[{"type":"journal_article","article_processing_charge":"Yes (via OA deal)","ddc":["520"],"page":"280-292","oa_version":"Published Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","scopus_import":"1","quality_controlled":"1","doi":"10.1038/s41550-024-02424-3","publication_identifier":{"eissn":["2397-3366"]},"status":"public","day":"01","date_updated":"2025-05-19T14:01:21Z","OA_type":"hybrid","OA_place":"publisher","_id":"18631","title":"Efficient formation of a massive quiescent galaxy at redshift 4.9","citation":{"ista":"De Graaff A, Setton DJ, Brammer G, Cutler S, Suess KA, Labbé I, Leja J, Weibel A, Maseda MV, Whitaker KE, Bezanson R, Boogaard LA, Cleri NJ, De Lucia G, Franx M, Greene JE, Hirschmann M, Matthee JJ, Mcconachie I, Naidu RP, Oesch PA, Price SH, Rix HW, Valentino F, Wang B, Williams CC. 2025. Efficient formation of a massive quiescent galaxy at redshift 4.9. Nature Astronomy. 9, 280–292.","chicago":"De Graaff, Anna, David J. Setton, Gabriel Brammer, Sam Cutler, Katherine A. Suess, Ivo Labbé, Joel Leja, et al. “Efficient Formation of a Massive Quiescent Galaxy at Redshift 4.9.” <i>Nature Astronomy</i>. Springer Nature, 2025. <a href=\"https://doi.org/10.1038/s41550-024-02424-3\">https://doi.org/10.1038/s41550-024-02424-3</a>.","short":"A. De Graaff, D.J. Setton, G. Brammer, S. Cutler, K.A. Suess, I. Labbé, J. Leja, A. Weibel, M.V. Maseda, K.E. Whitaker, R. Bezanson, L.A. Boogaard, N.J. Cleri, G. De Lucia, M. Franx, J.E. Greene, M. Hirschmann, J.J. Matthee, I. Mcconachie, R.P. Naidu, P.A. Oesch, S.H. Price, H.W. Rix, F. Valentino, B. Wang, C.C. Williams, Nature Astronomy 9 (2025) 280–292.","mla":"De Graaff, Anna, et al. “Efficient Formation of a Massive Quiescent Galaxy at Redshift 4.9.” <i>Nature Astronomy</i>, vol. 9, Springer Nature, 2025, pp. 280–92, doi:<a href=\"https://doi.org/10.1038/s41550-024-02424-3\">10.1038/s41550-024-02424-3</a>.","apa":"De Graaff, A., Setton, D. J., Brammer, G., Cutler, S., Suess, K. A., Labbé, I., … Williams, C. C. (2025). Efficient formation of a massive quiescent galaxy at redshift 4.9. <i>Nature Astronomy</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41550-024-02424-3\">https://doi.org/10.1038/s41550-024-02424-3</a>","ieee":"A. De Graaff <i>et al.</i>, “Efficient formation of a massive quiescent galaxy at redshift 4.9,” <i>Nature Astronomy</i>, vol. 9. Springer Nature, pp. 280–292, 2025.","ama":"De Graaff A, Setton DJ, Brammer G, et al. Efficient formation of a massive quiescent galaxy at redshift 4.9. <i>Nature Astronomy</i>. 2025;9:280-292. doi:<a href=\"https://doi.org/10.1038/s41550-024-02424-3\">10.1038/s41550-024-02424-3</a>"},"has_accepted_license":"1","publication":"Nature Astronomy","publisher":"Springer Nature","department":[{"_id":"JoMa"}],"file":[{"content_type":"application/pdf","file_size":2034513,"creator":"dernst","access_level":"open_access","relation":"main_file","date_created":"2025-04-16T08:53:59Z","date_updated":"2025-04-16T08:53:59Z","file_name":"2025_NatureAstronomy_deGraaff.pdf","file_id":"19574","checksum":"fb9109951dfe72f08c04c72cd7cfba69","success":1}],"external_id":{"isi":["001420347200001"],"pmid":["39990236"]},"pmid":1,"tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"publication_status":"published","author":[{"full_name":"De Graaff, Anna","last_name":"De Graaff","first_name":"Anna"},{"full_name":"Setton, David J.","last_name":"Setton","first_name":"David J."},{"full_name":"Brammer, Gabriel","last_name":"Brammer","first_name":"Gabriel"},{"full_name":"Cutler, Sam","first_name":"Sam","last_name":"Cutler"},{"full_name":"Suess, Katherine A.","last_name":"Suess","first_name":"Katherine A."},{"last_name":"Labbé","first_name":"Ivo","full_name":"Labbé, Ivo"},{"full_name":"Leja, Joel","first_name":"Joel","last_name":"Leja"},{"full_name":"Weibel, Andrea","last_name":"Weibel","first_name":"Andrea"},{"first_name":"Michael V.","last_name":"Maseda","full_name":"Maseda, Michael V."},{"last_name":"Whitaker","first_name":"Katherine E.","full_name":"Whitaker, Katherine E."},{"full_name":"Bezanson, Rachel","last_name":"Bezanson","first_name":"Rachel"},{"full_name":"Boogaard, Leindert A.","last_name":"Boogaard","first_name":"Leindert A."},{"full_name":"Cleri, Nikko J.","first_name":"Nikko J.","last_name":"Cleri"},{"first_name":"Gabriella","last_name":"De Lucia","full_name":"De Lucia, Gabriella"},{"last_name":"Franx","first_name":"Marijn","full_name":"Franx, Marijn"},{"full_name":"Greene, Jenny E.","first_name":"Jenny E.","last_name":"Greene"},{"first_name":"Michaela","last_name":"Hirschmann","full_name":"Hirschmann, Michaela"},{"id":"7439a258-f3c0-11ec-9501-9df22fe06720","orcid":"0000-0003-2871-127X","full_name":"Matthee, Jorryt J","last_name":"Matthee","first_name":"Jorryt J"},{"first_name":"Ian","last_name":"Mcconachie","full_name":"Mcconachie, Ian"},{"first_name":"Rohan P.","last_name":"Naidu","full_name":"Naidu, Rohan P."},{"full_name":"Oesch, Pascal A.","first_name":"Pascal A.","last_name":"Oesch"},{"first_name":"Sedona H.","last_name":"Price","full_name":"Price, Sedona H."},{"full_name":"Rix, Hans Walter","first_name":"Hans Walter","last_name":"Rix"},{"full_name":"Valentino, Francesco","last_name":"Valentino","first_name":"Francesco"},{"full_name":"Wang, Bingjie","last_name":"Wang","first_name":"Bingjie"},{"first_name":"Christina C.","last_name":"Williams","full_name":"Williams, Christina C."}],"abstract":[{"lang":"eng","text":"Within the established framework of structure formation, galaxies start as systems of low stellar mass and gradually grow into far more massive galaxies. The existence of massive galaxies in the first billion years of the Universe, as suggested by recent observations, seems to challenge this model, as such galaxies would require highly efficient conversion of baryons into stars. An even greater challenge in this epoch is the existence of massive galaxies that have already ceased forming stars. However, robust detections of early massive quiescent galaxies have been challenging due to the coarse wavelength sampling of photometric surveys. Here we report the spectroscopic confirmation with the James Webb Space Telescope of the quiescent galaxy RUBIES-EGS-QG-1 at redshift z = 4.90, 1.2 billion years after the Big Bang. Deep stellar absorption features in the spectrum reveal that the stellar mass of the galaxy of 1011 M⊙ formed in a short 200 Myr burst of star formation, after which star formation activity dropped rapidly and persistently. According to current galaxy formation models, systems with such rapid stellar mass growth and early quenching are too rare to plausibly occur in the small area probed spectroscopically with JWST. Instead, the discovery of RUBIES-EGS-QG-1 implies that early massive quiescent galaxies can be quenched earlier or exhaust gas available for star formation more efficiently than assumed at present."}],"month":"02","volume":9,"year":"2025","article_type":"original","file_date_updated":"2025-04-16T08:53:59Z","date_published":"2025-02-01T00:00:00Z","date_created":"2024-12-08T23:01:56Z","acknowledgement":"We thank V. Buat, D. Burgarella and J. Zavala for sharing their NOEMA data and constraints on the dust-obscured star formation of RUBIES-EGS-QG-1. This work is partially based on observations carried out under project number W20CK with the IRAM NOEMA Interferometer. IRAM is supported by INSU/CNRS (France), MPG (Germany) and IGN (Spain). We thank C. Lagos for providing measurements from the SHARK simulation. This research was supported by the International Space Science Institute (ISSI) in Bern, through ISSI International Team Project No. 562. M.V.M., J.L. and B.W. acknowledge funding support from NASA through JWST-GO-4233. The Cosmic Dawn Center is funded by the Danish National Research Foundation (Grant No. DNRF140 to G.B., P.A.O. and K.E.W.). This work has received funding from the Swiss State Secretariat for Education, Research and Innovation (Contract No. MB22.00072) and the Swiss National Science Foundation (Project Grant No. 200020_207349 to P.A.O.). Support for this work was provided by the Brinson Foundation through a Brinson Prize Fellowship grant (D.J.S.). K.A.S. is a NHFP Hubble Fellow. Support for this work was provided by NASA through the NASA Hubble Fellowship Grant No. HST-HF2-51515.001-A awarded by the Space Telescope Science Institute, which is operated by the Association of Universities for Research in Astronomy, Incorporated, under NASA contract NAS 5-26555 (R.P.N.). This work is based on observations made with the NASA/ESA/CSA JWST. The data were obtained from the Mikulski Archive for Space Telescopes at the Space Telescope Science Institute, which is operated by the Association of Universities for Research in Astronomy, Inc., under NASA contract NAS 5-03127 for JWST. The observations in this work are associated with programmes ERS-1345, GO-2234, DDT-2750 and GO-4233. We gratefully acknowledge the CEERS and DDT-2750 teams for developing their observing programme with a zero-exclusive-access period. Open access funding provided by Max Planck Society.","language":[{"iso":"eng"}],"isi":1,"oa":1,"intvolume":"         9"},{"OA_type":"hybrid","date_updated":"2025-04-14T07:27:49Z","day":"01","file":[{"success":1,"checksum":"1dc50d156feb777c86d779fb1c9ac875","file_id":"18838","file_name":"2025_MathNachrichten_DelloSchiavo.pdf","date_updated":"2025-01-13T10:34:42Z","date_created":"2025-01-13T10:34:42Z","relation":"main_file","access_level":"open_access","creator":"dernst","file_size":1734511,"content_type":"application/pdf"}],"department":[{"_id":"JaMa"}],"publisher":"Wiley","publication":"Mathematische Nachrichten","has_accepted_license":"1","citation":{"ama":"Dello Schiavo L, Herry R, Kopfer E, Sturm KT. Polyharmonic fields and Liouville quantum gravity measures on tori of arbitrary dimension: From discrete to continuous. <i>Mathematische Nachrichten</i>. 2025;298(1):244-281. doi:<a href=\"https://doi.org/10.1002/mana.202400169\">10.1002/mana.202400169</a>","apa":"Dello Schiavo, L., Herry, R., Kopfer, E., &#38; Sturm, K. T. (2025). Polyharmonic fields and Liouville quantum gravity measures on tori of arbitrary dimension: From discrete to continuous. <i>Mathematische Nachrichten</i>. Wiley. <a href=\"https://doi.org/10.1002/mana.202400169\">https://doi.org/10.1002/mana.202400169</a>","mla":"Dello Schiavo, Lorenzo, et al. “Polyharmonic Fields and Liouville Quantum Gravity Measures on Tori of Arbitrary Dimension: From Discrete to Continuous.” <i>Mathematische Nachrichten</i>, vol. 298, no. 1, Wiley, 2025, pp. 244–81, doi:<a href=\"https://doi.org/10.1002/mana.202400169\">10.1002/mana.202400169</a>.","ieee":"L. Dello Schiavo, R. Herry, E. Kopfer, and K. T. Sturm, “Polyharmonic fields and Liouville quantum gravity measures on tori of arbitrary dimension: From discrete to continuous,” <i>Mathematische Nachrichten</i>, vol. 298, no. 1. Wiley, pp. 244–281, 2025.","short":"L. Dello Schiavo, R. Herry, E. Kopfer, K.T. Sturm, Mathematische Nachrichten 298 (2025) 244–281.","ista":"Dello Schiavo L, Herry R, Kopfer E, Sturm KT. 2025. Polyharmonic fields and Liouville quantum gravity measures on tori of arbitrary dimension: From discrete to continuous. Mathematische Nachrichten. 298(1), 244–281.","chicago":"Dello Schiavo, Lorenzo, Ronan Herry, Eva Kopfer, and Karl Theodor Sturm. “Polyharmonic Fields and Liouville Quantum Gravity Measures on Tori of Arbitrary Dimension: From Discrete to Continuous.” <i>Mathematische Nachrichten</i>. Wiley, 2025. <a href=\"https://doi.org/10.1002/mana.202400169\">https://doi.org/10.1002/mana.202400169</a>."},"_id":"18632","title":"Polyharmonic fields and Liouville quantum gravity measures on tori of arbitrary dimension: From discrete to continuous","OA_place":"publisher","ddc":["510"],"arxiv":1,"article_processing_charge":"Yes (via OA deal)","type":"journal_article","ec_funded":1,"status":"public","doi":"10.1002/mana.202400169","publication_identifier":{"eissn":["1522-2616"],"issn":["0025-584X"]},"quality_controlled":"1","oa_version":"Published Version","scopus_import":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","page":"244-281","volume":298,"month":"01","abstract":[{"text":"For an arbitrary dimension (Formula presented.), we study: the polyharmonic Gaussian field (Formula presented.) on the discrete torus (Formula presented.), that is the random field whose law on (Formula presented.) given by (Formula presented.) where (Formula presented.) is the Lebesgue measure and (Formula presented.) is the discrete Laplacian; the associated discrete Liouville quantum gravity (LQG) measure associated with it, that is, the random measure on (Formula presented.) (Formula presented.) where (Formula presented.) is a regularity parameter. As (Formula presented.), we prove convergence of the fields (Formula presented.) to the polyharmonic Gaussian field (Formula presented.) on the continuous torus (Formula presented.), as well as convergence of the random measures (Formula presented.) to the LQG measure (Formula presented.) on (Formula presented.), for all (Formula presented.). ","lang":"eng"}],"intvolume":"       298","acknowledgement":"KTS is grateful to Christoph Thiele for valuable discussions and helpful references. LDS is grateful to Nathanaël Berestycki for valuable discussions on Gaussian Multiplicative Chaoses. The authors are grateful to an anonymous reviewer for suggestions which improved the presentation.\r\nThe authors gratefully acknowledge funding by the Deutsche Forschungsgemeinschaft through the project ‘Random Riemannian Geometry’ within the SPP 2265 ‘Random Geometric Systems.'\r\nLDS gratefully acknowledges financial support from the European Research Council (grant agreement No. 716117, awarded to J. Maas) and from the Austrian Science Fund (FWF). His research was funded by the Austrian Science Fund (FWF) project 10.55776/F65 and project 10.55776/ESP208.\r\nRH, EK, and KTS gratefully acknowledge funding by the Hausdorff Center for Mathematics (project ID 390685813), and through project B03 within the CRC 1060 (project ID 211504053). RH and KTS also gratefully acknowledges financial support from the European Research Council through the ERC AdG ‘RicciBounds’ (grant agreement 694405).\r\nOpen access funding enabled and organized by Projekt DEAL.","language":[{"iso":"eng"}],"oa":1,"isi":1,"issue":"1","date_created":"2024-12-08T23:01:56Z","file_date_updated":"2025-01-13T10:34:42Z","date_published":"2025-01-01T00:00:00Z","year":"2025","article_type":"original","author":[{"orcid":"0000-0002-9881-6870","full_name":"Dello Schiavo, Lorenzo","id":"ECEBF480-9E4F-11EA-B557-B0823DDC885E","first_name":"Lorenzo","last_name":"Dello Schiavo"},{"last_name":"Herry","first_name":"Ronan","full_name":"Herry, Ronan"},{"full_name":"Kopfer, Eva","first_name":"Eva","last_name":"Kopfer"},{"full_name":"Sturm, Karl Theodor","last_name":"Sturm","first_name":"Karl Theodor"}],"publication_status":"published","tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"external_id":{"arxiv":["2302.02963"],"isi":["001366948500001"]},"project":[{"call_identifier":"H2020","grant_number":"716117","name":"Optimal Transport and Stochastic Dynamics","_id":"256E75B8-B435-11E9-9278-68D0E5697425"},{"_id":"fc31cba2-9c52-11eb-aca3-ff467d239cd2","grant_number":"F6504","name":"Taming Complexity in Partial Differential Systems"},{"_id":"34dbf174-11ca-11ed-8bc3-afe9d43d4b9c","grant_number":"E208","name":"Configuration Spaces over Non-Smooth Spaces"}]},{"date_created":"2024-12-20T09:22:20Z","date_published":"2025-03-03T00:00:00Z","file_date_updated":"2025-02-28T16:50:39Z","year":"2025","license":"https://creativecommons.org/licenses/by-nc-sa/4.0/","oa":1,"month":"03","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"},{"_id":"ScienComp"},{"_id":"PreCl"},{"_id":"M-Shop"},{"_id":"E-Lib"}],"abstract":[{"text":"The information-processing capability of the brain’s cellular network depends on the physical wiring pattern between neurons and their molecular and functional characteristics. Mapping neurons and resolving their individual synaptic connections can be achieved by volumetric imaging at nanoscale resolution with dense cellular labelling. Light microscopy is uniquely positioned to visualize specific molecules but dense, synapse-level circuit reconstruction by light microscopy has been out of reach due to limitations in resolution, contrast, and volumetric imaging capability. Here we developed light-microscopy based connectomics (LICONN). We integrated specifically engineered hydrogel embedding and expansion with comprehensive deep-learning based segmentation and analysis of connectivity, thus directly incorporating molecular information in synapse-level brain tissue reconstructions. LICONN will allow synapse-level brain tissue phenotyping in biological experiments in a readily adoptable manner.","lang":"eng"}],"tmp":{"name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","short":"CC BY-NC-SA (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","image":"/images/cc_by_nc_sa.png"},"corr_author":"1","author":[{"id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8559-3973","full_name":"Danzl, Johann G","last_name":"Danzl","first_name":"Johann G"},{"id":"46E28B80-F248-11E8-B48F-1D18A9856A87","full_name":"Lyudchik, Julia","last_name":"Lyudchik","first_name":"Julia"},{"full_name":"Kreuzinger, Caroline","id":"382077BA-F248-11E8-B48F-1D18A9856A87","first_name":"Caroline","last_name":"Kreuzinger"}],"_id":"18697","title":"Light-microscopy based connectomic reconstruction of mammalian brain 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The PTh-rGO-based electrodes in a symmetrical device with xanthan gum in 1 M aq. Na2SO4 as an electrolyte, delivers a specific capacitance (Csp) of 114.7 F g–1 (electrode) and 28.7 F g–1 (cell) at an applied current density of 0.2 A g−1. The maximum energy and power densities recorded from the device were 588.0 mWh kg−1 and 1.1 kW kg−1 at 1.5 A g−1. The device exhibited a remarkable retention of Csp of 98.9 % over 10,000 continuous galvanostatic charge–discharge cycles highlighting an excellent performance. Electrochemical impedance spectroscopy analysis emphasizes material’s excellent structural integrity. This is attributed to the crystalline phases present in the matrix."}],"month":"03","acknowledgement":"This work was partly supported by the Institute of Information & Communications Technology Planning & Evaluation (IITP) grant funded by the Korea government (MSIT) (No.RS-2021-II210077) and Korea Institute of Energy Technology Evaluation and Planning (KETEP) grant funded by the Korea government (MOTIE)(RS-2024-00398346, ESS BigData-Based O&M and Asset Management Technical Manpower Training).","isi":1,"language":[{"iso":"eng"}],"intvolume":"       382","date_published":"2025-03-01T00:00:00Z","article_type":"original","year":"2025","date_created":"2024-12-22T23:01:47Z","author":[{"last_name":"Mahato","first_name":"Neelima","full_name":"Mahato, Neelima"},{"full_name":"Singh, Saurabh","orcid":"0000-0003-2209-5269","id":"12d625da-9cb3-11ed-9667-af09d37d3f0a","first_name":"Saurabh","last_name":"Singh"},{"first_name":"T. V.M.","last_name":"Sreekanth","full_name":"Sreekanth, T. V.M."},{"full_name":"Yoo, Kisoo","first_name":"Kisoo","last_name":"Yoo"},{"last_name":"Kim","first_name":"Jonghoon","full_name":"Kim, Jonghoon"}],"external_id":{"isi":["001433664000001"]},"publication_status":"published","article_number":"137869","date_updated":"2025-05-19T14:05:22Z","OA_type":"closed access","day":"01","publication":"Materials Letters","citation":{"short":"N. Mahato, S. Singh, T.V.M. Sreekanth, K. Yoo, J. Kim, Materials Letters 382 (2025).","chicago":"Mahato, Neelima, Saurabh Singh, T. V.M. Sreekanth, Kisoo Yoo, and Jonghoon Kim. “In-Situ Engineered Highly-Crystalline Polythiophene Empowered Electrochemical Capacitor-II: Anomalous Electrochemical Charge Storage Behavior of Polythiophene-RGO Composite.” <i>Materials Letters</i>. Elsevier, 2025. <a href=\"https://doi.org/10.1016/j.matlet.2024.137869\">https://doi.org/10.1016/j.matlet.2024.137869</a>.","ista":"Mahato N, Singh S, Sreekanth TVM, Yoo K, Kim J. 2025. In-situ engineered highly-crystalline Polythiophene empowered electrochemical capacitor-II: Anomalous electrochemical charge storage behavior of Polythiophene-rGO composite. Materials Letters. 382, 137869.","ama":"Mahato N, Singh S, Sreekanth TVM, Yoo K, Kim J. In-situ engineered highly-crystalline Polythiophene empowered electrochemical capacitor-II: Anomalous electrochemical charge storage behavior of Polythiophene-rGO composite. <i>Materials Letters</i>. 2025;382. doi:<a href=\"https://doi.org/10.1016/j.matlet.2024.137869\">10.1016/j.matlet.2024.137869</a>","ieee":"N. Mahato, S. Singh, T. V. M. Sreekanth, K. Yoo, and J. Kim, “In-situ engineered highly-crystalline Polythiophene empowered electrochemical capacitor-II: Anomalous electrochemical charge storage behavior of Polythiophene-rGO composite,” <i>Materials Letters</i>, vol. 382. Elsevier, 2025.","apa":"Mahato, N., Singh, S., Sreekanth, T. V. M., Yoo, K., &#38; Kim, J. (2025). In-situ engineered highly-crystalline Polythiophene empowered electrochemical capacitor-II: Anomalous electrochemical charge storage behavior of Polythiophene-rGO composite. <i>Materials Letters</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.matlet.2024.137869\">https://doi.org/10.1016/j.matlet.2024.137869</a>","mla":"Mahato, Neelima, et al. “In-Situ Engineered Highly-Crystalline Polythiophene Empowered Electrochemical Capacitor-II: Anomalous Electrochemical Charge Storage Behavior of Polythiophene-RGO Composite.” <i>Materials Letters</i>, vol. 382, 137869, Elsevier, 2025, doi:<a href=\"https://doi.org/10.1016/j.matlet.2024.137869\">10.1016/j.matlet.2024.137869</a>."},"publisher":"Elsevier","department":[{"_id":"MaIb"}],"title":"In-situ engineered highly-crystalline Polythiophene empowered electrochemical capacitor-II: Anomalous electrochemical charge storage behavior of Polythiophene-rGO composite","_id":"18701","type":"journal_article","article_processing_charge":"No","publication_identifier":{"issn":["0167-577X"],"eissn":["1873-4979"]},"doi":"10.1016/j.matlet.2024.137869","quality_controlled":"1","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"None","scopus_import":"1"},{"article_type":"original","year":"2025","date_published":"2025-04-01T00:00:00Z","file_date_updated":"2025-04-16T09:38:55Z","date_created":"2024-12-22T23:01:48Z","isi":1,"acknowledgement":"Open Access funding enabled and organized by Projekt DEAL.\r\nThe authors would like to thank Tim Browning for suggesting this project. Further they are grateful for his and Damaris Schindler’s helpful comments. We would also like to thank Efthymios Sofos for bringing Davenport’s question to our attention and Keith Matthews for providing us with scanned copies of the original correspondence. Finally we would like to thank the reviewer for helpful comments.","oa":1,"language":[{"iso":"eng"}],"intvolume":"       391","abstract":[{"lang":"eng","text":"Given a non-singular diagonal cubic hypersurface X⊂Pn−1 over Fq(t) with char(Fq)≠3, we show that the number of rational points of height at most |P| is O(|P|3+ε) for n=6 and O(|P|2+ε) for n=4. In fact, if n=4 and char(Fq)>3 we prove that the number of rational points away from any rational line contained in X is bounded by O(|P|3/2+ε). From the result in 6 variables we deduce weak approximation for diagonal cubic hypersurfaces for n≥7 over Fq(t) when char(Fq)>3 and handle Waring's problem for cubes in 7 variables over Fq(t) when char(Fq)≠3. Our results answer a question of Davenport regarding the number of solutions of bounded height to x31+x32+x33=x34+x35+x36 with xi∈Fq[t]."}],"month":"04","volume":391,"corr_author":"1","external_id":{"isi":["001376740400001"],"arxiv":["2208.05422"]},"tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"publication_status":"published","author":[{"id":"d6423cba-dc74-11ea-a0a7-ee61689ff5fb","full_name":"Glas, Jakob","last_name":"Glas","first_name":"Jakob"},{"full_name":"Hochfilzer, Leonhard","first_name":"Leonhard","last_name":"Hochfilzer"}],"OA_place":"publisher","title":"On a question of Davenport and diagonal cubic forms over Fq(t)","_id":"18705","citation":{"ista":"Glas J, Hochfilzer L. 2025. On a question of Davenport and diagonal cubic forms over Fq(t). Mathematische Annalen. 391, 5485–5533.","chicago":"Glas, Jakob, and Leonhard Hochfilzer. “On a Question of Davenport and Diagonal Cubic Forms over Fq(T).” <i>Mathematische Annalen</i>. Springer Nature, 2025. <a href=\"https://doi.org/10.1007/s00208-024-03035-z\">https://doi.org/10.1007/s00208-024-03035-z</a>.","short":"J. Glas, L. Hochfilzer, Mathematische Annalen 391 (2025) 5485–5533.","mla":"Glas, Jakob, and Leonhard Hochfilzer. “On a Question of Davenport and Diagonal Cubic Forms over Fq(T).” <i>Mathematische Annalen</i>, vol. 391, Springer Nature, 2025, pp. 5485–533, doi:<a href=\"https://doi.org/10.1007/s00208-024-03035-z\">10.1007/s00208-024-03035-z</a>.","apa":"Glas, J., &#38; Hochfilzer, L. (2025). On a question of Davenport and diagonal cubic forms over Fq(t). <i>Mathematische Annalen</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s00208-024-03035-z\">https://doi.org/10.1007/s00208-024-03035-z</a>","ieee":"J. Glas and L. Hochfilzer, “On a question of Davenport and diagonal cubic forms over Fq(t),” <i>Mathematische Annalen</i>, vol. 391. Springer Nature, pp. 5485–5533, 2025.","ama":"Glas J, Hochfilzer L. On a question of Davenport and diagonal cubic forms over Fq(t). <i>Mathematische Annalen</i>. 2025;391:5485-5533. doi:<a href=\"https://doi.org/10.1007/s00208-024-03035-z\">10.1007/s00208-024-03035-z</a>"},"publication":"Mathematische Annalen","has_accepted_license":"1","department":[{"_id":"TiBr"}],"publisher":"Springer Nature","file":[{"file_size":650021,"content_type":"application/pdf","creator":"dernst","access_level":"open_access","relation":"main_file","date_created":"2025-04-16T09:38:55Z","date_updated":"2025-04-16T09:38:55Z","file_name":"2025_MathAnnalen_Glas.pdf","checksum":"dcf57a8b01332c36e0cf2b0d1aeecb36","file_id":"19579","success":1}],"day":"01","date_updated":"2025-05-19T14:04:46Z","OA_type":"hybrid","page":"5485-5533","related_material":{"record":[{"status":"public","relation":"earlier_version","id":"18293"}]},"oa_version":"Published Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","scopus_import":"1","quality_controlled":"1","publication_identifier":{"eissn":["1432-1807"],"issn":["0025-5831"]},"doi":"10.1007/s00208-024-03035-z","status":"public","type":"journal_article","arxiv":1,"article_processing_charge":"Yes (via OA deal)","ddc":["510"]},{"abstract":[{"lang":"eng","text":"Lead Sulfide (PbS) has garnered attention as a promising thermoelectric (TE) material due to its natural abundance and cost-effectiveness. However, its practical application is hindered by inherently high lattice thermal conductivity and low electrical conductivity. In this study, we address these challenges by surface functionalization of PbS nanocrystals using Cu2S molecular complexes-based ligand displacement. The molecular complexes facilitate the incorporation of Cu into the PbS matrix and leads to the formation of nanoscale defects, dislocations, and strain fields while optimizing the charge carrier transport. The structural modulations enhance the phonon scattering and lead to a significant reduction in lattice thermal conductivity of 0.60 W m−1K−1 at 867 K in the PbS-Cu2S system. Simultaneously, the Cu incorporation improves electrical conductivity by increasing both carrier concentration and mobility with carefully optimized the content of Cu2S molecular complexes. These synergistic modifications yield a peak figure-of-merit (zT) of 1.05 at 867 K for the PbS-1.0 %Cu2S sample, representing an almost twofold enhancement in TE performance compared to pristine PbS. This work highlights the effectiveness of surface treatment in overcoming the intrinsic limitations of PbS-based materials and presents a promising strategy for the development of high-efficiency TE systems."}],"month":"04","volume":683,"date_published":"2025-04-01T00:00:00Z","year":"2025","article_type":"original","date_created":"2024-12-29T23:01:56Z","language":[{"iso":"eng"}],"isi":1,"acknowledgement":"Y.L. acknowledges funding from the National Natural Science Foundation of China (NSFC) (Grants No. 22209034), the Innovation and Entrepreneurship Project of Overseas Returnees in Anhui Province (Grant No. 2022LCX002) and the Fundamental Research Funds for the Central Universities (JZ2024HGTB0239). M.I. acknowledges financial support from ISTA and the Werner Siemens Foundation. K.H.L. acknowledges financial support from the National Natural Science Foundation of China (NSFC) (Grant No. 22208293). M.H acknowledges funding from Australian Research Council (FT230100316 and IH200100035) and iLAuNCH, Trailblazer Universities Program. L. H. and S. W. acknowledge the Fundamental Research Funds for the Central Universities (JZ2023HGTA0179, JZ2024HGTA0170).","intvolume":"       683","external_id":{"pmid":["39706089"],"isi":["001393340800001"]},"publication_status":"published","pmid":1,"author":[{"full_name":"Shu, Haibo","last_name":"Shu","first_name":"Haibo"},{"full_name":"Zhao, Mingjun","first_name":"Mingjun","last_name":"Zhao"},{"first_name":"Shaoqing","last_name":"Lu","full_name":"Lu, Shaoqing"},{"full_name":"Wan, Shanhong","last_name":"Wan","first_name":"Shanhong"},{"full_name":"Genç, Aziz","first_name":"Aziz","last_name":"Genç"},{"last_name":"Huang","first_name":"Lulu","full_name":"Huang, Lulu"},{"last_name":"Ibáñez","first_name":"Maria","id":"43C61214-F248-11E8-B48F-1D18A9856A87","full_name":"Ibáñez, Maria","orcid":"0000-0001-5013-2843"},{"full_name":"Lim, Khak Ho","last_name":"Lim","first_name":"Khak Ho"},{"last_name":"Hong","first_name":"Min","full_name":"Hong, Min"},{"id":"2A70014E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7313-6740","full_name":"Liu, Yu","last_name":"Liu","first_name":"Yu"}],"project":[{"name":"HighTE: The Werner Siemens Laboratory for the High Throughput Discovery of Semiconductors for Waste Heat Recovery","_id":"9B8F7476-BA93-11EA-9121-9846C619BF3A"}],"day":"01","date_updated":"2025-05-19T14:03:54Z","OA_type":"closed access","title":"Influence of surface engineering on the transport properties of lead sulfide nanomaterials","_id":"18707","publication":"Journal of Colloid and Interface Science","citation":{"ista":"Shu H, Zhao M, Lu S, Wan S, Genç A, Huang L, Ibáñez M, Lim KH, Hong M, Liu Y. 2025. Influence of surface engineering on the transport properties of lead sulfide nanomaterials. Journal of Colloid and Interface Science. 683, 703–712.","chicago":"Shu, Haibo, Mingjun Zhao, Shaoqing Lu, Shanhong Wan, Aziz Genç, Lulu Huang, Maria Ibáñez, Khak Ho Lim, Min Hong, and Yu Liu. “Influence of Surface Engineering on the Transport Properties of Lead Sulfide Nanomaterials.” <i>Journal of Colloid and Interface Science</i>. Elsevier, 2025. <a href=\"https://doi.org/10.1016/j.jcis.2024.12.067\">https://doi.org/10.1016/j.jcis.2024.12.067</a>.","short":"H. Shu, M. Zhao, S. Lu, S. Wan, A. Genç, L. Huang, M. Ibáñez, K.H. Lim, M. Hong, Y. Liu, Journal of Colloid and Interface Science 683 (2025) 703–712.","apa":"Shu, H., Zhao, M., Lu, S., Wan, S., Genç, A., Huang, L., … Liu, Y. (2025). Influence of surface engineering on the transport properties of lead sulfide nanomaterials. <i>Journal of Colloid and Interface Science</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.jcis.2024.12.067\">https://doi.org/10.1016/j.jcis.2024.12.067</a>","mla":"Shu, Haibo, et al. “Influence of Surface Engineering on the Transport Properties of Lead Sulfide Nanomaterials.” <i>Journal of Colloid and Interface Science</i>, vol. 683, Elsevier, 2025, pp. 703–12, doi:<a href=\"https://doi.org/10.1016/j.jcis.2024.12.067\">10.1016/j.jcis.2024.12.067</a>.","ieee":"H. Shu <i>et al.</i>, “Influence of surface engineering on the transport properties of lead sulfide nanomaterials,” <i>Journal of Colloid and Interface Science</i>, vol. 683. Elsevier, pp. 703–712, 2025.","ama":"Shu H, Zhao M, Lu S, et al. Influence of surface engineering on the transport properties of lead sulfide nanomaterials. <i>Journal of Colloid and Interface Science</i>. 2025;683:703-712. doi:<a href=\"https://doi.org/10.1016/j.jcis.2024.12.067\">10.1016/j.jcis.2024.12.067</a>"},"department":[{"_id":"MaIb"}],"publisher":"Elsevier","type":"journal_article","article_processing_charge":"No","oa_version":"None","scopus_import":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","page":"703-712","doi":"10.1016/j.jcis.2024.12.067","publication_identifier":{"eissn":["1095-7103"],"issn":["0021-9797"]},"quality_controlled":"1","status":"public"},{"publication_status":"published","tmp":{"short":"CC BY-NC (3.0)","name":"Creative Commons Attribution-NonCommercial 3.0 Unported (CC BY-NC 3.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/3.0/legalcode","image":"/images/cc_by_nc.png"},"pmid":1,"external_id":{"isi":["001379819100001"],"pmid":["39698879"]},"corr_author":"1","author":[{"first_name":"Mateja","last_name":"Hrast","full_name":"Hrast, Mateja","id":"48dbb294-2a9c-11ef-905d-f56be71f0e5d"},{"first_name":"Marko","last_name":"Ljubotina","orcid":"0000-0003-0038-7068","full_name":"Ljubotina, Marko","id":"F75EE9BE-5C90-11EA-905D-16643DDC885E"},{"first_name":"Matjaz","last_name":"Zitnik","full_name":"Zitnik, Matjaz"}],"project":[{"call_identifier":"H2020","grant_number":"801770","name":"Angulon: physics and applications of a new quasiparticle","_id":"2688CF98-B435-11E9-9278-68D0E5697425"}],"month":"01","abstract":[{"lang":"eng","text":"We present an ab initio theoretical method to calculate the resonant Auger spectrum in the presence of ultrafast dissociation. The method is demonstrated by deriving the L-VV resonant Auger spectrum mediated by the 2p3/2−1σ* resonance in HCl, where the electronic Auger decay and nuclear dissociation occur on the same time scale. The Auger decay rates are calculated within the one-center approximation and are shown to vary significantly with the inter-nuclear distance. A quantum-mechanical description of dissociation is effectuated by propagating the corresponding Franck–Condon factors. The calculated profiles of Auger spectral lines resemble those of atomic Auger decay but here the characteristic tails extend towards lower electron kinetic energies, which reflect specific features of the potential energy curves. The presented method can describe the resonant Auger spectrum for an arbitrary speed of dissociation and simplifies to known approximations in the limiting cases."}],"volume":27,"date_created":"2024-12-29T23:01:58Z","date_published":"2025-01-21T00:00:00Z","file_date_updated":"2025-04-16T09:46:45Z","article_type":"original","year":"2025","intvolume":"        27","acknowledgement":"This publication is based upon work from COST Action CA18212 – Molecular Dynamics in the GAS phase (MD-GAS), supported by COST (European Cooperation in Science and Technology). This work was financially supported by the Slovenian Research Agency in the framework of research program P1-0112 Studies of Atoms, Molecules and Structures by Photons and Particles. Part of this work was financed by the European Research Council (ERC) through the Starting Grant No. 801770 (ANGULON). The authors acknowledge P. Lablanquie, H. Iwayama, F. Penent, K. Soejima and E. Shigemasa for sharing their unpublished experimental spectra on HCl.","license":"https://creativecommons.org/licenses/by-nc/3.0/","issue":"3","language":[{"iso":"eng"}],"isi":1,"oa":1,"article_processing_charge":"Yes (via OA deal)","type":"journal_article","ddc":["530"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Published Version","scopus_import":"1","page":"1473-1482","related_material":{"record":[{"status":"public","relation":"research_data","id":"18716"}]},"ec_funded":1,"status":"public","publication_identifier":{"issn":["1463-9076"]},"doi":"10.1039/d4cp03727h","quality_controlled":"1","day":"21","OA_type":"hybrid","date_updated":"2025-05-19T14:03:19Z","_id":"18710","title":"Ab initio Auger spectrum of the ultrafast dissociating 2p3/2−1σ* resonance in HCl","OA_place":"publisher","file":[{"file_name":"2025_PCCP_Hrast.pdf","date_updated":"2025-04-16T09:46:45Z","success":1,"file_id":"19581","checksum":"d035683179547b41b811107a8649aab0","creator":"dernst","file_size":1270582,"content_type":"application/pdf","relation":"main_file","date_created":"2025-04-16T09:46:45Z","access_level":"open_access"}],"publisher":"Royal Society of Chemistry","department":[{"_id":"MiLe"},{"_id":"MaSe"}],"publication":"Physical Chemistry Chemical Physics","has_accepted_license":"1","citation":{"apa":"Hrast, M., Ljubotina, M., &#38; Zitnik, M. (2025). Ab initio Auger spectrum of the ultrafast dissociating 2p3/2−1σ* resonance in HCl. <i>Physical Chemistry Chemical Physics</i>. Royal Society of Chemistry. <a href=\"https://doi.org/10.1039/d4cp03727h\">https://doi.org/10.1039/d4cp03727h</a>","mla":"Hrast, Mateja, et al. “Ab Initio Auger Spectrum of the Ultrafast Dissociating 2p3/2−1σ* Resonance in HCl.” <i>Physical Chemistry Chemical Physics</i>, vol. 27, no. 3, Royal Society of Chemistry, 2025, pp. 1473–82, doi:<a href=\"https://doi.org/10.1039/d4cp03727h\">10.1039/d4cp03727h</a>.","ieee":"M. Hrast, M. Ljubotina, and M. Zitnik, “Ab initio Auger spectrum of the ultrafast dissociating 2p3/2−1σ* resonance in HCl,” <i>Physical Chemistry Chemical Physics</i>, vol. 27, no. 3. Royal Society of Chemistry, pp. 1473–1482, 2025.","ama":"Hrast M, Ljubotina M, Zitnik M. Ab initio Auger spectrum of the ultrafast dissociating 2p3/2−1σ* resonance in HCl. <i>Physical Chemistry Chemical Physics</i>. 2025;27(3):1473-1482. doi:<a href=\"https://doi.org/10.1039/d4cp03727h\">10.1039/d4cp03727h</a>","ista":"Hrast M, Ljubotina M, Zitnik M. 2025. Ab initio Auger spectrum of the ultrafast dissociating 2p3/2−1σ* resonance in HCl. Physical Chemistry Chemical Physics. 27(3), 1473–1482.","chicago":"Hrast, Mateja, Marko Ljubotina, and Matjaz Zitnik. “Ab Initio Auger Spectrum of the Ultrafast Dissociating 2p3/2−1σ* Resonance in HCl.” <i>Physical Chemistry Chemical Physics</i>. Royal Society of Chemistry, 2025. <a href=\"https://doi.org/10.1039/d4cp03727h\">https://doi.org/10.1039/d4cp03727h</a>.","short":"M. Hrast, M. Ljubotina, M. Zitnik, Physical Chemistry Chemical Physics 27 (2025) 1473–1482."}},{"status":"public","doi":"10.15479/AT:ISTA:17344","related_material":{"record":[{"status":"public","id":"19876","relation":"used_in_publication"}]},"user_id":"9947682f-b9fa-11ee-9c4a-b3ffaafe6614","oa_version":"Published Version","author":[{"id":"455235B8-F248-11E8-B48F-1D18A9856A87","full_name":"Surendranadh, Parvathy","orcid":"0000-0001-6395-386X","last_name":"Surendranadh","first_name":"Parvathy"},{"full_name":"Sachdeva, Himani","last_name":"Sachdeva","first_name":"Himani"}],"ddc":["576"],"tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"article_processing_charge":"No","corr_author":"1","type":"research_data","department":[{"_id":"GradSch"},{"_id":"NiBa"}],"publisher":"Institute of Science and Technology Austria","file":[{"access_level":"open_access","date_created":"2025-01-02T12:30:27Z","relation":"main_file","content_type":"application/zip","file_size":326835,"creator":"psurendr","file_id":"18722","checksum":"9c5f91876014706990a0728c3675cd2a","success":1,"date_updated":"2025-01-02T12:30:27Z","file_name":"Codes.zip"},{"file_id":"18723","checksum":"47fe98b7cc526e634e42de58f5eae288","success":1,"date_updated":"2025-01-02T12:30:39Z","file_name":"ReadMe.txt","access_level":"open_access","date_created":"2025-01-02T12:30:39Z","relation":"main_file","content_type":"text/plain","file_size":620,"creator":"psurendr"}],"oa":1,"citation":{"ieee":"P. Surendranadh and H. Sachdeva, “Mathematica notebook and Fortran code for ‘Effect of assortative mating and sexual selection on polygenic barriers to gene flow.’” Institute of Science and Technology Austria, 2025.","apa":"Surendranadh, P., &#38; Sachdeva, H. (2025). Mathematica notebook and Fortran code for “Effect of assortative mating and sexual selection on polygenic barriers to gene flow.” Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:17344\">https://doi.org/10.15479/AT:ISTA:17344</a>","mla":"Surendranadh, Parvathy, and Himani Sachdeva. <i>Mathematica Notebook and Fortran Code for “Effect of Assortative Mating and Sexual Selection on Polygenic Barriers to Gene Flow.”</i> Institute of Science and Technology Austria, 2025, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:17344\">10.15479/AT:ISTA:17344</a>.","ama":"Surendranadh P, Sachdeva H. Mathematica notebook and Fortran code for “Effect of assortative mating and sexual selection on polygenic barriers to gene flow.” 2025. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:17344\">10.15479/AT:ISTA:17344</a>","chicago":"Surendranadh, Parvathy, and Himani Sachdeva. “Mathematica Notebook and Fortran Code for ‘Effect of Assortative Mating and Sexual Selection on Polygenic Barriers to Gene Flow.’” Institute of Science and Technology Austria, 2025. <a href=\"https://doi.org/10.15479/AT:ISTA:17344\">https://doi.org/10.15479/AT:ISTA:17344</a>.","ista":"Surendranadh P, Sachdeva H. 2025. Mathematica notebook and Fortran code for ‘Effect of assortative mating and sexual selection on polygenic barriers to gene flow’, Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:17344\">10.15479/AT:ISTA:17344</a>.","short":"P. Surendranadh, H. Sachdeva, (2025)."},"has_accepted_license":"1","_id":"18712","title":"Mathematica notebook and Fortran code for 'Effect of assortative mating and sexual selection on polygenic barriers to gene flow'","date_created":"2025-01-01T15:28:27Z","year":"2025","file_date_updated":"2025-01-02T12:30:39Z","date_published":"2025-01-07T00:00:00Z","date_updated":"2025-12-30T08:44:12Z","acknowledged_ssus":[{"_id":"ScienComp"}],"month":"01","day":"07","abstract":[{"text":"This file contains the code associated with the manuscript 'Effect of assortative mating and sexual selection on polygenic barriers to gene flow'. ","lang":"eng"}]},{"publication":"European Journal of Combinatorics","has_accepted_license":"1","citation":{"ista":"Carbonero A, Koerts H, Moore B, Spirkl S. 2025. On heroes in digraphs with forbidden induced forests. European Journal of Combinatorics. 125, 104104.","chicago":"Carbonero, Alvaro, Hidde Koerts, Benjamin Moore, and Sophie Spirkl. “On Heroes in Digraphs with Forbidden Induced Forests.” <i>European Journal of Combinatorics</i>. Elsevier, 2025. <a href=\"https://doi.org/10.1016/j.ejc.2024.104104\">https://doi.org/10.1016/j.ejc.2024.104104</a>.","short":"A. Carbonero, H. Koerts, B. Moore, S. Spirkl, European Journal of Combinatorics 125 (2025).","mla":"Carbonero, Alvaro, et al. “On Heroes in Digraphs with Forbidden Induced Forests.” <i>European Journal of Combinatorics</i>, vol. 125, 104104, Elsevier, 2025, doi:<a href=\"https://doi.org/10.1016/j.ejc.2024.104104\">10.1016/j.ejc.2024.104104</a>.","apa":"Carbonero, A., Koerts, H., Moore, B., &#38; Spirkl, S. (2025). On heroes in digraphs with forbidden induced forests. <i>European Journal of Combinatorics</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.ejc.2024.104104\">https://doi.org/10.1016/j.ejc.2024.104104</a>","ieee":"A. Carbonero, H. Koerts, B. Moore, and S. Spirkl, “On heroes in digraphs with forbidden induced forests,” <i>European Journal of Combinatorics</i>, vol. 125. Elsevier, 2025.","ama":"Carbonero A, Koerts H, Moore B, Spirkl S. On heroes in digraphs with forbidden induced forests. <i>European Journal of Combinatorics</i>. 2025;125. doi:<a href=\"https://doi.org/10.1016/j.ejc.2024.104104\">10.1016/j.ejc.2024.104104</a>"},"file":[{"success":1,"file_id":"19577","checksum":"2c75f78f40ebb93d16fe3765bda2905a","file_name":"2025_EuropJournCombinatorics_Carbonero.pdf","date_updated":"2025-04-16T09:16:25Z","date_created":"2025-04-16T09:16:25Z","relation":"main_file","access_level":"open_access","creator":"dernst","file_size":1110657,"content_type":"application/pdf"}],"department":[{"_id":"MaKw"}],"publisher":"Elsevier","OA_place":"publisher","_id":"18753","title":"On heroes in digraphs with forbidden induced forests","date_updated":"2025-05-19T14:06:00Z","OA_type":"hybrid","day":"01","publication_identifier":{"issn":["0195-6698"]},"doi":"10.1016/j.ejc.2024.104104","quality_controlled":"1","status":"public","scopus_import":"1","oa_version":"Published Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["510"],"type":"journal_article","article_processing_charge":"Yes (in subscription journal)","arxiv":1,"oa":1,"language":[{"iso":"eng"}],"isi":1,"acknowledgement":"We thank the anonymous referees for their careful proofreading which helped improve the presentation of this paper. We also thank one of the anonymous referees for pointing out our construction implies Theorem 1.7!\r\nBenjamin Moore finished this project while a postdoctoral researcher at Charles University, and was supported by project 22-17398S (Flows and cycles in graphs on surfaces) of the Czech Science Foundation. Benjamin Moore is currently funded by RANDSTRUCT No. 101076777, and appreciates the gracious support. We acknowledge the support of the Natural Sciences and Engineering Research Council of Canada (NSERC), [funding reference number RGPIN-2020-03912]. Cette recherche a été financée par le Conseil de recherches en sciences naturelles et en génie du Canada (CRSNG), [numéro de référence RGPIN-2020-03912]. This project was funded in part by the Government of Ontario .","intvolume":"       125","date_published":"2025-03-01T00:00:00Z","file_date_updated":"2025-04-16T09:16:25Z","article_type":"original","year":"2025","date_created":"2025-01-05T23:01:55Z","volume":125,"abstract":[{"text":"We continue a line of research which studies which hereditary families of digraphs have bounded dichromatic number. For a class of digraphs  C, a hero in  C  is any digraph  H\r\n  such that  H -free digraphs in  C  have bounded dichromatic number. We show that if  F\r\n  is an oriented star of degree at least five, the only heroes for the class of  F -free digraphs are transitive tournaments. For oriented stars  F  of degree exactly four, we show the only heroes in  F -free digraphs are transitive tournaments, or possibly special joins of transitive tournaments. Aboulker et al. characterized the set of heroes of  {H,K1+P2→} -free digraphs almost completely, and we show the same characterization for the class of  {H,rK1+P3→} -free digraphs. Lastly, we show that if we forbid two \"valid\" orientations of brooms, then every transitive tournament is a hero for this class of digraphs.","lang":"eng"}],"month":"03","project":[{"grant_number":"101076777","name":"Randomness and structure in combinatorics","_id":"bd95085b-d553-11ed-ba76-e55d3349be45"}],"author":[{"first_name":"Alvaro","last_name":"Carbonero","full_name":"Carbonero, Alvaro"},{"last_name":"Koerts","first_name":"Hidde","full_name":"Koerts, Hidde"},{"id":"6dc1a1be-bf1c-11ed-8d2b-d044840f49d6","full_name":"Moore, Benjamin","last_name":"Moore","first_name":"Benjamin"},{"full_name":"Spirkl, Sophie","last_name":"Spirkl","first_name":"Sophie"}],"external_id":{"isi":["001400113700001"],"arxiv":["2306.04710"]},"corr_author":"1","publication_status":"published","article_number":"104104","tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"}},{"publication_status":"published","tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"pmid":1,"external_id":{"isi":["001412498600001"],"pmid":["39706196"]},"author":[{"full_name":"Smith, Hannah M.","first_name":"Hannah M.","last_name":"Smith"},{"full_name":"Ng, Hong Kiat","last_name":"Ng","first_name":"Hong Kiat"},{"last_name":"Moodie","first_name":"Joanna E.","full_name":"Moodie, Joanna E."},{"first_name":"Danni A.","last_name":"Gadd","full_name":"Gadd, Danni A."},{"last_name":"Mccartney","first_name":"Daniel L.","full_name":"Mccartney, Daniel L."},{"first_name":"Elena","last_name":"Bernabeu","full_name":"Bernabeu, Elena"},{"full_name":"Campbell, Archie","first_name":"Archie","last_name":"Campbell"},{"full_name":"Redmond, Paul","last_name":"Redmond","first_name":"Paul"},{"full_name":"Taylor, Adele","last_name":"Taylor","first_name":"Adele"},{"full_name":"Page, Danielle","first_name":"Danielle","last_name":"Page"},{"full_name":"Corley, Janie","last_name":"Corley","first_name":"Janie"},{"full_name":"Harris, Sarah E.","last_name":"Harris","first_name":"Sarah E."},{"first_name":"Darwin","last_name":"Tay","full_name":"Tay, Darwin"},{"last_name":"Deary","first_name":"Ian J.","full_name":"Deary, Ian J."},{"first_name":"Kathryn L.","last_name":"Evans","full_name":"Evans, Kathryn L."},{"last_name":"Robinson","first_name":"Matthew Richard","id":"E5D42276-F5DA-11E9-8E24-6303E6697425","orcid":"0000-0001-8982-8813","full_name":"Robinson, Matthew Richard"},{"full_name":"Chambers, John C.","first_name":"John C.","last_name":"Chambers"},{"full_name":"Loh, Marie","first_name":"Marie","last_name":"Loh"},{"first_name":"Simon R.","last_name":"Cox","full_name":"Cox, Simon R."},{"full_name":"Marioni, Riccardo E.","last_name":"Marioni","first_name":"Riccardo E."},{"first_name":"Robert F.","last_name":"Hillary","full_name":"Hillary, Robert F."}],"date_created":"2025-01-05T23:01:56Z","file_date_updated":"2025-01-08T09:26:42Z","date_published":"2025-01-02T00:00:00Z","year":"2025","article_type":"original","intvolume":"       112","isi":1,"oa":1,"issue":"1","language":[{"iso":"eng"}],"month":"01","abstract":[{"lang":"eng","text":"Exploring the molecular correlates of metabolic health measures may identify their shared and unique biological processes and pathways. Molecular proxies of these traits may also provide a more objective approach to their measurement. Here, DNA methylation (DNAm) data were used in epigenome-wide association studies (EWASs) and for training epigenetic scores (EpiScores) of six metabolic traits: body mass index (BMI), body fat percentage, waist-hip ratio, and blood-based measures of glucose, high-density lipoprotein cholesterol, and total cholesterol in >17,000 volunteers from the Generation Scotland (GS) cohort. We observed a maximum of 12,033 significant findings (p < 3.6 × 10−8) for BMI in a marginal linear regression EWAS. By contrast, a joint and conditional Bayesian penalized regression approach yielded 27 high-confidence associations with BMI. EpiScores trained in GS performed well in both Scottish and Singaporean test cohorts (Lothian Birth Cohort 1936 [LBC1936] and Health for Life in Singapore [HELIOS]). The EpiScores for BMI and total cholesterol performed best in HELIOS, explaining 20.8% and 7.1% of the variance in the measured traits, respectively. The corresponding results in LBC1936 were 14.4% and 3.2%, respectively. Differences were observed in HELIOS for body fat, where the EpiScore explained ∼9% of the variance in Chinese and Malay -subgroups but ∼3% in the Indian subgroup. The EpiScores also correlated with cognitive function in LBC1936 (standardized βrange: 0.08–0.12, false discovery rate p [pFDR] < 0.05). Accounting for the correlation structure across the methylome can vastly affect the number of lead findings in EWASs. The EpiScores of metabolic traits are broadly applicable across populations and can reflect differences in cognition."}],"volume":112,"scopus_import":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Published Version","related_material":{"link":[{"url":"https://github.com/marioni-group/Metabolic_trait","relation":"software"}]},"page":"106-115","status":"public","doi":"10.1016/j.ajhg.2024.11.012","publication_identifier":{"issn":["0002-9297"],"eissn":["1537-6605"]},"quality_controlled":"1","article_processing_charge":"No","type":"journal_article","ddc":["570"],"title":"DNA methylation-based predictors of metabolic traits in Scottish and Singaporean cohorts","_id":"18754","OA_place":"publisher","file":[{"file_name":"2025_AJHG_Smith.pdf","date_updated":"2025-01-08T09:26:42Z","success":1,"checksum":"891d120554f07da2c35d38388c29a690","file_id":"18776","creator":"dernst","content_type":"application/pdf","file_size":2266488,"relation":"main_file","date_created":"2025-01-08T09:26:42Z","access_level":"open_access"}],"department":[{"_id":"MaRo"}],"publisher":"Elsevier","publication":"American Journal of Human Genetics","has_accepted_license":"1","citation":{"ama":"Smith HM, Ng HK, Moodie JE, et al. DNA methylation-based predictors of metabolic traits in Scottish and Singaporean cohorts. <i>American Journal of Human Genetics</i>. 2025;112(1):106-115. doi:<a href=\"https://doi.org/10.1016/j.ajhg.2024.11.012\">10.1016/j.ajhg.2024.11.012</a>","apa":"Smith, H. M., Ng, H. K., Moodie, J. E., Gadd, D. A., Mccartney, D. L., Bernabeu, E., … Hillary, R. F. (2025). DNA methylation-based predictors of metabolic traits in Scottish and Singaporean cohorts. <i>American Journal of Human Genetics</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.ajhg.2024.11.012\">https://doi.org/10.1016/j.ajhg.2024.11.012</a>","mla":"Smith, Hannah M., et al. “DNA Methylation-Based Predictors of Metabolic Traits in Scottish and Singaporean Cohorts.” <i>American Journal of Human Genetics</i>, vol. 112, no. 1, Elsevier, 2025, pp. 106–15, doi:<a href=\"https://doi.org/10.1016/j.ajhg.2024.11.012\">10.1016/j.ajhg.2024.11.012</a>.","ieee":"H. M. Smith <i>et al.</i>, “DNA methylation-based predictors of metabolic traits in Scottish and Singaporean cohorts,” <i>American Journal of Human Genetics</i>, vol. 112, no. 1. Elsevier, pp. 106–115, 2025.","short":"H.M. Smith, H.K. Ng, J.E. Moodie, D.A. Gadd, D.L. Mccartney, E. Bernabeu, A. Campbell, P. Redmond, A. Taylor, D. Page, J. Corley, S.E. Harris, D. Tay, I.J. Deary, K.L. Evans, M.R. Robinson, J.C. Chambers, M. Loh, S.R. Cox, R.E. Marioni, R.F. Hillary, American Journal of Human Genetics 112 (2025) 106–115.","ista":"Smith HM, Ng HK, Moodie JE, Gadd DA, Mccartney DL, Bernabeu E, Campbell A, Redmond P, Taylor A, Page D, Corley J, Harris SE, Tay D, Deary IJ, Evans KL, Robinson MR, Chambers JC, Loh M, Cox SR, Marioni RE, Hillary RF. 2025. DNA methylation-based predictors of metabolic traits in Scottish and Singaporean cohorts. American Journal of Human Genetics. 112(1), 106–115.","chicago":"Smith, Hannah M., Hong Kiat Ng, Joanna E. Moodie, Danni A. Gadd, Daniel L. Mccartney, Elena Bernabeu, Archie Campbell, et al. “DNA Methylation-Based Predictors of Metabolic Traits in Scottish and Singaporean Cohorts.” <i>American Journal of Human Genetics</i>. Elsevier, 2025. <a href=\"https://doi.org/10.1016/j.ajhg.2024.11.012\">https://doi.org/10.1016/j.ajhg.2024.11.012</a>."},"day":"02","OA_type":"hybrid","date_updated":"2025-02-27T12:38:23Z"},{"acknowledgement":"All authors were supported by the ERC Advanced Grant “RMTBeyond” No. 101020331.\r\nJ.R. was additionally supported by the ERC Advanced Grant “LDRaM” No. 884584.\r\nWe thank Peter Reimann and Lennart Dabelow for helpful comments. Open access funding provided by Institute of Science and Technology (IST Austria).","isi":1,"oa":1,"language":[{"iso":"eng"}],"intvolume":"        26","date_published":"2025-06-01T00:00:00Z","file_date_updated":"2025-06-25T05:38:34Z","year":"2025","article_type":"original","date_created":"2025-01-05T23:01:59Z","volume":26,"abstract":[{"lang":"eng","text":"We prove that a class of weakly perturbed Hamiltonians of the form H_λ= H_0 + λW, with W being a Wigner matrix, exhibits prethermalization. That is, the time evolution generated by H_λ relaxes to its ultimate thermal state via an intermediate prethermal state with a lifetime of order λ^{-2}. Moreover, we obtain a general relaxation formula, expressing the perturbed dynamics via the unperturbed dynamics and the ultimate thermal state. The proof relies on a two-resolvent law for the deformed Wigner matrix H_λ."}],"month":"06","project":[{"name":"Random matrices beyond Wigner-Dyson-Mehta","call_identifier":"H2020","grant_number":"101020331","_id":"62796744-2b32-11ec-9570-940b20777f1d"}],"author":[{"orcid":"0000-0001-5366-9603","full_name":"Erdös, László","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","first_name":"László","last_name":"Erdös"},{"id":"31d731d7-d235-11ea-ad11-b50331c8d7fb","orcid":"0000-0003-1106-327X","full_name":"Henheik, Sven Joscha","last_name":"Henheik","first_name":"Sven Joscha"},{"last_name":"Reker","first_name":"Jana","id":"e796e4f9-dc8d-11ea-abe3-97e26a0323e9","full_name":"Reker, Jana"},{"last_name":"Riabov","first_name":"Volodymyr","id":"1949f904-edfb-11eb-afb5-e2dfddabb93b","full_name":"Riabov, Volodymyr"}],"external_id":{"isi":["001385326500001"],"arxiv":["2310.06677"]},"corr_author":"1","publication_status":"published","tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"has_accepted_license":"1","publication":"Annales Henri Poincare","citation":{"ama":"Erdös L, Henheik SJ, Reker J, Riabov V. Prethermalization for deformed Wigner matrices. <i>Annales Henri Poincare</i>. 2025;26:1991-2033. doi:<a href=\"https://doi.org/10.1007/s00023-024-01518-y\">10.1007/s00023-024-01518-y</a>","ieee":"L. Erdös, S. J. Henheik, J. Reker, and V. Riabov, “Prethermalization for deformed Wigner matrices,” <i>Annales Henri Poincare</i>, vol. 26. Springer Nature, pp. 1991–2033, 2025.","apa":"Erdös, L., Henheik, S. J., Reker, J., &#38; Riabov, V. (2025). Prethermalization for deformed Wigner matrices. <i>Annales Henri Poincare</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s00023-024-01518-y\">https://doi.org/10.1007/s00023-024-01518-y</a>","mla":"Erdös, László, et al. “Prethermalization for Deformed Wigner Matrices.” <i>Annales Henri Poincare</i>, vol. 26, Springer Nature, 2025, pp. 1991–2033, doi:<a href=\"https://doi.org/10.1007/s00023-024-01518-y\">10.1007/s00023-024-01518-y</a>.","short":"L. Erdös, S.J. Henheik, J. Reker, V. Riabov, Annales Henri Poincare 26 (2025) 1991–2033.","chicago":"Erdös, László, Sven Joscha Henheik, Jana Reker, and Volodymyr Riabov. “Prethermalization for Deformed Wigner Matrices.” <i>Annales Henri Poincare</i>. Springer Nature, 2025. <a href=\"https://doi.org/10.1007/s00023-024-01518-y\">https://doi.org/10.1007/s00023-024-01518-y</a>.","ista":"Erdös L, Henheik SJ, Reker J, Riabov V. 2025. Prethermalization for deformed Wigner matrices. Annales Henri Poincare. 26, 1991–2033."},"file":[{"relation":"main_file","date_created":"2025-06-25T05:38:34Z","access_level":"open_access","creator":"dernst","content_type":"application/pdf","file_size":977773,"success":1,"checksum":"49e6a934db540206f7eaa0c798553ded","file_id":"19895","file_name":"2025_AnnalesHenriPoincare_Erdoes.pdf","date_updated":"2025-06-25T05:38:34Z"}],"publisher":"Springer Nature","department":[{"_id":"LaEr"}],"OA_place":"publisher","_id":"18764","title":"Prethermalization for deformed Wigner matrices","date_updated":"2026-04-07T12:37:11Z","OA_type":"hybrid","day":"01","doi":"10.1007/s00023-024-01518-y","publication_identifier":{"issn":["1424-0637"]},"quality_controlled":"1","status":"public","ec_funded":1,"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","scopus_import":"1","oa_version":"Published Version","page":"1991-2033","related_material":{"record":[{"status":"public","relation":"earlier_version","id":"17174"},{"status":"public","relation":"dissertation_contains","id":"20575"},{"id":"19540","relation":"dissertation_contains","status":"public"}]},"ddc":["510"],"type":"journal_article","arxiv":1,"article_processing_charge":"Yes (via OA deal)"},{"_id":"18765","title":"Probing Cell-Type Specificity of Mutant Phenotype at Transcriptomic Level Using Mosaic Analysis with Double Markers (MADM)","citation":{"ieee":"G. T. Cheung, F. Pauler, and S. Hippenmeyer, “Probing Cell-Type Specificity of Mutant Phenotype at Transcriptomic Level Using Mosaic Analysis with Double Markers (MADM),” in <i>Lineage Tracing</i>, vol. 2886, J. Garcia-Marques and T. Lee, Eds. New York, NY: Springer Nature, 2025, pp. 139–151.","mla":"Cheung, Giselle T., et al. “Probing Cell-Type Specificity of Mutant Phenotype at Transcriptomic Level Using Mosaic Analysis with Double Markers (MADM).” <i>Lineage Tracing</i>, edited by Jorge Garcia-Marques and Tzumin Lee, vol. 2886, Springer Nature, 2025, pp. 139–51, doi:<a href=\"https://doi.org/10.1007/978-1-0716-4310-5_7\">10.1007/978-1-0716-4310-5_7</a>.","apa":"Cheung, G. T., Pauler, F., &#38; Hippenmeyer, S. (2025). Probing Cell-Type Specificity of Mutant Phenotype at Transcriptomic Level Using Mosaic Analysis with Double Markers (MADM). In J. Garcia-Marques &#38; T. Lee (Eds.), <i>Lineage Tracing</i> (Vol. 2886, pp. 139–151). New York, NY: Springer Nature. <a href=\"https://doi.org/10.1007/978-1-0716-4310-5_7\">https://doi.org/10.1007/978-1-0716-4310-5_7</a>","ama":"Cheung GT, Pauler F, Hippenmeyer S. Probing Cell-Type Specificity of Mutant Phenotype at Transcriptomic Level Using Mosaic Analysis with Double Markers (MADM). In: Garcia-Marques J, Lee T, eds. <i>Lineage Tracing</i>. Vol 2886. MIMB. New York, NY: Springer Nature; 2025:139-151. doi:<a href=\"https://doi.org/10.1007/978-1-0716-4310-5_7\">10.1007/978-1-0716-4310-5_7</a>","chicago":"Cheung, Giselle T, Florian Pauler, and Simon Hippenmeyer. “Probing Cell-Type Specificity of Mutant Phenotype at Transcriptomic Level Using Mosaic Analysis with Double Markers (MADM).” In <i>Lineage Tracing</i>, edited by Jorge Garcia-Marques and Tzumin Lee, 2886:139–51. MIMB. New York, NY: Springer Nature, 2025. <a href=\"https://doi.org/10.1007/978-1-0716-4310-5_7\">https://doi.org/10.1007/978-1-0716-4310-5_7</a>.","ista":"Cheung GT, Pauler F, Hippenmeyer S. 2025.Probing Cell-Type Specificity of Mutant Phenotype at Transcriptomic Level Using Mosaic Analysis with Double Markers (MADM). In: Lineage Tracing. Methods in Molecular Biology, vol. 2886, 139–151.","short":"G.T. Cheung, F. Pauler, S. Hippenmeyer, in:, J. Garcia-Marques, T. Lee (Eds.), Lineage Tracing, Springer Nature, New York, NY, 2025, pp. 139–151."},"place":"New York, NY","publication":"Lineage Tracing","department":[{"_id":"SiHi"}],"publisher":"Springer Nature","alternative_title":["Methods in Molecular Biology"],"day":"03","date_updated":"2025-04-14T07:43:46Z","OA_type":"closed access","page":"139-151","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","scopus_import":"1","oa_version":"None","quality_controlled":"1","doi":"10.1007/978-1-0716-4310-5_7","publication_identifier":{"issn":["1064-3745"],"eisbn":["9781071643105"],"isbn":["9781071643099"],"eissn":["1940-6029"]},"ec_funded":1,"status":"public","type":"book_chapter","article_processing_charge":"No","year":"2025","date_published":"2025-01-03T00:00:00Z","date_created":"2025-01-07T08:36:47Z","editor":[{"last_name":"Garcia-Marques","first_name":"Jorge","full_name":"Garcia-Marques, Jorge"},{"first_name":"Tzumin","last_name":"Lee","full_name":"Lee, Tzumin"}],"acknowledgement":"We thank all Hippenmeyer lab members for support and discussions. Experimental steps described were optimized with support provided by the Imaging & Optics Facility (IOF) and Preclinical Facility (PCF) at ISTA, Vienna BioCenter Core Facilities (VBCF), and Christoph Bock lab at Center for Molecular Medicine (CeMM). G.C. received funding from European Commission (IST plus postdoctoral fellowship). This work was supported by ISTA institutional funds: The Austrian Science Fund Special Research Programmes (FWF SFB F78 Neuro Stem Modulation) to S.H.","language":[{"iso":"eng"}],"intvolume":"      2886","abstract":[{"text":"Mosaic Analysis with Double Markers (MADM) represents a mouse genetic approach coupling differential fluorescent labeling to genetic manipulations in dividing cells and their lineages. MADM uniquely enables the generation and visualization of individual control or homozygous mutant cells in a heterozygous genetic environment. Among its diverse applications, MADM has been used to dissect cell-autonomous gene functions important for cortical development and neural development in general. The high cellular resolution offered by MADM also permits the analysis of transcriptomic changes of individual cells upon genetic manipulations. In this chapter, we describe an experimental protocol combining the generation and isolation of MADM-labeled cells with downstream single-cell RNA-sequencing technologies to probe cell-type specific phenotypes due to genetic mutations at single-cell resolution.","lang":"eng"}],"acknowledged_ssus":[{"_id":"Bio"}],"month":"01","volume":2886,"series_title":"MIMB","project":[{"grant_number":"754411","call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships","_id":"260C2330-B435-11E9-9278-68D0E5697425"}],"corr_author":"1","external_id":{"pmid":["39745639"]},"pmid":1,"publication_status":"published","author":[{"first_name":"Giselle T","last_name":"Cheung","orcid":"0000-0001-8457-2572","full_name":"Cheung, Giselle T","id":"471195F6-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Florian","last_name":"Pauler","orcid":"0000-0002-7462-0048","full_name":"Pauler, Florian","id":"48EA0138-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Hippenmeyer","first_name":"Simon","id":"37B36620-F248-11E8-B48F-1D18A9856A87","full_name":"Hippenmeyer, Simon","orcid":"0000-0003-2279-1061"}]},{"author":[{"full_name":"Tluckova, Katarina","id":"4AC7D980-F248-11E8-B48F-1D18A9856A87","first_name":"Katarina","last_name":"Tluckova"},{"last_name":"Kaczmarek","first_name":"Beata M","id":"36FA4AFA-F248-11E8-B48F-1D18A9856A87","full_name":"Kaczmarek, Beata M"},{"last_name":"Testa Salmazo","first_name":"Anita P","id":"41F1F098-F248-11E8-B48F-1D18A9856A87","full_name":"Testa Salmazo, Anita P"},{"full_name":"Bernecky, Carrie A","orcid":"0000-0003-0893-7036","id":"2CB9DFE2-F248-11E8-B48F-1D18A9856A87","first_name":"Carrie A","last_name":"Bernecky"}],"tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"pmid":1,"publication_status":"published","corr_author":"1","external_id":{"pmid":["39762629"],"isi":["001390268000001"]},"project":[{"grant_number":"P34185","name":"Regulation of mammalian transcription by noncoding RNA","_id":"c08a6700-5a5b-11eb-8a69-82a722b2bc30"}],"APC_amount":"12348 EUR","volume":32,"acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"EM-Fac"},{"_id":"ScienComp"},{"_id":"PreCl"}],"month":"04","abstract":[{"text":"Transcription by RNA polymerase II (Pol II) can be repressed by noncoding RNA, including the human RNA Alu. However, the mechanism by which endogenous RNAs repress transcription remains unclear. Here we present cryogenic-electron microscopy structures of Pol II bound to Alu RNA, which reveal that Alu RNA mimics how DNA and RNA bind to Pol II during transcription elongation. Further, we show how distinct domains of the general transcription factor TFIIF control repressive activity. Together, we reveal how a noncoding RNA can regulate mammalian gene expression.","lang":"eng"}],"intvolume":"        32","isi":1,"oa":1,"acknowledgement":"We thank the members of the Bernecky laboratory for helpful discussions and A. Hlavata for providing Pol II for use in the fluorescence anisotropy binding assay. We thank V.-V. Hodirnau for SerialEM data collection and support with EPU data collection. We thank D. Slade (Max Perutz Laboratories and Medical University of Vienna, Vienna, Austria) for the wild-type TFIIF expression plasmid. We thank N. Thompson and R. Burgess (McArdle Laboratory for Cancer Research, University of Wisconsin-Madison, Madison, WI, USA) for the 8WG16 hybridoma cell line. We thank C. Plaschka and M. Loose for critical reading of the manuscript. This work was supported by Austrian Science Fund (FWF) grant no. P34185 (DOI 10.55776/P34185) (C.B.). The funders had no role in study design, data collection and analysis, decision to publish or preparation of the manuscript. This research was further supported by the Scientific Service Units of ISTA through resources provided by the Laboratory Support Facility, Electron Microscopy Facility, Scientific Computing and the Preclinical Facility.","language":[{"iso":"eng"}],"date_created":"2025-01-08T11:20:20Z","article_type":"original","year":"2025","date_published":"2025-04-01T00:00:00Z","file_date_updated":"2025-04-16T08:17:27Z","ddc":["570"],"article_processing_charge":"Yes (in subscription journal)","type":"journal_article","status":"public","quality_controlled":"1","publication_identifier":{"eissn":["1545-9985"],"issn":["1545-9993"]},"doi":"10.1038/s41594-024-01448-7","related_material":{"record":[{"status":"public","id":"14644","relation":"earlier_version"}]},"page":"607-612","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","scopus_import":"1","oa_version":"Published Version","OA_type":"hybrid","date_updated":"2025-11-20T10:28:36Z","day":"01","department":[{"_id":"CaBe"}],"publisher":"Springer Nature","file":[{"access_level":"open_access","date_created":"2025-04-16T08:17:27Z","relation":"main_file","file_size":9306639,"content_type":"application/pdf","creator":"dernst","file_id":"19573","checksum":"2919b30b271f395888e880076a680d73","success":1,"date_updated":"2025-04-16T08:17:27Z","file_name":"2025_NatureStrucMolBiol_Tluckova.pdf"}],"citation":{"apa":"Tluckova, K., Kaczmarek, B. M., Testa Salmazo, A. P., &#38; Bernecky, C. (2025). Mechanism of mammalian transcriptional repression by noncoding RNA. <i>Nature Structural &#38; Molecular Biology</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41594-024-01448-7\">https://doi.org/10.1038/s41594-024-01448-7</a>","mla":"Tluckova, Katarina, et al. “Mechanism of Mammalian Transcriptional Repression by Noncoding RNA.” <i>Nature Structural &#38; Molecular Biology</i>, vol. 32, Springer Nature, 2025, pp. 607–12, doi:<a href=\"https://doi.org/10.1038/s41594-024-01448-7\">10.1038/s41594-024-01448-7</a>.","ieee":"K. Tluckova, B. M. Kaczmarek, A. P. Testa Salmazo, and C. Bernecky, “Mechanism of mammalian transcriptional repression by noncoding RNA,” <i>Nature Structural &#38; Molecular Biology</i>, vol. 32. Springer Nature, pp. 607–612, 2025.","ama":"Tluckova K, Kaczmarek BM, Testa Salmazo AP, Bernecky C. Mechanism of mammalian transcriptional repression by noncoding RNA. <i>Nature Structural &#38; Molecular Biology</i>. 2025;32:607-612. doi:<a href=\"https://doi.org/10.1038/s41594-024-01448-7\">10.1038/s41594-024-01448-7</a>","ista":"Tluckova K, Kaczmarek BM, Testa Salmazo AP, Bernecky C. 2025. Mechanism of mammalian transcriptional repression by noncoding RNA. Nature Structural &#38; Molecular Biology. 32, 607–612.","chicago":"Tluckova, Katarina, Beata M Kaczmarek, Anita P Testa Salmazo, and Carrie Bernecky. “Mechanism of Mammalian Transcriptional Repression by Noncoding RNA.” <i>Nature Structural &#38; Molecular Biology</i>. Springer Nature, 2025. <a href=\"https://doi.org/10.1038/s41594-024-01448-7\">https://doi.org/10.1038/s41594-024-01448-7</a>.","short":"K. Tluckova, B.M. Kaczmarek, A.P. Testa Salmazo, C. Bernecky, Nature Structural &#38; Molecular Biology 32 (2025) 607–612."},"publication":"Nature Structural & Molecular Biology","has_accepted_license":"1","title":"Mechanism of mammalian transcriptional repression by noncoding RNA","_id":"18778","OA_place":"publisher"},{"type":"journal_article","article_processing_charge":"Yes","ddc":["570"],"oa_version":"Published Version","scopus_import":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","quality_controlled":"1","publication_identifier":{"eissn":["2041-1723"]},"doi":"10.1038/s41467-024-55449-7","status":"public","day":"02","date_updated":"2025-02-27T12:41:25Z","OA_type":"gold","OA_place":"publisher","title":"Automatic feature selection and weighting in molecular systems using Differentiable Information Imbalance","_id":"18820","citation":{"ieee":"R. Wild, F. Wodaczek, V. Del Tatto, B. Cheng, and A. Laio, “Automatic feature selection and weighting in molecular systems using Differentiable Information Imbalance,” <i>Nature Communications</i>, vol. 16. Springer Nature, 2025.","apa":"Wild, R., Wodaczek, F., Del Tatto, V., Cheng, B., &#38; Laio, A. (2025). Automatic feature selection and weighting in molecular systems using Differentiable Information Imbalance. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-024-55449-7\">https://doi.org/10.1038/s41467-024-55449-7</a>","mla":"Wild, Romina, et al. “Automatic Feature Selection and Weighting in Molecular Systems Using Differentiable Information Imbalance.” <i>Nature Communications</i>, vol. 16, 270, Springer Nature, 2025, doi:<a href=\"https://doi.org/10.1038/s41467-024-55449-7\">10.1038/s41467-024-55449-7</a>.","ama":"Wild R, Wodaczek F, Del Tatto V, Cheng B, Laio A. Automatic feature selection and weighting in molecular systems using Differentiable Information Imbalance. <i>Nature Communications</i>. 2025;16. doi:<a href=\"https://doi.org/10.1038/s41467-024-55449-7\">10.1038/s41467-024-55449-7</a>","chicago":"Wild, Romina, Felix Wodaczek, Vittorio Del Tatto, Bingqing Cheng, and Alessandro Laio. “Automatic Feature Selection and Weighting in Molecular Systems Using Differentiable Information Imbalance.” <i>Nature Communications</i>. Springer Nature, 2025. <a href=\"https://doi.org/10.1038/s41467-024-55449-7\">https://doi.org/10.1038/s41467-024-55449-7</a>.","ista":"Wild R, Wodaczek F, Del Tatto V, Cheng B, Laio A. 2025. Automatic feature selection and weighting in molecular systems using Differentiable Information Imbalance. Nature Communications. 16, 270.","short":"R. Wild, F. Wodaczek, V. Del Tatto, B. Cheng, A. Laio, Nature Communications 16 (2025)."},"has_accepted_license":"1","publication":"Nature Communications","department":[{"_id":"AnSa"},{"_id":"BiCh"}],"publisher":"Springer Nature","file":[{"file_size":1216738,"content_type":"application/pdf","creator":"dernst","access_level":"open_access","relation":"main_file","date_created":"2025-01-14T06:59:25Z","date_updated":"2025-01-14T06:59:25Z","file_name":"2025_NatureComm_Wild.pdf","checksum":"b3d0f3568d9a87c494cf231a5324029a","file_id":"18846","success":1}],"external_id":{"pmid":["39747013"],"isi":["001389959100009"]},"pmid":1,"tmp":{"image":"/images/cc_by_nc_nd.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","short":"CC BY-NC-ND (4.0)"},"article_number":"270","publication_status":"published","author":[{"last_name":"Wild","first_name":"Romina","full_name":"Wild, Romina"},{"id":"8b4b6a9f-32b0-11ee-9fa8-bbe85e26258e","full_name":"Wodaczek, Felix","orcid":"0009-0000-1457-795X","last_name":"Wodaczek","first_name":"Felix"},{"full_name":"Del Tatto, Vittorio","first_name":"Vittorio","last_name":"Del Tatto"},{"id":"cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9","orcid":"0000-0002-3584-9632","full_name":"Cheng, Bingqing","last_name":"Cheng","first_name":"Bingqing"},{"last_name":"Laio","first_name":"Alessandro","full_name":"Laio, Alessandro"}],"DOAJ_listed":"1","abstract":[{"lang":"eng","text":"Feature selection is essential in the analysis of molecular systems and many other fields, but several uncertainties remain: What is the optimal number of features for a simplified, interpretable model that retains essential information? How should features with different units be aligned, and how should their relative importance be weighted? Here, we introduce the Differentiable Information Imbalance (DII), an automated method to rank information content between sets of features. Using distances in a ground truth feature space, DII identifies a low-dimensional subset of features that best preserves these relationships. Each feature is scaled by a weight, which is optimized by minimizing the DII through gradient descent. This allows simultaneously performing unit alignment and relative importance scaling, while preserving interpretability. DII can also produce sparse solutions and determine the optimal size of the reduced feature space. We demonstrate the usefulness of this approach on two benchmark molecular problems: (1) identifying collective variables that describe conformations of a biomolecule, and (2) selecting features for training a machine-learning force field. These results show the potential of DII in addressing feature selection challenges and optimizing dimensionality in various applications. The method is available in the Python library DADApy."}],"month":"01","volume":16,"article_type":"original","year":"2025","file_date_updated":"2025-01-14T06:59:25Z","date_published":"2025-01-02T00:00:00Z","date_created":"2025-01-12T23:04:00Z","isi":1,"oa":1,"language":[{"iso":"eng"}],"acknowledgement":"The authors thank Dr. Matteo Carli for providing the CLN025 replica exchange MD trajectory and Matteo Allione for the fruitful discussions connected with the idea of the linear scaling estimator. This work was partially funded by NextGenerationEU through the Italian National Centre for HPC, Big Data, and Quantum Computing (Grant No. CN00000013 received by A.L.). A.L. also acknowledges financial support by the region Friuli Venezia Giulia (project F53C22001770002 received by A.L.).","intvolume":"        16"},{"abstract":[{"text":"Even though the one-dimensional contact interaction requires no regularization, renormalization methods have been shown to improve the convergence of numerical calculations considerably. In this work, we compare and contrast these methods: “the running coupling constant” where the two-body ground-state energy is used as a renormalization condition, and two effective interaction approaches that include information about the ground as well as excited states. In particular, we calculate the energies and densities of few-fermion systems in a harmonic oscillator with the configuration-interaction method and compare the results based upon renormalized and bare interactions. We find that the use of the running coupling constant instead of the bare interaction improves convergence significantly. A comparison with an effective interaction, which is designed to reproduce the relative part of the energy spectrum of two particles, showed a similar improvement. The effective interaction provides an additional improvement if the center-of-mass excitations are included in the construction. Finally, we discuss the transformation of observables alongside the renormalization of the potential, and demonstrate that this might be an essential ingredient for accurate numerical calculations.","lang":"eng"}],"month":"01","volume":111,"article_type":"original","year":"2025","date_published":"2025-01-03T00:00:00Z","date_created":"2025-01-12T23:04:00Z","language":[{"iso":"eng"}],"acknowledgement":"We thank J. Cremon and J. Bjerlin for earlier contributions to the configuration-interaction calculations used in this work (see Refs. [49,50]). F.B. and S.M.R. acknowledge helpful discussions with Carl Heintze, Sandra Brandstetter, and Lila Chergui. We further want to thank Lila Chergui for helpful comments on the paper. This research was financially supported by the Knut and Alice Wallenberg Foundation (Grant No. KAW 2018.0217) and the Swedish Research Council (Grant No. 2022-03654 VR).","oa":1,"issue":"1","isi":1,"intvolume":"       111","external_id":{"isi":["001398791400004"],"arxiv":["2408.10052"]},"article_number":"013303","publication_status":"published","author":[{"full_name":"Brauneis, Fabian","first_name":"Fabian","last_name":"Brauneis"},{"full_name":"Hammer, Hans Werner","first_name":"Hans Werner","last_name":"Hammer"},{"full_name":"Reimann, Stephanie M.","first_name":"Stephanie M.","last_name":"Reimann"},{"last_name":"Volosniev","first_name":"Artem","id":"37D278BC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-0393-5525","full_name":"Volosniev, Artem"}],"day":"03","date_updated":"2025-02-27T12:41:58Z","OA_type":"green","OA_place":"repository","title":"Comparison of renormalized interactions using one-dimensional few-body systems as a testbed","_id":"18821","citation":{"chicago":"Brauneis, Fabian, Hans Werner Hammer, Stephanie M. Reimann, and Artem Volosniev. “Comparison of Renormalized Interactions Using One-Dimensional Few-Body Systems as a Testbed.” <i>Physical Review A</i>. American Physical Society, 2025. <a href=\"https://doi.org/10.1103/PhysRevA.111.013303\">https://doi.org/10.1103/PhysRevA.111.013303</a>.","ista":"Brauneis F, Hammer HW, Reimann SM, Volosniev A. 2025. Comparison of renormalized interactions using one-dimensional few-body systems as a testbed. Physical Review A. 111(1), 013303.","short":"F. Brauneis, H.W. Hammer, S.M. Reimann, A. Volosniev, Physical Review A 111 (2025).","ieee":"F. Brauneis, H. W. Hammer, S. M. Reimann, and A. Volosniev, “Comparison of renormalized interactions using one-dimensional few-body systems as a testbed,” <i>Physical Review A</i>, vol. 111, no. 1. American Physical Society, 2025.","apa":"Brauneis, F., Hammer, H. W., Reimann, S. M., &#38; Volosniev, A. (2025). Comparison of renormalized interactions using one-dimensional few-body systems as a testbed. <i>Physical Review A</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevA.111.013303\">https://doi.org/10.1103/PhysRevA.111.013303</a>","mla":"Brauneis, Fabian, et al. “Comparison of Renormalized Interactions Using One-Dimensional Few-Body Systems as a Testbed.” <i>Physical Review A</i>, vol. 111, no. 1, 013303, American Physical Society, 2025, doi:<a href=\"https://doi.org/10.1103/PhysRevA.111.013303\">10.1103/PhysRevA.111.013303</a>.","ama":"Brauneis F, Hammer HW, Reimann SM, Volosniev A. Comparison of renormalized interactions using one-dimensional few-body systems as a testbed. <i>Physical Review A</i>. 2025;111(1). doi:<a href=\"https://doi.org/10.1103/PhysRevA.111.013303\">10.1103/PhysRevA.111.013303</a>"},"publication":"Physical Review A","department":[{"_id":"MiLe"}],"publisher":"American Physical Society","main_file_link":[{"url":" https://doi.org/10.48550/arXiv.2408.10052","open_access":"1"}],"type":"journal_article","article_processing_charge":"No","arxiv":1,"oa_version":"Preprint","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","scopus_import":"1","quality_controlled":"1","doi":"10.1103/PhysRevA.111.013303","publication_identifier":{"eissn":["2469-9934"],"issn":["2469-9926"]},"status":"public"},{"ec_funded":1,"status":"public","quality_controlled":"1","publication_identifier":{"eissn":["2041-7942"],"issn":["0025-5793"]},"doi":"10.1112/mtk.70008","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","scopus_import":"1","oa_version":"Published Version","ddc":["510"],"article_processing_charge":"Yes (via OA deal)","type":"journal_article","publisher":"London Mathematical Society","department":[{"_id":"TiBr"}],"file":[{"content_type":"application/pdf","file_size":309893,"creator":"dernst","access_level":"open_access","relation":"main_file","date_created":"2025-01-14T06:52:09Z","date_updated":"2025-01-14T06:52:09Z","file_name":"2025_Mathematika_Wang.pdf","checksum":"700a8596b4bffce2320d074120962c22","file_id":"18845","success":1}],"citation":{"ista":"Wang V. 2025. Diagonal cubic forms and the large sieve. Mathematika. 71(1), e70008.","chicago":"Wang, Victor. “Diagonal Cubic Forms and the Large Sieve.” <i>Mathematika</i>. London Mathematical Society, 2025. <a href=\"https://doi.org/10.1112/mtk.70008\">https://doi.org/10.1112/mtk.70008</a>.","short":"V. Wang, Mathematika 71 (2025).","mla":"Wang, Victor. “Diagonal Cubic Forms and the Large Sieve.” <i>Mathematika</i>, vol. 71, no. 1, e70008, London Mathematical Society, 2025, doi:<a href=\"https://doi.org/10.1112/mtk.70008\">10.1112/mtk.70008</a>.","apa":"Wang, V. (2025). Diagonal cubic forms and the large sieve. <i>Mathematika</i>. London Mathematical Society. <a href=\"https://doi.org/10.1112/mtk.70008\">https://doi.org/10.1112/mtk.70008</a>","ieee":"V. Wang, “Diagonal cubic forms and the large sieve,” <i>Mathematika</i>, vol. 71, no. 1. London Mathematical Society, 2025.","ama":"Wang V. Diagonal cubic forms and the large sieve. <i>Mathematika</i>. 2025;71(1). doi:<a href=\"https://doi.org/10.1112/mtk.70008\">10.1112/mtk.70008</a>"},"has_accepted_license":"1","publication":"Mathematika","title":"Diagonal cubic forms and the large sieve","_id":"18822","OA_place":"publisher","OA_type":"hybrid","date_updated":"2025-04-14T07:54:56Z","day":"02","project":[{"grant_number":"101034413","call_identifier":"H2020","name":"IST-BRIDGE: International postdoctoral program","_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c"}],"author":[{"first_name":"Victor","last_name":"Wang","orcid":"0000-0002-0704-7026","full_name":"Wang, Victor","id":"76096395-aea4-11ed-a680-ab8ebbd3f1b9"}],"tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"article_number":"e70008","publication_status":"published","corr_author":"1","external_id":{"isi":["001388255500001"]},"intvolume":"        71","isi":1,"oa":1,"issue":"1","language":[{"iso":"eng"}],"acknowledgement":"I thank Peter Sarnak for suggesting projects that ultimately led to the present paper. I also thank him for many encouraging discussions, helpful comments, and references. Thanks also to Tim Browning, Trevor Wooley, and Nina Zubrilina for helpful comments, and to Levent Alpöge and Will Sawin for some interesting old discussions. I thank Yang Liu, Evan O'Dorney, Ashwin Sah, and Mark Sellke for conversations illuminating the combinatorics of an older, counting version of the present Lemma 4.9. Finally, special thanks are due to the editors and referees for their patience and help with the exposition. This work was partially supported by NSF Grant DMS-1802211, and the European Union's Horizon 2020 research and innovation program under the Marie Skłodowska-Curie Grant Agreement No. 101034413.","date_created":"2025-01-12T23:04:01Z","article_type":"original","year":"2025","date_published":"2025-01-02T00:00:00Z","file_date_updated":"2025-01-14T06:52:09Z","volume":71,"month":"01","abstract":[{"lang":"eng","text":"Let N(X) be the number of integral zeros (mathematical equation). Works of Hooley and Heath-Brown imply (mathematical equation), if one assumes automorphy and grand Riemann hypothesis for certain Hasse–Weil L-functions. Assuming instead a natural large sieve inequality, we recover the same bound on N(X). This is part of a more general statement, for diagonal cubic forms in (mathematical equation) variables, where we allow approximations to Hasse–Weil L-functions."}]},{"oa_version":"Published Version","scopus_import":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_identifier":{"eissn":["1532-2548"]},"doi":"10.1093/plphys/kiae651","quality_controlled":"1","status":"public","type":"journal_article","article_processing_charge":"Yes (in subscription journal)","ddc":["580"],"OA_place":"publisher","title":"Memory of maternal temperatures: DNA methylation alterations across generations","_id":"18823","publication":"Plant Physiology","has_accepted_license":"1","citation":{"ista":"Cao D, De Jaeger-Braet JG. 2025. Memory of maternal temperatures: DNA methylation alterations across generations. Plant Physiology. 197(1), kiae651.","chicago":"Cao, Dechang, and Joke G De Jaeger-Braet. “Memory of Maternal Temperatures: DNA Methylation Alterations across Generations.” <i>Plant Physiology</i>. Oxford University Press, 2025. <a href=\"https://doi.org/10.1093/plphys/kiae651\">https://doi.org/10.1093/plphys/kiae651</a>.","short":"D. Cao, J.G. De Jaeger-Braet, Plant Physiology 197 (2025).","apa":"Cao, D., &#38; De Jaeger-Braet, J. G. (2025). Memory of maternal temperatures: DNA methylation alterations across generations. <i>Plant Physiology</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/plphys/kiae651\">https://doi.org/10.1093/plphys/kiae651</a>","mla":"Cao, Dechang, and Joke G. De Jaeger-Braet. “Memory of Maternal Temperatures: DNA Methylation Alterations across Generations.” <i>Plant Physiology</i>, vol. 197, no. 1, kiae651, Oxford University Press, 2025, doi:<a href=\"https://doi.org/10.1093/plphys/kiae651\">10.1093/plphys/kiae651</a>.","ieee":"D. Cao and J. G. De Jaeger-Braet, “Memory of maternal temperatures: DNA methylation alterations across generations,” <i>Plant Physiology</i>, vol. 197, no. 1. Oxford University Press, 2025.","ama":"Cao D, De Jaeger-Braet JG. 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of Science and Technology Austria","date_published":"2025-04-01T00:00:00Z","file_date_updated":"2025-03-07T11:09:13Z","year":"2025","date_created":"2025-01-13T09:51:29Z","title":"Research Data for the publication \"Super-resolution expansion microscopy in plant roots\"","_id":"18837","date_updated":"2026-06-10T08:30:20Z","abstract":[{"text":"Super-resolution methods provide far better spatial resolution than the optical diffraction limit of about half the wavelength of light (∼200-300 nm). Nevertheless, they have yet to attain widespread use in plants, largely due to plants’ challenging optical properties. Expansion microscopy improves effective resolution by isotropically increasing the physical distances between sample structures while preserving relative spatial arrangements and clearing the sample. However, its application to plants has been hindered by the rigid, mechanically cohesive structure of plant tissues. Here, we report on whole-mount expansion microscopy of thale cress (Arabidopsis thaliana) root tissues (PlantEx), achieving a four-fold resolution increase over conventional microscopy. Our results highlight the microtubule cytoskeleton organization and interaction between molecularly defined cellular constituents. Combining PlantEx with stimulated emission depletion (STED) microscopy, we increase nanoscale resolution and visualize the complex organization of subcellular organelles from intact tissues by example of the densely packed COPI-coated vesicles associated with the Golgi apparatus and put these into a cellular structural context. Our results show that expansion microscopy can be applied to increase effective imaging resolution in Arabidopsis root specimens.","lang":"eng"}],"month":"04","doi":"10.15479/AT:ISTA:18837","status":"public","user_id":"68b8ca59-c5b3-11ee-8790-cd641c68093d","contributor":[{"last_name":"Gallei","contributor_type":"researcher","first_name":"Michelle C","id":"35A03822-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1286-7368"},{"first_name":"Sven M","contributor_type":"researcher","last_name":"Truckenbrodt","id":"45812BD4-F248-11E8-B48F-1D18A9856A87"},{"contributor_type":"researcher","first_name":"Caroline","last_name":"Kreuzinger","id":"382077BA-F248-11E8-B48F-1D18A9856A87"},{"id":"F8660870-D756-11E9-98C5-34DFE5697425","contributor_type":"researcher","first_name":"Syamala","last_name":"Inumella"},{"contributor_type":"researcher","first_name":"Vitali","last_name":"Vistunou","id":"7e146587-8972-11ed-ae7b-d7a32ea86a81"},{"orcid":"0000-0003-1216-9105","id":"4DF26D8C-F248-11E8-B48F-1D18A9856A87","contributor_type":"researcher","first_name":"Christoph M","last_name":"Sommer"},{"id":"3A0A06F4-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7667-6854","last_name":"Tavakoli","contributor_type":"researcher","first_name":"Mojtaba"},{"id":"40E7F008-F248-11E8-B48F-1D18A9856A87","contributor_type":"researcher","first_name":"Nathalie","last_name":"Agudelo Duenas"},{"first_name":"Jakob","contributor_type":"researcher","last_name":"Vorlaufer","id":"937696FA-C996-11E9-8C7C-CF13E6697425"},{"id":"425C1CE8-F248-11E8-B48F-1D18A9856A87","contributor_type":"researcher","first_name":"Wiebke","last_name":"Jahr"},{"id":"6ac4636d-15b2-11ec-abd3-fb8df79972ae","last_name":"Randuch","contributor_type":"researcher","first_name":"Marek"},{"orcid":"0000-0002-2739-8843","id":"46A62C3A-F248-11E8-B48F-1D18A9856A87","first_name":"Alexander J","contributor_type":"researcher","last_name":"Johnson"},{"id":"38F4F166-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8510-9739","last_name":"Benková","contributor_type":"researcher","first_name":"Eva"},{"first_name":"Jiří","contributor_type":"researcher","last_name":"Friml","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87"},{"contributor_type":"researcher","first_name":"Johann G","last_name":"Danzl","orcid":"0000-0001-8559-3973","id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87"}],"oa_version":"Published Version","related_material":{"record":[{"relation":"used_in_publication","id":"19003","status":"public"}]},"author":[{"first_name":"Johann G","last_name":"Danzl","full_name":"Danzl, Johann G","orcid":"0000-0001-8559-3973","id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Kreuzinger","first_name":"Caroline","id":"382077BA-F248-11E8-B48F-1D18A9856A87","full_name":"Kreuzinger, Caroline"}],"type":"research_data","corr_author":"1","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","short":"CC BY-NC (4.0)"},"article_processing_charge":"No"},{"date_created":"2025-01-19T23:01:50Z","file_date_updated":"2025-01-22T14:35:22Z","date_published":"2025-01-07T00:00:00Z","article_type":"original","year":"2025","intvolume":"        16","oa":1,"language":[{"iso":"eng"}],"acknowledgement":"We would like to thank M. Ocampo Camacho and M.F. Canedo Ocampo for assistance with the figures. We thank M. Hooper for assistance developing the GFP assay and operating the CE machine for in vitro cleavage analysis. We thank E. Schwartz and A. Brilot for expert cryo-EM support in the Sauer Structural Biology Laboratory at UT Austin. This work was funded, in part, by a sponsored research agreement with Metagenomi, Inc. (to D.W.T), a Welch Foundation Research Grant F-1938 (to D.W.T), and the Robert J. Kleberg, Jr. and Helen C. Kleberg Foundation Medical Research Grant (to D.W.T), and a grant from the National Institute of Allergy and Infectious Diseases (NIAID 1R01AI110577 to K.A.J.).","month":"01","abstract":[{"lang":"eng","text":"Type II CRISPR endonucleases are widely used programmable genome editing tools. Recently, CRISPR-Cas systems with highly compact nucleases have been discovered, including Cas9d (a type II-D nuclease). Here, we report the cryo-EM structures of a Cas9d nuclease (747 amino acids in length) in multiple functional states, revealing a stepwise process of DNA targeting involving a conformational switch in a REC2 domain insertion. Our structures provide insights into the intricately folded guide RNA which acts as a structural scaffold to anchor small, flexible protein domains for DNA recognition. The sgRNA can be truncated by up to ~25% yet still retain activity in vivo. Using ancestral sequence reconstruction, we generated compact nucleases capable of efficient genome editing in mammalian cells. Collectively, our results provide mechanistic insights into the evolution and DNA targeting of diverse type II CRISPR-Cas systems, providing a blueprint for future re-engineering of minimal RNA-guided DNA endonucleases."}],"volume":16,"DOAJ_listed":"1","publication_status":"published","tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"pmid":1,"article_number":"457","external_id":{"pmid":["39774105"]},"author":[{"first_name":"Rodrigo Fregoso","last_name":"Ocampo","full_name":"Ocampo, Rodrigo Fregoso"},{"first_name":"Jack Peter Kelly","last_name":"Bravo","orcid":"0000-0003-0456-0753","full_name":"Bravo, Jack Peter Kelly","id":"96aecfa5-8931-11ee-af30-aa6a5d6eee0e"},{"full_name":"Dangerfield, Tyler L.","last_name":"Dangerfield","first_name":"Tyler L."},{"full_name":"Nocedal, Isabel","first_name":"Isabel","last_name":"Nocedal"},{"full_name":"Jirde, Samatar A.","last_name":"Jirde","first_name":"Samatar A."},{"last_name":"Alexander","first_name":"Lisa M.","full_name":"Alexander, Lisa M."},{"first_name":"Nicole C.","last_name":"Thomas","full_name":"Thomas, Nicole C."},{"first_name":"Anjali","last_name":"Das","full_name":"Das, Anjali"},{"full_name":"Nielson, Sarah","first_name":"Sarah","last_name":"Nielson"},{"first_name":"Kenneth A.","last_name":"Johnson","full_name":"Johnson, Kenneth A."},{"last_name":"Brown","first_name":"Christopher T.","full_name":"Brown, Christopher T."},{"full_name":"Butterfield, Cristina N.","last_name":"Butterfield","first_name":"Cristina N."},{"first_name":"Daniela S.A.","last_name":"Goltsman","full_name":"Goltsman, Daniela S.A."},{"last_name":"Taylor","first_name":"David W.","full_name":"Taylor, David W."}],"_id":"18848","title":"DNA targeting by compact Cas9d and its resurrected ancestor","OA_place":"publisher","file":[{"content_type":"application/pdf","file_size":5450660,"creator":"dernst","access_level":"open_access","relation":"main_file","date_created":"2025-01-22T14:35:22Z","date_updated":"2025-01-22T14:35:22Z","file_name":"2025_NatureComm_Ocampo.pdf","file_id":"18869","checksum":"885e96690620790d5c9f188a1587b4cd","success":1}],"department":[{"_id":"JaBr"}],"publisher":"Springer Nature","publication":"Nature Communications","has_accepted_license":"1","citation":{"short":"R.F. Ocampo, J.P.K. Bravo, T.L. Dangerfield, I. Nocedal, S.A. Jirde, L.M. Alexander, N.C. Thomas, A. Das, S. Nielson, K.A. Johnson, C.T. Brown, C.N. Butterfield, D.S.A. Goltsman, D.W. Taylor, Nature Communications 16 (2025).","chicago":"Ocampo, Rodrigo Fregoso, Jack Peter Kelly Bravo, Tyler L. Dangerfield, Isabel Nocedal, Samatar A. Jirde, Lisa M. Alexander, Nicole C. Thomas, et al. “DNA Targeting by Compact Cas9d and Its Resurrected Ancestor.” <i>Nature Communications</i>. Springer Nature, 2025. <a href=\"https://doi.org/10.1038/s41467-024-55573-4\">https://doi.org/10.1038/s41467-024-55573-4</a>.","ista":"Ocampo RF, Bravo JPK, Dangerfield TL, Nocedal I, Jirde SA, Alexander LM, Thomas NC, Das A, Nielson S, Johnson KA, Brown CT, Butterfield CN, Goltsman DSA, Taylor DW. 2025. DNA targeting by compact Cas9d and its resurrected ancestor. Nature Communications. 16, 457.","ama":"Ocampo RF, Bravo JPK, Dangerfield TL, et al. DNA targeting by compact Cas9d and its resurrected ancestor. <i>Nature Communications</i>. 2025;16. doi:<a href=\"https://doi.org/10.1038/s41467-024-55573-4\">10.1038/s41467-024-55573-4</a>","ieee":"R. F. Ocampo <i>et al.</i>, “DNA targeting by compact Cas9d and its resurrected ancestor,” <i>Nature Communications</i>, vol. 16. Springer Nature, 2025.","apa":"Ocampo, R. F., Bravo, J. P. K., Dangerfield, T. L., Nocedal, I., Jirde, S. A., Alexander, L. M., … Taylor, D. W. (2025). DNA targeting by compact Cas9d and its resurrected ancestor. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-024-55573-4\">https://doi.org/10.1038/s41467-024-55573-4</a>","mla":"Ocampo, Rodrigo Fregoso, et al. “DNA Targeting by Compact Cas9d and Its Resurrected Ancestor.” <i>Nature Communications</i>, vol. 16, 457, Springer Nature, 2025, doi:<a href=\"https://doi.org/10.1038/s41467-024-55573-4\">10.1038/s41467-024-55573-4</a>."},"day":"07","OA_type":"gold","date_updated":"2025-07-03T11:58:22Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","scopus_import":"1","oa_version":"Published Version","status":"public","publication_identifier":{"eissn":["2041-1723"]},"doi":"10.1038/s41467-024-55573-4","quality_controlled":"1","article_processing_charge":"Yes","type":"journal_article","ddc":["570"]},{"date_created":"2025-01-19T23:01:50Z","article_type":"original","year":"2025","date_published":"2025-01-07T00:00:00Z","file_date_updated":"2025-01-20T10:10:04Z","intvolume":"       122","issue":"1","oa":1,"isi":1,"language":[{"iso":"eng"}],"acknowledgement":"We thank Nicholas H. Barton for his comments on the manuscript, Benjamin Zoller for helpful discussions, and Aleksandra Walczak and Curtis Callan for early collaborations that shaped this work. Special thanks to Eric F. Wieschaus for many persistently inspiring conversations. This work was supported in part by the Human Frontiers Science Program; the Austrian Science Fund (FWF P28844); by the European Research Council grant DynaTrans (101118866); by U.S. NSF, through the Center for the Physics of Biological Function (PHY–1734030); by NIH Grants R01GM097275, U01DA047730, and U01DK127429; by the John Simon Guggenheim Memorial Foundation; and by the LOEWE priority program “Center for Multiscale Modeling in Life Sciences” (CMMS), sponsored by the Hessian Ministry for Science and Research, Arts and Culture (HMWK).","month":"01","abstract":[{"lang":"eng","text":"Many biological systems operate near the physical limits to their performance, suggesting that aspects of their behavior and underlying mechanisms could be derived from optimization principles. However, such principles have often been applied only in simplified models. Here, we explore a detailed mechanistic model of the gap gene network in the Drosophila embryo, optimizing its 50+ parameters to maximize the information that gene expression levels provide about nuclear positions. This optimization is conducted under realistic constraints, such as limits on the number of available molecules. Remarkably, the optimal networks we derive closely match the architecture and spatial gene expression profiles observed in the real organism. Our framework quantifies the tradeoffs involved in maximizing functional performance and allows for the exploration of alternative network configurations, addressing the question of which features are necessary and which are contingent. Our results suggest that multiple solutions to the optimization problem might exist across closely related organisms, offering insights into the evolution of gene regulatory networks."}],"volume":122,"project":[{"_id":"254E9036-B435-11E9-9278-68D0E5697425","name":"Biophysics of information processing in gene regulation","grant_number":"P28844-B27","call_identifier":"FWF"},{"grant_number":"101118866","name":"Transcription in 4D: the dynamic interplay between chromatin architecture and gene expression in developing pseudo-embryos","_id":"7bfe6a29-9f16-11ee-852c-c0da5e2045d9"},{"_id":"2665AAFE-B435-11E9-9278-68D0E5697425","name":"Can evolution minimize spurious signaling crosstalk to reach optimal performance?","grant_number":"RGP0034/2018"}],"tmp":{"image":"/images/cc_by_nc_nd.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","short":"CC BY-NC-ND (4.0)"},"article_number":"e2402925121","pmid":1,"publication_status":"published","corr_author":"1","external_id":{"pmid":["39752518"],"isi":["001392772400001"]},"author":[{"orcid":"0000-0002-1287-3779","full_name":"Sokolowski, Thomas R","id":"3E999752-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas R","last_name":"Sokolowski"},{"full_name":"Gregor, Thomas","first_name":"Thomas","last_name":"Gregor"},{"full_name":"Bialek, William","first_name":"William","last_name":"Bialek"},{"first_name":"Gašper","last_name":"Tkačik","orcid":"0000-0002-6699-1455","full_name":"Tkačik, Gašper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87"}],"title":"Deriving a genetic regulatory network from an optimization principle","_id":"18849","OA_place":"publisher","department":[{"_id":"GaTk"}],"publisher":"National Academy of Sciences","file":[{"checksum":"8dbfc7d495413340225ebfae69b0cf9a","file_id":"18862","success":1,"date_updated":"2025-01-20T10:10:04Z","file_name":"2025_PNAS_Sokolowski.pdf","access_level":"open_access","date_created":"2025-01-20T10:10:04Z","relation":"main_file","file_size":19073585,"content_type":"application/pdf","creator":"dernst"}],"citation":{"ama":"Sokolowski TR, Gregor T, Bialek W, Tkačik G. Deriving a genetic regulatory network from an optimization principle. <i>Proceedings of the National Academy of Sciences</i>. 2025;122(1). doi:<a href=\"https://doi.org/10.1073/pnas.2402925121\">10.1073/pnas.2402925121</a>","ieee":"T. R. Sokolowski, T. Gregor, W. Bialek, and G. Tkačik, “Deriving a genetic regulatory network from an optimization principle,” <i>Proceedings of the National Academy of Sciences</i>, vol. 122, no. 1. National Academy of Sciences, 2025.","mla":"Sokolowski, Thomas R., et al. “Deriving a Genetic Regulatory Network from an Optimization Principle.” <i>Proceedings of the National Academy of Sciences</i>, vol. 122, no. 1, e2402925121, National Academy of Sciences, 2025, doi:<a href=\"https://doi.org/10.1073/pnas.2402925121\">10.1073/pnas.2402925121</a>.","apa":"Sokolowski, T. R., Gregor, T., Bialek, W., &#38; Tkačik, G. (2025). Deriving a genetic regulatory network from an optimization principle. <i>Proceedings of the National Academy of Sciences</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.2402925121\">https://doi.org/10.1073/pnas.2402925121</a>","short":"T.R. Sokolowski, T. Gregor, W. Bialek, G. Tkačik, Proceedings of the National Academy of Sciences 122 (2025).","chicago":"Sokolowski, Thomas R, Thomas Gregor, William Bialek, and Gašper Tkačik. “Deriving a Genetic Regulatory Network from an Optimization Principle.” <i>Proceedings of the National Academy of Sciences</i>. National Academy of Sciences, 2025. <a href=\"https://doi.org/10.1073/pnas.2402925121\">https://doi.org/10.1073/pnas.2402925121</a>.","ista":"Sokolowski TR, Gregor T, Bialek W, Tkačik G. 2025. Deriving a genetic regulatory network from an optimization principle. Proceedings of the National Academy of Sciences. 122(1), e2402925121."},"has_accepted_license":"1","publication":"Proceedings of the National Academy of Sciences","day":"07","OA_type":"hybrid","date_updated":"2026-02-16T12:26:51Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","scopus_import":"1","oa_version":"Published Version","status":"public","quality_controlled":"1","doi":"10.1073/pnas.2402925121","publication_identifier":{"issn":["0027-8424"],"eissn":["1091-6490"]},"article_processing_charge":"Yes (in subscription journal)","type":"journal_article","ddc":["570"]}]