[{"publication_status":"published","external_id":{"pmid":["34667153"],"isi":["000709050300016"]},"language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"year":"2021","related_material":{"link":[{"description":"Preprint","relation":"earlier_version","url":"https://doi.org/10.1101/2020.11.23.394171 "}]},"publication":"Nature Communications","citation":{"mla":"Pradhan, Saurabh J., et al. “Satb2 Acts as a Gatekeeper for Major Developmental Transitions during Early Vertebrate Embryogenesis.” <i>Nature Communications</i>, vol. 12, no. 1, 6094, Springer Nature, 2021, doi:<a href=\"https://doi.org/10.1038/s41467-021-26234-7\">10.1038/s41467-021-26234-7</a>.","ista":"Pradhan SJ, Reddy PC, Smutny M, Sharma A, Sako K, Oak MS, Shah R, Pal M, Deshpande O, Dsilva G, Tang Y, Mishra R, Deshpande G, Giraldez AJ, Sonawane M, Heisenberg C-PJ, Galande S. 2021. Satb2 acts as a gatekeeper for major developmental transitions during early vertebrate embryogenesis. Nature Communications. 12(1), 6094.","ieee":"S. J. Pradhan <i>et al.</i>, “Satb2 acts as a gatekeeper for major developmental transitions during early vertebrate embryogenesis,” <i>Nature Communications</i>, vol. 12, no. 1. Springer Nature, 2021.","ama":"Pradhan SJ, Reddy PC, Smutny M, et al. Satb2 acts as a gatekeeper for major developmental transitions during early vertebrate embryogenesis. <i>Nature Communications</i>. 2021;12(1). doi:<a href=\"https://doi.org/10.1038/s41467-021-26234-7\">10.1038/s41467-021-26234-7</a>","chicago":"Pradhan, Saurabh J., Puli Chandramouli Reddy, Michael Smutny, Ankita Sharma, Keisuke Sako, Meghana S. Oak, Rini Shah, et al. “Satb2 Acts as a Gatekeeper for Major Developmental Transitions during Early Vertebrate Embryogenesis.” <i>Nature Communications</i>. Springer Nature, 2021. <a href=\"https://doi.org/10.1038/s41467-021-26234-7\">https://doi.org/10.1038/s41467-021-26234-7</a>.","short":"S.J. Pradhan, P.C. Reddy, M. Smutny, A. Sharma, K. Sako, M.S. Oak, R. Shah, M. Pal, O. Deshpande, G. Dsilva, Y. Tang, R. Mishra, G. Deshpande, A.J. Giraldez, M. Sonawane, C.-P.J. Heisenberg, S. Galande, Nature Communications 12 (2021).","apa":"Pradhan, S. J., Reddy, P. C., Smutny, M., Sharma, A., Sako, K., Oak, M. S., … Galande, S. (2021). Satb2 acts as a gatekeeper for major developmental transitions during early vertebrate embryogenesis. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-021-26234-7\">https://doi.org/10.1038/s41467-021-26234-7</a>"},"isi":1,"month":"10","date_updated":"2026-04-02T11:57:41Z","date_created":"2021-10-31T23:01:29Z","file":[{"date_created":"2021-11-09T13:59:26Z","content_type":"application/pdf","file_id":"10262","checksum":"c40a69ae94435ecd3a30c9874a11ef2b","access_level":"open_access","file_name":"2021_NatureComm_Pradhan.pdf","relation":"main_file","creator":"cziletti","success":1,"date_updated":"2021-11-09T13:59:26Z","file_size":7144437}],"issue":"1","scopus_import":"1","volume":12,"file_date_updated":"2021-11-09T13:59:26Z","article_type":"original","author":[{"first_name":"Saurabh J.","last_name":"Pradhan","full_name":"Pradhan, Saurabh J."},{"full_name":"Reddy, Puli Chandramouli","last_name":"Reddy","first_name":"Puli Chandramouli"},{"last_name":"Smutny","id":"3FE6E4E8-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-5920-9090","first_name":"Michael","full_name":"Smutny, Michael"},{"last_name":"Sharma","first_name":"Ankita","full_name":"Sharma, Ankita"},{"id":"3BED66BE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6453-8075","first_name":"Keisuke","last_name":"Sako","full_name":"Sako, Keisuke"},{"full_name":"Oak, Meghana S.","last_name":"Oak","first_name":"Meghana S."},{"first_name":"Rini","last_name":"Shah","full_name":"Shah, Rini"},{"first_name":"Mrinmoy","last_name":"Pal","full_name":"Pal, Mrinmoy"},{"last_name":"Deshpande","first_name":"Ojas","full_name":"Deshpande, Ojas"},{"last_name":"Dsilva","first_name":"Greg","full_name":"Dsilva, Greg"},{"first_name":"Yin","last_name":"Tang","full_name":"Tang, Yin"},{"first_name":"Rakesh","last_name":"Mishra","full_name":"Mishra, Rakesh"},{"first_name":"Girish","last_name":"Deshpande","full_name":"Deshpande, Girish"},{"full_name":"Giraldez, Antonio J.","first_name":"Antonio J.","last_name":"Giraldez"},{"full_name":"Sonawane, Mahendra","last_name":"Sonawane","first_name":"Mahendra"},{"last_name":"Heisenberg","first_name":"Carl-Philipp J","orcid":"0000-0002-0912-4566","id":"39427864-F248-11E8-B48F-1D18A9856A87","full_name":"Heisenberg, Carl-Philipp J"},{"full_name":"Galande, Sanjeev","last_name":"Galande","first_name":"Sanjeev"}],"title":"Satb2 acts as a gatekeeper for major developmental transitions during early vertebrate embryogenesis","day":"19","intvolume":"        12","acknowledgement":"We are grateful to the members of C.-P.H. and SG lab for discussions. Authors thank Shubha Tole for providing embryonic mouse tissues. Authors are grateful to Alessandro Mongera and Chetana Sachidanandan for generous help with Tg: Sox10: GFP line. Authors would like to thank Satyajeet Khare, Vanessa Barone, Jyothish S., Shalini Mishra, Yoshita Bhide, and Keshav Jha for assistance in experiments. We would also like to thank Chaitanya Dingare for valuable suggestions. We thank Diana Pinhiero and Alexandra Schauer for critical reading of early versions of the manuscript. This work was supported by the Centre of Excellence in Epigenetics program of the Department of Biotechnology, Government of India Phase I (BT/01/COE/09/07) to S.G. and R.K.M., and Phase II (BT/COE/34/SP17426/2016) to S.G. and JC Bose Fellowship (JCB/2019/000013) from Science and Engineering Research Board, Government of India to S.G., DST-BMWF Indo-Austrian bilateral program grant to S.G. and C.-P.H. The work using animal models was partly supported by the infrastructure support grants from the Department of Biotechnology (National Facility for Laboratory Model Organisms: BT/INF/22/SP17358/2016 and Establishment of a Pune Biotech Cluster, Model Organism to Human Disease: B-2 Whole Animal Imaging & Tissue Processing FacilityBT/Pune-Biocluster/01/2015). S.J.P. was supported by Fellowship from the Council of Scientific and Industrial Research, India and travel fellowship from the Company of Biologists, UK. P.C.R. was supported by the Early Career Fellowship of the Wellcome Trust-DBT India Alliance (IA/E/16/1/503057). A.S. was supported by UGC and R.S. was supported by CSIR India. M.S. was supported by core funding from the Tata Institute of Fundamental Research (TIFR 12P-121).","publication_identifier":{"eissn":["2041-1723"]},"department":[{"_id":"CaHe"}],"ddc":["570"],"_id":"10202","type":"journal_article","date_published":"2021-10-19T00:00:00Z","status":"public","article_processing_charge":"Yes","article_number":"6094","oa":1,"oa_version":"Published Version","has_accepted_license":"1","doi":"10.1038/s41467-021-26234-7","pmid":1,"abstract":[{"text":"Zygotic genome activation (ZGA) initiates regionalized transcription underlying distinct cellular identities. ZGA is dependent upon dynamic chromatin architecture sculpted by conserved DNA-binding proteins. However, the direct mechanistic link between the onset of ZGA and the tissue-specific transcription remains unclear. Here, we have addressed the involvement of chromatin organizer Satb2 in orchestrating both processes during zebrafish embryogenesis. Integrative analysis of transcriptome, genome-wide occupancy and chromatin accessibility reveals contrasting molecular activities of maternally deposited and zygotically synthesized Satb2. Maternal Satb2 prevents premature transcription of zygotic genes by influencing the interplay between the pluripotency factors. By contrast, zygotic Satb2 activates transcription of the same group of genes during neural crest development and organogenesis. Thus, our comparative analysis of maternal versus zygotic function of Satb2 underscores how these antithetical activities are temporally coordinated and functionally implemented highlighting the evolutionary implications of the biphasic and bimodal regulation of landmark developmental transitions by a single determinant.","lang":"eng"}],"publisher":"Springer Nature","corr_author":"1","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","quality_controlled":"1"},{"date_updated":"2026-04-02T13:15:46Z","isi":1,"month":"10","author":[{"last_name":"Martín-Sánchez","first_name":"Javier","full_name":"Martín-Sánchez, Javier"},{"first_name":"Jiahua","last_name":"Duan","full_name":"Duan, Jiahua"},{"last_name":"Taboada-Gutiérrez","first_name":"Javier","full_name":"Taboada-Gutiérrez, Javier"},{"full_name":"Álvarez-Pérez, Gonzalo","last_name":"Álvarez-Pérez","first_name":"Gonzalo"},{"first_name":"Kirill V.","last_name":"Voronin","full_name":"Voronin, Kirill V."},{"last_name":"Prieto Gonzalez","first_name":"Ivan","orcid":"0000-0002-7370-5357","id":"2A307FE2-F248-11E8-B48F-1D18A9856A87","full_name":"Prieto Gonzalez, Ivan"},{"last_name":"Ma","first_name":"Weiliang","full_name":"Ma, Weiliang"},{"full_name":"Bao, Qiaoliang","first_name":"Qiaoliang","last_name":"Bao"},{"last_name":"Volkov","first_name":"Valentyn S.","full_name":"Volkov, Valentyn S."},{"last_name":"Hillenbrand","first_name":"Rainer","full_name":"Hillenbrand, Rainer"},{"full_name":"Nikitin, Alexey Y.","first_name":"Alexey Y.","last_name":"Nikitin"},{"first_name":"Pablo","last_name":"Alonso-González","full_name":"Alonso-González, Pablo"}],"file_date_updated":"2021-10-27T14:16:06Z","article_type":"original","volume":7,"file":[{"file_size":2441163,"creator":"cziletti","success":1,"date_updated":"2021-10-27T14:16:06Z","file_name":"2021_ScienceAdv_Martin-Sanchez.pdf","relation":"main_file","date_created":"2021-10-27T14:16:06Z","file_id":"10189","content_type":"application/pdf","checksum":"0a470ef6a47d2b8a96ede4c4d28cfacd","access_level":"open_access"}],"issue":"41","scopus_import":"1","date_created":"2021-10-24T22:01:33Z","language":[{"iso":"eng"}],"external_id":{"isi":["000704912700024"],"arxiv":["2103.10852"]},"publication_status":"published","citation":{"apa":"Martín-Sánchez, J., Duan, J., Taboada-Gutiérrez, J., Álvarez-Pérez, G., Voronin, K. V., Prieto Gonzalez, I., … Alonso-González, P. (2021). Focusing of in-plane hyperbolic polaritons in van der Waals crystals with tailored infrared nanoantennas. <i>Science Advances</i>. American Association for the Advancement of Science. <a href=\"https://doi.org/10.1126/sciadv.abj0127\">https://doi.org/10.1126/sciadv.abj0127</a>","short":"J. Martín-Sánchez, J. Duan, J. Taboada-Gutiérrez, G. Álvarez-Pérez, K.V. Voronin, I. Prieto Gonzalez, W. Ma, Q. Bao, V.S. Volkov, R. Hillenbrand, A.Y. Nikitin, P. Alonso-González, Science Advances 7 (2021).","chicago":"Martín-Sánchez, Javier, Jiahua Duan, Javier Taboada-Gutiérrez, Gonzalo Álvarez-Pérez, Kirill V. Voronin, Ivan Prieto Gonzalez, Weiliang Ma, et al. “Focusing of In-Plane Hyperbolic Polaritons in van Der Waals Crystals with Tailored Infrared Nanoantennas.” <i>Science Advances</i>. American Association for the Advancement of Science, 2021. <a href=\"https://doi.org/10.1126/sciadv.abj0127\">https://doi.org/10.1126/sciadv.abj0127</a>.","ista":"Martín-Sánchez J, Duan J, Taboada-Gutiérrez J, Álvarez-Pérez G, Voronin KV, Prieto Gonzalez I, Ma W, Bao Q, Volkov VS, Hillenbrand R, Nikitin AY, Alonso-González P. 2021. Focusing of in-plane hyperbolic polaritons in van der Waals crystals with tailored infrared nanoantennas. Science Advances. 7(41), abj0127.","ieee":"J. Martín-Sánchez <i>et al.</i>, “Focusing of in-plane hyperbolic polaritons in van der Waals crystals with tailored infrared nanoantennas,” <i>Science Advances</i>, vol. 7, no. 41. American Association for the Advancement of Science, 2021.","ama":"Martín-Sánchez J, Duan J, Taboada-Gutiérrez J, et al. Focusing of in-plane hyperbolic polaritons in van der Waals crystals with tailored infrared nanoantennas. <i>Science Advances</i>. 2021;7(41). doi:<a href=\"https://doi.org/10.1126/sciadv.abj0127\">10.1126/sciadv.abj0127</a>","mla":"Martín-Sánchez, Javier, et al. “Focusing of In-Plane Hyperbolic Polaritons in van Der Waals Crystals with Tailored Infrared Nanoantennas.” <i>Science Advances</i>, vol. 7, no. 41, abj0127, American Association for the Advancement of Science, 2021, doi:<a href=\"https://doi.org/10.1126/sciadv.abj0127\">10.1126/sciadv.abj0127</a>."},"publication":"Science Advances","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","short":"CC BY-NC (4.0)","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","image":"/images/cc_by_nc.png"},"year":"2021","doi":"10.1126/sciadv.abj0127","oa_version":"Published Version","has_accepted_license":"1","oa":1,"license":"https://creativecommons.org/licenses/by-nc/4.0/","article_number":"abj0127","arxiv":1,"quality_controlled":"1","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","publisher":"American Association for the Advancement of Science","abstract":[{"text":"Phonon polaritons (PhPs)—light coupled to lattice vibrations—with in-plane hyperbolic dispersion exhibit ray-like propagation with large wave vectors and enhanced density of optical states along certain directions on a surface. As such, they have raised a surge of interest, promising unprecedented manipulation of infrared light at the nanoscale in a planar circuitry. Here, we demonstrate focusing of in-plane hyperbolic PhPs propagating along thin slabs of α-MoO3. To that end, we developed metallic nanoantennas of convex geometries for both efficient launching and focusing of the polaritons. The foci obtained exhibit enhanced near-field confinement and absorption compared to foci produced by in-plane isotropic PhPs. Foci sizes as small as λp/4.5 = λ0/50 were achieved (λp is the polariton wavelength and λ0 is the photon wavelength). Focusing of in-plane hyperbolic polaritons introduces a first and most basic building block developing planar polariton optics using in-plane anisotropic van der Waals materials.","lang":"eng"}],"ddc":["530"],"_id":"10177","department":[{"_id":"NanoFab"}],"publication_identifier":{"eissn":["2375-2548"]},"acknowledgement":"J.M.-S. acknowledges financial support from the Ramón y Cajal Program of the Government of Spain and FSE (RYC2018-026196-I) and the Spanish Ministry of Science and Innovation (State Plan for Scientific and Technical Research and Innovation grant number PID2019-110308GA-I00). P.A.-G. acknowledges support from the European Research Council under starting grant no. 715496, 2DNANOPTICA, and the Spanish Ministry of Science and Innovation (State Plan for Scientific and Technical Research and Innovation grant number PID2019-111156GB-I00). J.T.-G. acknowledges support through the Severo Ochoa Program from the Government of the Principality of Asturias (PA-18-PF-BP17-126). G.A.-P. acknowledges support through the Severo Ochoa Program from the Government of the Principality of Asturias (PA-20-PF-BP19-053). K.V.V. and V.S.V. acknowledge the financial support from the Ministry of Science and Higher Education of the Russian Federation (agreement no. 075-15-2021-606). A.Y.N. acknowledges the Spanish Ministry of Science, Innovation, and Universities (national projects MAT2017-88358-C3-3-R and PID2020-115221GB-C42) and the Basque Department of Education (PIBA-2020-1-0014). R.H. acknowledges financial support from the Spanish Ministry of Science, Innovation, and Universities (national project number RTI2018-094830-B-100 and project number MDM-2016-0618 of the Marie de Maeztu Units of Excellence Program) and the Basque Government (grant number IT1164-19).","intvolume":"         7","day":"08","title":"Focusing of in-plane hyperbolic polaritons in van der Waals crystals with tailored infrared nanoantennas","article_processing_charge":"Yes","status":"public","date_published":"2021-10-08T00:00:00Z","type":"journal_article"},{"pmid":1,"abstract":[{"lang":"eng","text":"While high risk of failure is an inherent part of developing innovative therapies, it can be reduced by adherence to evidence-based rigorous research practices. Numerous analyses conducted to date have clearly identified measures that need to be taken to improve research rigor. Supported through the European Union's Innovative Medicines Initiative, the EQIPD consortium has developed a novel preclinical research quality system that can be applied in both public and private sectors and is free for anyone to use. The EQIPD Quality System was designed to be suited to boost innovation by ensuring the generation of robust and reliable preclinical data while being lean, effective and not becoming a burden that could negatively impact the freedom to explore scientific questions. EQIPD defines research quality as the extent to which research data are fit for their intended use. Fitness, in this context, is defined by the stakeholders, who are the scientists directly involved in the research, but also their funders, sponsors, publishers, research tool manufacturers and collaboration partners such as peers in a multi-site research project. The essence of the EQIPD Quality System is the set of 18 core requirements that can be addressed flexibly, according to user-specific needs and following a user-defined trajectory. The EQIPD Quality System proposes guidance on expectations for quality-related measures, defines criteria for adequate processes (i.e., performance standards) and provides examples of how such measures can be developed and implemented. However, it does not prescribe any pre-determined solutions. EQIPD has also developed tools (for optional use) to support users in implementing the system and assessment services for those research units that successfully implement the quality system and seek formal accreditation. Building upon the feedback from users and continuous improvement, a sustainable EQIPD Quality System will ultimately serve the entire community of scientists conducting non-regulated preclinical research, by helping them generate reliable data that are fit for their intended use."}],"publisher":"eLife Sciences Publications","quality_controlled":"1","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","oa":1,"has_accepted_license":"1","oa_version":"Published Version","doi":"10.7554/eLife.63294","date_published":"2021-05-24T00:00:00Z","type":"journal_article","status":"public","article_processing_charge":"No","day":"24","title":"Introduction to the EQIPD quality system","intvolume":"        10","publication_identifier":{"eissn":["2050-084X"]},"acknowledgement":"This project has received funding from the Innovative Medicines Initiative 2 Joint Undertaking under grant agreement No 777364. This Joint Undertaking receives support from the European Union’s Horizon 2020 research and innovation programme and EFPIA. The authors are very grateful to Martin Heinrich (Abbvie, Ludwigshafen, Germany) for the exceptional IT support and programming the EQIPD Planning Tool and the Creator Tool and to Dr Shai Silberberg (NINDS, USA), Dr. Renza Roncarati (PAASP Italy) and Dr Judith Homberg (Radboud University, Nijmegen) for highly stimulating contributions to the discussions and comments on earlier versions of this manuscript. We also wish to express our thanks to Dr. Sara Stöber (concentris research management GmbH, Fürstenfeldbruck, Germany) for excellent and continuous support of this project. Creation of the EQIPD Stakeholder group was supported by Noldus Information Technology bv (Wageningen, the Netherlands).","_id":"9607","ddc":["570"],"department":[{"_id":"PreCl"}],"scopus_import":"1","file":[{"file_size":2500720,"creator":"asandaue","success":1,"date_updated":"2021-06-28T11:35:30Z","file_name":"2021_ELife_Bespalov.pdf","relation":"main_file","date_created":"2021-06-28T11:35:30Z","content_type":"application/pdf","file_id":"9609","checksum":"885b746051a7a6b6e24e3d2781a48fde","access_level":"open_access"}],"date_created":"2021-06-27T22:01:49Z","volume":10,"article_type":"original","file_date_updated":"2021-06-28T11:35:30Z","author":[{"full_name":"Bespalov, Anton","first_name":"Anton","last_name":"Bespalov"},{"first_name":"René","last_name":"Bernard","full_name":"Bernard, René"},{"last_name":"Gilis","first_name":"Anja","full_name":"Gilis, Anja"},{"full_name":"Gerlach, Björn","first_name":"Björn","last_name":"Gerlach"},{"full_name":"Guillén, Javier","last_name":"Guillén","first_name":"Javier"},{"first_name":"Vincent","last_name":"Castagné","full_name":"Castagné, Vincent"},{"full_name":"Lefevre, Isabel A.","first_name":"Isabel A.","last_name":"Lefevre"},{"full_name":"Ducrey, Fiona","first_name":"Fiona","last_name":"Ducrey"},{"full_name":"Monk, Lee","last_name":"Monk","first_name":"Lee"},{"last_name":"Bongiovanni","first_name":"Sandrine","full_name":"Bongiovanni, Sandrine"},{"first_name":"Bruce","last_name":"Altevogt","full_name":"Altevogt, Bruce"},{"full_name":"Arroyo-Araujo, María","first_name":"María","last_name":"Arroyo-Araujo"},{"first_name":"Lior","last_name":"Bikovski","full_name":"Bikovski, Lior"},{"last_name":"De Bruin","first_name":"Natasja","full_name":"De Bruin, Natasja"},{"last_name":"Castaños-Vélez","first_name":"Esmeralda","full_name":"Castaños-Vélez, Esmeralda"},{"first_name":"Alexander","last_name":"Dityatev","full_name":"Dityatev, Alexander"},{"full_name":"Emmerich, Christoph H.","last_name":"Emmerich","first_name":"Christoph H."},{"last_name":"Fares","first_name":"Raafat","full_name":"Fares, Raafat"},{"last_name":"Ferland-Beckham","first_name":"Chantelle","full_name":"Ferland-Beckham, Chantelle"},{"first_name":"Christelle","last_name":"Froger-Colléaux","full_name":"Froger-Colléaux, Christelle"},{"last_name":"Gailus-Durner","first_name":"Valerie","full_name":"Gailus-Durner, Valerie"},{"last_name":"Hölter","first_name":"Sabine M.","full_name":"Hölter, Sabine M."},{"last_name":"Hofmann","first_name":"Martine Cj","full_name":"Hofmann, Martine Cj"},{"full_name":"Kabitzke, Patricia","last_name":"Kabitzke","first_name":"Patricia"},{"full_name":"Kas, Martien Jh","last_name":"Kas","first_name":"Martien Jh"},{"full_name":"Kurreck, Claudia","last_name":"Kurreck","first_name":"Claudia"},{"last_name":"Moser","first_name":"Paul","full_name":"Moser, Paul"},{"full_name":"Pietraszek, Malgorzata","first_name":"Malgorzata","last_name":"Pietraszek"},{"full_name":"Popik, Piotr","last_name":"Popik","first_name":"Piotr"},{"last_name":"Potschka","first_name":"Heidrun","full_name":"Potschka, Heidrun"},{"full_name":"Prado Montes De Oca, Ernesto","last_name":"Prado Montes De Oca","first_name":"Ernesto"},{"first_name":"Leonardo","last_name":"Restivo","full_name":"Restivo, Leonardo"},{"full_name":"Riedel, Gernot","last_name":"Riedel","first_name":"Gernot"},{"full_name":"Ritskes-Hoitinga, Merel","first_name":"Merel","last_name":"Ritskes-Hoitinga"},{"full_name":"Samardzic, Janko","first_name":"Janko","last_name":"Samardzic"},{"last_name":"Schunn","id":"4272DB4A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4326-5300","first_name":"Michael","full_name":"Schunn, Michael"},{"first_name":"Claudia","last_name":"Stöger","full_name":"Stöger, Claudia"},{"last_name":"Voikar","first_name":"Vootele","full_name":"Voikar, Vootele"},{"first_name":"Jan","last_name":"Vollert","full_name":"Vollert, Jan"},{"first_name":"Kimberley E.","last_name":"Wever","full_name":"Wever, Kimberley E."},{"first_name":"Kathleen","last_name":"Wuyts","full_name":"Wuyts, Kathleen"},{"full_name":"Macleod, Malcolm R.","last_name":"Macleod","first_name":"Malcolm R."},{"full_name":"Dirnagl, Ulrich","last_name":"Dirnagl","first_name":"Ulrich"},{"last_name":"Steckler","first_name":"Thomas","full_name":"Steckler, Thomas"}],"date_updated":"2026-04-02T13:55:57Z","month":"05","isi":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"year":"2021","publication":"eLife","citation":{"short":"A. Bespalov, R. Bernard, A. Gilis, B. Gerlach, J. Guillén, V. Castagné, I.A. Lefevre, F. Ducrey, L. Monk, S. Bongiovanni, B. Altevogt, M. Arroyo-Araujo, L. Bikovski, N. De Bruin, E. Castaños-Vélez, A. Dityatev, C.H. Emmerich, R. Fares, C. Ferland-Beckham, C. Froger-Colléaux, V. Gailus-Durner, S.M. Hölter, M.C. Hofmann, P. Kabitzke, M.J. Kas, C. Kurreck, P. Moser, M. Pietraszek, P. Popik, H. Potschka, E. Prado Montes De Oca, L. Restivo, G. Riedel, M. Ritskes-Hoitinga, J. Samardzic, M. Schunn, C. Stöger, V. Voikar, J. Vollert, K.E. Wever, K. Wuyts, M.R. Macleod, U. Dirnagl, T. Steckler, ELife 10 (2021).","chicago":"Bespalov, Anton, René Bernard, Anja Gilis, Björn Gerlach, Javier Guillén, Vincent Castagné, Isabel A. Lefevre, et al. “Introduction to the EQIPD Quality System.” <i>ELife</i>. eLife Sciences Publications, 2021. <a href=\"https://doi.org/10.7554/eLife.63294\">https://doi.org/10.7554/eLife.63294</a>.","ama":"Bespalov A, Bernard R, Gilis A, et al. Introduction to the EQIPD quality system. <i>eLife</i>. 2021;10. doi:<a href=\"https://doi.org/10.7554/eLife.63294\">10.7554/eLife.63294</a>","ista":"Bespalov A, Bernard R, Gilis A, Gerlach B, Guillén J, Castagné V, Lefevre IA, Ducrey F, Monk L, Bongiovanni S, Altevogt B, Arroyo-Araujo M, Bikovski L, De Bruin N, Castaños-Vélez E, Dityatev A, Emmerich CH, Fares R, Ferland-Beckham C, Froger-Colléaux C, Gailus-Durner V, Hölter SM, Hofmann MC, Kabitzke P, Kas MJ, Kurreck C, Moser P, Pietraszek M, Popik P, Potschka H, Prado Montes De Oca E, Restivo L, Riedel G, Ritskes-Hoitinga M, Samardzic J, Schunn M, Stöger C, Voikar V, Vollert J, Wever KE, Wuyts K, Macleod MR, Dirnagl U, Steckler T. 2021. Introduction to the EQIPD quality system. eLife. 10.","ieee":"A. Bespalov <i>et al.</i>, “Introduction to the EQIPD quality system,” <i>eLife</i>, vol. 10. eLife Sciences Publications, 2021.","mla":"Bespalov, Anton, et al. “Introduction to the EQIPD Quality System.” <i>ELife</i>, vol. 10, eLife Sciences Publications, 2021, doi:<a href=\"https://doi.org/10.7554/eLife.63294\">10.7554/eLife.63294</a>.","apa":"Bespalov, A., Bernard, R., Gilis, A., Gerlach, B., Guillén, J., Castagné, V., … Steckler, T. (2021). Introduction to the EQIPD quality system. <i>ELife</i>. eLife Sciences Publications. <a href=\"https://doi.org/10.7554/eLife.63294\">https://doi.org/10.7554/eLife.63294</a>"},"publication_status":"published","external_id":{"pmid":["34028353"],"isi":["000661272000001"]},"language":[{"iso":"eng"}]},{"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","quality_controlled":"1","publisher":"MDPI","abstract":[{"lang":"eng","text":"Layered materials in which individual atomic layers are bonded by weak van der Waals forces (vdW materials) constitute one of the most prominent platforms for materials research. Particularly, polar vdW crystals, such as hexagonal boron nitride (h-BN), alpha-molybdenum trioxide (α-MoO3) or alpha-vanadium pentoxide (α-V2O5), have received significant attention in nano-optics, since they support phonon polaritons (PhPs)―light coupled to lattice vibrations― with strong electromagnetic confinement and low optical losses. Recently, correlative far- and near-field studies of α-MoO3 have been demonstrated as an effective strategy to accurately extract the permittivity of this material. Here, we use this accurately characterized and low-loss polaritonic material to sense its local dielectric environment, namely silica (SiO2), one of the most widespread substrates in nanotechnology. By studying the propagation of PhPs on α-MoO3 flakes with different thicknesses laying on SiO2 substrates via near-field microscopy (s-SNOM), we extract locally the infrared permittivity of SiO2. Our work reveals PhPs nanoimaging as a versatile method for the quantitative characterization of the local optical properties of dielectric substrates, crucial for understanding and predicting the response of nanomaterials and for the future scalability of integrated nanophotonic devices. "}],"pmid":1,"doi":"10.3390/nano11010120","has_accepted_license":"1","oa_version":"Published Version","oa":1,"article_number":"120","article_processing_charge":"No","status":"public","type":"journal_article","date_published":"2021-01-07T00:00:00Z","department":[{"_id":"NanoFab"}],"ddc":["620"],"_id":"9038","acknowledgement":"P.A.-M. acknowledges financial support through JAE Intro program from the Superior\r\nCouncil of Scientific Investigations and the Spanish Ministry of Science and Innovation (grant number JAEINT_20_00589). G.Á.-P. and J.T.-G. acknowledge financial support through the Severo Ochoa Program from the Government of the Principality of Asturias (grant numbers PA-20-PF-BP19-053 and PA-18-PF-BP17-126, respectively). J.M.-S. acknowledges financial support from the Ramón y Cajal Program of the Government of Spain (RYC2018-026196-I) and the Spanish Ministry of Science and Innovation (State Plan for Scientific and Technical Research and Innovation grant number PID2019-110308GA-I00). P.A.-G. acknowledges support from the European Research Council under starting grant no. 715496, 2DNANOPTICA and the Spanish Ministry of Science and Innovation (State Plan for Scientific and Technical Research and Innovation grant number PID2019-111156GB-I00).","publication_identifier":{"eissn":["2079-4991"]},"intvolume":"        11","title":"Extracting the infrared permittivity of SiO2 substrates locally by near-field imaging of phonon polaritons in a van der Waals crystal","day":"07","author":[{"full_name":"Aguilar-Merino, Patricia","first_name":"Patricia","last_name":"Aguilar-Merino"},{"full_name":"Álvarez-Pérez, Gonzalo","first_name":"Gonzalo","last_name":"Álvarez-Pérez"},{"full_name":"Taboada-Gutiérrez, Javier","first_name":"Javier","last_name":"Taboada-Gutiérrez"},{"first_name":"Jiahua","last_name":"Duan","full_name":"Duan, Jiahua"},{"full_name":"Prieto Gonzalez, Ivan","last_name":"Prieto Gonzalez","first_name":"Ivan","id":"2A307FE2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7370-5357"},{"last_name":"Álvarez-Prado","first_name":"Luis Manuel","full_name":"Álvarez-Prado, Luis Manuel"},{"full_name":"Nikitin, Alexey Y.","last_name":"Nikitin","first_name":"Alexey Y."},{"first_name":"Javier","last_name":"Martín-Sánchez","full_name":"Martín-Sánchez, Javier"},{"last_name":"Alonso-González","first_name":"Pablo","full_name":"Alonso-González, Pablo"}],"article_type":"original","file_date_updated":"2021-01-25T08:02:32Z","volume":11,"date_created":"2021-01-24T23:01:09Z","file":[{"access_level":"open_access","checksum":"1edc13eeda83df5cd9fff9504727b1f5","content_type":"application/pdf","file_id":"9042","date_created":"2021-01-25T08:02:32Z","relation":"main_file","file_name":"2020_Nanomaterials_Aguilar_Merino.pdf","date_updated":"2021-01-25T08:02:32Z","success":1,"creator":"dernst","file_size":2730267}],"scopus_import":"1","issue":"1","isi":1,"month":"01","date_updated":"2026-04-02T13:57:24Z","citation":{"apa":"Aguilar-Merino, P., Álvarez-Pérez, G., Taboada-Gutiérrez, J., Duan, J., Prieto Gonzalez, I., Álvarez-Prado, L. M., … Alonso-González, P. (2021). Extracting the infrared permittivity of SiO2 substrates locally by near-field imaging of phonon polaritons in a van der Waals crystal. <i>Nanomaterials</i>. MDPI. <a href=\"https://doi.org/10.3390/nano11010120\">https://doi.org/10.3390/nano11010120</a>","short":"P. Aguilar-Merino, G. Álvarez-Pérez, J. Taboada-Gutiérrez, J. Duan, I. Prieto Gonzalez, L.M. Álvarez-Prado, A.Y. Nikitin, J. Martín-Sánchez, P. Alonso-González, Nanomaterials 11 (2021).","chicago":"Aguilar-Merino, Patricia, Gonzalo Álvarez-Pérez, Javier Taboada-Gutiérrez, Jiahua Duan, Ivan Prieto Gonzalez, Luis Manuel Álvarez-Prado, Alexey Y. Nikitin, Javier Martín-Sánchez, and Pablo Alonso-González. “Extracting the Infrared Permittivity of SiO2 Substrates Locally by Near-Field Imaging of Phonon Polaritons in a van Der Waals Crystal.” <i>Nanomaterials</i>. MDPI, 2021. <a href=\"https://doi.org/10.3390/nano11010120\">https://doi.org/10.3390/nano11010120</a>.","mla":"Aguilar-Merino, Patricia, et al. “Extracting the Infrared Permittivity of SiO2 Substrates Locally by Near-Field Imaging of Phonon Polaritons in a van Der Waals Crystal.” <i>Nanomaterials</i>, vol. 11, no. 1, 120, MDPI, 2021, doi:<a href=\"https://doi.org/10.3390/nano11010120\">10.3390/nano11010120</a>.","ieee":"P. Aguilar-Merino <i>et al.</i>, “Extracting the infrared permittivity of SiO2 substrates locally by near-field imaging of phonon polaritons in a van der Waals crystal,” <i>Nanomaterials</i>, vol. 11, no. 1. MDPI, 2021.","ista":"Aguilar-Merino P, Álvarez-Pérez G, Taboada-Gutiérrez J, Duan J, Prieto Gonzalez I, Álvarez-Prado LM, Nikitin AY, Martín-Sánchez J, Alonso-González P. 2021. Extracting the infrared permittivity of SiO2 substrates locally by near-field imaging of phonon polaritons in a van der Waals crystal. Nanomaterials. 11(1), 120.","ama":"Aguilar-Merino P, Álvarez-Pérez G, Taboada-Gutiérrez J, et al. Extracting the infrared permittivity of SiO2 substrates locally by near-field imaging of phonon polaritons in a van der Waals crystal. <i>Nanomaterials</i>. 2021;11(1). doi:<a href=\"https://doi.org/10.3390/nano11010120\">10.3390/nano11010120</a>"},"publication":"Nanomaterials","year":"2021","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"language":[{"iso":"eng"}],"external_id":{"pmid":["33430225"],"isi":["000610636600001"]},"publication_status":"published"},{"language":[{"iso":"eng"}],"publication_status":"published","external_id":{"isi":["000667248600005"]},"citation":{"chicago":"Santini, Laura, Florian Halbritter, Fabian Titz-Teixeira, Toru Suzuki, Maki Asami, Xiaoyan Ma, Julia Ramesmayer, et al. “Genomic Imprinting in Mouse Blastocysts Is Predominantly Associated with H3K27me3.” <i>Nature Communications</i>. Springer Nature, 2021. <a href=\"https://doi.org/10.1038/s41467-021-23510-4\">https://doi.org/10.1038/s41467-021-23510-4</a>.","short":"L. Santini, F. Halbritter, F. Titz-Teixeira, T. Suzuki, M. Asami, X. Ma, J. Ramesmayer, A. Lackner, N. Warr, F. Pauler, S. Hippenmeyer, E. Laue, M. Farlik, C. Bock, A. Beyer, A.C.F. Perry, M. Leeb, Nature Communications 12 (2021).","mla":"Santini, Laura, et al. “Genomic Imprinting in Mouse Blastocysts Is Predominantly Associated with H3K27me3.” <i>Nature Communications</i>, vol. 12, no. 1, 3804, Springer Nature, 2021, doi:<a href=\"https://doi.org/10.1038/s41467-021-23510-4\">10.1038/s41467-021-23510-4</a>.","ieee":"L. Santini <i>et al.</i>, “Genomic imprinting in mouse blastocysts is predominantly associated with H3K27me3,” <i>Nature Communications</i>, vol. 12, no. 1. Springer Nature, 2021.","ista":"Santini L, Halbritter F, Titz-Teixeira F, Suzuki T, Asami M, Ma X, Ramesmayer J, Lackner A, Warr N, Pauler F, Hippenmeyer S, Laue E, Farlik M, Bock C, Beyer A, Perry ACF, Leeb M. 2021. Genomic imprinting in mouse blastocysts is predominantly associated with H3K27me3. Nature Communications. 12(1), 3804.","ama":"Santini L, Halbritter F, Titz-Teixeira F, et al. Genomic imprinting in mouse blastocysts is predominantly associated with H3K27me3. <i>Nature Communications</i>. 2021;12(1). doi:<a href=\"https://doi.org/10.1038/s41467-021-23510-4\">10.1038/s41467-021-23510-4</a>","apa":"Santini, L., Halbritter, F., Titz-Teixeira, F., Suzuki, T., Asami, M., Ma, X., … Leeb, M. (2021). Genomic imprinting in mouse blastocysts is predominantly associated with H3K27me3. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-021-23510-4\">https://doi.org/10.1038/s41467-021-23510-4</a>"},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"year":"2021","publication":"Nature Communications","date_updated":"2026-04-02T13:55:23Z","isi":1,"month":"07","file_date_updated":"2021-06-28T08:04:22Z","article_type":"original","author":[{"full_name":"Santini, Laura","first_name":"Laura","last_name":"Santini"},{"first_name":"Florian","last_name":"Halbritter","full_name":"Halbritter, Florian"},{"full_name":"Titz-Teixeira, Fabian","last_name":"Titz-Teixeira","first_name":"Fabian"},{"last_name":"Suzuki","first_name":"Toru","full_name":"Suzuki, Toru"},{"full_name":"Asami, Maki","first_name":"Maki","last_name":"Asami"},{"first_name":"Xiaoyan","last_name":"Ma","full_name":"Ma, Xiaoyan"},{"full_name":"Ramesmayer, Julia","last_name":"Ramesmayer","first_name":"Julia"},{"first_name":"Andreas","last_name":"Lackner","full_name":"Lackner, Andreas"},{"full_name":"Warr, Nick","first_name":"Nick","last_name":"Warr"},{"last_name":"Pauler","id":"48EA0138-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7462-0048","first_name":"Florian","full_name":"Pauler, Florian"},{"full_name":"Hippenmeyer, Simon","last_name":"Hippenmeyer","id":"37B36620-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2279-1061","first_name":"Simon"},{"full_name":"Laue, Ernest","first_name":"Ernest","last_name":"Laue"},{"full_name":"Farlik, Matthias","first_name":"Matthias","last_name":"Farlik"},{"last_name":"Bock","first_name":"Christoph","full_name":"Bock, Christoph"},{"last_name":"Beyer","first_name":"Andreas","full_name":"Beyer, Andreas"},{"first_name":"Anthony C.F.","last_name":"Perry","full_name":"Perry, Anthony C.F."},{"full_name":"Leeb, Martin","first_name":"Martin","last_name":"Leeb"}],"issue":"1","scopus_import":"1","file":[{"checksum":"75dd89d09945185b2d14b2434a0bcb50","access_level":"open_access","date_created":"2021-06-28T08:04:22Z","file_id":"9608","content_type":"application/pdf","relation":"main_file","file_name":"2021_NatureCommunications_Santini.pdf","date_updated":"2021-06-28T08:04:22Z","creator":"asandaue","success":1,"file_size":2156554}],"date_created":"2021-06-27T22:01:46Z","volume":12,"publication_identifier":{"eissn":["2041-1723"]},"acknowledgement":"The authors thank Robert Feil and Anton Wutz for helpful discussions and comments, Samuel Collombet and Peter Fraser for sharing embryo TAD coordinates, and Andy Riddel at the Cambridge Stem Cell Institute and Thomas Sauer at the Max Perutz Laboratories FACS facility for flow-sorting. We thank the team of the Biomedical Sequencing Facility at the CeMM and the Vienna Biocenter Core Facilities (VBCF) for support with next-generation sequencing. We are grateful to animal care teams at the University of Bath and MRC Harwell. A.C.F.P. acknowledges support from the UK Medical Research Council (MR/N000080/1 and MR/N020294/1) and Biotechnology and Biological Sciences Research Council (BB/P009506/1). L.S. is part of the FWF doctoral programme SMICH and supported by an Austrian Academy of Sciences DOC Fellowship. M.L. is funded by a Vienna Research Group for Young Investigators grant (VRG14-006) by the Vienna Science and Technology Fund (WWTF) and by the Austrian Science Fund FWF (I3786 and P31334).","ddc":["570"],"_id":"9601","department":[{"_id":"SiHi"}],"day":"12","title":"Genomic imprinting in mouse blastocysts is predominantly associated with H3K27me3","intvolume":"        12","status":"public","article_processing_charge":"No","date_published":"2021-07-12T00:00:00Z","type":"journal_article","has_accepted_license":"1","oa_version":"Published Version","doi":"10.1038/s41467-021-23510-4","article_number":"3804","oa":1,"publisher":"Springer Nature","quality_controlled":"1","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","abstract":[{"lang":"eng","text":"In mammalian genomes, differentially methylated regions (DMRs) and histone marks including trimethylation of histone 3 lysine 27 (H3K27me3) at imprinted genes are asymmetrically inherited to control parentally-biased gene expression. However, neither parent-of-origin-specific transcription nor imprints have been comprehensively mapped at the blastocyst stage of preimplantation development. Here, we address this by integrating transcriptomic and epigenomic approaches in mouse preimplantation embryos. We find that seventy-one genes exhibit previously unreported parent-of-origin-specific expression in blastocysts (nBiX: novel blastocyst-imprinted expressed). Uniparental expression of nBiX genes disappears soon after implantation. Micro-whole-genome bisulfite sequencing (µWGBS) of individual uniparental blastocysts detects 859 DMRs. We further find that 16% of nBiX genes are associated with a DMR, whereas most are associated with parentally-biased H3K27me3, suggesting a role for Polycomb-mediated imprinting in blastocysts. nBiX genes are clustered: five clusters contained at least one published imprinted gene, and five clusters exclusively contained nBiX genes. These data suggest that early development undergoes a complex program of stage-specific imprinting involving different tiers of regulation."}]},{"department":[{"_id":"SaSi"}],"ddc":["570"],"_id":"9761","acknowledgement":"The authors are grateful to Kazuya Oikawa and Gillian McLellan for generously sharing some of their data for this review, and to Janis Eells for helpful comments on the manuscript.","publication_identifier":{"eissn":["2073-4409"]},"intvolume":"        10","title":"The influence of mitochondrial dynamics and function on retinal ganglion cell susceptibility in optic nerve disease","day":"25","article_processing_charge":"Yes","status":"public","type":"journal_article","date_published":"2021-06-25T00:00:00Z","doi":"10.3390/cells10071593","has_accepted_license":"1","oa_version":"Published Version","oa":1,"article_number":"1593","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","quality_controlled":"1","publisher":"MDPI","abstract":[{"text":"The important roles of mitochondrial function and dysfunction in the process of neurodegeneration are widely acknowledged. Retinal ganglion cells (RGCs) appear to be a highly vulnerable neuronal cell type in the central nervous system with respect to mitochondrial dysfunction but the actual reasons for this are still incompletely understood. These cells have a unique circumstance where unmyelinated axons must bend nearly 90° to exit the eye and then cross a translaminar pressure gradient before becoming myelinated in the optic nerve. This region, the optic nerve head, contains some of the highest density of mitochondria present in these cells. Glaucoma represents a perfect storm of events occurring at this location, with a combination of changes in the translaminar pressure gradient and reassignment of the metabolic support functions of supporting glia, which appears to apply increased metabolic stress to the RGC axons leading to a failure of axonal transport mechanisms. However, RGCs themselves are also extremely sensitive to genetic mutations, particularly in genes affecting mitochondrial dynamics and mitochondrial clearance. These mutations, which systemically affect the mitochondria in every cell, often lead to an optic neuropathy as the sole pathologic defect in affected patients. This review summarizes knowledge of mitochondrial structure and function, the known energy demands of neurons in general, and places these in the context of normal and pathological characteristics of mitochondria attributed to RGCs. ","lang":"eng"}],"pmid":1,"language":[{"iso":"eng"}],"external_id":{"isi":["000678193300001"],"pmid":["34201955"]},"publication_status":"published","citation":{"short":"N.A. Muench, S. Patel, M.E. Maes, R.J. Donahue, A. Ikeda, R.W. Nickells, Cells 10 (2021).","chicago":"Muench, Nicole A., Sonia Patel, Margaret E Maes, Ryan J. Donahue, Akihiro Ikeda, and Robert W. Nickells. “The Influence of Mitochondrial Dynamics and Function on Retinal Ganglion Cell Susceptibility in Optic Nerve Disease.” <i>Cells</i>. MDPI, 2021. <a href=\"https://doi.org/10.3390/cells10071593\">https://doi.org/10.3390/cells10071593</a>.","ieee":"N. A. Muench, S. Patel, M. E. Maes, R. J. Donahue, A. Ikeda, and R. W. Nickells, “The influence of mitochondrial dynamics and function on retinal ganglion cell susceptibility in optic nerve disease,” <i>Cells</i>, vol. 10, no. 7. MDPI, 2021.","ama":"Muench NA, Patel S, Maes ME, Donahue RJ, Ikeda A, Nickells RW. The influence of mitochondrial dynamics and function on retinal ganglion cell susceptibility in optic nerve disease. <i>Cells</i>. 2021;10(7). doi:<a href=\"https://doi.org/10.3390/cells10071593\">10.3390/cells10071593</a>","ista":"Muench NA, Patel S, Maes ME, Donahue RJ, Ikeda A, Nickells RW. 2021. The influence of mitochondrial dynamics and function on retinal ganglion cell susceptibility in optic nerve disease. Cells. 10(7), 1593.","mla":"Muench, Nicole A., et al. “The Influence of Mitochondrial Dynamics and Function on Retinal Ganglion Cell Susceptibility in Optic Nerve Disease.” <i>Cells</i>, vol. 10, no. 7, 1593, MDPI, 2021, doi:<a href=\"https://doi.org/10.3390/cells10071593\">10.3390/cells10071593</a>.","apa":"Muench, N. A., Patel, S., Maes, M. E., Donahue, R. J., Ikeda, A., &#38; Nickells, R. W. (2021). The influence of mitochondrial dynamics and function on retinal ganglion cell susceptibility in optic nerve disease. <i>Cells</i>. MDPI. <a href=\"https://doi.org/10.3390/cells10071593\">https://doi.org/10.3390/cells10071593</a>"},"publication":"Cells","year":"2021","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"month":"06","isi":1,"date_updated":"2026-04-02T13:56:24Z","author":[{"first_name":"Nicole A.","last_name":"Muench","full_name":"Muench, Nicole A."},{"last_name":"Patel","first_name":"Sonia","full_name":"Patel, Sonia"},{"last_name":"Maes","orcid":"0000-0001-9642-1085","id":"3838F452-F248-11E8-B48F-1D18A9856A87","first_name":"Margaret E","full_name":"Maes, Margaret E"},{"last_name":"Donahue","first_name":"Ryan J.","full_name":"Donahue, Ryan J."},{"full_name":"Ikeda, Akihiro","first_name":"Akihiro","last_name":"Ikeda"},{"last_name":"Nickells","first_name":"Robert W.","full_name":"Nickells, Robert W."}],"file_date_updated":"2021-08-04T14:01:30Z","article_type":"original","volume":10,"date_created":"2021-08-01T22:01:22Z","scopus_import":"1","issue":"7","file":[{"file_size":4555611,"date_updated":"2021-08-04T14:01:30Z","creator":"cziletti","success":1,"relation":"main_file","file_name":"2021_Cells_Muench.pdf","checksum":"e0497ce5c77fa3b65a538c7d6e0f6c66","access_level":"open_access","date_created":"2021-08-04T14:01:30Z","content_type":"application/pdf","file_id":"9768"}]},{"scopus_import":"1","file":[{"success":1,"creator":"dernst","date_updated":"2021-03-22T11:18:58Z","file_size":8602096,"file_id":"9275","content_type":"application/pdf","date_created":"2021-03-22T11:18:58Z","access_level":"open_access","checksum":"e1022f3aee349853ded2b2b3e092362d","file_name":"2021_NatureComm_Hu.pdf","relation":"main_file"}],"date_created":"2021-03-21T23:01:19Z","volume":12,"file_date_updated":"2021-03-22T11:18:58Z","article_type":"original","author":[{"last_name":"Hu","first_name":"Yangjie","full_name":"Hu, Yangjie"},{"full_name":"Omary, Moutasem","last_name":"Omary","first_name":"Moutasem"},{"full_name":"Hu, Yun","first_name":"Yun","last_name":"Hu"},{"full_name":"Doron, Ohad","first_name":"Ohad","last_name":"Doron"},{"full_name":"Hörmayer, Lukas","first_name":"Lukas","orcid":"0000-0001-8295-2926","id":"2EEE7A2A-F248-11E8-B48F-1D18A9856A87","last_name":"Hörmayer"},{"full_name":"Chen, Qingguo","first_name":"Qingguo","last_name":"Chen"},{"first_name":"Or","last_name":"Megides","full_name":"Megides, Or"},{"full_name":"Chekli, Ori","first_name":"Ori","last_name":"Chekli"},{"full_name":"Ding, Zhaojun","last_name":"Ding","first_name":"Zhaojun"},{"last_name":"Friml","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jiří","full_name":"Friml, Jiří"},{"last_name":"Zhao","first_name":"Yunde","full_name":"Zhao, Yunde"},{"full_name":"Tsarfaty, Ilan","first_name":"Ilan","last_name":"Tsarfaty"},{"last_name":"Shani","first_name":"Eilon","full_name":"Shani, Eilon"}],"date_updated":"2026-04-02T13:57:40Z","month":"03","isi":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"year":"2021","publication":"Nature Communications","citation":{"ista":"Hu Y, Omary M, Hu Y, Doron O, Hörmayer L, Chen Q, Megides O, Chekli O, Ding Z, Friml J, Zhao Y, Tsarfaty I, Shani E. 2021. Cell kinetics of auxin transport and activity in Arabidopsis root growth and skewing. Nature Communications. 12, 1657.","ieee":"Y. Hu <i>et al.</i>, “Cell kinetics of auxin transport and activity in Arabidopsis root growth and skewing,” <i>Nature Communications</i>, vol. 12. Springer Nature, 2021.","ama":"Hu Y, Omary M, Hu Y, et al. Cell kinetics of auxin transport and activity in Arabidopsis root growth and skewing. <i>Nature Communications</i>. 2021;12. doi:<a href=\"https://doi.org/10.1038/s41467-021-21802-3\">10.1038/s41467-021-21802-3</a>","mla":"Hu, Yangjie, et al. “Cell Kinetics of Auxin Transport and Activity in Arabidopsis Root Growth and Skewing.” <i>Nature Communications</i>, vol. 12, 1657, Springer Nature, 2021, doi:<a href=\"https://doi.org/10.1038/s41467-021-21802-3\">10.1038/s41467-021-21802-3</a>.","chicago":"Hu, Yangjie, Moutasem Omary, Yun Hu, Ohad Doron, Lukas Hörmayer, Qingguo Chen, Or Megides, et al. “Cell Kinetics of Auxin Transport and Activity in Arabidopsis Root Growth and Skewing.” <i>Nature Communications</i>. Springer Nature, 2021. <a href=\"https://doi.org/10.1038/s41467-021-21802-3\">https://doi.org/10.1038/s41467-021-21802-3</a>.","short":"Y. Hu, M. Omary, Y. Hu, O. Doron, L. Hörmayer, Q. Chen, O. Megides, O. Chekli, Z. Ding, J. Friml, Y. Zhao, I. Tsarfaty, E. Shani, Nature Communications 12 (2021).","apa":"Hu, Y., Omary, M., Hu, Y., Doron, O., Hörmayer, L., Chen, Q., … Shani, E. (2021). Cell kinetics of auxin transport and activity in Arabidopsis root growth and skewing. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-021-21802-3\">https://doi.org/10.1038/s41467-021-21802-3</a>"},"publication_status":"published","external_id":{"pmid":["33712581"],"isi":["000630419400048"]},"language":[{"iso":"eng"}],"pmid":1,"abstract":[{"lang":"eng","text":"Auxin is a key regulator of plant growth and development. Local auxin biosynthesis and intercellular transport generates regional gradients in the root that are instructive for processes such as specification of developmental zones that maintain root growth and tropic responses. Here we present a toolbox to study auxin-mediated root development that features: (i) the ability to control auxin synthesis with high spatio-temporal resolution and (ii) single-cell nucleus tracking and morphokinetic analysis infrastructure. Integration of these two features enables cutting-edge analysis of root development at single-cell resolution based on morphokinetic parameters under normal growth conditions and during cell-type-specific induction of auxin biosynthesis. We show directional auxin flow in the root and refine the contributions of key players in this process. In addition, we determine the quantitative kinetics of Arabidopsis root meristem skewing, which depends on local auxin gradients but does not require PIN2 and AUX1 auxin transporter activities. Beyond the mechanistic insights into root development, the tools developed here will enable biologists to study kinetics and morphology of various critical processes at the single cell-level in whole organisms."}],"publisher":"Springer Nature","quality_controlled":"1","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","article_number":"1657","oa":1,"oa_version":"Published Version","has_accepted_license":"1","doi":"10.1038/s41467-021-21802-3","date_published":"2021-03-12T00:00:00Z","type":"journal_article","status":"public","article_processing_charge":"No","day":"12","title":"Cell kinetics of auxin transport and activity in Arabidopsis root growth and skewing","intvolume":"        12","publication_identifier":{"eissn":["2041-1723"]},"acknowledgement":"This work was supported by grants from the Israel Science Foundation (2378/19 to E.S.), the Joint NSFC-ISF Research Grant (3419/20 to E.S. and Z.D.), the Human Frontier Science Program (HFSP—LIY000540/2020 to E.S.), the European Research Council Starting Grant (757683- RobustHormoneTrans to E.S.), PBC postdoctoral fellowships (to Y.H. and M.O.), NIH (GM114660 to Y.Z.), Breast Cancer Research Foundation (BCRF to I.T.).","_id":"9254","ddc":["580"],"department":[{"_id":"JiFr"}]},{"date_updated":"2026-04-02T13:56:42Z","isi":1,"month":"07","author":[{"last_name":"Graff","first_name":"Grzegorz","full_name":"Graff, Grzegorz"},{"full_name":"Graff, Beata","last_name":"Graff","first_name":"Beata"},{"id":"3768D56A-F248-11E8-B48F-1D18A9856A87","first_name":"Pawel","last_name":"Pilarczyk","full_name":"Pilarczyk, Pawel"},{"last_name":"Jablonski","id":"4483EF78-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-3536-9866","first_name":"Grzegorz","full_name":"Jablonski, Grzegorz"},{"first_name":"Dariusz","last_name":"Gąsecki","full_name":"Gąsecki, Dariusz"},{"full_name":"Narkiewicz, Krzysztof","last_name":"Narkiewicz","first_name":"Krzysztof"}],"article_type":"original","file_date_updated":"2021-08-09T09:25:41Z","volume":16,"scopus_import":"1","issue":"7","file":[{"file_size":2706919,"success":1,"creator":"asandaue","date_updated":"2021-08-09T09:25:41Z","file_name":"2021_PLoSONE_Graff.pdf","relation":"main_file","content_type":"application/pdf","file_id":"9832","date_created":"2021-08-09T09:25:41Z","access_level":"open_access","checksum":"0277aa155d5db1febd2cb384768bba5f"}],"date_created":"2021-08-08T22:01:28Z","language":[{"iso":"eng"}],"external_id":{"pmid":["34292957"],"isi":["000678124900050"]},"publication_status":"published","citation":{"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>.","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.","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>","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.","short":"G. Graff, B. Graff, P. Pilarczyk, G. Jablonski, D. Gąsecki, K. Narkiewicz, PLoS ONE 16 (2021).","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>.","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>"},"publication":"PLoS ONE","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"year":"2021","doi":"10.1371/journal.pone.0253851","oa_version":"Published Version","has_accepted_license":"1","oa":1,"article_number":"e0253851","quality_controlled":"1","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","publisher":"Public Library of Science","abstract":[{"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.","lang":"eng"}],"pmid":1,"_id":"9821","ddc":["006"],"department":[{"_id":"HeEd"}],"publication_identifier":{"eissn":["1932-6203"]},"acknowledgement":"We express our gratitude to the anonymous referees who provided constructive comments that helped us improve the quality of the paper.","intvolume":"        16","day":"01","title":"Persistent homology as a new method of the assessment of heart rate variability","article_processing_charge":"Yes","status":"public","date_published":"2021-07-01T00:00:00Z","type":"journal_article"},{"doi":"10.1088/1367-2630/ac23f1","has_accepted_license":"1","oa_version":"Published Version","oa":1,"article_number":"093043","arxiv":1,"quality_controlled":"1","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","publisher":"IOP Publishing","abstract":[{"text":"In dense biological tissues, cell types performing different roles remain segregated by maintaining sharp interfaces. To better understand the mechanisms for such sharp compartmentalization, we study the effect of an imposed heterotypic tension at the interface between two distinct cell types in a fully 3D Voronoi model for confluent tissues. We find that cells rapidly sort and self-organize to generate a tissue-scale interface between cell types, and cells adjacent to this interface exhibit signature geometric features including nematic-like ordering, bimodal facet areas, and registration, or alignment, of cell centers on either side of the two-tissue interface. The magnitude of these features scales directly with the magnitude of the imposed tension, suggesting that biologists can estimate the magnitude of tissue surface tension between two tissue types simply by segmenting a 3D tissue. To uncover the underlying physical mechanisms driving these geometric features, we develop two minimal, ordered models using two different underlying lattices that identify an energetic competition between bulk cell shapes and tissue interface area. When the interface area dominates, changes to neighbor topology are costly and occur less frequently, which generates the observed geometric features.","lang":"eng"}],"ddc":["570"],"_id":"10178","department":[{"_id":"EdHa"}],"publication_identifier":{"eissn":["1367-2630"]},"acknowledgement":"We thank Paula Sanematsu, Matthias Merkel, Daniel Sussman, Cristina Marchetti and Edouard Hannezo for helpful discussions, and M Merkel for developing and sharing the original version of the 3D Voronoi code. This work was primarily funded by NSF-PHY-1607416, NSF-PHY-2014192 , and are in the division of physics at the National Science Foundation. PS and MLM acknowledge additional support from Simons Grant No. 454947.\r\n","intvolume":"        23","day":"29","title":"Geometric signatures of tissue surface tension in a three-dimensional model of confluent tissue","article_processing_charge":"Yes","status":"public","date_published":"2021-09-29T00:00:00Z","type":"journal_article","date_updated":"2026-04-02T13:54:56Z","isi":1,"month":"09","author":[{"full_name":"Sahu, Preeti","last_name":"Sahu","first_name":"Preeti","id":"55BA52EE-A185-11EA-88FD-18AD3DDC885E"},{"full_name":"Schwarz, J. M.","first_name":"J. M.","last_name":"Schwarz"},{"full_name":"Manning, M. Lisa","first_name":"M. Lisa","last_name":"Manning"}],"article_type":"original","file_date_updated":"2021-10-28T12:06:01Z","volume":23,"scopus_import":"1","file":[{"content_type":"application/pdf","file_id":"10193","date_created":"2021-10-28T12:06:01Z","access_level":"open_access","checksum":"ace603e8f0962b3ba55f23fa34f57764","file_name":"2021_NewJPhys_Sahu.pdf","relation":"main_file","success":1,"creator":"cziletti","date_updated":"2021-10-28T12:06:01Z","file_size":2215016}],"issue":"9","date_created":"2021-10-24T22:01:34Z","language":[{"iso":"eng"}],"external_id":{"arxiv":["2102.05397"],"isi":["000702042400001"]},"publication_status":"published","citation":{"apa":"Sahu, P., Schwarz, J. M., &#38; Manning, M. L. (2021). Geometric signatures of tissue surface tension in a three-dimensional model of confluent tissue. <i>New Journal of Physics</i>. IOP Publishing. <a href=\"https://doi.org/10.1088/1367-2630/ac23f1\">https://doi.org/10.1088/1367-2630/ac23f1</a>","short":"P. Sahu, J.M. Schwarz, M.L. Manning, New Journal of Physics 23 (2021).","chicago":"Sahu, Preeti, J. M. Schwarz, and M. Lisa Manning. “Geometric Signatures of Tissue Surface Tension in a Three-Dimensional Model of Confluent Tissue.” <i>New Journal of Physics</i>. IOP Publishing, 2021. <a href=\"https://doi.org/10.1088/1367-2630/ac23f1\">https://doi.org/10.1088/1367-2630/ac23f1</a>.","ieee":"P. Sahu, J. M. Schwarz, and M. L. Manning, “Geometric signatures of tissue surface tension in a three-dimensional model of confluent tissue,” <i>New Journal of Physics</i>, vol. 23, no. 9. IOP Publishing, 2021.","ama":"Sahu P, Schwarz JM, Manning ML. Geometric signatures of tissue surface tension in a three-dimensional model of confluent tissue. <i>New Journal of Physics</i>. 2021;23(9). doi:<a href=\"https://doi.org/10.1088/1367-2630/ac23f1\">10.1088/1367-2630/ac23f1</a>","ista":"Sahu P, Schwarz JM, Manning ML. 2021. Geometric signatures of tissue surface tension in a three-dimensional model of confluent tissue. New Journal of Physics. 23(9), 093043.","mla":"Sahu, Preeti, et al. “Geometric Signatures of Tissue Surface Tension in a Three-Dimensional Model of Confluent Tissue.” <i>New Journal of Physics</i>, vol. 23, no. 9, 093043, IOP Publishing, 2021, doi:<a href=\"https://doi.org/10.1088/1367-2630/ac23f1\">10.1088/1367-2630/ac23f1</a>."},"publication":"New Journal of Physics","year":"2021","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"}},{"title":"Arabidopsis hypocotyl adventitious root formation is suppressed by ABA signaling","day":"27","intvolume":"        12","acknowledgement":"We thank S. Cutler (Riverside, USA) for providing the ABA biosynthesis mutants and ABA signaling mutants.","publication_identifier":{"eissn":["2073-4425"]},"department":[{"_id":"JiFr"}],"ddc":["580","570"],"_id":"9909","type":"journal_article","date_published":"2021-07-27T00:00:00Z","status":"public","article_processing_charge":"Yes","article_number":"1141","oa":1,"oa_version":"Published Version","has_accepted_license":"1","doi":"10.3390/genes12081141","abstract":[{"text":"Roots are composed of different root types and, in the dicotyledonous Arabidopsis, typically consist of a primary root that branches into lateral roots. Adventitious roots emerge from non-root tissue and are formed upon wounding or other types of abiotic stress. Here, we investigated adventitious root (AR) formation in Arabidopsis hypocotyls under conditions of altered abscisic acid (ABA) signaling. Exogenously applied ABA suppressed AR formation at 0.25 µM or higher doses. AR formation was less sensitive to the synthetic ABA analog pyrabactin (PB). However, PB was a more potent inhibitor at concentrations above 1 µM, suggesting that it was more selective in triggering a root inhibition response. Analysis of a series of phosphonamide and phosphonate pyrabactin analogs suggested that adventitious root formation and lateral root branching are differentially regulated by ABA signaling. ABA biosynthesis and signaling mutants affirmed a general inhibitory role of ABA and point to PYL1 and PYL2 as candidate ABA receptors that regulate AR inhibition.","lang":"eng"}],"publisher":"MDPI","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","quality_controlled":"1","publication_status":"published","external_id":{"isi":["000690558000001"]},"language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"year":"2021","publication":"Genes","citation":{"ama":"Zeng Y, Verstraeten I, Trinh HK, et al. Arabidopsis hypocotyl adventitious root formation is suppressed by ABA signaling. <i>Genes</i>. 2021;12(8). doi:<a href=\"https://doi.org/10.3390/genes12081141\">10.3390/genes12081141</a>","ieee":"Y. Zeng <i>et al.</i>, “Arabidopsis hypocotyl adventitious root formation is suppressed by ABA signaling,” <i>Genes</i>, vol. 12, no. 8. MDPI, 2021.","ista":"Zeng Y, Verstraeten I, Trinh HK, Heugebaert T, Stevens CV, Garcia-Maquilon I, Rodriguez PL, Vanneste S, Geelen D. 2021. Arabidopsis hypocotyl adventitious root formation is suppressed by ABA signaling. Genes. 12(8), 1141.","mla":"Zeng, Yinwei, et al. “Arabidopsis Hypocotyl Adventitious Root Formation Is Suppressed by ABA Signaling.” <i>Genes</i>, vol. 12, no. 8, 1141, MDPI, 2021, doi:<a href=\"https://doi.org/10.3390/genes12081141\">10.3390/genes12081141</a>.","chicago":"Zeng, Yinwei, Inge Verstraeten, Hoang Khai Trinh, Thomas Heugebaert, Christian V. Stevens, Irene Garcia-Maquilon, Pedro L. Rodriguez, Steffen Vanneste, and Danny Geelen. “Arabidopsis Hypocotyl Adventitious Root Formation Is Suppressed by ABA Signaling.” <i>Genes</i>. MDPI, 2021. <a href=\"https://doi.org/10.3390/genes12081141\">https://doi.org/10.3390/genes12081141</a>.","short":"Y. Zeng, I. Verstraeten, H.K. Trinh, T. Heugebaert, C.V. Stevens, I. Garcia-Maquilon, P.L. Rodriguez, S. Vanneste, D. Geelen, Genes 12 (2021).","apa":"Zeng, Y., Verstraeten, I., Trinh, H. K., Heugebaert, T., Stevens, C. V., Garcia-Maquilon, I., … Geelen, D. (2021). Arabidopsis hypocotyl adventitious root formation is suppressed by ABA signaling. <i>Genes</i>. MDPI. <a href=\"https://doi.org/10.3390/genes12081141\">https://doi.org/10.3390/genes12081141</a>"},"month":"07","isi":1,"date_updated":"2026-04-02T13:57:06Z","date_created":"2021-08-15T22:01:28Z","file":[{"success":1,"creator":"asandaue","date_updated":"2021-08-16T09:02:40Z","file_size":1340305,"file_id":"9919","content_type":"application/pdf","date_created":"2021-08-16T09:02:40Z","access_level":"open_access","checksum":"3d99535618cf9a5b14d264408fa52e97","file_name":"2021_Genes_Zeng.pdf","relation":"main_file"}],"issue":"8","scopus_import":"1","volume":12,"file_date_updated":"2021-08-16T09:02:40Z","article_type":"original","author":[{"first_name":"Yinwei","last_name":"Zeng","full_name":"Zeng, Yinwei"},{"last_name":"Verstraeten","orcid":"0000-0001-7241-2328","id":"362BF7FE-F248-11E8-B48F-1D18A9856A87","first_name":"Inge","full_name":"Verstraeten, Inge"},{"full_name":"Trinh, Hoang Khai","first_name":"Hoang Khai","last_name":"Trinh"},{"last_name":"Heugebaert","first_name":"Thomas","full_name":"Heugebaert, Thomas"},{"last_name":"Stevens","first_name":"Christian V.","full_name":"Stevens, Christian V."},{"last_name":"Garcia-Maquilon","first_name":"Irene","full_name":"Garcia-Maquilon, Irene"},{"first_name":"Pedro L.","last_name":"Rodriguez","full_name":"Rodriguez, Pedro L."},{"full_name":"Vanneste, Steffen","last_name":"Vanneste","first_name":"Steffen"},{"first_name":"Danny","last_name":"Geelen","full_name":"Geelen, Danny"}]},{"date_updated":"2026-04-02T13:58:00Z","isi":1,"month":"04","file_date_updated":"2021-04-19T10:40:01Z","article_type":"original","author":[{"full_name":"Mitrouskas, David Johannes","last_name":"Mitrouskas","first_name":"David Johannes","id":"cbddacee-2b11-11eb-a02e-a2e14d04e52d"}],"scopus_import":"1","file":[{"file_name":"2021_LettersMathPhysics_Mitrouskas.pdf","relation":"main_file","date_created":"2021-04-19T10:40:01Z","file_id":"9341","content_type":"application/pdf","checksum":"be56c0845a43c0c5c772ee0b5053f7d7","access_level":"open_access","file_size":438084,"creator":"dernst","success":1,"date_updated":"2021-04-19T10:40:01Z"}],"date_created":"2021-04-18T22:01:41Z","volume":111,"language":[{"iso":"eng"}],"publication_status":"published","external_id":{"isi":["000637359300002"]},"citation":{"mla":"Mitrouskas, David Johannes. “A Note on the Fröhlich Dynamics in the Strong Coupling Limit.” <i>Letters in Mathematical Physics</i>, vol. 111, 45, Springer Nature, 2021, doi:<a href=\"https://doi.org/10.1007/s11005-021-01380-7\">10.1007/s11005-021-01380-7</a>.","ama":"Mitrouskas DJ. A note on the Fröhlich dynamics in the strong coupling limit. <i>Letters in Mathematical Physics</i>. 2021;111. doi:<a href=\"https://doi.org/10.1007/s11005-021-01380-7\">10.1007/s11005-021-01380-7</a>","ista":"Mitrouskas DJ. 2021. A note on the Fröhlich dynamics in the strong coupling limit. Letters in Mathematical Physics. 111, 45.","ieee":"D. J. Mitrouskas, “A note on the Fröhlich dynamics in the strong coupling limit,” <i>Letters in Mathematical Physics</i>, vol. 111. Springer Nature, 2021.","short":"D.J. Mitrouskas, Letters in Mathematical Physics 111 (2021).","chicago":"Mitrouskas, David Johannes. “A Note on the Fröhlich Dynamics in the Strong Coupling Limit.” <i>Letters in Mathematical Physics</i>. Springer Nature, 2021. <a href=\"https://doi.org/10.1007/s11005-021-01380-7\">https://doi.org/10.1007/s11005-021-01380-7</a>.","apa":"Mitrouskas, D. J. (2021). A note on the Fröhlich dynamics in the strong coupling limit. <i>Letters in Mathematical Physics</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s11005-021-01380-7\">https://doi.org/10.1007/s11005-021-01380-7</a>"},"year":"2021","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"publication":"Letters in Mathematical Physics","has_accepted_license":"1","oa_version":"Published Version","doi":"10.1007/s11005-021-01380-7","article_number":"45","oa":1,"publisher":"Springer Nature","quality_controlled":"1","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","abstract":[{"lang":"eng","text":"We revise a previous result about the Fröhlich dynamics in the strong coupling limit obtained in Griesemer (Rev Math Phys 29(10):1750030, 2017). In the latter it was shown that the Fröhlich time evolution applied to the initial state φ0⊗ξα, where φ0 is the electron ground state of the Pekar energy functional and ξα the associated coherent state of the phonons, can be approximated by a global phase for times small compared to α2. In the present note we prove that a similar approximation holds for t=O(α2) if one includes a nontrivial effective dynamics for the phonons that is generated by an operator proportional to α−2 and quadratic in creation and annihilation operators. Our result implies that the electron ground state remains close to its initial state for times of order α2, while the phonon fluctuations around the coherent state ξα can be described by a time-dependent Bogoliubov transformation."}],"publication_identifier":{"issn":["0377-9017"],"eissn":["1573-0530"]},"acknowledgement":"I thank Marcel Griesemer for many interesting discussions about the Fröhlich polaron and also for valuable comments on this manuscript. Helpful discussions with Nikolai Leopold and Robert Seiringer are also gratefully acknowledged. This work was partially supported by the Deutsche Forschungsgemeinschaft (DFG) through the Research Training Group 1838: Spectral Theory and Dynamics of Quantum Systems. Open Access funding enabled and organized by Projekt DEAL.","ddc":["510"],"_id":"9333","department":[{"_id":"RoSe"}],"day":"05","title":"A note on the Fröhlich dynamics in the strong coupling limit","intvolume":"       111","status":"public","article_processing_charge":"No","date_published":"2021-04-05T00:00:00Z","type":"journal_article"},{"file":[{"file_name":"2021_eLife_Hankeova.pdf","relation":"main_file","date_created":"2021-03-22T08:50:33Z","content_type":"application/pdf","file_id":"9271","checksum":"20ccf4dfe46c48cf986794c8bf4fd1cb","access_level":"open_access","file_size":9259690,"creator":"dernst","success":1,"date_updated":"2021-03-22T08:50:33Z"}],"project":[{"name":"Design Principles of Branching Morphogenesis","grant_number":"851288","call_identifier":"H2020","_id":"05943252-7A3F-11EA-A408-12923DDC885E"}],"scopus_import":"1","date_created":"2021-03-14T23:01:34Z","volume":10,"file_date_updated":"2021-03-22T08:50:33Z","article_type":"original","author":[{"first_name":"Simona","last_name":"Hankeova","full_name":"Hankeova, Simona"},{"full_name":"Salplachta, Jakub","first_name":"Jakub","last_name":"Salplachta"},{"full_name":"Zikmund, Tomas","last_name":"Zikmund","first_name":"Tomas"},{"full_name":"Kavkova, Michaela","first_name":"Michaela","last_name":"Kavkova"},{"last_name":"Van Hul","first_name":"Noémi","full_name":"Van Hul, Noémi"},{"first_name":"Adam","last_name":"Brinek","full_name":"Brinek, Adam"},{"last_name":"Smekalova","first_name":"Veronika","full_name":"Smekalova, Veronika"},{"full_name":"Laznovsky, Jakub","first_name":"Jakub","last_name":"Laznovsky"},{"last_name":"Dawit","first_name":"Feven","full_name":"Dawit, Feven"},{"full_name":"Jaros, Josef","first_name":"Josef","last_name":"Jaros"},{"full_name":"Bryja, Vítězslav","last_name":"Bryja","first_name":"Vítězslav"},{"last_name":"Lendahl","first_name":"Urban","full_name":"Lendahl, Urban"},{"first_name":"Ewa","last_name":"Ellis","full_name":"Ellis, Ewa"},{"last_name":"Nemeth","first_name":"Antal","full_name":"Nemeth, Antal"},{"first_name":"Björn","last_name":"Fischler","full_name":"Fischler, Björn"},{"last_name":"Hannezo","first_name":"Edouard B","orcid":"0000-0001-6005-1561","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","full_name":"Hannezo, Edouard B"},{"last_name":"Kaiser","first_name":"Jozef","full_name":"Kaiser, Jozef"},{"first_name":"Emma Rachel","last_name":"Andersson","full_name":"Andersson, Emma Rachel"}],"date_updated":"2026-04-02T14:00:00Z","isi":1,"month":"02","year":"2021","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"publication":"eLife","citation":{"ama":"Hankeova S, Salplachta J, Zikmund T, et al. DUCT reveals architectural mechanisms contributing to bile duct recovery in a mouse model for alagille syndrome. <i>eLife</i>. 2021;10. doi:<a href=\"https://doi.org/10.7554/eLife.60916\">10.7554/eLife.60916</a>","ista":"Hankeova S, Salplachta J, Zikmund T, Kavkova M, Van Hul N, Brinek A, Smekalova V, Laznovsky J, Dawit F, Jaros J, Bryja V, Lendahl U, Ellis E, Nemeth A, Fischler B, Hannezo EB, Kaiser J, Andersson ER. 2021. DUCT reveals architectural mechanisms contributing to bile duct recovery in a mouse model for alagille syndrome. eLife. 10, e60916.","ieee":"S. Hankeova <i>et al.</i>, “DUCT reveals architectural mechanisms contributing to bile duct recovery in a mouse model for alagille syndrome,” <i>eLife</i>, vol. 10. eLife Sciences Publications, 2021.","mla":"Hankeova, Simona, et al. “DUCT Reveals Architectural Mechanisms Contributing to Bile Duct Recovery in a Mouse Model for Alagille Syndrome.” <i>ELife</i>, vol. 10, e60916, eLife Sciences Publications, 2021, doi:<a href=\"https://doi.org/10.7554/eLife.60916\">10.7554/eLife.60916</a>.","short":"S. Hankeova, J. Salplachta, T. Zikmund, M. Kavkova, N. Van Hul, A. Brinek, V. Smekalova, J. Laznovsky, F. Dawit, J. Jaros, V. Bryja, U. Lendahl, E. Ellis, A. Nemeth, B. Fischler, E.B. Hannezo, J. Kaiser, E.R. Andersson, ELife 10 (2021).","chicago":"Hankeova, Simona, Jakub Salplachta, Tomas Zikmund, Michaela Kavkova, Noémi Van Hul, Adam Brinek, Veronika Smekalova, et al. “DUCT Reveals Architectural Mechanisms Contributing to Bile Duct Recovery in a Mouse Model for Alagille Syndrome.” <i>ELife</i>. eLife Sciences Publications, 2021. <a href=\"https://doi.org/10.7554/eLife.60916\">https://doi.org/10.7554/eLife.60916</a>.","apa":"Hankeova, S., Salplachta, J., Zikmund, T., Kavkova, M., Van Hul, N., Brinek, A., … Andersson, E. R. (2021). DUCT reveals architectural mechanisms contributing to bile duct recovery in a mouse model for alagille syndrome. <i>ELife</i>. eLife Sciences Publications. <a href=\"https://doi.org/10.7554/eLife.60916\">https://doi.org/10.7554/eLife.60916</a>"},"publication_status":"published","external_id":{"isi":["000625357100001"],"pmid":["33635272"]},"language":[{"iso":"eng"}],"pmid":1,"abstract":[{"text":"Organ function depends on tissues adopting the correct architecture. However, insights into organ architecture are currently hampered by an absence of standardized quantitative 3D analysis. We aimed to develop a robust technology to visualize, digitalize, and segment the architecture of two tubular systems in 3D: double resin casting micro computed tomography (DUCT). As proof of principle, we applied DUCT to a mouse model for Alagille syndrome (Jag1Ndr/Ndr mice), characterized by intrahepatic bile duct paucity, that can spontaneously generate a biliary system in adulthood. DUCT identified increased central biliary branching and peripheral bile duct tortuosity as two compensatory processes occurring in distinct regions of Jag1Ndr/Ndr liver, leading to full reconstitution of wild-type biliary volume and phenotypic recovery. DUCT is thus a powerful new technology for 3D analysis, which can reveal novel phenotypes and provide a standardized method of defining liver architecture in mouse models.","lang":"eng"}],"publisher":"eLife Sciences Publications","quality_controlled":"1","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","article_number":"e60916","oa":1,"has_accepted_license":"1","oa_version":"Published Version","doi":"10.7554/eLife.60916","date_published":"2021-02-26T00:00:00Z","type":"journal_article","status":"public","article_processing_charge":"No","day":"26","title":"DUCT reveals architectural mechanisms contributing to bile duct recovery in a mouse model for alagille syndrome","ec_funded":1,"intvolume":"        10","publication_identifier":{"eissn":["2050-084X"]},"acknowledgement":"Work in ERA lab is supported by the Swedish Research Council, the Center of Innovative Medicine (CIMED) Grant, Karolinska Institutet, and the Heart and Lung Foundation, and\r\nthe Daniel Alagille Award from the European Association for the Study of the Liver. One project in ERA lab is funded by ModeRNA, unrelated to this project. The funders have no role in the design or interpretation of the work. SH has been supported by a KI-MU PhD student program, and by a Wera Ekstro¨m Foundation Scholarship. We are grateful for support from Tornspiran foundation to NVH. JK: This research was carried out under the project CEITEC 2020 (LQ1601) with financial support from the Ministry of Education, Youth and Sports of the Czech Republic under the National Sustainability Programme II and CzechNanoLab Research Infrastructure supported by MEYS CR (LM2018110) . UL: The financial support from the Swedish Research Council and ICMC (Integrated CardioMetabolic Center) is acknowledged. JJ: The work was supported by the Grant Agency of Masaryk University (project no. MUNI/A/1565/2018). We thank Kari Huppert and Stacey Huppert for their expertise and help regarding bile duct cannulation and their laboratory hospitality. We also thank Nadja Schultz and Charlotte L Mattsson for their help with common bile duct cannulation. We thank Daniel Holl for his help with trachea cannulation. We thank Nikos Papadogiannakis for his assistance with mild Alagille biopsy samples and discussion. We thank Karolinska Biomedicum Imaging Core, especially Shigeaki Kanatani for his help with image analysis. We thank Jan Masek and Carolina Gutierrez for their scientific input in manuscript writing. We thank Peter Ranefall and the BioImage Informatics (SciLife national facility) for their help writing parts of the MATLAB pipeline.\r\nThe TROMA-III antibody developed by Rolf Kemler was obtained from the Developmental Studies Hybridoma (DSHB) Bank developed under the auspices of NICHD and maintained by The University of Iowa, Department of Biological Sciences, Iowa City, IA52242. We thank Goncalo M Brito for all illustrations. This work was supported by the European Union (European Research Council Starting grant 851288 to E.H.).","_id":"9244","ddc":["570"],"department":[{"_id":"EdHa"}]},{"quality_controlled":"1","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","publisher":"Rockefeller University Press","abstract":[{"text":"Assemblies of actin and its regulators underlie the dynamic morphology of all eukaryotic cells. To understand how actin regulatory proteins work together to generate actin-rich structures such as filopodia, we analyzed the localization of diverse actin regulators within filopodia in Drosophila embryos and in a complementary in vitro system of filopodia-like structures (FLSs). We found that the composition of the regulatory protein complex where actin is incorporated (the filopodial tip complex) is remarkably heterogeneous both in vivo and in vitro. Our data reveal that different pairs of proteins correlate with each other and with actin bundle length, suggesting the presence of functional subcomplexes. This is consistent with a theoretical framework where three or more redundant subcomplexes join the tip complex stochastically, with any two being sufficient to drive filopodia formation. We provide an explanation for the observed heterogeneity and suggest that a mechanism based on multiple components allows stereotypical filopodial dynamics to arise from diverse upstream signaling pathways.","lang":"eng"}],"pmid":1,"doi":"10.1083/jcb.202003052","has_accepted_license":"1","oa_version":"Published Version","oa":1,"article_number":"e202003052","article_processing_charge":"No","status":"public","date_published":"2021-03-19T00:00:00Z","type":"journal_article","_id":"9306","ddc":["576"],"department":[{"_id":"EdHa"}],"publication_identifier":{"eissn":["1540-8140"]},"acknowledgement":"This work was supported by European Research Council grant 281971, Wellcome Trust Research Career Development Fellowship WT095829AIA and Wellcome Trust Senior Research\r\nFellowship 219482/Z/19/Z to J.L. Gallop, a Wellcome Trust Senior Investigator Award 098357 to B.D. Simons, and an Austrian Science Fund grant (P31639) to E. Hannezo. We acknowledge\r\ncore funding by the Wellcome Trust (092096) and Cancer Research UK (C6946/A14492). U. Dobramysl was supported by a Wellcome Trust Junior Interdisciplinary Fellowship grant\r\n(105602/Z/14/Z) and a Herchel Smith Postdoctoral Fellowship. H. Shimo was supported by a Funai Foundation Overseas scholarship.","intvolume":"       220","day":"19","title":"Stochastic combinations of actin regulatory proteins are sufficient to drive filopodia formation","author":[{"last_name":"Dobramysl","first_name":"Ulrich","full_name":"Dobramysl, Ulrich"},{"last_name":"Jarsch","first_name":"Iris Katharina","full_name":"Jarsch, Iris Katharina"},{"full_name":"Inoue, Yoshiko","last_name":"Inoue","first_name":"Yoshiko"},{"first_name":"Hanae","last_name":"Shimo","full_name":"Shimo, Hanae"},{"first_name":"Benjamin","last_name":"Richier","full_name":"Richier, Benjamin"},{"first_name":"Jonathan R.","last_name":"Gadsby","full_name":"Gadsby, Jonathan R."},{"full_name":"Mason, Julia","first_name":"Julia","last_name":"Mason"},{"first_name":"Alicja","last_name":"Szałapak","full_name":"Szałapak, Alicja"},{"last_name":"Ioannou","first_name":"Pantelis Savvas","full_name":"Ioannou, Pantelis Savvas"},{"full_name":"Correia, Guilherme Pereira","last_name":"Correia","first_name":"Guilherme Pereira"},{"last_name":"Walrant","first_name":"Astrid","full_name":"Walrant, Astrid"},{"full_name":"Butler, Richard","first_name":"Richard","last_name":"Butler"},{"full_name":"Hannezo, Edouard B","orcid":"0000-0001-6005-1561","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","first_name":"Edouard B","last_name":"Hannezo"},{"full_name":"Simons, Benjamin D.","first_name":"Benjamin D.","last_name":"Simons"},{"first_name":"Jennifer L.","last_name":"Gallop","full_name":"Gallop, Jennifer L."}],"file_date_updated":"2021-04-06T10:39:08Z","article_type":"original","volume":220,"project":[{"grant_number":"P31639","_id":"268294B6-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Active mechano-chemical description of the cell cytoskeleton"}],"scopus_import":"1","file":[{"success":1,"creator":"dernst","date_updated":"2021-04-06T10:39:08Z","file_size":9019720,"file_id":"9310","content_type":"application/pdf","date_created":"2021-04-06T10:39:08Z","access_level":"open_access","checksum":"4739ffd90f2c7e05ac5b00f057c58aa2","file_name":"2021_JCB_Dobramysl.pdf","relation":"main_file"}],"issue":"4","date_created":"2021-04-04T22:01:21Z","date_updated":"2026-04-02T13:59:43Z","month":"03","isi":1,"citation":{"mla":"Dobramysl, Ulrich, et al. “Stochastic Combinations of Actin Regulatory Proteins Are Sufficient to Drive Filopodia Formation.” <i>Journal of Cell Biology</i>, vol. 220, no. 4, e202003052, Rockefeller University Press, 2021, doi:<a href=\"https://doi.org/10.1083/jcb.202003052\">10.1083/jcb.202003052</a>.","ista":"Dobramysl U, Jarsch IK, Inoue Y, Shimo H, Richier B, Gadsby JR, Mason J, Szałapak A, Ioannou PS, Correia GP, Walrant A, Butler R, Hannezo EB, Simons BD, Gallop JL. 2021. Stochastic combinations of actin regulatory proteins are sufficient to drive filopodia formation. Journal of Cell Biology. 220(4), e202003052.","ama":"Dobramysl U, Jarsch IK, Inoue Y, et al. Stochastic combinations of actin regulatory proteins are sufficient to drive filopodia formation. <i>Journal of Cell Biology</i>. 2021;220(4). doi:<a href=\"https://doi.org/10.1083/jcb.202003052\">10.1083/jcb.202003052</a>","ieee":"U. Dobramysl <i>et al.</i>, “Stochastic combinations of actin regulatory proteins are sufficient to drive filopodia formation,” <i>Journal of Cell Biology</i>, vol. 220, no. 4. Rockefeller University Press, 2021.","short":"U. Dobramysl, I.K. Jarsch, Y. Inoue, H. Shimo, B. Richier, J.R. Gadsby, J. Mason, A. Szałapak, P.S. Ioannou, G.P. Correia, A. Walrant, R. Butler, E.B. Hannezo, B.D. Simons, J.L. Gallop, Journal of Cell Biology 220 (2021).","chicago":"Dobramysl, Ulrich, Iris Katharina Jarsch, Yoshiko Inoue, Hanae Shimo, Benjamin Richier, Jonathan R. Gadsby, Julia Mason, et al. “Stochastic Combinations of Actin Regulatory Proteins Are Sufficient to Drive Filopodia Formation.” <i>Journal of Cell Biology</i>. Rockefeller University Press, 2021. <a href=\"https://doi.org/10.1083/jcb.202003052\">https://doi.org/10.1083/jcb.202003052</a>.","apa":"Dobramysl, U., Jarsch, I. K., Inoue, Y., Shimo, H., Richier, B., Gadsby, J. R., … Gallop, J. L. (2021). Stochastic combinations of actin regulatory proteins are sufficient to drive filopodia formation. <i>Journal of Cell Biology</i>. Rockefeller University Press. <a href=\"https://doi.org/10.1083/jcb.202003052\">https://doi.org/10.1083/jcb.202003052</a>"},"publication":"Journal of Cell Biology","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"year":"2021","language":[{"iso":"eng"}],"external_id":{"pmid":["33740033"],"isi":["000663160600002"]},"publication_status":"published"},{"day":"19","title":"Cryo-EM grid optimization for membrane proteins","ec_funded":1,"intvolume":"        24","publication_identifier":{"eissn":["2589-0042"]},"acknowledgement":"We thank the Electron Microscopy Facilities at the Institute of Science and Technology Austria and at the Vienna Biocenter for providing access and training for the electron microscopes. This project has received funding from the European Union's Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement no. 665385 .","_id":"9205","ddc":["570"],"department":[{"_id":"LeSa"}],"date_published":"2021-03-19T00:00:00Z","type":"journal_article","status":"public","article_processing_charge":"No","license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","article_number":"102139","oa":1,"has_accepted_license":"1","oa_version":"Published Version","doi":"10.1016/j.isci.2021.102139","pmid":1,"acknowledged_ssus":[{"_id":"EM-Fac"}],"abstract":[{"lang":"eng","text":"Cryo-EM grid preparation is an important bottleneck in protein structure determination, especially for membrane proteins, typically requiring screening of a large number of conditions. We systematically investigated the effects of buffer components, blotting conditions and grid types on the outcome of grid preparation of five different membrane protein samples. Aggregation was the most common type of problem which was addressed by changing detergents, salt concentration or reconstitution of proteins into nanodiscs or amphipols. We show that the optimal concentration of detergent is between 0.05 and 0.4% and that the presence of a low concentration of detergent with a high critical micellar concentration protects the proteins from denaturation at the air-water interface. Furthermore, we discuss the strategies for achieving an adequate ice thickness, particle coverage and orientation distribution on free ice and on support films. Our findings provide a clear roadmap for comprehensive screening of conditions for cryo-EM grid preparation of membrane proteins."}],"publisher":"Elsevier","quality_controlled":"1","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","publication_status":"published","external_id":{"pmid":["33665558"],"isi":["000631646000012"]},"language":[{"iso":"eng"}],"year":"2021","tmp":{"short":"CC BY-NC-ND (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","image":"/images/cc_by_nc_nd.png"},"publication":"iScience","citation":{"apa":"Kampjut, D., Steiner, J., &#38; Sazanov, L. A. (2021). Cryo-EM grid optimization for membrane proteins. <i>IScience</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.isci.2021.102139\">https://doi.org/10.1016/j.isci.2021.102139</a>","mla":"Kampjut, Domen, et al. “Cryo-EM Grid Optimization for Membrane Proteins.” <i>IScience</i>, vol. 24, no. 3, 102139, Elsevier, 2021, doi:<a href=\"https://doi.org/10.1016/j.isci.2021.102139\">10.1016/j.isci.2021.102139</a>.","ama":"Kampjut D, Steiner J, Sazanov LA. Cryo-EM grid optimization for membrane proteins. <i>iScience</i>. 2021;24(3). doi:<a href=\"https://doi.org/10.1016/j.isci.2021.102139\">10.1016/j.isci.2021.102139</a>","ieee":"D. Kampjut, J. Steiner, and L. A. Sazanov, “Cryo-EM grid optimization for membrane proteins,” <i>iScience</i>, vol. 24, no. 3. Elsevier, 2021.","ista":"Kampjut D, Steiner J, Sazanov LA. 2021. Cryo-EM grid optimization for membrane proteins. iScience. 24(3), 102139.","chicago":"Kampjut, Domen, Julia Steiner, and Leonid A Sazanov. “Cryo-EM Grid Optimization for Membrane Proteins.” <i>IScience</i>. Elsevier, 2021. <a href=\"https://doi.org/10.1016/j.isci.2021.102139\">https://doi.org/10.1016/j.isci.2021.102139</a>.","short":"D. Kampjut, J. Steiner, L.A. Sazanov, IScience 24 (2021)."},"date_updated":"2026-04-02T14:00:19Z","month":"03","isi":1,"issue":"3","scopus_import":"1","file":[{"success":1,"creator":"dernst","date_updated":"2021-03-03T07:38:14Z","file_size":7431411,"content_type":"application/pdf","file_id":"9219","date_created":"2021-03-03T07:38:14Z","access_level":"open_access","checksum":"50585447386fe5842f07ab9b3a66e7e9","file_name":"2021_iScience_Kampjut.pdf","relation":"main_file"}],"project":[{"grant_number":"665385","call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","name":"International IST Doctoral Program"}],"date_created":"2021-02-28T23:01:24Z","volume":24,"file_date_updated":"2021-03-03T07:38:14Z","article_type":"original","author":[{"full_name":"Kampjut, Domen","id":"37233050-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6018-3422","first_name":"Domen","last_name":"Kampjut"},{"full_name":"Steiner, Julia","first_name":"Julia","orcid":"0000-0003-0493-3775","id":"3BB67EB0-F248-11E8-B48F-1D18A9856A87","last_name":"Steiner"},{"first_name":"Leonid A","orcid":"0000-0002-0977-7989","id":"338D39FE-F248-11E8-B48F-1D18A9856A87","last_name":"Sazanov","full_name":"Sazanov, Leonid A"}]},{"date_created":"2021-04-18T22:01:42Z","file":[{"relation":"main_file","file_name":"2021_ScienceAdv_Duan.pdf","checksum":"4b383d4a1d484a71bbc64ecf401bbdbb","access_level":"open_access","date_created":"2021-04-19T11:17:29Z","file_id":"9343","content_type":"application/pdf","file_size":717489,"date_updated":"2021-04-19T11:17:29Z","creator":"dernst","success":1}],"issue":"14","scopus_import":"1","volume":7,"article_type":"original","file_date_updated":"2021-04-19T11:17:29Z","author":[{"first_name":"J.","last_name":"Duan","full_name":"Duan, J."},{"last_name":"Álvarez-Pérez","first_name":"G.","full_name":"Álvarez-Pérez, G."},{"last_name":"Voronin","first_name":"K. V.","full_name":"Voronin, K. V."},{"full_name":"Prieto Gonzalez, Ivan","last_name":"Prieto Gonzalez","orcid":"0000-0002-7370-5357","id":"2A307FE2-F248-11E8-B48F-1D18A9856A87","first_name":"Ivan"},{"last_name":"Taboada-Gutiérrez","first_name":"J.","full_name":"Taboada-Gutiérrez, J."},{"full_name":"Volkov, V. S.","last_name":"Volkov","first_name":"V. S."},{"full_name":"Martín-Sánchez, J.","last_name":"Martín-Sánchez","first_name":"J."},{"last_name":"Nikitin","first_name":"A. Y.","full_name":"Nikitin, A. Y."},{"first_name":"P.","last_name":"Alonso-González","full_name":"Alonso-González, P."}],"month":"04","isi":1,"date_updated":"2026-04-02T13:58:21Z","year":"2021","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","short":"CC BY-NC (4.0)","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","image":"/images/cc_by_nc.png"},"publication":"Science Advances","citation":{"ieee":"J. Duan <i>et al.</i>, “Enabling propagation of anisotropic polaritons along forbidden directions via a topological transition,” <i>Science Advances</i>, vol. 7, no. 14. AAAS, 2021.","ista":"Duan J, Álvarez-Pérez G, Voronin KV, Prieto Gonzalez I, Taboada-Gutiérrez J, Volkov VS, Martín-Sánchez J, Nikitin AY, Alonso-González P. 2021. Enabling propagation of anisotropic polaritons along forbidden directions via a topological transition. Science Advances. 7(14), eabf2690.","ama":"Duan J, Álvarez-Pérez G, Voronin KV, et al. Enabling propagation of anisotropic polaritons along forbidden directions via a topological transition. <i>Science Advances</i>. 2021;7(14). doi:<a href=\"https://doi.org/10.1126/sciadv.abf2690\">10.1126/sciadv.abf2690</a>","mla":"Duan, J., et al. “Enabling Propagation of Anisotropic Polaritons along Forbidden Directions via a Topological Transition.” <i>Science Advances</i>, vol. 7, no. 14, eabf2690, AAAS, 2021, doi:<a href=\"https://doi.org/10.1126/sciadv.abf2690\">10.1126/sciadv.abf2690</a>.","chicago":"Duan, J., G. Álvarez-Pérez, K. V. Voronin, Ivan Prieto Gonzalez, J. Taboada-Gutiérrez, V. S. Volkov, J. Martín-Sánchez, A. Y. Nikitin, and P. Alonso-González. “Enabling Propagation of Anisotropic Polaritons along Forbidden Directions via a Topological Transition.” <i>Science Advances</i>. AAAS, 2021. <a href=\"https://doi.org/10.1126/sciadv.abf2690\">https://doi.org/10.1126/sciadv.abf2690</a>.","short":"J. Duan, G. Álvarez-Pérez, K.V. Voronin, I. Prieto Gonzalez, J. Taboada-Gutiérrez, V.S. Volkov, J. Martín-Sánchez, A.Y. Nikitin, P. Alonso-González, Science Advances 7 (2021).","apa":"Duan, J., Álvarez-Pérez, G., Voronin, K. V., Prieto Gonzalez, I., Taboada-Gutiérrez, J., Volkov, V. S., … Alonso-González, P. (2021). Enabling propagation of anisotropic polaritons along forbidden directions via a topological transition. <i>Science Advances</i>. AAAS. <a href=\"https://doi.org/10.1126/sciadv.abf2690\">https://doi.org/10.1126/sciadv.abf2690</a>"},"publication_status":"published","external_id":{"pmid":["33811076"],"isi":["000636455600027"]},"language":[{"iso":"eng"}],"pmid":1,"abstract":[{"text":"Polaritons with directional in-plane propagation and ultralow losses in van der Waals (vdW) crystals promise unprecedented manipulation of light at the nanoscale. However, these polaritons present a crucial limitation: their directional propagation is intrinsically determined by the crystal structure of the host material, imposing forbidden directions of propagation. Here, we demonstrate that directional polaritons (in-plane hyperbolic phonon polaritons) in a vdW crystal (α-phase molybdenum trioxide) can be directed along forbidden directions by inducing an optical topological transition, which emerges when the slab is placed on a substrate with a given negative permittivity (4H–silicon carbide). By visualizing the transition in real space, we observe exotic polaritonic states between mutually orthogonal hyperbolic regimes, which unveil the topological origin of the transition: a gap opening in the dispersion. This work provides insights into optical topological transitions in vdW crystals, which introduce a route to direct light at the nanoscale.","lang":"eng"}],"publisher":"AAAS","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","quality_controlled":"1","article_number":"eabf2690","oa":1,"oa_version":"Published Version","has_accepted_license":"1","doi":"10.1126/sciadv.abf2690","type":"journal_article","date_published":"2021-04-02T00:00:00Z","status":"public","article_processing_charge":"No","title":"Enabling propagation of anisotropic polaritons along forbidden directions via a topological transition","day":"02","intvolume":"         7","acknowledgement":"G.Á.-P. and J.T.-G. acknowledge support through the Severo Ochoa Program from the government of the Principality of Asturias (grant nos. PA20-PF-BP19-053 and PA-18-PF-BP17-126, respectively). K.V.V. and V.S.V. acknowledge the Ministry of Science and Higher Education of the Russian Federation (no. 0714-2020-0002). J. M.-S. acknowledges financial support through the Ramón y Cajal Program from the government of Spain and FSE (RYC2018-026196-I). A.Y.N. acknowledges the Spanish Ministry of Science, Innovation and Universities (national project no. MAT201788358-C3-3-R), and the Basque Department of Education (PIBA-2020-1-0014). P.A.-G. acknowledges support from the European Research Council under starting grant no. 715496, 2DNANOPTICA. ","publication_identifier":{"eissn":["2375-2548"]},"department":[{"_id":"NanoFab"}],"ddc":["530"],"_id":"9334"},{"date_published":"2021-03-23T00:00:00Z","type":"journal_article","article_processing_charge":"No","status":"public","ec_funded":1,"intvolume":"        26","day":"23","title":"Fluctuation around the circular law for random matrices with real entries","_id":"9412","ddc":["510"],"department":[{"_id":"LaEr"}],"publication_identifier":{"eissn":["1083-6489"]},"abstract":[{"text":"We extend our recent result [22] on the central limit theorem for the linear eigenvalue statistics of non-Hermitian matrices X with independent, identically distributed complex entries to the real symmetry class. We find that the expectation and variance substantially differ from their complex counterparts, reflecting (i) the special spectral symmetry of real matrices onto the real axis; and (ii) the fact that real i.i.d. matrices have many real eigenvalues. Our result generalizes the previously known special cases where either the test function is analytic [49] or the first four moments of the matrix elements match the real Gaussian [59, 44]. The key element of the proof is the analysis of several weakly dependent Dyson Brownian motions (DBMs). The conceptual novelty of the real case compared with [22] is that the correlation structure of the stochastic differentials in each individual DBM is non-trivial, potentially even jeopardising its well-posedness.","lang":"eng"}],"arxiv":1,"quality_controlled":"1","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","publisher":"Institute of Mathematical Statistics","oa":1,"article_number":"24","doi":"10.1214/21-EJP591","oa_version":"Published Version","has_accepted_license":"1","publication":"Electronic Journal of Probability","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"year":"2021","citation":{"mla":"Cipolloni, Giorgio, et al. “Fluctuation around the Circular Law for Random Matrices with Real Entries.” <i>Electronic Journal of Probability</i>, vol. 26, 24, Institute of Mathematical Statistics, 2021, doi:<a href=\"https://doi.org/10.1214/21-EJP591\">10.1214/21-EJP591</a>.","ieee":"G. Cipolloni, L. Erdös, and D. J. Schröder, “Fluctuation around the circular law for random matrices with real entries,” <i>Electronic Journal of Probability</i>, vol. 26. Institute of Mathematical Statistics, 2021.","ama":"Cipolloni G, Erdös L, Schröder DJ. Fluctuation around the circular law for random matrices with real entries. <i>Electronic Journal of Probability</i>. 2021;26. doi:<a href=\"https://doi.org/10.1214/21-EJP591\">10.1214/21-EJP591</a>","ista":"Cipolloni G, Erdös L, Schröder DJ. 2021. Fluctuation around the circular law for random matrices with real entries. Electronic Journal of Probability. 26, 24.","short":"G. Cipolloni, L. Erdös, D.J. Schröder, Electronic Journal of Probability 26 (2021).","chicago":"Cipolloni, Giorgio, László Erdös, and Dominik J Schröder. “Fluctuation around the Circular Law for Random Matrices with Real Entries.” <i>Electronic Journal of Probability</i>. Institute of Mathematical Statistics, 2021. <a href=\"https://doi.org/10.1214/21-EJP591\">https://doi.org/10.1214/21-EJP591</a>.","apa":"Cipolloni, G., Erdös, L., &#38; Schröder, D. J. (2021). Fluctuation around the circular law for random matrices with real entries. <i>Electronic Journal of Probability</i>. Institute of Mathematical Statistics. <a href=\"https://doi.org/10.1214/21-EJP591\">https://doi.org/10.1214/21-EJP591</a>"},"external_id":{"arxiv":["2002.02438"],"isi":["000641855600001"]},"publication_status":"published","language":[{"iso":"eng"}],"volume":26,"project":[{"name":"International IST Doctoral Program","grant_number":"665385","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"file":[{"file_size":865148,"date_updated":"2021-05-25T13:24:19Z","creator":"kschuh","success":1,"relation":"main_file","file_name":"2021_EJP_Cipolloni.pdf","checksum":"864ab003ad4cffea783f65aa8c2ba69f","access_level":"open_access","date_created":"2021-05-25T13:24:19Z","content_type":"application/pdf","file_id":"9423"}],"scopus_import":"1","date_created":"2021-05-23T22:01:44Z","author":[{"full_name":"Cipolloni, Giorgio","first_name":"Giorgio","orcid":"0000-0002-4901-7992","id":"42198EFA-F248-11E8-B48F-1D18A9856A87","last_name":"Cipolloni"},{"id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5366-9603","first_name":"László","last_name":"Erdös","full_name":"Erdös, László"},{"full_name":"Schröder, Dominik J","orcid":"0000-0002-2904-1856","id":"408ED176-F248-11E8-B48F-1D18A9856A87","first_name":"Dominik J","last_name":"Schröder"}],"file_date_updated":"2021-05-25T13:24:19Z","date_updated":"2026-04-02T14:00:37Z","month":"03","isi":1},{"citation":{"apa":"Gast, M., Kadzioch, N. P., Milius, D., Origgi, F., &#38; Plattet, P. (2021). Oligomerization and cell egress controlled by two microdomains of canine distemper virus matrix protein. <i>MSphere</i>. American Society for Microbiology. <a href=\"https://doi.org/10.1128/mSphere.01024-20\">https://doi.org/10.1128/mSphere.01024-20</a>","short":"M. Gast, N.P. Kadzioch, D. Milius, F. Origgi, P. Plattet, MSphere 6 (2021).","chicago":"Gast, Matthieu, Nicole P. Kadzioch, Doreen Milius, Francesco Origgi, and Philippe Plattet. “Oligomerization and Cell Egress Controlled by Two Microdomains of Canine Distemper Virus Matrix Protein.” <i>MSphere</i>. American Society for Microbiology, 2021. <a href=\"https://doi.org/10.1128/mSphere.01024-20\">https://doi.org/10.1128/mSphere.01024-20</a>.","ieee":"M. Gast, N. P. Kadzioch, D. Milius, F. Origgi, and P. Plattet, “Oligomerization and cell egress controlled by two microdomains of canine distemper virus matrix protein,” <i>mSphere</i>, vol. 6, no. 2. American Society for Microbiology, 2021.","ista":"Gast M, Kadzioch NP, Milius D, Origgi F, Plattet P. 2021. Oligomerization and cell egress controlled by two microdomains of canine distemper virus matrix protein. mSphere. 6(2), e01024-20.","ama":"Gast M, Kadzioch NP, Milius D, Origgi F, Plattet P. Oligomerization and cell egress controlled by two microdomains of canine distemper virus matrix protein. <i>mSphere</i>. 2021;6(2). doi:<a href=\"https://doi.org/10.1128/mSphere.01024-20\">10.1128/mSphere.01024-20</a>","mla":"Gast, Matthieu, et al. “Oligomerization and Cell Egress Controlled by Two Microdomains of Canine Distemper Virus Matrix Protein.” <i>MSphere</i>, vol. 6, no. 2, e01024-20, American Society for Microbiology, 2021, doi:<a href=\"https://doi.org/10.1128/mSphere.01024-20\">10.1128/mSphere.01024-20</a>."},"year":"2021","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"publication":"mSphere","language":[{"iso":"eng"}],"publication_status":"published","external_id":{"isi":["000663823400025"],"pmid":["33853875"]},"file_date_updated":"2021-05-04T12:41:38Z","author":[{"first_name":"Matthieu","last_name":"Gast","full_name":"Gast, Matthieu"},{"full_name":"Kadzioch, Nicole P.","last_name":"Kadzioch","first_name":"Nicole P."},{"last_name":"Milius","first_name":"Doreen","id":"384050BC-F248-11E8-B48F-1D18A9856A87","full_name":"Milius, Doreen"},{"first_name":"Francesco","last_name":"Origgi","full_name":"Origgi, Francesco"},{"first_name":"Philippe","last_name":"Plattet","full_name":"Plattet, Philippe"}],"date_created":"2021-05-02T22:01:28Z","file":[{"date_updated":"2021-05-04T12:41:38Z","success":1,"creator":"kschuh","file_size":3379349,"access_level":"open_access","checksum":"310748d140c8838335c1314431095898","file_id":"9370","content_type":"application/pdf","date_created":"2021-05-04T12:41:38Z","relation":"main_file","file_name":"2021_mSphere_Gast.pdf"}],"issue":"2","scopus_import":"1","volume":6,"isi":1,"month":"04","date_updated":"2026-04-02T13:58:38Z","status":"public","article_processing_charge":"No","type":"journal_article","date_published":"2021-04-14T00:00:00Z","acknowledgement":"This work was supported by the Swiss National Science Foundation (referencenumber 310030_173185 to P. P.).","publication_identifier":{"eissn":["2379-5042"]},"department":[{"_id":"Bio"}],"_id":"9361","ddc":["570"],"title":"Oligomerization and cell egress controlled by two microdomains of canine distemper virus matrix protein","day":"14","intvolume":"         6","publisher":"American Society for Microbiology","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","quality_controlled":"1","pmid":1,"abstract":[{"lang":"eng","text":"The multimeric matrix (M) protein of clinically relevant paramyxoviruses orchestrates assembly and budding activity of viral particles at the plasma membrane (PM). We identified within the canine distemper virus (CDV) M protein two microdomains, potentially assuming α-helix structures, which are essential for membrane budding activity. Remarkably, while two rationally designed microdomain M mutants (E89R, microdomain 1 and L239D, microdomain 2) preserved proper folding, dimerization, interaction with the nucleocapsid protein, localization at and deformation of the PM, the virus-like particle formation, as well as production of infectious virions (as monitored using a membrane budding-complementation system), were, in sharp contrast, strongly impaired. Of major importance, raster image correlation spectroscopy (RICS) revealed that both microdomains contributed to finely tune M protein mobility specifically at the PM. Collectively, our data highlighted the cornerstone membrane budding-priming activity of two spatially discrete M microdomains, potentially by coordinating the assembly of productive higher oligomers at the PM."}],"has_accepted_license":"1","oa_version":"Published Version","doi":"10.1128/mSphere.01024-20","article_number":"e01024-20","oa":1},{"quality_controlled":"1","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","publisher":"Public Library of Science","abstract":[{"text":"A central goal in systems neuroscience is to understand the functions performed by neural circuits. Previous top-down models addressed this question by comparing the behaviour of an ideal model circuit, optimised to perform a given function, with neural recordings. However, this requires guessing in advance what function is being performed, which may not be possible for many neural systems. To address this, we propose an inverse reinforcement learning (RL) framework for inferring the function performed by a neural network from data. We assume that the responses of each neuron in a network are optimised so as to drive the network towards ‘rewarded’ states, that are desirable for performing a given function. We then show how one can use inverse RL to infer the reward function optimised by the network from observing its responses. This inferred reward function can be used to predict how the neural network should adapt its dynamics to perform the same function when the external environment or network structure changes. This could lead to theoretical predictions about how neural network dynamics adapt to deal with cell death and/or varying sensory stimulus statistics.","lang":"eng"}],"pmid":1,"doi":"10.1371/journal.pone.0248940","oa_version":"Published Version","has_accepted_license":"1","oa":1,"article_number":"e0248940","article_processing_charge":"No","status":"public","date_published":"2021-04-15T00:00:00Z","type":"journal_article","ddc":["570"],"_id":"9362","department":[{"_id":"GaTk"}],"publication_identifier":{"eissn":["1932-6203"]},"acknowledgement":"The authors would like to thank Ulisse Ferrari for useful discussions and feedback.","intvolume":"        16","day":"15","title":"Inferring the function performed by a recurrent neural network","author":[{"last_name":"Chalk","orcid":"0000-0001-7782-4436","id":"2BAAC544-F248-11E8-B48F-1D18A9856A87","first_name":"Matthew J","full_name":"Chalk, Matthew J"},{"full_name":"Tkačik, Gašper","first_name":"Gašper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6699-1455","last_name":"Tkačik"},{"full_name":"Marre, Olivier","first_name":"Olivier","last_name":"Marre"}],"file_date_updated":"2021-05-04T13:22:19Z","article_type":"original","volume":16,"scopus_import":"1","file":[{"file_name":"2021_pone_Chalk.pdf","relation":"main_file","date_created":"2021-05-04T13:22:19Z","file_id":"9371","content_type":"application/pdf","checksum":"c52da133850307d2031f552d998f00e8","access_level":"open_access","file_size":2768282,"creator":"kschuh","success":1,"date_updated":"2021-05-04T13:22:19Z"}],"issue":"4","date_created":"2021-05-02T22:01:28Z","date_updated":"2026-04-02T13:58:56Z","isi":1,"month":"04","citation":{"apa":"Chalk, M. J., Tkačik, G., &#38; Marre, O. (2021). Inferring the function performed by a recurrent neural network. <i>PLoS ONE</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pone.0248940\">https://doi.org/10.1371/journal.pone.0248940</a>","mla":"Chalk, Matthew J., et al. “Inferring the Function Performed by a Recurrent Neural Network.” <i>PLoS ONE</i>, vol. 16, no. 4, e0248940, Public Library of Science, 2021, doi:<a href=\"https://doi.org/10.1371/journal.pone.0248940\">10.1371/journal.pone.0248940</a>.","ieee":"M. J. Chalk, G. Tkačik, and O. Marre, “Inferring the function performed by a recurrent neural network,” <i>PLoS ONE</i>, vol. 16, no. 4. Public Library of Science, 2021.","ista":"Chalk MJ, Tkačik G, Marre O. 2021. Inferring the function performed by a recurrent neural network. PLoS ONE. 16(4), e0248940.","ama":"Chalk MJ, Tkačik G, Marre O. Inferring the function performed by a recurrent neural network. <i>PLoS ONE</i>. 2021;16(4). doi:<a href=\"https://doi.org/10.1371/journal.pone.0248940\">10.1371/journal.pone.0248940</a>","chicago":"Chalk, Matthew J, Gašper Tkačik, and Olivier Marre. “Inferring the Function Performed by a Recurrent Neural Network.” <i>PLoS ONE</i>. Public Library of Science, 2021. <a href=\"https://doi.org/10.1371/journal.pone.0248940\">https://doi.org/10.1371/journal.pone.0248940</a>.","short":"M.J. Chalk, G. Tkačik, O. Marre, PLoS ONE 16 (2021)."},"publication":"PLoS ONE","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"year":"2021","language":[{"iso":"eng"}],"external_id":{"pmid":["33857170"],"isi":["000641474900072"]},"publication_status":"published"},{"doi":"10.1016/j.cub.2021.03.060","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1016/j.cub.2021.03.060"}],"oa_version":"Published Version","oa":1,"quality_controlled":"1","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","corr_author":"1","publisher":"Cell Press","abstract":[{"text":"Humans conceptualize the diversity of life by classifying individuals into types we call ‘species’1. The species we recognize influence political and financial decisions and guide our understanding of how units of diversity evolve and interact. Although the idea of species may seem intuitive, a debate about the best way to define them has raged even before Darwin2. So much energy has been devoted to the so-called ‘species problem’ that no amount of discourse will ever likely solve it2,3. Dozens of species concepts are currently recognized3, but we lack a concrete understanding of how much researchers actually disagree and the factors that cause them to think differently1,2. To address this, we used a survey to quantify the species problem for the first time. The results indicate that the disagreement is extensive: two randomly chosen respondents will most likely disagree on the nature of species. The probability of disagreement is not predicted by researcher experience or broad study system, but tended to be lower among researchers with similar focus, training and who study the same organism. Should we see this diversity of perspectives as a problem? We argue that we should not.","lang":"eng"}],"pmid":1,"_id":"9392","department":[{"_id":"NiBa"}],"publication_identifier":{"eissn":["1879-0445"],"issn":["0960-9822"]},"acknowledgement":"We thank Christopher Cooney, Martin Garlovsky, Anja M. Westram, Carina Baskett, Stefanie Belohlavy, Michal Hledik, Arka Pal, Nicholas H. Barton, Roger K. Butlin and members of the University of Sheffield Speciation Journal Club for feedback on draft survey questions and/or comments on a draft manuscript. Three anonymous reviewers gave thoughtful feedback that improved the manuscript. We thank Ahmad Nadeem, who was paid to build the Shiny app. We are especially grateful to everyone who took part in the survey. Ethical approval for the survey was obtained through the University of Sheffield Ethics Review Procedure (Application 029768). S.S. was supported by a NERC grant awarded to Roger K. Butlin.","intvolume":"        31","day":"10","title":"Quantifying the use of species concepts","article_processing_charge":"No","status":"public","date_published":"2021-05-10T00:00:00Z","type":"journal_article","date_updated":"2026-04-02T13:59:25Z","month":"05","isi":1,"author":[{"full_name":"Stankowski, Sean","first_name":"Sean","id":"43161670-5719-11EA-8025-FABC3DDC885E","last_name":"Stankowski"},{"full_name":"Ravinet, Mark","first_name":"Mark","last_name":"Ravinet"}],"article_type":"original","page":"R428-R429","volume":31,"scopus_import":"1","issue":"9","date_created":"2021-05-16T22:01:46Z","language":[{"iso":"eng"}],"external_id":{"isi":["000654741200004"],"pmid":["33974865"]},"publication_status":"published","citation":{"apa":"Stankowski, S., &#38; Ravinet, M. (2021). Quantifying the use of species concepts. <i>Current Biology</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.cub.2021.03.060\">https://doi.org/10.1016/j.cub.2021.03.060</a>","chicago":"Stankowski, Sean, and Mark Ravinet. “Quantifying the Use of Species Concepts.” <i>Current Biology</i>. Cell Press, 2021. <a href=\"https://doi.org/10.1016/j.cub.2021.03.060\">https://doi.org/10.1016/j.cub.2021.03.060</a>.","short":"S. Stankowski, M. Ravinet, Current Biology 31 (2021) R428–R429.","ista":"Stankowski S, Ravinet M. 2021. Quantifying the use of species concepts. Current Biology. 31(9), R428–R429.","ieee":"S. Stankowski and M. Ravinet, “Quantifying the use of species concepts,” <i>Current Biology</i>, vol. 31, no. 9. Cell Press, pp. R428–R429, 2021.","ama":"Stankowski S, Ravinet M. Quantifying the use of species concepts. <i>Current Biology</i>. 2021;31(9):R428-R429. doi:<a href=\"https://doi.org/10.1016/j.cub.2021.03.060\">10.1016/j.cub.2021.03.060</a>","mla":"Stankowski, Sean, and Mark Ravinet. “Quantifying the Use of Species Concepts.” <i>Current Biology</i>, vol. 31, no. 9, Cell Press, 2021, pp. R428–29, doi:<a href=\"https://doi.org/10.1016/j.cub.2021.03.060\">10.1016/j.cub.2021.03.060</a>."},"publication":"Current Biology","year":"2021"},{"author":[{"first_name":"David","last_name":"Huber","full_name":"Huber, David"},{"first_name":"Oleksandr V.","last_name":"Marchukov","full_name":"Marchukov, Oleksandr V."},{"full_name":"Hammer, Hans Werner","first_name":"Hans Werner","last_name":"Hammer"},{"last_name":"Volosniev","id":"37D278BC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-0393-5525","first_name":"Artem","full_name":"Volosniev, Artem"}],"file_date_updated":"2021-07-19T11:47:16Z","article_type":"original","volume":23,"date_created":"2021-07-18T22:01:22Z","issue":"6","scopus_import":"1","file":[{"access_level":"open_access","checksum":"e39164ce7ea228d287cf8924e1a0f9fe","file_id":"9690","content_type":"application/pdf","date_created":"2021-07-19T11:47:16Z","relation":"main_file","file_name":"2021_NewJPhys_Huber.pdf","date_updated":"2021-07-19T11:47:16Z","success":1,"creator":"cziletti","file_size":3868445}],"project":[{"name":"ISTplus - Postdoctoral Fellowships","_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"754411"}],"month":"06","isi":1,"date_updated":"2026-04-02T14:01:49Z","citation":{"mla":"Huber, David, et al. “Morphology of Three-Body Quantum States from Machine Learning.” <i>New Journal of Physics</i>, vol. 23, no. 6, 065009, IOP Publishing, 2021, doi:<a href=\"https://doi.org/10.1088/1367-2630/ac0576\">10.1088/1367-2630/ac0576</a>.","ama":"Huber D, Marchukov OV, Hammer HW, Volosniev A. Morphology of three-body quantum states from machine learning. <i>New Journal of Physics</i>. 2021;23(6). doi:<a href=\"https://doi.org/10.1088/1367-2630/ac0576\">10.1088/1367-2630/ac0576</a>","ieee":"D. Huber, O. V. Marchukov, H. W. Hammer, and A. Volosniev, “Morphology of three-body quantum states from machine learning,” <i>New Journal of Physics</i>, vol. 23, no. 6. IOP Publishing, 2021.","ista":"Huber D, Marchukov OV, Hammer HW, Volosniev A. 2021. Morphology of three-body quantum states from machine learning. New Journal of Physics. 23(6), 065009.","short":"D. Huber, O.V. Marchukov, H.W. Hammer, A. Volosniev, New Journal of Physics 23 (2021).","chicago":"Huber, David, Oleksandr V. Marchukov, Hans Werner Hammer, and Artem Volosniev. “Morphology of Three-Body Quantum States from Machine Learning.” <i>New Journal of Physics</i>. IOP Publishing, 2021. <a href=\"https://doi.org/10.1088/1367-2630/ac0576\">https://doi.org/10.1088/1367-2630/ac0576</a>.","apa":"Huber, D., Marchukov, O. V., Hammer, H. W., &#38; Volosniev, A. (2021). Morphology of three-body quantum states from machine learning. <i>New Journal of Physics</i>. IOP Publishing. <a href=\"https://doi.org/10.1088/1367-2630/ac0576\">https://doi.org/10.1088/1367-2630/ac0576</a>"},"publication":"New Journal of Physics","year":"2021","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"language":[{"iso":"eng"}],"external_id":{"isi":["000664736300001"],"arxiv":["2102.04961"]},"publication_status":"published","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","quality_controlled":"1","arxiv":1,"publisher":"IOP Publishing","abstract":[{"text":"The relative motion of three impenetrable particles on a ring, in our case two identical fermions and one impurity, is isomorphic to a triangular quantum billiard. Depending on the ratio κ of the impurity and fermion masses, the billiards can be integrable or non-integrable (also referred to in the main text as chaotic). To set the stage, we first investigate the energy level distributions of the billiards as a function of 1/κ ∈ [0, 1] and find no evidence of integrable cases beyond the limiting values 1/κ = 1 and 1/κ = 0. Then, we use machine learning tools to analyze properties of probability distributions of individual quantum states. We find that convolutional neural networks can correctly classify integrable and non-integrable states. The decisive features of the wave functions are the normalization and a large number of zero elements, corresponding to the existence of a nodal line. The network achieves typical accuracies of 97%, suggesting that machine learning tools can be used to analyze and classify the morphology of probability densities obtained in theory or experiment.","lang":"eng"}],"doi":"10.1088/1367-2630/ac0576","oa_version":"Published Version","has_accepted_license":"1","oa":1,"article_number":"065009","article_processing_charge":"Yes","status":"public","type":"journal_article","date_published":"2021-06-23T00:00:00Z","department":[{"_id":"MiLe"}],"ddc":["530"],"_id":"9679","acknowledgement":"We thank Aidan Tracy for his input during the initial stages of this project. We thank Nathan Harshman, Achim Richter, Wojciech Rzadkowski, and Dane Hudson Smith for helpful discussions and comments on the manuscript. This work has been supported by European Union's Horizon 2020 research and innovation program under the Marie Skłodowska-Curie Grant Agreement No. 754411 (AGV); by the German Aeronautics and Space Administration (DLR) through Grant No. 50 WM 1957 (OVM); by the Deutsche Forschungsgemeinschaft through Project VO 2437/1-1 (Project No. 413495248) (AGV and HWH); by the Deutsche Forschungsgemeinschaft through Collaborative Research Center SFB 1245 (Project No. 279384907) and by the Bundesministerium für Bildung und Forschung under Contract 05P18RDFN1 (HWH). HWH also thanks the ECT* for hospitality during the workshop 'Universal physics in Many-Body Quantum Systems—From Atoms to Quarks'. This infrastructure is part of a project that has received funding from the European Union's Horizon 2020 research and innovation program under Grant Agreement No. 824093. We acknowledge support by the Deutsche Forschungsgemeinschaft and the Open Access Publishing Fund of Technische Universität Darmstadt.","publication_identifier":{"eissn":["1367-2630"]},"ec_funded":1,"intvolume":"        23","title":"Morphology of three-body quantum states from machine learning","day":"23"}]