[{"date_published":"2021-08-30T00:00:00Z","year":"2021","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"oa":1,"abstract":[{"text":"In this article we introduce a complete gradient estimate for symmetric quantum Markov semigroups on von Neumann algebras equipped with a normal faithful tracial state, which implies semi-convexity of the entropy with respect to the recently introduced noncommutative 2-Wasserstein distance. We show that this complete gradient estimate is stable under tensor products and free products and establish its validity for a number of examples. As an application we prove a complete modified logarithmic Sobolev inequality with optimal constant for Poisson-type semigroups on free group factors.","lang":"eng"}],"intvolume":"       387","date_created":"2021-08-30T10:07:44Z","quality_controlled":"1","keyword":["Mathematical Physics","Statistical and Nonlinear Physics"],"publication":"Communications in Mathematical Physics","volume":387,"ec_funded":1,"article_type":"original","title":"Complete gradient estimates of quantum Markov semigroups","_id":"9973","publisher":"Springer Nature","arxiv":1,"day":"30","ddc":["621"],"pmid":1,"date_updated":"2025-06-12T06:30:13Z","department":[{"_id":"JaMa"}],"article_processing_charge":"Yes (via OA deal)","author":[{"full_name":"Wirth, Melchior","last_name":"Wirth","id":"88644358-0A0E-11EA-8FA5-49A33DDC885E","orcid":"0000-0002-0519-4241","first_name":"Melchior"},{"first_name":"Haonan","id":"D8F41E38-9E66-11E9-A9E2-65C2E5697425","last_name":"Zhang","full_name":"Zhang, Haonan"}],"publication_status":"published","doi":"10.1007/s00220-021-04199-4","type":"journal_article","oa_version":"Published Version","isi":1,"status":"public","page":"761–791","file":[{"file_id":"9990","date_created":"2021-09-08T07:34:24Z","access_level":"open_access","content_type":"application/pdf","creator":"cchlebak","date_updated":"2021-09-08T09:46:34Z","file_name":"2021_CommunMathPhys_Wirth.pdf","checksum":"8a602f916b1c2b0dc1159708b7cb204b","relation":"main_file","file_size":505971}],"acknowledgement":"Both authors would like to thank Jan Maas for fruitful discussions and helpful comments.","external_id":{"arxiv":["2007.13506"],"pmid":["34776525"],"isi":["000691214200001"]},"publication_identifier":{"issn":["0010-3616"],"eissn":["1432-0916"]},"month":"08","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","scopus_import":"1","corr_author":"1","project":[{"_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854","name":"IST Austria Open Access Fund"},{"grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425","name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020"},{"_id":"fc31cba2-9c52-11eb-aca3-ff467d239cd2","name":"Taming Complexity in Partial Differential Systems","grant_number":"F6504"}],"file_date_updated":"2021-09-08T09:46:34Z","citation":{"mla":"Wirth, Melchior, and Haonan Zhang. “Complete Gradient Estimates of Quantum Markov Semigroups.” <i>Communications in Mathematical Physics</i>, vol. 387, Springer Nature, 2021, pp. 761–791, doi:<a href=\"https://doi.org/10.1007/s00220-021-04199-4\">10.1007/s00220-021-04199-4</a>.","ieee":"M. Wirth and H. Zhang, “Complete gradient estimates of quantum Markov semigroups,” <i>Communications in Mathematical Physics</i>, vol. 387. Springer Nature, pp. 761–791, 2021.","short":"M. Wirth, H. Zhang, Communications in Mathematical Physics 387 (2021) 761–791.","ista":"Wirth M, Zhang H. 2021. Complete gradient estimates of quantum Markov semigroups. Communications in Mathematical Physics. 387, 761–791.","chicago":"Wirth, Melchior, and Haonan Zhang. “Complete Gradient Estimates of Quantum Markov Semigroups.” <i>Communications in Mathematical Physics</i>. Springer Nature, 2021. <a href=\"https://doi.org/10.1007/s00220-021-04199-4\">https://doi.org/10.1007/s00220-021-04199-4</a>.","apa":"Wirth, M., &#38; Zhang, H. (2021). Complete gradient estimates of quantum Markov semigroups. <i>Communications in Mathematical Physics</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s00220-021-04199-4\">https://doi.org/10.1007/s00220-021-04199-4</a>","ama":"Wirth M, Zhang H. Complete gradient estimates of quantum Markov semigroups. <i>Communications in Mathematical Physics</i>. 2021;387:761–791. doi:<a href=\"https://doi.org/10.1007/s00220-021-04199-4\">10.1007/s00220-021-04199-4</a>"},"has_accepted_license":"1","language":[{"iso":"eng"}]},{"day":"18","publisher":"Research Square","_id":"9978","ddc":["541"],"keyword":["Catalysis","Energy engineering","Materials theory and modeling"],"publication":"Research Square","title":"Sharp kinetic acceleration potentials during mediated redox catalysis of insulators","abstract":[{"text":"Redox mediators could catalyse otherwise slow and energy-inefficient cycling of Li-S and Li-O 2 batteries by shuttling electrons/holes between the electrode and the solid insulating storage materials. For mediators to work efficiently they need to oxidize the solid with fast kinetics yet the lowest possible overpotential. Here, we found that when the redox potentials of mediators are tuned via, e.g., Li + concentration in the electrolyte, they exhibit distinct threshold potentials, where the kinetics accelerate several-fold within a range as small as 10 mV. This phenomenon is independent of types of mediators and electrolyte. The acceleration originates from the overpotentials required to activate fast Li + /e – extraction and the following chemical step at specific abundant surface facets. Efficient redox catalysis at insulating solids requires therefore carefully considering the surface conditions of the storage materials and electrolyte-dependent redox potentials, which may be tuned by salt concentrations or solvents.","lang":"eng"}],"date_created":"2021-08-31T12:54:16Z","year":"2021","date_published":"2021-08-18T00:00:00Z","oa":1,"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"file_date_updated":"2021-08-31T14:02:19Z","corr_author":"1","language":[{"iso":"eng"}],"has_accepted_license":"1","citation":{"mla":"Cao, Deqing, et al. “Sharp Kinetic Acceleration Potentials during Mediated Redox Catalysis of Insulators.” <i>Research Square</i>, Research Square, doi:<a href=\"https://doi.org/10.21203/rs.3.rs-750965/v1\">10.21203/rs.3.rs-750965/v1</a>.","short":"D. Cao, X. Shen, A. Wang, F. Yu, Y. Wu, S. Shi, S.A. Freunberger, Y. Chen, Research Square (n.d.).","ista":"Cao D, Shen X, Wang A, Yu F, Wu Y, Shi S, Freunberger SA, Chen Y. Sharp kinetic acceleration potentials during mediated redox catalysis of insulators. Research Square, <a href=\"https://doi.org/10.21203/rs.3.rs-750965/v1\">10.21203/rs.3.rs-750965/v1</a>.","ieee":"D. Cao <i>et al.</i>, “Sharp kinetic acceleration potentials during mediated redox catalysis of insulators,” <i>Research Square</i>. Research Square.","ama":"Cao D, Shen X, Wang A, et al. Sharp kinetic acceleration potentials during mediated redox catalysis of insulators. <i>Research Square</i>. doi:<a href=\"https://doi.org/10.21203/rs.3.rs-750965/v1\">10.21203/rs.3.rs-750965/v1</a>","chicago":"Cao, Deqing, Xiaoxiao Shen, Aiping Wang, Fengjiao Yu, Yuping Wu, Siqi Shi, Stefan Alexander Freunberger, and Yuhui Chen. “Sharp Kinetic Acceleration Potentials during Mediated Redox Catalysis of Insulators.” <i>Research Square</i>. Research Square, n.d. <a href=\"https://doi.org/10.21203/rs.3.rs-750965/v1\">https://doi.org/10.21203/rs.3.rs-750965/v1</a>.","apa":"Cao, D., Shen, X., Wang, A., Yu, F., Wu, Y., Shi, S., … Chen, Y. (n.d.). Sharp kinetic acceleration potentials during mediated redox catalysis of insulators. <i>Research Square</i>. Research Square. <a href=\"https://doi.org/10.21203/rs.3.rs-750965/v1\">https://doi.org/10.21203/rs.3.rs-750965/v1</a>"},"publication_identifier":{"eissn":["2693-5015"]},"file":[{"date_updated":"2021-08-31T14:02:19Z","file_name":"2021_ResearchSquare_Cao.pdf","relation":"main_file","checksum":"1878e91c29d5769ed5a827b0b7addf00","file_size":1019662,"file_id":"9979","success":1,"access_level":"open_access","date_created":"2021-08-31T14:02:19Z","creator":"cchlebak","content_type":"application/pdf"}],"related_material":{"record":[{"relation":"later_version","status":"public","id":"10813"}]},"page":"21","acknowledgement":"This work was financially supported by the National Natural Science Foundation of China (51773092, 21975124, 11874254, 51802187, U2030206). S.A.F. is indebted to IST Austria for support. ","month":"08","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Preprint","type":"preprint","doi":"10.21203/rs.3.rs-750965/v1","publication_status":"submitted","status":"public","department":[{"_id":"StFr"}],"date_updated":"2024-10-09T21:01:46Z","author":[{"first_name":"Deqing","full_name":"Cao, Deqing","last_name":"Cao"},{"first_name":"Xiaoxiao","last_name":"Shen","full_name":"Shen, Xiaoxiao"},{"full_name":"Wang, Aiping","last_name":"Wang","first_name":"Aiping"},{"first_name":"Fengjiao","full_name":"Yu, Fengjiao","last_name":"Yu"},{"first_name":"Yuping","full_name":"Wu, Yuping","last_name":"Wu"},{"last_name":"Shi","full_name":"Shi, Siqi","first_name":"Siqi"},{"full_name":"Freunberger, Stefan Alexander","last_name":"Freunberger","orcid":"0000-0003-2902-5319","id":"A8CA28E6-CE23-11E9-AD2D-EC27E6697425","first_name":"Stefan Alexander"},{"last_name":"Chen","full_name":"Chen, Yuhui","first_name":"Yuhui"}],"article_processing_charge":"No"},{"ddc":["621"],"citation":{"short":"C. Prehal, S.D. Talian, A. Vizintin, H. Amenitsch, R. Dominko, S.A. Freunberger, V. Wood, Research Square (n.d.).","ieee":"C. Prehal <i>et al.</i>, “Mechanism of Li2S formation and dissolution in Lithium-Sulphur batteries,” <i>Research Square</i>. .","ista":"Prehal C, Talian SD, Vizintin A, Amenitsch H, Dominko R, Freunberger SA, Wood V. Mechanism of Li2S formation and dissolution in Lithium-Sulphur batteries. Research Square, <a href=\"https://doi.org/10.21203/rs.3.rs-818607/v1\">10.21203/rs.3.rs-818607/v1</a>.","mla":"Prehal, Christian, et al. “Mechanism of Li2S Formation and Dissolution in Lithium-Sulphur Batteries.” <i>Research Square</i>, doi:<a href=\"https://doi.org/10.21203/rs.3.rs-818607/v1\">10.21203/rs.3.rs-818607/v1</a>.","ama":"Prehal C, Talian SD, Vizintin A, et al. Mechanism of Li2S formation and dissolution in Lithium-Sulphur batteries. <i>Research Square</i>. doi:<a href=\"https://doi.org/10.21203/rs.3.rs-818607/v1\">10.21203/rs.3.rs-818607/v1</a>","apa":"Prehal, C., Talian, S. D., Vizintin, A., Amenitsch, H., Dominko, R., Freunberger, S. A., &#38; Wood, V. (n.d.). Mechanism of Li2S formation and dissolution in Lithium-Sulphur batteries. <i>Research Square</i>. <a href=\"https://doi.org/10.21203/rs.3.rs-818607/v1\">https://doi.org/10.21203/rs.3.rs-818607/v1</a>","chicago":"Prehal, Christian, Sara Drvarič Talian, Alen Vizintin, Heinz Amenitsch, Robert Dominko, Stefan Alexander Freunberger, and Vanessa Wood. “Mechanism of Li2S Formation and Dissolution in Lithium-Sulphur Batteries.” <i>Research Square</i>, n.d. <a href=\"https://doi.org/10.21203/rs.3.rs-818607/v1\">https://doi.org/10.21203/rs.3.rs-818607/v1</a>."},"language":[{"iso":"eng"}],"_id":"9980","day":"16","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","month":"08","title":"Mechanism of Li2S formation and dissolution in Lithium-Sulphur batteries","keyword":["Li2S","Lithium Sulphur Batteries","SAXS","WAXS"],"page":"21","acknowledgement":"This project has received funding from the European Union’s Horizon 2020 research and innovation program under the Marie Skłodowska-Curie grant NanoEvolution, grant agreement No 894042. The authors acknowledge TU Graz for support through the Lead Project LP-03. Likewise, the use of SOMAPP Lab, a core facility supported by the Austrian Federal Ministry of Education, Science and Research, the Graz University\r\n6 of Technology, the University of Graz, and Anton Paar GmbH is acknowledged. S.D.T, A.V. and R.D. acknowledge the financial support by the Slovenian Research Agency (ARRS) research core funding P2-0393. Furthermore, A.V. acknowledge the funding from the Slovenian Research Agency, research project Z2-1863. S.A.F. is indebted to IST Austria for support. ","publication":"Research Square","status":"public","publication_status":"submitted","date_created":"2021-09-02T08:45:00Z","abstract":[{"text":"Insufficient understanding of the mechanism that reversibly converts sulphur into lithium sulphide (Li2S) via soluble polysulphides (PS) hampers the realization of high performance lithium-sulphur cells. Typically Li2S formation is explained by direct electroreduction of a PS to Li2S; however, this is not consistent with the size of the insulating Li2S deposits. Here, we use in situ small and wide angle X-ray scattering (SAXS/WAXS) to track the growth and dissolution of crystalline and amorphous deposits from atomic to sub-micron scales during charge and discharge. Stochastic modelling based on the SAXS data allows quantification of the chemical phase evolution during discharge and charge. We show that Li2S deposits predominantly via disproportionation of transient, solid Li2S2 to form primary Li2S crystallites and solid Li2S4 particles. We further demonstrate that this process happens in reverse during charge. These findings show that the discharge capacity and rate capability in Li-S battery cathodes are therefore limited by mass transport through the increasingly tortuous network of Li2S / Li2S4 / carbon pores rather than electron transport through a passivating surface film.","lang":"eng"}],"main_file_link":[{"open_access":"1","url":"https://www.researchsquare.com/article/rs-818607/v1"}],"doi":"10.21203/rs.3.rs-818607/v1","type":"preprint","oa_version":"Preprint","article_processing_charge":"No","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"author":[{"last_name":"Prehal","full_name":"Prehal, Christian","first_name":"Christian"},{"first_name":"Sara Drvarič","last_name":"Talian","full_name":"Talian, Sara Drvarič"},{"last_name":"Vizintin","full_name":"Vizintin, Alen","first_name":"Alen"},{"full_name":"Amenitsch, Heinz","last_name":"Amenitsch","first_name":"Heinz"},{"first_name":"Robert","last_name":"Dominko","full_name":"Dominko, Robert"},{"full_name":"Freunberger, Stefan Alexander","last_name":"Freunberger","first_name":"Stefan Alexander","orcid":"0000-0003-2902-5319","id":"A8CA28E6-CE23-11E9-AD2D-EC27E6697425"},{"last_name":"Wood","full_name":"Wood, Vanessa","first_name":"Vanessa"}],"oa":1,"date_published":"2021-08-16T00:00:00Z","date_updated":"2021-12-03T10:35:42Z","year":"2021","department":[{"_id":"StFr"}]},{"ddc":["519"],"arxiv":1,"publisher":"SciPost Foundation","day":"02","_id":"9981","ec_funded":1,"article_type":"original","title":"Importance sampling scheme for the stochastic simulation of quantum spin dynamics","volume":11,"keyword":["General Physics and Astronomy"],"publication":"SciPost Physics","quality_controlled":"1","date_created":"2021-09-02T11:49:47Z","abstract":[{"text":"The numerical simulation of dynamical phenomena in interacting quantum systems is a notoriously hard problem. Although a number of promising numerical methods exist, they often have limited applicability due to the growth of entanglement or the presence of the so-called sign problem. In this work, we develop an importance sampling scheme for the simulation of quantum spin dynamics, building on a recent approach mapping quantum spin systems to classical stochastic processes. The importance sampling scheme is based on identifying the classical trajectory that yields the largest contribution to a given quantum observable. An exact transformation is then carried out to preferentially sample trajectories that are close to the dominant one. We demonstrate that this approach is capable of reducing the temporal growth of fluctuations in the stochastic quantities, thus extending the range of accessible times and system sizes compared to direct sampling. We discuss advantages and limitations of the proposed approach, outlining directions\r\nfor further developments.","lang":"eng"}],"intvolume":"        11","oa":1,"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"year":"2021","issue":"3","date_published":"2021-09-02T00:00:00Z","language":[{"iso":"eng"}],"citation":{"ama":"De Nicola S. Importance sampling scheme for the stochastic simulation of quantum spin dynamics. <i>SciPost Physics</i>. 2021;11(3). doi:<a href=\"https://doi.org/10.21468/scipostphys.11.3.048\">10.21468/scipostphys.11.3.048</a>","chicago":"De Nicola, Stefano. “Importance Sampling Scheme for the Stochastic Simulation of Quantum Spin Dynamics.” <i>SciPost Physics</i>. SciPost Foundation, 2021. <a href=\"https://doi.org/10.21468/scipostphys.11.3.048\">https://doi.org/10.21468/scipostphys.11.3.048</a>.","apa":"De Nicola, S. (2021). Importance sampling scheme for the stochastic simulation of quantum spin dynamics. <i>SciPost Physics</i>. SciPost Foundation. <a href=\"https://doi.org/10.21468/scipostphys.11.3.048\">https://doi.org/10.21468/scipostphys.11.3.048</a>","mla":"De Nicola, Stefano. “Importance Sampling Scheme for the Stochastic Simulation of Quantum Spin Dynamics.” <i>SciPost Physics</i>, vol. 11, no. 3, 048, SciPost Foundation, 2021, doi:<a href=\"https://doi.org/10.21468/scipostphys.11.3.048\">10.21468/scipostphys.11.3.048</a>.","ieee":"S. De Nicola, “Importance sampling scheme for the stochastic simulation of quantum spin dynamics,” <i>SciPost Physics</i>, vol. 11, no. 3. SciPost Foundation, 2021.","ista":"De Nicola S. 2021. Importance sampling scheme for the stochastic simulation of quantum spin dynamics. SciPost Physics. 11(3), 048.","short":"S. De Nicola, SciPost Physics 11 (2021)."},"article_number":"048","has_accepted_license":"1","project":[{"name":"ISTplus - Postdoctoral Fellowships","_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"754411"}],"file_date_updated":"2021-09-02T14:05:43Z","scopus_import":"1","month":"09","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_identifier":{"issn":["2542-4653"],"eissn":["2666-9366"]},"file":[{"content_type":"application/pdf","creator":"cchlebak","file_id":"9984","success":1,"access_level":"open_access","date_created":"2021-09-02T14:05:43Z","relation":"main_file","checksum":"e4ec69d893e31811efc6093cb6ea8eb7","file_size":373833,"date_updated":"2021-09-02T14:05:43Z","file_name":"2021_SciPostPhys_DeNicola.pdf"}],"external_id":{"isi":["000692534200001"],"arxiv":["2103.16468"]},"status":"public","isi":1,"type":"journal_article","oa_version":"Published Version","publication_status":"published","doi":"10.21468/scipostphys.11.3.048","article_processing_charge":"No","author":[{"full_name":"De Nicola, Stefano","last_name":"De Nicola","orcid":"0000-0002-4842-6671","id":"42832B76-F248-11E8-B48F-1D18A9856A87","first_name":"Stefano"}],"department":[{"_id":"MaSe"}],"date_updated":"2025-05-14T10:51:45Z"},{"date_updated":"2023-08-11T11:07:51Z","department":[{"_id":"PeJo"}],"author":[{"full_name":"Watson, Jake","last_name":"Watson","first_name":"Jake","id":"63836096-4690-11EA-BD4E-32803DDC885E","orcid":"0000-0002-8698-3823"},{"first_name":"Alexandra","full_name":"Pinggera, Alexandra","last_name":"Pinggera"},{"last_name":"Ho","full_name":"Ho, Hinze","first_name":"Hinze"},{"full_name":"Greger, Ingo H.","last_name":"Greger","first_name":"Ingo H."}],"article_processing_charge":"Yes","publication_status":"published","doi":"10.1038/s41467-021-25281-4","type":"journal_article","oa_version":"Published Version","isi":1,"status":"public","acknowledgement":"The authors are very grateful to Andrew Penn for advice and discussions on surface receptor labelling in slice tissue, dissociated culture transfection, and for providing tdTomato and BirAER expression plasmids. This work would not have been possible without support from the Biological Services teams at both the Laboratory of Molecular Biology and Ares facilities. We are also very grateful to Nick Barry and Jerome Boulanger of the LMB Light Microscopy facility for support with confocal and STORM imaging and analysis, Junichi Takagi for providing scFv-Clasp expression constructs, Veronica Chang for assistance with scFv-Clasp protein production, and Nejc Kejzar for assistance with cluster analysis. We would like to thank Teru Nakagawa and Ole Paulsen for critical reading of the manuscript and constructive feedback. This work was supported by grants from the Medical Research Council (MC_U105174197) and BBSRC (BB/N002113/1).","file":[{"date_created":"2021-09-08T12:57:06Z","success":1,"access_level":"open_access","file_id":"9991","creator":"cchlebak","content_type":"application/pdf","date_updated":"2021-09-08T12:57:06Z","file_name":"2021_NatureCommunications_Watson.pdf","file_size":18310502,"checksum":"1bf4f6a561f96bc426d754de9cb57710","relation":"main_file"}],"external_id":{"isi":["000687672000006"],"pmid":["34426577 "]},"publication_identifier":{"eissn":["2041-1723"]},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","month":"08","scopus_import":"1","file_date_updated":"2021-09-08T12:57:06Z","citation":{"mla":"Watson, Jake, et al. “AMPA Receptor Anchoring at CA1 Synapses Is Determined by N-Terminal Domain and TARP Γ8 Interactions.” <i>Nature Communications</i>, vol. 12, no. 1, 5083, Nature Publishing Group, 2021, doi:<a href=\"https://doi.org/10.1038/s41467-021-25281-4\">10.1038/s41467-021-25281-4</a>.","ista":"Watson J, Pinggera A, Ho H, Greger IH. 2021. AMPA receptor anchoring at CA1 synapses is determined by N-terminal domain and TARP γ8 interactions. Nature Communications. 12(1), 5083.","ieee":"J. Watson, A. Pinggera, H. Ho, and I. H. Greger, “AMPA receptor anchoring at CA1 synapses is determined by N-terminal domain and TARP γ8 interactions,” <i>Nature Communications</i>, vol. 12, no. 1. Nature Publishing Group, 2021.","short":"J. Watson, A. Pinggera, H. Ho, I.H. Greger, Nature Communications 12 (2021).","chicago":"Watson, Jake, Alexandra Pinggera, Hinze Ho, and Ingo H. Greger. “AMPA Receptor Anchoring at CA1 Synapses Is Determined by N-Terminal Domain and TARP Γ8 Interactions.” <i>Nature Communications</i>. Nature Publishing Group, 2021. <a href=\"https://doi.org/10.1038/s41467-021-25281-4\">https://doi.org/10.1038/s41467-021-25281-4</a>.","apa":"Watson, J., Pinggera, A., Ho, H., &#38; Greger, I. H. (2021). AMPA receptor anchoring at CA1 synapses is determined by N-terminal domain and TARP γ8 interactions. <i>Nature Communications</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/s41467-021-25281-4\">https://doi.org/10.1038/s41467-021-25281-4</a>","ama":"Watson J, Pinggera A, Ho H, Greger IH. AMPA receptor anchoring at CA1 synapses is determined by N-terminal domain and TARP γ8 interactions. <i>Nature Communications</i>. 2021;12(1). doi:<a href=\"https://doi.org/10.1038/s41467-021-25281-4\">10.1038/s41467-021-25281-4</a>"},"has_accepted_license":"1","article_number":"5083","language":[{"iso":"eng"}],"date_published":"2021-08-23T00:00:00Z","year":"2021","issue":"1","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"oa":1,"date_created":"2021-09-05T22:01:23Z","intvolume":"        12","abstract":[{"lang":"eng","text":"AMPA receptor (AMPAR) abundance and positioning at excitatory synapses regulates the strength of transmission. Changes in AMPAR localisation can enact synaptic plasticity, allowing long-term information storage, and is therefore tightly controlled. Multiple mechanisms regulating AMPAR synaptic anchoring have been described, but with limited coherence or comparison between reports, our understanding of this process is unclear. Here, combining synaptic recordings from mouse hippocampal slices and super-resolution imaging in dissociated cultures, we compare the contributions of three AMPAR interaction domains controlling transmission at hippocampal CA1 synapses. We show that the AMPAR C-termini play only a modulatory role, whereas the extracellular N-terminal domain (NTD) and PDZ interactions of the auxiliary subunit TARP γ8 are both crucial, and each is sufficient to maintain transmission. Our data support a model in which γ8 accumulates AMPARs at the postsynaptic density, where the NTD further tunes their positioning. This interplay between cytosolic (TARP γ8) and synaptic cleft (NTD) interactions provides versatility to regulate synaptic transmission and plasticity."}],"quality_controlled":"1","publication":"Nature Communications","volume":12,"article_type":"original","title":"AMPA receptor anchoring at CA1 synapses is determined by N-terminal domain and TARP γ8 interactions","_id":"9985","publisher":"Nature Publishing Group","day":"23","ddc":["612"],"pmid":1},{"status":"public","isi":1,"type":"journal_article","oa_version":"Published Version","publication_status":"published","doi":"10.3390/ijms22179222","article_processing_charge":"Yes","author":[{"full_name":"Velasquez, Silvia Melina","last_name":"Velasquez","first_name":"Silvia Melina"},{"first_name":"Xiaoyuan","last_name":"Guo","full_name":"Guo, Xiaoyuan"},{"id":"460C6802-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4675-6893","first_name":"Marçal","last_name":"Gallemi","full_name":"Gallemi, Marçal"},{"first_name":"Bibek","full_name":"Aryal, Bibek","last_name":"Aryal"},{"full_name":"Venhuizen, Peter","last_name":"Venhuizen","first_name":"Peter"},{"full_name":"Barbez, Elke","last_name":"Barbez","first_name":"Elke"},{"full_name":"Dünser, Kai Alexander","last_name":"Dünser","first_name":"Kai Alexander"},{"full_name":"Darino, Martin","last_name":"Darino","first_name":"Martin"},{"last_name":"Pӗnčík","full_name":"Pӗnčík, Aleš","first_name":"Aleš"},{"last_name":"Novák","full_name":"Novák, Ondřej","first_name":"Ondřej"},{"full_name":"Kalyna, Maria","last_name":"Kalyna","first_name":"Maria"},{"full_name":"Mouille, Gregory","last_name":"Mouille","first_name":"Gregory"},{"first_name":"Eva","orcid":"0000-0002-8510-9739","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","last_name":"Benková","full_name":"Benková, Eva"},{"first_name":"Rishikesh P.","last_name":"Bhalerao","full_name":"Bhalerao, Rishikesh P."},{"last_name":"Mravec","full_name":"Mravec, Jozef","first_name":"Jozef"},{"first_name":"Jürgen","last_name":"Kleine-Vehn","full_name":"Kleine-Vehn, Jürgen"}],"department":[{"_id":"EvBe"}],"date_updated":"2024-10-09T21:00:50Z","language":[{"iso":"eng"}],"citation":{"mla":"Velasquez, Silvia Melina, et al. “Xyloglucan Remodeling Defines Auxin-Dependent Differential Tissue Expansion in Plants.” <i>International Journal of Molecular Sciences</i>, vol. 22, no. 17, 9222, MDPI, 2021, doi:<a href=\"https://doi.org/10.3390/ijms22179222\">10.3390/ijms22179222</a>.","ista":"Velasquez SM, Guo X, Gallemi M, Aryal B, Venhuizen P, Barbez E, Dünser KA, Darino M, Pӗnčík A, Novák O, Kalyna M, Mouille G, Benková E, Bhalerao RP, Mravec J, Kleine-Vehn J. 2021. Xyloglucan remodeling defines auxin-dependent differential tissue expansion in plants. International Journal of Molecular Sciences. 22(17), 9222.","short":"S.M. Velasquez, X. Guo, M. Gallemi, B. Aryal, P. Venhuizen, E. Barbez, K.A. Dünser, M. Darino, A. Pӗnčík, O. Novák, M. Kalyna, G. Mouille, E. Benková, R.P. Bhalerao, J. Mravec, J. Kleine-Vehn, International Journal of Molecular Sciences 22 (2021).","ieee":"S. M. Velasquez <i>et al.</i>, “Xyloglucan remodeling defines auxin-dependent differential tissue expansion in plants,” <i>International Journal of Molecular Sciences</i>, vol. 22, no. 17. MDPI, 2021.","ama":"Velasquez SM, Guo X, Gallemi M, et al. Xyloglucan remodeling defines auxin-dependent differential tissue expansion in plants. <i>International Journal of Molecular Sciences</i>. 2021;22(17). doi:<a href=\"https://doi.org/10.3390/ijms22179222\">10.3390/ijms22179222</a>","chicago":"Velasquez, Silvia Melina, Xiaoyuan Guo, Marçal Gallemi, Bibek Aryal, Peter Venhuizen, Elke Barbez, Kai Alexander Dünser, et al. “Xyloglucan Remodeling Defines Auxin-Dependent Differential Tissue Expansion in Plants.” <i>International Journal of Molecular Sciences</i>. MDPI, 2021. <a href=\"https://doi.org/10.3390/ijms22179222\">https://doi.org/10.3390/ijms22179222</a>.","apa":"Velasquez, S. M., Guo, X., Gallemi, M., Aryal, B., Venhuizen, P., Barbez, E., … Kleine-Vehn, J. (2021). Xyloglucan remodeling defines auxin-dependent differential tissue expansion in plants. <i>International Journal of Molecular Sciences</i>. MDPI. <a href=\"https://doi.org/10.3390/ijms22179222\">https://doi.org/10.3390/ijms22179222</a>"},"article_number":"9222","has_accepted_license":"1","corr_author":"1","file_date_updated":"2021-09-07T09:04:53Z","scopus_import":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"08","publication_identifier":{"issn":["1661-6596"],"eissn":["1422-0067"]},"file":[{"file_id":"9988","access_level":"open_access","date_created":"2021-09-06T12:50:19Z","content_type":"application/pdf","creator":"cchlebak","date_updated":"2021-09-07T09:04:53Z","file_name":"2021_IntJMolecularSciences_Velasquez.pdf","relation":"main_file","checksum":"6b7055cf89f1b7ed8594c3fdf56f000b","file_size":2162247}],"acknowledgement":"We are grateful to Paul Knox, Markus Pauly, Malcom O’Neill, and Ignacio Zarra for providing published material; the BOKU-VIBT Imaging Center for access and M. Debreczeny for expertise; J.I. Thaker and Georg Seifert for critical reading.\r\n","external_id":{"pmid":["34502129"],"isi":["000694347100001"]},"quality_controlled":"1","intvolume":"        22","abstract":[{"lang":"eng","text":"Size control is a fundamental question in biology, showing incremental complexity in plants, whose cells possess a rigid cell wall. The phytohormone auxin is a vital growth regulator with central importance for differential growth control. Our results indicate that auxin-reliant growth programs affect the molecular complexity of xyloglucans, the major type of cell wall hemicellulose in eudicots. Auxin-dependent induction and repression of growth coincide with reduced and enhanced molecular complexity of xyloglucans, respectively. In agreement with a proposed function in growth control, genetic interference with xyloglucan side decorations distinctly modulates auxin-dependent differential growth rates. Our work proposes that auxin-dependent growth programs have a spatially defined effect on xyloglucan’s molecular structure, which in turn affects cell wall mechanics and specifies differential, gravitropic hypocotyl growth."}],"date_created":"2021-09-05T22:01:24Z","oa":1,"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"year":"2021","issue":"17","date_published":"2021-08-26T00:00:00Z","pmid":1,"ddc":["575"],"publisher":"MDPI","day":"26","_id":"9986","title":"Xyloglucan remodeling defines auxin-dependent differential tissue expansion in plants","article_type":"original","volume":22,"publication":"International Journal of Molecular Sciences","keyword":["auxin","growth","cell wall","xyloglucans","hypocotyls","gravitropism"]},{"month":"08","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","external_id":{"isi":["000692795200001"]},"acknowledgement":"First of all we would like to thank Andrei Okounkov for invaluable discussions, advises and sharing with us his fantastic viewpoint on modern quantum geometry. We are also grateful to D. Korb and Z. Zhou for their interest and comments. The work of A. Smirnov was supported in part by RFBR Grants under Numbers 15-02-04175 and 15-01-04217 and in part by NSF Grant DMS–2054527. The work of P. Koroteev, A.M. Zeitlin and A. Smirnov is supported in part by AMS Simons travel Grant. A. M. Zeitlin is partially supported by Simons Collaboration Grant, Award ID: 578501. Open access funding provided by Institute of Science and Technology (IST Austria).","file":[{"date_created":"2021-09-13T11:31:34Z","success":1,"access_level":"open_access","file_id":"10010","creator":"cchlebak","content_type":"application/pdf","file_name":"2021_SelectaMath_Koroteev.pdf","date_updated":"2021-09-13T11:31:34Z","file_size":584648,"checksum":"beadc5a722ffb48190e1e63ee2dbfee5","relation":"main_file"}],"publication_identifier":{"eissn":["1420-9020"],"issn":["1022-1824"]},"article_number":"87","has_accepted_license":"1","citation":{"mla":"Koroteev, Peter, et al. “Quantum K-Theory of Quiver Varieties and Many-Body Systems.” <i>Selecta Mathematica</i>, vol. 27, no. 5, 87, Springer Nature, 2021, doi:<a href=\"https://doi.org/10.1007/s00029-021-00698-3\">10.1007/s00029-021-00698-3</a>.","short":"P. Koroteev, P. Pushkar, A.V. Smirnov, A.M. Zeitlin, Selecta Mathematica 27 (2021).","ieee":"P. Koroteev, P. Pushkar, A. V. Smirnov, and A. M. Zeitlin, “Quantum K-theory of quiver varieties and many-body systems,” <i>Selecta Mathematica</i>, vol. 27, no. 5. Springer Nature, 2021.","ista":"Koroteev P, Pushkar P, Smirnov AV, Zeitlin AM. 2021. Quantum K-theory of quiver varieties and many-body systems. Selecta Mathematica. 27(5), 87.","chicago":"Koroteev, Peter, Petr Pushkar, Andrey V. Smirnov, and Anton M. Zeitlin. “Quantum K-Theory of Quiver Varieties and Many-Body Systems.” <i>Selecta Mathematica</i>. Springer Nature, 2021. <a href=\"https://doi.org/10.1007/s00029-021-00698-3\">https://doi.org/10.1007/s00029-021-00698-3</a>.","apa":"Koroteev, P., Pushkar, P., Smirnov, A. V., &#38; Zeitlin, A. M. (2021). Quantum K-theory of quiver varieties and many-body systems. <i>Selecta Mathematica</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s00029-021-00698-3\">https://doi.org/10.1007/s00029-021-00698-3</a>","ama":"Koroteev P, Pushkar P, Smirnov AV, Zeitlin AM. Quantum K-theory of quiver varieties and many-body systems. <i>Selecta Mathematica</i>. 2021;27(5). doi:<a href=\"https://doi.org/10.1007/s00029-021-00698-3\">10.1007/s00029-021-00698-3</a>"},"language":[{"iso":"eng"}],"scopus_import":"1","file_date_updated":"2021-09-13T11:31:34Z","project":[{"name":"IST Austria Open Access Fund","_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854"}],"article_processing_charge":"Yes (via OA deal)","author":[{"last_name":"Koroteev","full_name":"Koroteev, Peter","first_name":"Peter"},{"first_name":"Petr","id":"151DCEB6-9EC3-11E9-8480-ABECE5697425","full_name":"Pushkar, Petr","last_name":"Pushkar"},{"last_name":"Smirnov","full_name":"Smirnov, Andrey V.","first_name":"Andrey V."},{"first_name":"Anton M.","full_name":"Zeitlin, Anton M.","last_name":"Zeitlin"}],"date_updated":"2025-04-15T06:53:09Z","department":[{"_id":"TaHa"}],"isi":1,"status":"public","doi":"10.1007/s00029-021-00698-3","publication_status":"published","oa_version":"Published Version","type":"journal_article","volume":27,"title":"Quantum K-theory of quiver varieties and many-body systems","article_type":"original","publication":"Selecta Mathematica","ddc":["530"],"_id":"9998","day":"30","publisher":"Springer Nature","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"oa":1,"date_published":"2021-08-30T00:00:00Z","issue":"5","year":"2021","abstract":[{"text":"We define quantum equivariant K-theory of Nakajima quiver varieties. We discuss type A in detail as well as its connections with quantum XXZ spin chains and trigonometric Ruijsenaars-Schneider models. Finally we study a limit which produces a K-theoretic version of results of Givental and Kim, connecting quantum geometry of flag varieties and Toda lattice.","lang":"eng"}],"intvolume":"        27","date_created":"2021-09-12T22:01:22Z","quality_controlled":"1"},{"day":"27","publisher":"eLife Sciences Publications","_id":"9999","pmid":1,"ddc":["570"],"keyword":["cell delamination","apical constriction","dragging","mechanical forces","collective 18 locomotion","dorsal forerunner cells","zebrafish"],"publication":"eLife","article_type":"original","title":"Apical contacts stemming from incomplete delamination guide progenitor cell allocation through a dragging mechanism","ec_funded":1,"volume":10,"quality_controlled":"1","date_created":"2021-09-12T22:01:23Z","abstract":[{"lang":"eng","text":"The developmental strategies used by progenitor cells to endure a safe journey from their induction place towards the site of terminal differentiation are still poorly understood. Here we uncovered a progenitor cell allocation mechanism that stems from an incomplete process of epithelial delamination that allows progenitors to coordinate their movement with adjacent extra-embryonic tissues. Progenitors of the zebrafish laterality organ originate from the surface epithelial enveloping layer by an apical constriction process of cell delamination. During this process, progenitors retain long-term apical contacts that enable the epithelial layer to pull a subset of progenitors along their way towards the vegetal pole. The remaining delaminated progenitors follow apically-attached progenitors’ movement by a co-attraction mechanism, avoiding sequestration by the adjacent endoderm, ensuring their fate and collective allocation at the differentiation site. Thus, we reveal that incomplete delamination serves as a cellular platform for coordinated tissue movements during development. Impact Statement: Incomplete delamination serves as a cellular platform for coordinated tissue movements during development, guiding newly formed progenitor cell groups to the differentiation site."}],"intvolume":"        10","year":"2021","date_published":"2021-08-27T00:00:00Z","oa":1,"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"project":[{"call_identifier":"H2020","name":"Interaction and feedback between cell mechanics and fate specification in vertebrate gastrulation","_id":"260F1432-B435-11E9-9278-68D0E5697425","grant_number":"742573"}],"file_date_updated":"2022-05-13T08:03:37Z","scopus_import":"1","language":[{"iso":"eng"}],"article_number":"e66483","has_accepted_license":"1","citation":{"chicago":"Pulgar, Eduardo, Cornelia Schwayer, Néstor Guerrero, Loreto López, Susana Márquez, Steffen Härtel, Rodrigo Soto, Carl Philipp Heisenberg, and Miguel L. Concha. “Apical Contacts Stemming from Incomplete Delamination Guide Progenitor Cell Allocation through a Dragging Mechanism.” <i>ELife</i>. eLife Sciences Publications, 2021. <a href=\"https://doi.org/10.7554/eLife.66483\">https://doi.org/10.7554/eLife.66483</a>.","apa":"Pulgar, E., Schwayer, C., Guerrero, N., López, L., Márquez, S., Härtel, S., … Concha, M. L. (2021). Apical contacts stemming from incomplete delamination guide progenitor cell allocation through a dragging mechanism. <i>ELife</i>. eLife Sciences Publications. <a href=\"https://doi.org/10.7554/eLife.66483\">https://doi.org/10.7554/eLife.66483</a>","ama":"Pulgar E, Schwayer C, Guerrero N, et al. Apical contacts stemming from incomplete delamination guide progenitor cell allocation through a dragging mechanism. <i>eLife</i>. 2021;10. doi:<a href=\"https://doi.org/10.7554/eLife.66483\">10.7554/eLife.66483</a>","mla":"Pulgar, Eduardo, et al. “Apical Contacts Stemming from Incomplete Delamination Guide Progenitor Cell Allocation through a Dragging Mechanism.” <i>ELife</i>, vol. 10, e66483, eLife Sciences Publications, 2021, doi:<a href=\"https://doi.org/10.7554/eLife.66483\">10.7554/eLife.66483</a>.","ieee":"E. Pulgar <i>et al.</i>, “Apical contacts stemming from incomplete delamination guide progenitor cell allocation through a dragging mechanism,” <i>eLife</i>, vol. 10. eLife Sciences Publications, 2021.","short":"E. Pulgar, C. Schwayer, N. Guerrero, L. López, S. Márquez, S. Härtel, R. Soto, C.P. Heisenberg, M.L. Concha, ELife 10 (2021).","ista":"Pulgar E, Schwayer C, Guerrero N, López L, Márquez S, Härtel S, Soto R, Heisenberg CP, Concha ML. 2021. Apical contacts stemming from incomplete delamination guide progenitor cell allocation through a dragging mechanism. eLife. 10, e66483."},"publication_identifier":{"eissn":["2050-084X"]},"external_id":{"isi":["000700428500001"],"pmid":["34448451"]},"file":[{"file_id":"11371","success":1,"access_level":"open_access","date_created":"2022-05-13T08:03:37Z","creator":"dernst","content_type":"application/pdf","file_name":"2021_eLife_Pulgar.pdf","date_updated":"2022-05-13T08:03:37Z","relation":"main_file","checksum":"a3f82b0499cc822ac1eab48a01f3f57e","file_size":9010446}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","month":"08","oa_version":"Published Version","type":"journal_article","doi":"10.7554/eLife.66483","publication_status":"published","status":"public","isi":1,"department":[{"_id":"CaHe"}],"date_updated":"2025-04-14T07:46:58Z","article_processing_charge":"Yes","author":[{"last_name":"Pulgar","full_name":"Pulgar, Eduardo","first_name":"Eduardo"},{"last_name":"Schwayer","full_name":"Schwayer, Cornelia","first_name":"Cornelia","id":"3436488C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5130-2226"},{"first_name":"Néstor","last_name":"Guerrero","full_name":"Guerrero, Néstor"},{"full_name":"López, Loreto","last_name":"López","first_name":"Loreto"},{"first_name":"Susana","full_name":"Márquez, Susana","last_name":"Márquez"},{"first_name":"Steffen","full_name":"Härtel, Steffen","last_name":"Härtel"},{"first_name":"Rodrigo","last_name":"Soto","full_name":"Soto, Rodrigo"},{"last_name":"Heisenberg","full_name":"Heisenberg, Carl Philipp","first_name":"Carl Philipp"},{"first_name":"Miguel L.","full_name":"Concha, Miguel L.","last_name":"Concha"}]},{"oa":1,"year":"2021","issue":"6550","date_published":"2021-07-02T00:00:00Z","quality_controlled":"1","abstract":[{"text":"Genomes of germ cells present an existential vulnerability to organisms because germ cell mutations will propagate to future generations. Transposable elements are one source of such mutations. In the small flowering plant Arabidopsis, Long et al. found that genome methylation in the male germline is directed by small interfering RNAs (siRNAs) imperfectly transcribed from transposons (see the Perspective by Mosher). These germline siRNAs silence germline transposons and establish inherited methylation patterns in sperm, thus maintaining the integrity of the plant genome across generations.","lang":"eng"}],"date_created":"2023-01-16T09:15:14Z","intvolume":"       373","main_file_link":[{"url":"https://doi.org/10.1101/2021.01.25.428150","open_access":"1"}],"article_type":"original","title":"Nurse cell-derived small RNAs define paternal epigenetic inheritance in Arabidopsis","OA_place":"repository","volume":373,"keyword":["Multidisciplinary"],"publication":"Science","pmid":1,"publisher":"American Association for the Advancement of Science","day":"02","_id":"12187","article_processing_charge":"No","author":[{"first_name":"Jincheng","full_name":"Long, Jincheng","last_name":"Long"},{"last_name":"Walker","full_name":"Walker, James","first_name":"James"},{"last_name":"She","full_name":"She, Wenjing","first_name":"Wenjing"},{"last_name":"Aldridge","full_name":"Aldridge, Billy","first_name":"Billy"},{"first_name":"Hongbo","full_name":"Gao, Hongbo","last_name":"Gao"},{"full_name":"Deans, Samuel","last_name":"Deans","first_name":"Samuel"},{"full_name":"Vickers, Martin","last_name":"Vickers","first_name":"Martin"},{"first_name":"Xiaoqi","orcid":"0000-0002-4008-1234","id":"e0164712-22ee-11ed-b12a-d80fcdf35958","full_name":"Feng, Xiaoqi","last_name":"Feng"}],"department":[{"_id":"XiFe"}],"date_updated":"2026-03-19T10:52:21Z","status":"public","type":"journal_article","oa_version":"Preprint","publication_status":"published","doi":"10.1126/science.abh0556","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","month":"07","publication_identifier":{"issn":["0036-8075"],"eissn":["1095-9203"]},"acknowledgement":"We thank the John Innes Centre Bioimaging Facility (S. Lopez, E. Wegel, and K. Findlay) for their assistance with microscopy and the Norwich BioScience Institute Partnership Computing Infrastructure for Science Group for high-performance computing resources. Funding: This work was funded by a European Research Council Starting Grant (“SexMeth” 804981; J.L., J.W., and X.F.), a Sainsbury Charitable Foundation studentship (J.W.), two Biotechnology and Biological Sciences Research Council (BBSRC) grants (BBS0096201 and BBP0135111; W.S., M.V., and X.F.), two John Innes Foundation studentships (B.A. and S.D.), and a BBSRC David Phillips Fellowship (BBL0250431; H.G. and X.F.). Author contributions: J.L., J.W., and X.F. designed the study and wrote the manuscript; J.L., W.S., B.A., H.G., and S.D. performed the experiments; and J.L., J.W., B.A., H.G., S.D., M.V., and X.F. analyzed the data. Competing interests: The authors declare no competing interests. Data and material availability: All sequencing data have been deposited in the Gene Expression Omnibus (GEO) under accession no. GSE161625. Accession nos. of published datasets used in this study are listed in table S6. Published software used in this study include Bowtie v1.2.2 (https://doi.org/10.1002/0471250953.bi1107s32), Bismark v0.22.2 (https://doi.org/10.1093/bioinformatics/btr167), Kallisto v0.43.0 (https://doi.org/10.1038/nbt0816-888d), Shortstack v3.8.5 (https://doi.org/10.1534/g3.116.030452), and Cutadapt v1.15 (https://doi.org/10.1089/cmb.2017.0096). TrimGalore v0.4.1 and MarkDuplicates v1.141 are available from https://github.com/FelixKrueger/TrimGalore and https://github.com/broadinstitute/picard, respectively. All remaining data are in the main paper or the supplementary materials.","external_id":{"pmid":["34210850"]},"OA_type":"green","language":[{"iso":"eng"}],"citation":{"ama":"Long J, Walker J, She W, et al. Nurse cell-derived small RNAs define paternal epigenetic inheritance in Arabidopsis. <i>Science</i>. 2021;373(6550). doi:<a href=\"https://doi.org/10.1126/science.abh0556\">10.1126/science.abh0556</a>","chicago":"Long, Jincheng, James Walker, Wenjing She, Billy Aldridge, Hongbo Gao, Samuel Deans, Martin Vickers, and Xiaoqi Feng. “Nurse Cell-Derived Small RNAs Define Paternal Epigenetic Inheritance in Arabidopsis.” <i>Science</i>. American Association for the Advancement of Science, 2021. <a href=\"https://doi.org/10.1126/science.abh0556\">https://doi.org/10.1126/science.abh0556</a>.","apa":"Long, J., Walker, J., She, W., Aldridge, B., Gao, H., Deans, S., … Feng, X. (2021). Nurse cell-derived small RNAs define paternal epigenetic inheritance in Arabidopsis. <i>Science</i>. American Association for the Advancement of Science. <a href=\"https://doi.org/10.1126/science.abh0556\">https://doi.org/10.1126/science.abh0556</a>","mla":"Long, Jincheng, et al. “Nurse Cell-Derived Small RNAs Define Paternal Epigenetic Inheritance in Arabidopsis.” <i>Science</i>, vol. 373, no. 6550, American Association for the Advancement of Science, 2021, doi:<a href=\"https://doi.org/10.1126/science.abh0556\">10.1126/science.abh0556</a>.","ista":"Long J, Walker J, She W, Aldridge B, Gao H, Deans S, Vickers M, Feng X. 2021. Nurse cell-derived small RNAs define paternal epigenetic inheritance in Arabidopsis. Science. 373(6550).","short":"J. Long, J. Walker, W. She, B. Aldridge, H. Gao, S. Deans, M. Vickers, X. Feng, Science 373 (2021).","ieee":"J. Long <i>et al.</i>, “Nurse cell-derived small RNAs define paternal epigenetic inheritance in Arabidopsis,” <i>Science</i>, vol. 373, no. 6550. American Association for the Advancement of Science, 2021."},"extern":"1","scopus_import":"1"},{"external_id":{"isi":["000659894300001"],"pmid":["34107249 "]},"file":[{"checksum":"7def3d42ebc8f5675efb6f38819e3e2e","relation":"main_file","file_size":8900385,"date_updated":"2021-06-15T14:01:35Z","file_name":"2021_CellReports_Zhang.pdf","content_type":"application/pdf","creator":"cziletti","file_id":"9554","date_created":"2021-06-15T14:01:35Z","access_level":"open_access","success":1}],"related_material":{"link":[{"relation":"earlier_version","url":"https://doi.org/10.1101/2020.03.18.997205"}]},"acknowledgement":"This work was supported by the program “Investissements d’avenir” ANR-10-IAIHU-06 , ICM , a Sorbonne Université Emergence grant, an Allen Distinguished Investigator Award , and the Roger De Spoelberch Foundation Prize (to B.A.H.); Armenise-Harvard Foundation , AIRC , and CARITRO (to L.T.); and the European Research Council under the European Union’s Horizon 2020 research and innovation programme grant agreement no. 725780 LinPro (to S.H.). T.Z. and T.L. were supported by doctoral fellowships from the China Scholarship Council and A.H.H. by a doctoral DOC fellowship of the Austrian Academy of Sciences ( 24812 ). All animal work was conducted at the PHENO-ICMice facility. The Core is supported by 2 “Investissements d’avenir” (ANR-10- IAIHU-06 and ANR-11-INBS-0011-NeurATRIS) and the “Fondation pour la Recherche Médicale.” Light microscopy work was carried out at ICM’s imaging core facility, ICM.Quant, and analysis of scRNA-seq data was carried out at ICM’s bioinformatics core facility, iCONICS. We thank Paulina Ejsmont, Natalia Danda, and Nathalie De Geest for technical support. We are grateful to Dr. Shahragim TAJBAKHSH for providing R26Rstop-NICD-nGFP transgenic mice, Dr. Bart De Strooper for Psn1-deficient mice, Dr. Jean-Christophe Marine for Gt(ROSA)26SortdTom reporter mice, and Dr. Martinez Barbera for Sox2CreERT2 mice. We also give thanks to Dr. Mikio Hoshino for providing Atoh1 and Ptf1a antibodies. B.A.H. is an Einstein Visiting Fellow of the Berlin Institute of Health .","publication_identifier":{"eissn":[" 2211-1247"]},"month":"06","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","scopus_import":"1","file_date_updated":"2021-06-15T14:01:35Z","project":[{"grant_number":"725780","_id":"260018B0-B435-11E9-9278-68D0E5697425","name":"Principles of Neural Stem Cell Lineage Progression in Cerebral Cortex Development","call_identifier":"H2020"},{"name":"Molecular mechanisms of radial neuronal migration","_id":"2625A13E-B435-11E9-9278-68D0E5697425","grant_number":"24812"}],"article_number":"109208","has_accepted_license":"1","citation":{"apa":"Zhang, T., Liu, T., Mora, N., Guegan, J., Bertrand, M., Contreras, X., … Hassan, B. A. (2021). Generation of excitatory and inhibitory neurons from common progenitors via Notch signaling in the cerebellum. <i>Cell Reports</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.celrep.2021.109208\">https://doi.org/10.1016/j.celrep.2021.109208</a>","chicago":"Zhang, Tingting, Tengyuan Liu, Natalia Mora, Justine Guegan, Mathilde Bertrand, Ximena Contreras, Andi H Hansen, et al. “Generation of Excitatory and Inhibitory Neurons from Common Progenitors via Notch Signaling in the Cerebellum.” <i>Cell Reports</i>. Elsevier, 2021. <a href=\"https://doi.org/10.1016/j.celrep.2021.109208\">https://doi.org/10.1016/j.celrep.2021.109208</a>.","ama":"Zhang T, Liu T, Mora N, et al. Generation of excitatory and inhibitory neurons from common progenitors via Notch signaling in the cerebellum. <i>Cell Reports</i>. 2021;35(10). doi:<a href=\"https://doi.org/10.1016/j.celrep.2021.109208\">10.1016/j.celrep.2021.109208</a>","ieee":"T. Zhang <i>et al.</i>, “Generation of excitatory and inhibitory neurons from common progenitors via Notch signaling in the cerebellum,” <i>Cell Reports</i>, vol. 35, no. 10. Elsevier, 2021.","ista":"Zhang T, Liu T, Mora N, Guegan J, Bertrand M, Contreras X, Hansen AH, Streicher C, Anderle M, Danda N, Tiberi L, Hippenmeyer S, Hassan BA. 2021. Generation of excitatory and inhibitory neurons from common progenitors via Notch signaling in the cerebellum. Cell Reports. 35(10), 109208.","short":"T. Zhang, T. Liu, N. Mora, J. Guegan, M. Bertrand, X. Contreras, A.H. Hansen, C. Streicher, M. Anderle, N. Danda, L. Tiberi, S. Hippenmeyer, B.A. Hassan, Cell Reports 35 (2021).","mla":"Zhang, Tingting, et al. “Generation of Excitatory and Inhibitory Neurons from Common Progenitors via Notch Signaling in the Cerebellum.” <i>Cell Reports</i>, vol. 35, no. 10, 109208, Elsevier, 2021, doi:<a href=\"https://doi.org/10.1016/j.celrep.2021.109208\">10.1016/j.celrep.2021.109208</a>."},"language":[{"iso":"eng"}],"date_updated":"2026-04-02T11:52:30Z","department":[{"_id":"SiHi"}],"author":[{"full_name":"Zhang, Tingting","last_name":"Zhang","first_name":"Tingting"},{"first_name":"Tengyuan","last_name":"Liu","full_name":"Liu, Tengyuan"},{"first_name":"Natalia","full_name":"Mora, Natalia","last_name":"Mora"},{"first_name":"Justine","full_name":"Guegan, Justine","last_name":"Guegan"},{"last_name":"Bertrand","full_name":"Bertrand, Mathilde","first_name":"Mathilde"},{"first_name":"Ximena","id":"475990FE-F248-11E8-B48F-1D18A9856A87","last_name":"Contreras","full_name":"Contreras, Ximena"},{"last_name":"Hansen","full_name":"Hansen, Andi H","id":"38853E16-F248-11E8-B48F-1D18A9856A87","first_name":"Andi H"},{"first_name":"Carmen","id":"36BCB99C-F248-11E8-B48F-1D18A9856A87","last_name":"Streicher","full_name":"Streicher, Carmen"},{"first_name":"Marica","last_name":"Anderle","full_name":"Anderle, Marica"},{"last_name":"Danda","full_name":"Danda, Natasha","first_name":"Natasha"},{"first_name":"Luca","last_name":"Tiberi","full_name":"Tiberi, Luca"},{"last_name":"Hippenmeyer","full_name":"Hippenmeyer, Simon","first_name":"Simon","id":"37B36620-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2279-1061"},{"last_name":"Hassan","full_name":"Hassan, Bassem A.","first_name":"Bassem A."}],"article_processing_charge":"No","doi":"10.1016/j.celrep.2021.109208","publication_status":"published","oa_version":"Published Version","type":"journal_article","isi":1,"status":"public","publication":"Cell Reports","volume":35,"title":"Generation of excitatory and inhibitory neurons from common progenitors via Notch signaling in the cerebellum","article_type":"original","ec_funded":1,"_id":"8546","day":"08","publisher":"Elsevier","ddc":["570"],"pmid":1,"date_published":"2021-06-08T00:00:00Z","issue":"10","year":"2021","tmp":{"short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png"},"oa":1,"abstract":[{"lang":"eng","text":"Brain neurons arise from relatively few progenitors generating an enormous diversity of neuronal types. Nonetheless, a cardinal feature of mammalian brain neurogenesis is thought to be that excitatory and inhibitory neurons derive from separate, spatially segregated progenitors. Whether bi-potential progenitors with an intrinsic capacity to generate both lineages exist and how such a fate decision may be regulated are unknown. Using cerebellar development as a model, we discover that individual progenitors can give rise to both inhibitory and excitatory lineages. Gradations of Notch activity determine the fates of the progenitors and their daughters. Daughters with the highest levels of Notch activity retain the progenitor fate, while intermediate levels of Notch activity generate inhibitory neurons, and daughters with very low levels of Notch signaling adopt the excitatory fate. Therefore, Notch-mediated binary cell fate choice is a mechanism for regulating the ratio of excitatory to inhibitory neurons from common progenitors."}],"date_created":"2020-09-21T12:00:48Z","intvolume":"        35","quality_controlled":"1"},{"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","month":"10","external_id":{"pmid":["34667153"],"isi":["000709050300016"]},"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).","file":[{"relation":"main_file","checksum":"c40a69ae94435ecd3a30c9874a11ef2b","file_size":7144437,"date_updated":"2021-11-09T13:59:26Z","file_name":"2021_NatureComm_Pradhan.pdf","creator":"cziletti","content_type":"application/pdf","file_id":"10262","success":1,"access_level":"open_access","date_created":"2021-11-09T13:59:26Z"}],"related_material":{"link":[{"description":"Preprint","url":"https://doi.org/10.1101/2020.11.23.394171 ","relation":"earlier_version"}]},"publication_identifier":{"eissn":["2041-1723"]},"article_number":"6094","has_accepted_license":"1","citation":{"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.","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).","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.","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>.","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>","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>","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>."},"language":[{"iso":"eng"}],"scopus_import":"1","file_date_updated":"2021-11-09T13:59:26Z","corr_author":"1","article_processing_charge":"Yes","author":[{"first_name":"Saurabh J.","last_name":"Pradhan","full_name":"Pradhan, Saurabh J."},{"first_name":"Puli Chandramouli","full_name":"Reddy, Puli Chandramouli","last_name":"Reddy"},{"last_name":"Smutny","full_name":"Smutny, Michael","id":"3FE6E4E8-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-5920-9090","first_name":"Michael"},{"first_name":"Ankita","last_name":"Sharma","full_name":"Sharma, Ankita"},{"last_name":"Sako","full_name":"Sako, Keisuke","first_name":"Keisuke","id":"3BED66BE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6453-8075"},{"first_name":"Meghana S.","full_name":"Oak, Meghana S.","last_name":"Oak"},{"full_name":"Shah, Rini","last_name":"Shah","first_name":"Rini"},{"first_name":"Mrinmoy","full_name":"Pal, Mrinmoy","last_name":"Pal"},{"last_name":"Deshpande","full_name":"Deshpande, Ojas","first_name":"Ojas"},{"first_name":"Greg","last_name":"Dsilva","full_name":"Dsilva, Greg"},{"last_name":"Tang","full_name":"Tang, Yin","first_name":"Yin"},{"first_name":"Rakesh","full_name":"Mishra, Rakesh","last_name":"Mishra"},{"full_name":"Deshpande, Girish","last_name":"Deshpande","first_name":"Girish"},{"first_name":"Antonio J.","full_name":"Giraldez, Antonio J.","last_name":"Giraldez"},{"first_name":"Mahendra","last_name":"Sonawane","full_name":"Sonawane, Mahendra"},{"orcid":"0000-0002-0912-4566","id":"39427864-F248-11E8-B48F-1D18A9856A87","first_name":"Carl-Philipp J","full_name":"Heisenberg, Carl-Philipp J","last_name":"Heisenberg"},{"first_name":"Sanjeev","full_name":"Galande, Sanjeev","last_name":"Galande"}],"date_updated":"2026-04-02T11:57:41Z","department":[{"_id":"CaHe"}],"isi":1,"status":"public","doi":"10.1038/s41467-021-26234-7","publication_status":"published","oa_version":"Published Version","type":"journal_article","volume":12,"article_type":"original","title":"Satb2 acts as a gatekeeper for major developmental transitions during early vertebrate embryogenesis","publication":"Nature Communications","ddc":["570"],"pmid":1,"_id":"10202","day":"19","publisher":"Springer Nature","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"oa":1,"date_published":"2021-10-19T00:00:00Z","issue":"1","year":"2021","abstract":[{"lang":"eng","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."}],"date_created":"2021-10-31T23:01:29Z","intvolume":"        12","quality_controlled":"1"},{"isi":1,"status":"public","doi":"10.1126/sciadv.abj0127","publication_status":"published","oa_version":"Published Version","type":"journal_article","author":[{"first_name":"Javier","last_name":"Martín-Sánchez","full_name":"Martín-Sánchez, Javier"},{"last_name":"Duan","full_name":"Duan, Jiahua","first_name":"Jiahua"},{"first_name":"Javier","full_name":"Taboada-Gutiérrez, Javier","last_name":"Taboada-Gutiérrez"},{"first_name":"Gonzalo","last_name":"Álvarez-Pérez","full_name":"Álvarez-Pérez, Gonzalo"},{"first_name":"Kirill V.","last_name":"Voronin","full_name":"Voronin, Kirill V."},{"last_name":"Prieto Gonzalez","full_name":"Prieto Gonzalez, Ivan","first_name":"Ivan","id":"2A307FE2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7370-5357"},{"first_name":"Weiliang","last_name":"Ma","full_name":"Ma, Weiliang"},{"full_name":"Bao, Qiaoliang","last_name":"Bao","first_name":"Qiaoliang"},{"first_name":"Valentyn S.","full_name":"Volkov, Valentyn S.","last_name":"Volkov"},{"first_name":"Rainer","last_name":"Hillenbrand","full_name":"Hillenbrand, Rainer"},{"first_name":"Alexey Y.","last_name":"Nikitin","full_name":"Nikitin, Alexey Y."},{"full_name":"Alonso-González, Pablo","last_name":"Alonso-González","first_name":"Pablo"}],"article_processing_charge":"Yes","date_updated":"2026-04-02T13:15:46Z","department":[{"_id":"NanoFab"}],"article_number":"abj0127","has_accepted_license":"1","citation":{"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.","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).","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.","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>.","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>","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>.","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>"},"language":[{"iso":"eng"}],"scopus_import":"1","file_date_updated":"2021-10-27T14:16:06Z","license":"https://creativecommons.org/licenses/by-nc/4.0/","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","month":"10","external_id":{"arxiv":["2103.10852"],"isi":["000704912700024"]},"file":[{"file_name":"2021_ScienceAdv_Martin-Sanchez.pdf","date_updated":"2021-10-27T14:16:06Z","file_size":2441163,"relation":"main_file","checksum":"0a470ef6a47d2b8a96ede4c4d28cfacd","access_level":"open_access","success":1,"date_created":"2021-10-27T14:16:06Z","file_id":"10189","creator":"cziletti","content_type":"application/pdf"}],"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).","publication_identifier":{"eissn":["2375-2548"]},"intvolume":"         7","date_created":"2021-10-24T22:01:33Z","abstract":[{"lang":"eng","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."}],"quality_controlled":"1","tmp":{"short":"CC BY-NC (4.0)","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png"},"oa":1,"date_published":"2021-10-08T00:00:00Z","issue":"41","year":"2021","ddc":["530"],"_id":"10177","day":"08","arxiv":1,"publisher":"American Association for the Advancement of Science","volume":7,"title":"Focusing of in-plane hyperbolic polaritons in van der Waals crystals with tailored infrared nanoantennas","article_type":"original","publication":"Science Advances"},{"quality_controlled":"1","intvolume":"        10","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."}],"date_created":"2021-06-27T22:01:49Z","year":"2021","date_published":"2021-05-24T00:00:00Z","oa":1,"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"publisher":"eLife Sciences Publications","day":"24","_id":"9607","pmid":1,"ddc":["570"],"publication":"eLife","title":"Introduction to the EQIPD quality system","article_type":"original","volume":10,"type":"journal_article","oa_version":"Published Version","publication_status":"published","doi":"10.7554/eLife.63294","status":"public","isi":1,"department":[{"_id":"PreCl"}],"date_updated":"2026-04-02T13:55:57Z","article_processing_charge":"No","author":[{"last_name":"Bespalov","full_name":"Bespalov, Anton","first_name":"Anton"},{"first_name":"René","last_name":"Bernard","full_name":"Bernard, René"},{"first_name":"Anja","last_name":"Gilis","full_name":"Gilis, Anja"},{"first_name":"Björn","full_name":"Gerlach, Björn","last_name":"Gerlach"},{"full_name":"Guillén, Javier","last_name":"Guillén","first_name":"Javier"},{"full_name":"Castagné, Vincent","last_name":"Castagné","first_name":"Vincent"},{"first_name":"Isabel A.","last_name":"Lefevre","full_name":"Lefevre, Isabel A."},{"last_name":"Ducrey","full_name":"Ducrey, Fiona","first_name":"Fiona"},{"first_name":"Lee","full_name":"Monk, Lee","last_name":"Monk"},{"first_name":"Sandrine","last_name":"Bongiovanni","full_name":"Bongiovanni, Sandrine"},{"full_name":"Altevogt, Bruce","last_name":"Altevogt","first_name":"Bruce"},{"full_name":"Arroyo-Araujo, María","last_name":"Arroyo-Araujo","first_name":"María"},{"first_name":"Lior","full_name":"Bikovski, Lior","last_name":"Bikovski"},{"first_name":"Natasja","last_name":"De Bruin","full_name":"De Bruin, Natasja"},{"first_name":"Esmeralda","full_name":"Castaños-Vélez, Esmeralda","last_name":"Castaños-Vélez"},{"first_name":"Alexander","full_name":"Dityatev, Alexander","last_name":"Dityatev"},{"first_name":"Christoph H.","last_name":"Emmerich","full_name":"Emmerich, Christoph H."},{"first_name":"Raafat","last_name":"Fares","full_name":"Fares, Raafat"},{"first_name":"Chantelle","full_name":"Ferland-Beckham, Chantelle","last_name":"Ferland-Beckham"},{"first_name":"Christelle","full_name":"Froger-Colléaux, Christelle","last_name":"Froger-Colléaux"},{"full_name":"Gailus-Durner, Valerie","last_name":"Gailus-Durner","first_name":"Valerie"},{"first_name":"Sabine M.","last_name":"Hölter","full_name":"Hölter, Sabine M."},{"first_name":"Martine Cj","full_name":"Hofmann, Martine Cj","last_name":"Hofmann"},{"first_name":"Patricia","last_name":"Kabitzke","full_name":"Kabitzke, Patricia"},{"first_name":"Martien Jh","full_name":"Kas, Martien Jh","last_name":"Kas"},{"first_name":"Claudia","last_name":"Kurreck","full_name":"Kurreck, Claudia"},{"full_name":"Moser, Paul","last_name":"Moser","first_name":"Paul"},{"first_name":"Malgorzata","last_name":"Pietraszek","full_name":"Pietraszek, Malgorzata"},{"last_name":"Popik","full_name":"Popik, Piotr","first_name":"Piotr"},{"full_name":"Potschka, Heidrun","last_name":"Potschka","first_name":"Heidrun"},{"last_name":"Prado Montes De Oca","full_name":"Prado Montes De Oca, Ernesto","first_name":"Ernesto"},{"first_name":"Leonardo","full_name":"Restivo, Leonardo","last_name":"Restivo"},{"full_name":"Riedel, Gernot","last_name":"Riedel","first_name":"Gernot"},{"last_name":"Ritskes-Hoitinga","full_name":"Ritskes-Hoitinga, Merel","first_name":"Merel"},{"full_name":"Samardzic, Janko","last_name":"Samardzic","first_name":"Janko"},{"orcid":"0000-0003-4326-5300","id":"4272DB4A-F248-11E8-B48F-1D18A9856A87","first_name":"Michael","last_name":"Schunn","full_name":"Schunn, Michael"},{"first_name":"Claudia","full_name":"Stöger, Claudia","last_name":"Stöger"},{"first_name":"Vootele","full_name":"Voikar, Vootele","last_name":"Voikar"},{"full_name":"Vollert, Jan","last_name":"Vollert","first_name":"Jan"},{"first_name":"Kimberley E.","full_name":"Wever, Kimberley E.","last_name":"Wever"},{"first_name":"Kathleen","last_name":"Wuyts","full_name":"Wuyts, Kathleen"},{"last_name":"Macleod","full_name":"Macleod, Malcolm R.","first_name":"Malcolm R."},{"first_name":"Ulrich","last_name":"Dirnagl","full_name":"Dirnagl, Ulrich"},{"first_name":"Thomas","full_name":"Steckler, Thomas","last_name":"Steckler"}],"file_date_updated":"2021-06-28T11:35:30Z","scopus_import":"1","language":[{"iso":"eng"}],"citation":{"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>","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>.","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>","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>.","ieee":"A. Bespalov <i>et al.</i>, “Introduction to the EQIPD quality system,” <i>eLife</i>, vol. 10. eLife Sciences Publications, 2021.","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.","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)."},"has_accepted_license":"1","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).","file":[{"file_size":2500720,"checksum":"885b746051a7a6b6e24e3d2781a48fde","relation":"main_file","file_name":"2021_ELife_Bespalov.pdf","date_updated":"2021-06-28T11:35:30Z","creator":"asandaue","content_type":"application/pdf","date_created":"2021-06-28T11:35:30Z","access_level":"open_access","success":1,"file_id":"9609"}],"external_id":{"isi":["000661272000001"],"pmid":["34028353"]},"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","month":"05"},{"publication":"Nanomaterials","title":"Extracting the infrared permittivity of SiO2 substrates locally by near-field imaging of phonon polaritons in a van der Waals crystal","article_type":"original","volume":11,"publisher":"MDPI","day":"07","_id":"9038","pmid":1,"ddc":["620"],"year":"2021","issue":"1","date_published":"2021-01-07T00:00:00Z","oa":1,"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"quality_controlled":"1","abstract":[{"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. ","lang":"eng"}],"date_created":"2021-01-24T23:01:09Z","intvolume":"        11","publication_identifier":{"eissn":["2079-4991"]},"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).","file":[{"date_updated":"2021-01-25T08:02:32Z","file_name":"2020_Nanomaterials_Aguilar_Merino.pdf","relation":"main_file","checksum":"1edc13eeda83df5cd9fff9504727b1f5","file_size":2730267,"file_id":"9042","access_level":"open_access","success":1,"date_created":"2021-01-25T08:02:32Z","content_type":"application/pdf","creator":"dernst"}],"external_id":{"pmid":["33430225"],"isi":["000610636600001"]},"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","month":"01","file_date_updated":"2021-01-25T08:02:32Z","scopus_import":"1","language":[{"iso":"eng"}],"citation":{"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.","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).","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>","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>.","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>"},"article_number":"120","has_accepted_license":"1","department":[{"_id":"NanoFab"}],"date_updated":"2026-04-02T13:57:24Z","author":[{"last_name":"Aguilar-Merino","full_name":"Aguilar-Merino, Patricia","first_name":"Patricia"},{"first_name":"Gonzalo","last_name":"Álvarez-Pérez","full_name":"Álvarez-Pérez, Gonzalo"},{"first_name":"Javier","full_name":"Taboada-Gutiérrez, Javier","last_name":"Taboada-Gutiérrez"},{"last_name":"Duan","full_name":"Duan, Jiahua","first_name":"Jiahua"},{"orcid":"0000-0002-7370-5357","id":"2A307FE2-F248-11E8-B48F-1D18A9856A87","first_name":"Ivan","last_name":"Prieto Gonzalez","full_name":"Prieto Gonzalez, Ivan"},{"last_name":"Álvarez-Prado","full_name":"Álvarez-Prado, Luis Manuel","first_name":"Luis Manuel"},{"first_name":"Alexey Y.","last_name":"Nikitin","full_name":"Nikitin, Alexey Y."},{"first_name":"Javier","last_name":"Martín-Sánchez","full_name":"Martín-Sánchez, Javier"},{"first_name":"Pablo","last_name":"Alonso-González","full_name":"Alonso-González, Pablo"}],"article_processing_charge":"No","type":"journal_article","oa_version":"Published Version","publication_status":"published","doi":"10.3390/nano11010120","status":"public","isi":1},{"volume":12,"title":"Genomic imprinting in mouse blastocysts is predominantly associated with H3K27me3","article_type":"original","publication":"Nature Communications","ddc":["570"],"_id":"9601","publisher":"Springer Nature","day":"12","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"oa":1,"date_published":"2021-07-12T00:00:00Z","year":"2021","issue":"1","abstract":[{"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.","lang":"eng"}],"date_created":"2021-06-27T22:01:46Z","intvolume":"        12","quality_controlled":"1","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","month":"07","file":[{"content_type":"application/pdf","creator":"asandaue","date_created":"2021-06-28T08:04:22Z","access_level":"open_access","success":1,"file_id":"9608","file_size":2156554,"checksum":"75dd89d09945185b2d14b2434a0bcb50","relation":"main_file","file_name":"2021_NatureCommunications_Santini.pdf","date_updated":"2021-06-28T08:04:22Z"}],"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).","external_id":{"isi":["000667248600005"]},"publication_identifier":{"eissn":["2041-1723"]},"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>.","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>","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>","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.","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).","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."},"has_accepted_license":"1","article_number":"3804","language":[{"iso":"eng"}],"scopus_import":"1","file_date_updated":"2021-06-28T08:04:22Z","author":[{"first_name":"Laura","full_name":"Santini, Laura","last_name":"Santini"},{"first_name":"Florian","last_name":"Halbritter","full_name":"Halbritter, Florian"},{"last_name":"Titz-Teixeira","full_name":"Titz-Teixeira, Fabian","first_name":"Fabian"},{"last_name":"Suzuki","full_name":"Suzuki, Toru","first_name":"Toru"},{"first_name":"Maki","full_name":"Asami, Maki","last_name":"Asami"},{"full_name":"Ma, Xiaoyan","last_name":"Ma","first_name":"Xiaoyan"},{"first_name":"Julia","full_name":"Ramesmayer, Julia","last_name":"Ramesmayer"},{"first_name":"Andreas","full_name":"Lackner, Andreas","last_name":"Lackner"},{"last_name":"Warr","full_name":"Warr, Nick","first_name":"Nick"},{"id":"48EA0138-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7462-0048","first_name":"Florian","full_name":"Pauler, Florian","last_name":"Pauler"},{"last_name":"Hippenmeyer","full_name":"Hippenmeyer, Simon","orcid":"0000-0003-2279-1061","id":"37B36620-F248-11E8-B48F-1D18A9856A87","first_name":"Simon"},{"first_name":"Ernest","last_name":"Laue","full_name":"Laue, Ernest"},{"first_name":"Matthias","last_name":"Farlik","full_name":"Farlik, Matthias"},{"first_name":"Christoph","last_name":"Bock","full_name":"Bock, Christoph"},{"last_name":"Beyer","full_name":"Beyer, Andreas","first_name":"Andreas"},{"full_name":"Perry, Anthony C.F.","last_name":"Perry","first_name":"Anthony C.F."},{"last_name":"Leeb","full_name":"Leeb, Martin","first_name":"Martin"}],"article_processing_charge":"No","date_updated":"2026-04-02T13:55:23Z","department":[{"_id":"SiHi"}],"isi":1,"status":"public","publication_status":"published","doi":"10.1038/s41467-021-23510-4","type":"journal_article","oa_version":"Published Version"},{"language":[{"iso":"eng"}],"has_accepted_license":"1","article_number":"1593","citation":{"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>","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>.","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>","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>.","short":"N.A. Muench, S. Patel, M.E. Maes, R.J. Donahue, A. Ikeda, R.W. Nickells, Cells 10 (2021).","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.","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."},"file_date_updated":"2021-08-04T14:01:30Z","scopus_import":"1","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","month":"06","publication_identifier":{"eissn":["2073-4409"]},"external_id":{"isi":["000678193300001"],"pmid":["34201955"]},"file":[{"success":1,"access_level":"open_access","date_created":"2021-08-04T14:01:30Z","file_id":"9768","creator":"cziletti","content_type":"application/pdf","file_name":"2021_Cells_Muench.pdf","date_updated":"2021-08-04T14:01:30Z","file_size":4555611,"relation":"main_file","checksum":"e0497ce5c77fa3b65a538c7d6e0f6c66"}],"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.","status":"public","isi":1,"oa_version":"Published Version","type":"journal_article","doi":"10.3390/cells10071593","publication_status":"published","article_processing_charge":"Yes","author":[{"last_name":"Muench","full_name":"Muench, Nicole A.","first_name":"Nicole A."},{"first_name":"Sonia","last_name":"Patel","full_name":"Patel, Sonia"},{"id":"3838F452-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9642-1085","first_name":"Margaret E","last_name":"Maes","full_name":"Maes, Margaret E"},{"first_name":"Ryan J.","full_name":"Donahue, Ryan J.","last_name":"Donahue"},{"last_name":"Ikeda","full_name":"Ikeda, Akihiro","first_name":"Akihiro"},{"first_name":"Robert W.","last_name":"Nickells","full_name":"Nickells, Robert W."}],"department":[{"_id":"SaSi"}],"date_updated":"2026-04-02T13:56:24Z","pmid":1,"ddc":["570"],"day":"25","publisher":"MDPI","_id":"9761","title":"The influence of mitochondrial dynamics and function on retinal ganglion cell susceptibility in optic nerve disease","article_type":"original","volume":10,"publication":"Cells","quality_controlled":"1","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"}],"date_created":"2021-08-01T22:01:22Z","intvolume":"        10","oa":1,"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"issue":"7","year":"2021","date_published":"2021-06-25T00:00:00Z"},{"author":[{"first_name":"Yangjie","last_name":"Hu","full_name":"Hu, Yangjie"},{"full_name":"Omary, Moutasem","last_name":"Omary","first_name":"Moutasem"},{"first_name":"Yun","full_name":"Hu, Yun","last_name":"Hu"},{"first_name":"Ohad","last_name":"Doron","full_name":"Doron, Ohad"},{"last_name":"Hörmayer","full_name":"Hörmayer, Lukas","first_name":"Lukas","orcid":"0000-0001-8295-2926","id":"2EEE7A2A-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Qingguo","last_name":"Chen","full_name":"Chen, Qingguo"},{"first_name":"Or","full_name":"Megides, Or","last_name":"Megides"},{"last_name":"Chekli","full_name":"Chekli, Ori","first_name":"Ori"},{"last_name":"Ding","full_name":"Ding, Zhaojun","first_name":"Zhaojun"},{"last_name":"Friml","full_name":"Friml, Jiří","first_name":"Jiří","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Zhao","full_name":"Zhao, Yunde","first_name":"Yunde"},{"first_name":"Ilan","last_name":"Tsarfaty","full_name":"Tsarfaty, Ilan"},{"full_name":"Shani, Eilon","last_name":"Shani","first_name":"Eilon"}],"article_processing_charge":"No","date_updated":"2026-04-02T13:57:40Z","department":[{"_id":"JiFr"}],"isi":1,"status":"public","doi":"10.1038/s41467-021-21802-3","publication_status":"published","oa_version":"Published Version","type":"journal_article","month":"03","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","external_id":{"isi":["000630419400048"],"pmid":["33712581"]},"file":[{"file_id":"9275","access_level":"open_access","success":1,"date_created":"2021-03-22T11:18:58Z","content_type":"application/pdf","creator":"dernst","date_updated":"2021-03-22T11:18:58Z","file_name":"2021_NatureComm_Hu.pdf","relation":"main_file","checksum":"e1022f3aee349853ded2b2b3e092362d","file_size":8602096}],"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.).","publication_identifier":{"eissn":["2041-1723"]},"article_number":"1657","has_accepted_license":"1","citation":{"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>.","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).","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.","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>.","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>","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>"},"language":[{"iso":"eng"}],"scopus_import":"1","file_date_updated":"2021-03-22T11:18:58Z","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"oa":1,"date_published":"2021-03-12T00:00:00Z","year":"2021","intvolume":"        12","abstract":[{"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.","lang":"eng"}],"date_created":"2021-03-21T23:01:19Z","quality_controlled":"1","volume":12,"article_type":"original","title":"Cell kinetics of auxin transport and activity in Arabidopsis root growth and skewing","publication":"Nature Communications","ddc":["580"],"pmid":1,"_id":"9254","day":"12","publisher":"Springer Nature"},{"date_published":"2021-07-01T00:00:00Z","issue":"7","year":"2021","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"oa":1,"date_created":"2021-08-08T22:01:28Z","intvolume":"        16","abstract":[{"lang":"eng","text":"Heart rate variability (hrv) is a physiological phenomenon of the variation in the length of the time interval between consecutive heartbeats. In many cases it could be an indicator of the development of pathological states. The classical approach to the analysis of hrv includes time domain methods and frequency domain methods. However, attempts are still being made to define new and more effective hrv assessment tools. Persistent homology is a novel data analysis tool developed in the recent decades that is rooted at algebraic topology. The Topological Data Analysis (TDA) approach focuses on examining the shape of the data in terms of connectedness and holes, and has recently proved to be very effective in various fields of research. In this paper we propose the use of persistent homology to the hrv analysis. We recall selected topological descriptors used in the literature and we introduce some new topological descriptors that reflect the specificity of hrv, and we discuss their relation to the standard hrv measures. In particular, we show that this novel approach provides a collection of indices that might be at least as useful as the classical parameters in differentiating between series of beat-to-beat intervals (RR-intervals) in healthy subjects and patients suffering from a stroke episode."}],"quality_controlled":"1","publication":"PLoS ONE","volume":16,"title":"Persistent homology as a new method of the assessment of heart rate variability","article_type":"original","_id":"9821","day":"01","publisher":"Public Library of Science","ddc":["006"],"pmid":1,"date_updated":"2026-04-02T13:56:42Z","department":[{"_id":"HeEd"}],"author":[{"first_name":"Grzegorz","last_name":"Graff","full_name":"Graff, Grzegorz"},{"first_name":"Beata","last_name":"Graff","full_name":"Graff, Beata"},{"last_name":"Pilarczyk","full_name":"Pilarczyk, Pawel","id":"3768D56A-F248-11E8-B48F-1D18A9856A87","first_name":"Pawel"},{"full_name":"Jablonski, Grzegorz","last_name":"Jablonski","first_name":"Grzegorz","id":"4483EF78-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-3536-9866"},{"first_name":"Dariusz","full_name":"Gąsecki, Dariusz","last_name":"Gąsecki"},{"last_name":"Narkiewicz","full_name":"Narkiewicz, Krzysztof","first_name":"Krzysztof"}],"article_processing_charge":"Yes","doi":"10.1371/journal.pone.0253851","publication_status":"published","oa_version":"Published Version","type":"journal_article","isi":1,"status":"public","external_id":{"pmid":["34292957"],"isi":["000678124900050"]},"file":[{"file_size":2706919,"relation":"main_file","checksum":"0277aa155d5db1febd2cb384768bba5f","file_name":"2021_PLoSONE_Graff.pdf","date_updated":"2021-08-09T09:25:41Z","creator":"asandaue","content_type":"application/pdf","success":1,"access_level":"open_access","date_created":"2021-08-09T09:25:41Z","file_id":"9832"}],"acknowledgement":"We express our gratitude to the anonymous referees who provided constructive comments that helped us improve the quality of the paper.","publication_identifier":{"eissn":["1932-6203"]},"month":"07","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","scopus_import":"1","file_date_updated":"2021-08-09T09:25:41Z","has_accepted_license":"1","article_number":"e0253851","citation":{"short":"G. Graff, B. Graff, P. Pilarczyk, G. Jablonski, D. Gąsecki, K. Narkiewicz, PLoS ONE 16 (2021).","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.","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.","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>.","apa":"Graff, G., Graff, B., Pilarczyk, P., Jablonski, G., Gąsecki, D., &#38; Narkiewicz, K. (2021). Persistent homology as a new method of the assessment of heart rate variability. <i>PLoS ONE</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pone.0253851\">https://doi.org/10.1371/journal.pone.0253851</a>","chicago":"Graff, Grzegorz, Beata Graff, Pawel Pilarczyk, Grzegorz Jablonski, Dariusz Gąsecki, and Krzysztof Narkiewicz. “Persistent Homology as a New Method of the Assessment of Heart Rate Variability.” <i>PLoS ONE</i>. Public Library of Science, 2021. <a href=\"https://doi.org/10.1371/journal.pone.0253851\">https://doi.org/10.1371/journal.pone.0253851</a>.","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>"},"language":[{"iso":"eng"}]},{"date_updated":"2026-04-02T13:54:56Z","department":[{"_id":"EdHa"}],"article_processing_charge":"Yes","author":[{"full_name":"Sahu, Preeti","last_name":"Sahu","first_name":"Preeti","id":"55BA52EE-A185-11EA-88FD-18AD3DDC885E"},{"last_name":"Schwarz","full_name":"Schwarz, J. M.","first_name":"J. M."},{"full_name":"Manning, M. Lisa","last_name":"Manning","first_name":"M. Lisa"}],"publication_status":"published","doi":"10.1088/1367-2630/ac23f1","type":"journal_article","oa_version":"Published Version","isi":1,"status":"public","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","file":[{"file_id":"10193","date_created":"2021-10-28T12:06:01Z","access_level":"open_access","success":1,"creator":"cziletti","content_type":"application/pdf","file_name":"2021_NewJPhys_Sahu.pdf","date_updated":"2021-10-28T12:06:01Z","checksum":"ace603e8f0962b3ba55f23fa34f57764","relation":"main_file","file_size":2215016}],"external_id":{"isi":["000702042400001"],"arxiv":["2102.05397"]},"publication_identifier":{"eissn":["1367-2630"]},"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","month":"09","scopus_import":"1","file_date_updated":"2021-10-28T12:06:01Z","citation":{"short":"P. Sahu, J.M. Schwarz, M.L. Manning, New Journal of Physics 23 (2021).","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.","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>.","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>","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>.","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>"},"article_number":"093043","has_accepted_license":"1","language":[{"iso":"eng"}],"date_published":"2021-09-29T00:00:00Z","year":"2021","issue":"9","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"oa":1,"abstract":[{"lang":"eng","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."}],"intvolume":"        23","date_created":"2021-10-24T22:01:34Z","quality_controlled":"1","publication":"New Journal of Physics","volume":23,"article_type":"original","title":"Geometric signatures of tissue surface tension in a three-dimensional model of confluent tissue","_id":"10178","publisher":"IOP Publishing","arxiv":1,"day":"29","ddc":["570"]},{"department":[{"_id":"JiFr"}],"date_updated":"2026-04-02T13:57:06Z","article_processing_charge":"Yes","author":[{"last_name":"Zeng","full_name":"Zeng, Yinwei","first_name":"Yinwei"},{"last_name":"Verstraeten","full_name":"Verstraeten, Inge","first_name":"Inge","orcid":"0000-0001-7241-2328","id":"362BF7FE-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Hoang Khai","full_name":"Trinh, Hoang Khai","last_name":"Trinh"},{"full_name":"Heugebaert, Thomas","last_name":"Heugebaert","first_name":"Thomas"},{"full_name":"Stevens, Christian V.","last_name":"Stevens","first_name":"Christian V."},{"first_name":"Irene","full_name":"Garcia-Maquilon, Irene","last_name":"Garcia-Maquilon"},{"last_name":"Rodriguez","full_name":"Rodriguez, Pedro L.","first_name":"Pedro L."},{"full_name":"Vanneste, Steffen","last_name":"Vanneste","first_name":"Steffen"},{"last_name":"Geelen","full_name":"Geelen, Danny","first_name":"Danny"}],"oa_version":"Published Version","type":"journal_article","doi":"10.3390/genes12081141","publication_status":"published","status":"public","isi":1,"publication_identifier":{"eissn":["2073-4425"]},"external_id":{"isi":["000690558000001"]},"file":[{"date_updated":"2021-08-16T09:02:40Z","file_name":"2021_Genes_Zeng.pdf","file_size":1340305,"checksum":"3d99535618cf9a5b14d264408fa52e97","relation":"main_file","date_created":"2021-08-16T09:02:40Z","access_level":"open_access","success":1,"file_id":"9919","creator":"asandaue","content_type":"application/pdf"}],"acknowledgement":"We thank S. Cutler (Riverside, USA) for providing the ABA biosynthesis mutants and ABA signaling mutants.","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","month":"07","file_date_updated":"2021-08-16T09:02:40Z","scopus_import":"1","language":[{"iso":"eng"}],"article_number":"1141","has_accepted_license":"1","citation":{"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>","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>.","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>","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).","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.","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.","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>."},"issue":"8","year":"2021","date_published":"2021-07-27T00:00:00Z","oa":1,"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"quality_controlled":"1","abstract":[{"lang":"eng","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."}],"date_created":"2021-08-15T22:01:28Z","intvolume":"        12","publication":"Genes","article_type":"original","title":"Arabidopsis hypocotyl adventitious root formation is suppressed by ABA signaling","volume":12,"day":"27","publisher":"MDPI","_id":"9909","ddc":["580","570"]}]