--- OA_type: closed access _id: '18701' abstract: - lang: eng text: We developed in-situ engineered polycrystalline polythiophene (PTh) and its composite with reduced graphene oxide (PTh-rGO) via a simple chemical synthesis. 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. 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). article_number: '137869' article_processing_charge: No article_type: original author: - first_name: Neelima full_name: Mahato, Neelima last_name: Mahato - first_name: Saurabh full_name: Singh, Saurabh id: 12d625da-9cb3-11ed-9667-af09d37d3f0a last_name: Singh orcid: 0000-0003-2209-5269 - first_name: T. V.M. full_name: Sreekanth, T. V.M. last_name: Sreekanth - first_name: Kisoo full_name: Yoo, Kisoo last_name: Yoo - first_name: Jonghoon full_name: Kim, Jonghoon last_name: Kim citation: 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. Materials Letters. 2025;382. doi:10.1016/j.matlet.2024.137869' apa: 'Mahato, N., Singh, S., Sreekanth, T. V. M., 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. Elsevier. https://doi.org/10.1016/j.matlet.2024.137869' 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.” Materials Letters. Elsevier, 2025. https://doi.org/10.1016/j.matlet.2024.137869.' 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,” Materials Letters, vol. 382. Elsevier, 2025.' 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.' mla: 'Mahato, Neelima, et al. “In-Situ Engineered Highly-Crystalline Polythiophene Empowered Electrochemical Capacitor-II: Anomalous Electrochemical Charge Storage Behavior of Polythiophene-RGO Composite.” Materials Letters, vol. 382, 137869, Elsevier, 2025, doi:10.1016/j.matlet.2024.137869.' short: N. Mahato, S. Singh, T.V.M. Sreekanth, K. Yoo, J. Kim, Materials Letters 382 (2025). date_created: 2024-12-22T23:01:47Z date_published: 2025-03-01T00:00:00Z date_updated: 2025-05-19T14:05:22Z day: '01' department: - _id: MaIb doi: 10.1016/j.matlet.2024.137869 external_id: isi: - '001433664000001' intvolume: ' 382' isi: 1 language: - iso: eng month: '03' oa_version: None publication: Materials Letters publication_identifier: eissn: - 1873-4979 issn: - 0167-577X publication_status: published publisher: Elsevier quality_controlled: '1' scopus_import: '1' status: public title: 'In-situ engineered highly-crystalline Polythiophene empowered electrochemical capacitor-II: Anomalous electrochemical charge storage behavior of Polythiophene-rGO composite' type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 382 year: '2025' ... --- OA_place: publisher OA_type: hybrid _id: '18705' 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]. 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." article_processing_charge: Yes (via OA deal) article_type: original arxiv: 1 author: - first_name: Jakob full_name: Glas, Jakob id: d6423cba-dc74-11ea-a0a7-ee61689ff5fb last_name: Glas - first_name: Leonhard full_name: Hochfilzer, Leonhard last_name: Hochfilzer citation: ama: Glas J, Hochfilzer L. On a question of Davenport and diagonal cubic forms over Fq(t). Mathematische Annalen. 2025;391:5485-5533. doi:10.1007/s00208-024-03035-z apa: Glas, J., & Hochfilzer, L. (2025). On a question of Davenport and diagonal cubic forms over Fq(t). Mathematische Annalen. Springer Nature. https://doi.org/10.1007/s00208-024-03035-z chicago: Glas, Jakob, and Leonhard Hochfilzer. “On a Question of Davenport and Diagonal Cubic Forms over Fq(T).” Mathematische Annalen. Springer Nature, 2025. https://doi.org/10.1007/s00208-024-03035-z. ieee: J. Glas and L. Hochfilzer, “On a question of Davenport and diagonal cubic forms over Fq(t),” Mathematische Annalen, vol. 391. Springer Nature, pp. 5485–5533, 2025. ista: Glas J, Hochfilzer L. 2025. On a question of Davenport and diagonal cubic forms over Fq(t). Mathematische Annalen. 391, 5485–5533. mla: Glas, Jakob, and Leonhard Hochfilzer. “On a Question of Davenport and Diagonal Cubic Forms over Fq(T).” Mathematische Annalen, vol. 391, Springer Nature, 2025, pp. 5485–533, doi:10.1007/s00208-024-03035-z. short: J. Glas, L. Hochfilzer, Mathematische Annalen 391 (2025) 5485–5533. corr_author: '1' date_created: 2024-12-22T23:01:48Z date_published: 2025-04-01T00:00:00Z date_updated: 2025-05-19T14:04:46Z day: '01' ddc: - '510' department: - _id: TiBr doi: 10.1007/s00208-024-03035-z external_id: arxiv: - '2208.05422' isi: - '001376740400001' file: - access_level: open_access checksum: dcf57a8b01332c36e0cf2b0d1aeecb36 content_type: application/pdf creator: dernst date_created: 2025-04-16T09:38:55Z date_updated: 2025-04-16T09:38:55Z file_id: '19579' file_name: 2025_MathAnnalen_Glas.pdf file_size: 650021 relation: main_file success: 1 file_date_updated: 2025-04-16T09:38:55Z has_accepted_license: '1' intvolume: ' 391' isi: 1 language: - iso: eng month: '04' oa: 1 oa_version: Published Version page: 5485-5533 publication: Mathematische Annalen publication_identifier: eissn: - 1432-1807 issn: - 0025-5831 publication_status: published publisher: Springer Nature quality_controlled: '1' related_material: record: - id: '18293' relation: earlier_version status: public scopus_import: '1' status: public title: On a question of Davenport and diagonal cubic forms over Fq(t) tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 391 year: '2025' ... --- OA_type: closed access _id: '18707' 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. 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). article_processing_charge: No article_type: original author: - first_name: Haibo full_name: Shu, Haibo last_name: Shu - first_name: Mingjun full_name: Zhao, Mingjun last_name: Zhao - first_name: Shaoqing full_name: Lu, Shaoqing last_name: Lu - first_name: Shanhong full_name: Wan, Shanhong last_name: Wan - first_name: Aziz full_name: Genç, Aziz last_name: Genç - first_name: Lulu full_name: Huang, Lulu last_name: Huang - first_name: Maria full_name: Ibáñez, Maria id: 43C61214-F248-11E8-B48F-1D18A9856A87 last_name: Ibáñez orcid: 0000-0001-5013-2843 - first_name: Khak Ho full_name: Lim, Khak Ho last_name: Lim - first_name: Min full_name: Hong, Min last_name: Hong - first_name: Yu full_name: Liu, Yu id: 2A70014E-F248-11E8-B48F-1D18A9856A87 last_name: Liu orcid: 0000-0001-7313-6740 citation: ama: Shu H, Zhao M, Lu S, et al. Influence of surface engineering on the transport properties of lead sulfide nanomaterials. Journal of Colloid and Interface Science. 2025;683:703-712. doi:10.1016/j.jcis.2024.12.067 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. Journal of Colloid and Interface Science. Elsevier. https://doi.org/10.1016/j.jcis.2024.12.067 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.” Journal of Colloid and Interface Science. Elsevier, 2025. https://doi.org/10.1016/j.jcis.2024.12.067. ieee: H. Shu et al., “Influence of surface engineering on the transport properties of lead sulfide nanomaterials,” Journal of Colloid and Interface Science, vol. 683. Elsevier, pp. 703–712, 2025. 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. mla: Shu, Haibo, et al. “Influence of Surface Engineering on the Transport Properties of Lead Sulfide Nanomaterials.” Journal of Colloid and Interface Science, vol. 683, Elsevier, 2025, pp. 703–12, doi:10.1016/j.jcis.2024.12.067. 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. date_created: 2024-12-29T23:01:56Z date_published: 2025-04-01T00:00:00Z date_updated: 2025-05-19T14:03:54Z day: '01' department: - _id: MaIb doi: 10.1016/j.jcis.2024.12.067 external_id: isi: - '001393340800001' pmid: - '39706089' intvolume: ' 683' isi: 1 language: - iso: eng month: '04' oa_version: None page: 703-712 pmid: 1 project: - _id: 9B8F7476-BA93-11EA-9121-9846C619BF3A name: 'HighTE: The Werner Siemens Laboratory for the High Throughput Discovery of Semiconductors for Waste Heat Recovery' publication: Journal of Colloid and Interface Science publication_identifier: eissn: - 1095-7103 issn: - 0021-9797 publication_status: published publisher: Elsevier quality_controlled: '1' scopus_import: '1' status: public title: Influence of surface engineering on the transport properties of lead sulfide nanomaterials type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 683 year: '2025' ... --- OA_place: publisher OA_type: hybrid _id: '18710' 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. 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. article_processing_charge: Yes (via OA deal) article_type: original author: - first_name: Mateja full_name: Hrast, Mateja id: 48dbb294-2a9c-11ef-905d-f56be71f0e5d last_name: Hrast - first_name: Marko full_name: Ljubotina, Marko id: F75EE9BE-5C90-11EA-905D-16643DDC885E last_name: Ljubotina orcid: 0000-0003-0038-7068 - first_name: Matjaz full_name: Zitnik, Matjaz last_name: Zitnik citation: ama: Hrast M, Ljubotina M, Zitnik M. Ab initio Auger spectrum of the ultrafast dissociating 2p3/2−1σ* resonance in HCl. Physical Chemistry Chemical Physics. 2025;27(3):1473-1482. doi:10.1039/d4cp03727h apa: 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. Royal Society of Chemistry. https://doi.org/10.1039/d4cp03727h chicago: Hrast, Mateja, Marko Ljubotina, and Matjaz Zitnik. “Ab Initio Auger Spectrum of the Ultrafast Dissociating 2p3/2−1σ* Resonance in HCl.” Physical Chemistry Chemical Physics. Royal Society of Chemistry, 2025. https://doi.org/10.1039/d4cp03727h. ieee: M. Hrast, M. Ljubotina, and M. Zitnik, “Ab initio Auger spectrum of the ultrafast dissociating 2p3/2−1σ* resonance in HCl,” Physical Chemistry Chemical Physics, vol. 27, no. 3. Royal Society of Chemistry, pp. 1473–1482, 2025. 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. mla: Hrast, Mateja, et al. “Ab Initio Auger Spectrum of the Ultrafast Dissociating 2p3/2−1σ* Resonance in HCl.” Physical Chemistry Chemical Physics, vol. 27, no. 3, Royal Society of Chemistry, 2025, pp. 1473–82, doi:10.1039/d4cp03727h. short: M. Hrast, M. Ljubotina, M. Zitnik, Physical Chemistry Chemical Physics 27 (2025) 1473–1482. corr_author: '1' date_created: 2024-12-29T23:01:58Z date_published: 2025-01-21T00:00:00Z date_updated: 2025-05-19T14:03:19Z day: '21' ddc: - '530' department: - _id: MiLe - _id: MaSe doi: 10.1039/d4cp03727h ec_funded: 1 external_id: isi: - '001379819100001' pmid: - '39698879' file: - access_level: open_access checksum: d035683179547b41b811107a8649aab0 content_type: application/pdf creator: dernst date_created: 2025-04-16T09:46:45Z date_updated: 2025-04-16T09:46:45Z file_id: '19581' file_name: 2025_PCCP_Hrast.pdf file_size: 1270582 relation: main_file success: 1 file_date_updated: 2025-04-16T09:46:45Z has_accepted_license: '1' intvolume: ' 27' isi: 1 issue: '3' language: - iso: eng license: https://creativecommons.org/licenses/by-nc/3.0/ month: '01' oa: 1 oa_version: Published Version page: 1473-1482 pmid: 1 project: - _id: 2688CF98-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '801770' name: 'Angulon: physics and applications of a new quasiparticle' publication: Physical Chemistry Chemical Physics publication_identifier: issn: - 1463-9076 publication_status: published publisher: Royal Society of Chemistry quality_controlled: '1' related_material: record: - id: '18716' relation: research_data status: public scopus_import: '1' status: public title: Ab initio Auger spectrum of the ultrafast dissociating 2p3/2−1σ* resonance in HCl tmp: image: /images/cc_by_nc.png legal_code_url: https://creativecommons.org/licenses/by-nc/3.0/legalcode name: Creative Commons Attribution-NonCommercial 3.0 Unported (CC BY-NC 3.0) short: CC BY-NC (3.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 27 year: '2025' ... --- _id: '18712' abstract: - lang: eng text: 'This file contains the code associated with the manuscript ''Effect of assortative mating and sexual selection on polygenic barriers to gene flow''. ' acknowledged_ssus: - _id: ScienComp article_processing_charge: No author: - first_name: Parvathy full_name: Surendranadh, Parvathy id: 455235B8-F248-11E8-B48F-1D18A9856A87 last_name: Surendranadh orcid: 0000-0001-6395-386X - first_name: Himani full_name: Sachdeva, Himani last_name: Sachdeva citation: 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:10.15479/AT:ISTA:17344 apa: 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. https://doi.org/10.15479/AT:ISTA:17344 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. https://doi.org/10.15479/AT:ISTA:17344. 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. 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, 10.15479/AT:ISTA:17344. mla: 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, doi:10.15479/AT:ISTA:17344. short: P. Surendranadh, H. Sachdeva, (2025). corr_author: '1' date_created: 2025-01-01T15:28:27Z date_published: 2025-01-07T00:00:00Z date_updated: 2025-12-30T08:44:12Z day: '07' ddc: - '576' department: - _id: GradSch - _id: NiBa doi: 10.15479/AT:ISTA:17344 file: - access_level: open_access checksum: 9c5f91876014706990a0728c3675cd2a content_type: application/zip creator: psurendr date_created: 2025-01-02T12:30:27Z date_updated: 2025-01-02T12:30:27Z file_id: '18722' file_name: Codes.zip file_size: 326835 relation: main_file success: 1 - access_level: open_access checksum: 47fe98b7cc526e634e42de58f5eae288 content_type: text/plain creator: psurendr date_created: 2025-01-02T12:30:39Z date_updated: 2025-01-02T12:30:39Z file_id: '18723' file_name: ReadMe.txt file_size: 620 relation: main_file success: 1 file_date_updated: 2025-01-02T12:30:39Z has_accepted_license: '1' month: '01' oa: 1 oa_version: Published Version publisher: Institute of Science and Technology Austria related_material: record: - id: '19876' relation: used_in_publication status: public status: public title: Mathematica notebook and Fortran code for 'Effect of assortative mating and sexual selection on polygenic barriers to gene flow' tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: research_data user_id: 9947682f-b9fa-11ee-9c4a-b3ffaafe6614 year: '2025' ... --- OA_place: publisher OA_type: hybrid _id: '18753' abstract: - lang: eng 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." 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 ." article_number: '104104' article_processing_charge: Yes (in subscription journal) article_type: original arxiv: 1 author: - first_name: Alvaro full_name: Carbonero, Alvaro last_name: Carbonero - first_name: Hidde full_name: Koerts, Hidde last_name: Koerts - first_name: Benjamin full_name: Moore, Benjamin id: 6dc1a1be-bf1c-11ed-8d2b-d044840f49d6 last_name: Moore - first_name: Sophie full_name: Spirkl, Sophie last_name: Spirkl citation: ama: Carbonero A, Koerts H, Moore B, Spirkl S. On heroes in digraphs with forbidden induced forests. European Journal of Combinatorics. 2025;125. doi:10.1016/j.ejc.2024.104104 apa: Carbonero, A., Koerts, H., Moore, B., & Spirkl, S. (2025). On heroes in digraphs with forbidden induced forests. European Journal of Combinatorics. Elsevier. https://doi.org/10.1016/j.ejc.2024.104104 chicago: Carbonero, Alvaro, Hidde Koerts, Benjamin Moore, and Sophie Spirkl. “On Heroes in Digraphs with Forbidden Induced Forests.” European Journal of Combinatorics. Elsevier, 2025. https://doi.org/10.1016/j.ejc.2024.104104. ieee: A. Carbonero, H. Koerts, B. Moore, and S. Spirkl, “On heroes in digraphs with forbidden induced forests,” European Journal of Combinatorics, vol. 125. Elsevier, 2025. ista: Carbonero A, Koerts H, Moore B, Spirkl S. 2025. On heroes in digraphs with forbidden induced forests. European Journal of Combinatorics. 125, 104104. mla: Carbonero, Alvaro, et al. “On Heroes in Digraphs with Forbidden Induced Forests.” European Journal of Combinatorics, vol. 125, 104104, Elsevier, 2025, doi:10.1016/j.ejc.2024.104104. short: A. Carbonero, H. Koerts, B. Moore, S. Spirkl, European Journal of Combinatorics 125 (2025). corr_author: '1' date_created: 2025-01-05T23:01:55Z date_published: 2025-03-01T00:00:00Z date_updated: 2025-05-19T14:06:00Z day: '01' ddc: - '510' department: - _id: MaKw doi: 10.1016/j.ejc.2024.104104 external_id: arxiv: - '2306.04710' isi: - '001400113700001' file: - access_level: open_access checksum: 2c75f78f40ebb93d16fe3765bda2905a content_type: application/pdf creator: dernst date_created: 2025-04-16T09:16:25Z date_updated: 2025-04-16T09:16:25Z file_id: '19577' file_name: 2025_EuropJournCombinatorics_Carbonero.pdf file_size: 1110657 relation: main_file success: 1 file_date_updated: 2025-04-16T09:16:25Z has_accepted_license: '1' intvolume: ' 125' isi: 1 language: - iso: eng month: '03' oa: 1 oa_version: Published Version project: - _id: bd95085b-d553-11ed-ba76-e55d3349be45 grant_number: '101076777' name: Randomness and structure in combinatorics publication: European Journal of Combinatorics publication_identifier: issn: - 0195-6698 publication_status: published publisher: Elsevier quality_controlled: '1' scopus_import: '1' status: public title: On heroes in digraphs with forbidden induced forests tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 125 year: '2025' ... --- OA_place: publisher OA_type: hybrid _id: '18754' 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.' article_processing_charge: No article_type: original author: - first_name: Hannah M. full_name: Smith, Hannah M. last_name: Smith - first_name: Hong Kiat full_name: Ng, Hong Kiat last_name: Ng - first_name: Joanna E. full_name: Moodie, Joanna E. last_name: Moodie - first_name: Danni A. full_name: Gadd, Danni A. last_name: Gadd - first_name: Daniel L. full_name: Mccartney, Daniel L. last_name: Mccartney - first_name: Elena full_name: Bernabeu, Elena last_name: Bernabeu - first_name: Archie full_name: Campbell, Archie last_name: Campbell - first_name: Paul full_name: Redmond, Paul last_name: Redmond - first_name: Adele full_name: Taylor, Adele last_name: Taylor - first_name: Danielle full_name: Page, Danielle last_name: Page - first_name: Janie full_name: Corley, Janie last_name: Corley - first_name: Sarah E. full_name: Harris, Sarah E. last_name: Harris - first_name: Darwin full_name: Tay, Darwin last_name: Tay - first_name: Ian J. full_name: Deary, Ian J. last_name: Deary - first_name: Kathryn L. full_name: Evans, Kathryn L. last_name: Evans - first_name: Matthew Richard full_name: Robinson, Matthew Richard id: E5D42276-F5DA-11E9-8E24-6303E6697425 last_name: Robinson orcid: 0000-0001-8982-8813 - first_name: John C. full_name: Chambers, John C. last_name: Chambers - first_name: Marie full_name: Loh, Marie last_name: Loh - first_name: Simon R. full_name: Cox, Simon R. last_name: Cox - first_name: Riccardo E. full_name: Marioni, Riccardo E. last_name: Marioni - first_name: Robert F. full_name: Hillary, Robert F. last_name: Hillary citation: ama: Smith HM, Ng HK, Moodie JE, et al. DNA methylation-based predictors of metabolic traits in Scottish and Singaporean cohorts. American Journal of Human Genetics. 2025;112(1):106-115. doi:10.1016/j.ajhg.2024.11.012 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. American Journal of Human Genetics. Elsevier. https://doi.org/10.1016/j.ajhg.2024.11.012 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.” American Journal of Human Genetics. Elsevier, 2025. https://doi.org/10.1016/j.ajhg.2024.11.012. ieee: H. M. Smith et al., “DNA methylation-based predictors of metabolic traits in Scottish and Singaporean cohorts,” American Journal of Human Genetics, vol. 112, no. 1. Elsevier, pp. 106–115, 2025. 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. mla: Smith, Hannah M., et al. “DNA Methylation-Based Predictors of Metabolic Traits in Scottish and Singaporean Cohorts.” American Journal of Human Genetics, vol. 112, no. 1, Elsevier, 2025, pp. 106–15, doi:10.1016/j.ajhg.2024.11.012. 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. date_created: 2025-01-05T23:01:56Z date_published: 2025-01-02T00:00:00Z date_updated: 2025-02-27T12:38:23Z day: '02' ddc: - '570' department: - _id: MaRo doi: 10.1016/j.ajhg.2024.11.012 external_id: isi: - '001412498600001' pmid: - '39706196' file: - access_level: open_access checksum: 891d120554f07da2c35d38388c29a690 content_type: application/pdf creator: dernst date_created: 2025-01-08T09:26:42Z date_updated: 2025-01-08T09:26:42Z file_id: '18776' file_name: 2025_AJHG_Smith.pdf file_size: 2266488 relation: main_file success: 1 file_date_updated: 2025-01-08T09:26:42Z has_accepted_license: '1' intvolume: ' 112' isi: 1 issue: '1' language: - iso: eng month: '01' oa: 1 oa_version: Published Version page: 106-115 pmid: 1 publication: American Journal of Human Genetics publication_identifier: eissn: - 1537-6605 issn: - 0002-9297 publication_status: published publisher: Elsevier quality_controlled: '1' related_material: link: - relation: software url: https://github.com/marioni-group/Metabolic_trait scopus_import: '1' status: public title: DNA methylation-based predictors of metabolic traits in Scottish and Singaporean cohorts tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 112 year: '2025' ... --- OA_place: publisher OA_type: hybrid _id: '18764' 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. 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)." article_processing_charge: Yes (via OA deal) article_type: original arxiv: 1 author: - first_name: László full_name: Erdös, László id: 4DBD5372-F248-11E8-B48F-1D18A9856A87 last_name: Erdös orcid: 0000-0001-5366-9603 - first_name: Sven Joscha full_name: Henheik, Sven Joscha id: 31d731d7-d235-11ea-ad11-b50331c8d7fb last_name: Henheik orcid: 0000-0003-1106-327X - first_name: Jana full_name: Reker, Jana id: e796e4f9-dc8d-11ea-abe3-97e26a0323e9 last_name: Reker - first_name: Volodymyr full_name: Riabov, Volodymyr id: 1949f904-edfb-11eb-afb5-e2dfddabb93b last_name: Riabov citation: ama: Erdös L, Henheik SJ, Reker J, Riabov V. Prethermalization for deformed Wigner matrices. Annales Henri Poincare. 2025;26:1991-2033. doi:10.1007/s00023-024-01518-y apa: Erdös, L., Henheik, S. J., Reker, J., & Riabov, V. (2025). Prethermalization for deformed Wigner matrices. Annales Henri Poincare. Springer Nature. https://doi.org/10.1007/s00023-024-01518-y chicago: Erdös, László, Sven Joscha Henheik, Jana Reker, and Volodymyr Riabov. “Prethermalization for Deformed Wigner Matrices.” Annales Henri Poincare. Springer Nature, 2025. https://doi.org/10.1007/s00023-024-01518-y. ieee: L. Erdös, S. J. Henheik, J. Reker, and V. Riabov, “Prethermalization for deformed Wigner matrices,” Annales Henri Poincare, vol. 26. Springer Nature, pp. 1991–2033, 2025. ista: Erdös L, Henheik SJ, Reker J, Riabov V. 2025. Prethermalization for deformed Wigner matrices. Annales Henri Poincare. 26, 1991–2033. mla: Erdös, László, et al. “Prethermalization for Deformed Wigner Matrices.” Annales Henri Poincare, vol. 26, Springer Nature, 2025, pp. 1991–2033, doi:10.1007/s00023-024-01518-y. short: L. Erdös, S.J. Henheik, J. Reker, V. Riabov, Annales Henri Poincare 26 (2025) 1991–2033. corr_author: '1' date_created: 2025-01-05T23:01:59Z date_published: 2025-06-01T00:00:00Z date_updated: 2026-04-07T12:37:11Z day: '01' ddc: - '510' department: - _id: LaEr doi: 10.1007/s00023-024-01518-y ec_funded: 1 external_id: arxiv: - '2310.06677' isi: - '001385326500001' file: - access_level: open_access checksum: 49e6a934db540206f7eaa0c798553ded content_type: application/pdf creator: dernst date_created: 2025-06-25T05:38:34Z date_updated: 2025-06-25T05:38:34Z file_id: '19895' file_name: 2025_AnnalesHenriPoincare_Erdoes.pdf file_size: 977773 relation: main_file success: 1 file_date_updated: 2025-06-25T05:38:34Z has_accepted_license: '1' intvolume: ' 26' isi: 1 language: - iso: eng month: '06' oa: 1 oa_version: Published Version page: 1991-2033 project: - _id: 62796744-2b32-11ec-9570-940b20777f1d call_identifier: H2020 grant_number: '101020331' name: Random matrices beyond Wigner-Dyson-Mehta publication: Annales Henri Poincare publication_identifier: issn: - 1424-0637 publication_status: published publisher: Springer Nature quality_controlled: '1' related_material: record: - id: '17174' relation: earlier_version status: public - id: '20575' relation: dissertation_contains status: public - id: '19540' relation: dissertation_contains status: public scopus_import: '1' status: public title: Prethermalization for deformed Wigner matrices tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 317138e5-6ab7-11ef-aa6d-ffef3953e345 volume: 26 year: '2025' ... --- OA_type: closed access _id: '18765' abstract: - lang: eng 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. acknowledged_ssus: - _id: Bio 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.' alternative_title: - Methods in Molecular Biology article_processing_charge: No author: - first_name: Giselle T full_name: Cheung, Giselle T id: 471195F6-F248-11E8-B48F-1D18A9856A87 last_name: Cheung orcid: 0000-0001-8457-2572 - first_name: Florian full_name: Pauler, Florian id: 48EA0138-F248-11E8-B48F-1D18A9856A87 last_name: Pauler orcid: 0000-0002-7462-0048 - first_name: Simon full_name: Hippenmeyer, Simon id: 37B36620-F248-11E8-B48F-1D18A9856A87 last_name: Hippenmeyer orcid: 0000-0003-2279-1061 citation: 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. Lineage Tracing. Vol 2886. MIMB. New York, NY: Springer Nature; 2025:139-151. doi:10.1007/978-1-0716-4310-5_7' apa: 'Cheung, G. T., Pauler, F., & Hippenmeyer, S. (2025). Probing Cell-Type Specificity of Mutant Phenotype at Transcriptomic Level Using Mosaic Analysis with Double Markers (MADM). In J. Garcia-Marques & T. Lee (Eds.), Lineage Tracing (Vol. 2886, pp. 139–151). New York, NY: Springer Nature. https://doi.org/10.1007/978-1-0716-4310-5_7' 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 Lineage Tracing, edited by Jorge Garcia-Marques and Tzumin Lee, 2886:139–51. MIMB. New York, NY: Springer Nature, 2025. https://doi.org/10.1007/978-1-0716-4310-5_7.' 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 Lineage Tracing, vol. 2886, J. Garcia-Marques and T. Lee, Eds. New York, NY: Springer Nature, 2025, pp. 139–151.' 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.' mla: Cheung, Giselle T., et al. “Probing Cell-Type Specificity of Mutant Phenotype at Transcriptomic Level Using Mosaic Analysis with Double Markers (MADM).” Lineage Tracing, edited by Jorge Garcia-Marques and Tzumin Lee, vol. 2886, Springer Nature, 2025, pp. 139–51, doi:10.1007/978-1-0716-4310-5_7. 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. corr_author: '1' date_created: 2025-01-07T08:36:47Z date_published: 2025-01-03T00:00:00Z date_updated: 2025-04-14T07:43:46Z day: '03' department: - _id: SiHi doi: 10.1007/978-1-0716-4310-5_7 ec_funded: 1 editor: - first_name: Jorge full_name: Garcia-Marques, Jorge last_name: Garcia-Marques - first_name: Tzumin full_name: Lee, Tzumin last_name: Lee external_id: pmid: - '39745639' intvolume: ' 2886' language: - iso: eng month: '01' oa_version: None page: 139-151 place: New York, NY pmid: 1 project: - _id: 260C2330-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '754411' name: ISTplus - Postdoctoral Fellowships publication: Lineage Tracing publication_identifier: eisbn: - '9781071643105' eissn: - 1940-6029 isbn: - '9781071643099' issn: - 1064-3745 publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' series_title: MIMB status: public title: Probing Cell-Type Specificity of Mutant Phenotype at Transcriptomic Level Using Mosaic Analysis with Double Markers (MADM) type: book_chapter user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 2886 year: '2025' ... --- APC_amount: 12348 EUR OA_place: publisher OA_type: hybrid _id: '18778' abstract: - lang: eng 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. acknowledged_ssus: - _id: LifeSc - _id: EM-Fac - _id: ScienComp - _id: PreCl 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. article_processing_charge: Yes (in subscription journal) article_type: original author: - first_name: Katarina full_name: Tluckova, Katarina id: 4AC7D980-F248-11E8-B48F-1D18A9856A87 last_name: Tluckova - first_name: Beata M full_name: Kaczmarek, Beata M id: 36FA4AFA-F248-11E8-B48F-1D18A9856A87 last_name: Kaczmarek - first_name: Anita P full_name: Testa Salmazo, Anita P id: 41F1F098-F248-11E8-B48F-1D18A9856A87 last_name: Testa Salmazo - first_name: Carrie A full_name: Bernecky, Carrie A id: 2CB9DFE2-F248-11E8-B48F-1D18A9856A87 last_name: Bernecky orcid: 0000-0003-0893-7036 citation: ama: Tluckova K, Kaczmarek BM, Testa Salmazo AP, Bernecky C. Mechanism of mammalian transcriptional repression by noncoding RNA. Nature Structural & Molecular Biology. 2025;32:607-612. doi:10.1038/s41594-024-01448-7 apa: Tluckova, K., Kaczmarek, B. M., Testa Salmazo, A. P., & Bernecky, C. (2025). Mechanism of mammalian transcriptional repression by noncoding RNA. Nature Structural & Molecular Biology. Springer Nature. https://doi.org/10.1038/s41594-024-01448-7 chicago: Tluckova, Katarina, Beata M Kaczmarek, Anita P Testa Salmazo, and Carrie Bernecky. “Mechanism of Mammalian Transcriptional Repression by Noncoding RNA.” Nature Structural & Molecular Biology. Springer Nature, 2025. https://doi.org/10.1038/s41594-024-01448-7. ieee: K. Tluckova, B. M. Kaczmarek, A. P. Testa Salmazo, and C. Bernecky, “Mechanism of mammalian transcriptional repression by noncoding RNA,” Nature Structural & Molecular Biology, vol. 32. Springer Nature, pp. 607–612, 2025. ista: Tluckova K, Kaczmarek BM, Testa Salmazo AP, Bernecky C. 2025. Mechanism of mammalian transcriptional repression by noncoding RNA. Nature Structural & Molecular Biology. 32, 607–612. mla: Tluckova, Katarina, et al. “Mechanism of Mammalian Transcriptional Repression by Noncoding RNA.” Nature Structural & Molecular Biology, vol. 32, Springer Nature, 2025, pp. 607–12, doi:10.1038/s41594-024-01448-7. short: K. Tluckova, B.M. Kaczmarek, A.P. Testa Salmazo, C. Bernecky, Nature Structural & Molecular Biology 32 (2025) 607–612. corr_author: '1' date_created: 2025-01-08T11:20:20Z date_published: 2025-04-01T00:00:00Z date_updated: 2025-11-20T10:28:36Z day: '01' ddc: - '570' department: - _id: CaBe doi: 10.1038/s41594-024-01448-7 external_id: isi: - '001390268000001' pmid: - '39762629' file: - access_level: open_access checksum: 2919b30b271f395888e880076a680d73 content_type: application/pdf creator: dernst date_created: 2025-04-16T08:17:27Z date_updated: 2025-04-16T08:17:27Z file_id: '19573' file_name: 2025_NatureStrucMolBiol_Tluckova.pdf file_size: 9306639 relation: main_file success: 1 file_date_updated: 2025-04-16T08:17:27Z has_accepted_license: '1' intvolume: ' 32' isi: 1 language: - iso: eng month: '04' oa: 1 oa_version: Published Version page: 607-612 pmid: 1 project: - _id: c08a6700-5a5b-11eb-8a69-82a722b2bc30 grant_number: P34185 name: Regulation of mammalian transcription by noncoding RNA publication: Nature Structural & Molecular Biology publication_identifier: eissn: - 1545-9985 issn: - 1545-9993 publication_status: published publisher: Springer Nature quality_controlled: '1' related_material: record: - id: '14644' relation: earlier_version status: public scopus_import: '1' status: public title: Mechanism of mammalian transcriptional repression by noncoding RNA tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 32 year: '2025' ... --- DOAJ_listed: '1' OA_place: publisher OA_type: gold _id: '18820' 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.' 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.). article_number: '270' article_processing_charge: Yes article_type: original author: - first_name: Romina full_name: Wild, Romina last_name: Wild - first_name: Felix full_name: Wodaczek, Felix id: 8b4b6a9f-32b0-11ee-9fa8-bbe85e26258e last_name: Wodaczek orcid: 0009-0000-1457-795X - first_name: Vittorio full_name: Del Tatto, Vittorio last_name: Del Tatto - first_name: Bingqing full_name: Cheng, Bingqing id: cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9 last_name: Cheng orcid: 0000-0002-3584-9632 - first_name: Alessandro full_name: Laio, Alessandro last_name: Laio citation: ama: Wild R, Wodaczek F, Del Tatto V, Cheng B, Laio A. Automatic feature selection and weighting in molecular systems using Differentiable Information Imbalance. Nature Communications. 2025;16. doi:10.1038/s41467-024-55449-7 apa: 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. Springer Nature. https://doi.org/10.1038/s41467-024-55449-7 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.” Nature Communications. Springer Nature, 2025. https://doi.org/10.1038/s41467-024-55449-7. 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,” Nature Communications, vol. 16. Springer Nature, 2025. 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. mla: Wild, Romina, et al. “Automatic Feature Selection and Weighting in Molecular Systems Using Differentiable Information Imbalance.” Nature Communications, vol. 16, 270, Springer Nature, 2025, doi:10.1038/s41467-024-55449-7. short: R. Wild, F. Wodaczek, V. Del Tatto, B. Cheng, A. Laio, Nature Communications 16 (2025). date_created: 2025-01-12T23:04:00Z date_published: 2025-01-02T00:00:00Z date_updated: 2025-02-27T12:41:25Z day: '02' ddc: - '570' department: - _id: AnSa - _id: BiCh doi: 10.1038/s41467-024-55449-7 external_id: isi: - '001389959100009' pmid: - '39747013' file: - access_level: open_access checksum: b3d0f3568d9a87c494cf231a5324029a content_type: application/pdf creator: dernst date_created: 2025-01-14T06:59:25Z date_updated: 2025-01-14T06:59:25Z file_id: '18846' file_name: 2025_NatureComm_Wild.pdf file_size: 1216738 relation: main_file success: 1 file_date_updated: 2025-01-14T06:59:25Z has_accepted_license: '1' intvolume: ' 16' isi: 1 language: - iso: eng month: '01' oa: 1 oa_version: Published Version pmid: 1 publication: Nature Communications publication_identifier: eissn: - 2041-1723 publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: Automatic feature selection and weighting in molecular systems using Differentiable Information Imbalance 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) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 16 year: '2025' ... --- OA_place: repository OA_type: green _id: '18821' abstract: - lang: eng 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.' 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). article_number: '013303' article_processing_charge: No article_type: original arxiv: 1 author: - first_name: Fabian full_name: Brauneis, Fabian last_name: Brauneis - first_name: Hans Werner full_name: Hammer, Hans Werner last_name: Hammer - first_name: Stephanie M. full_name: Reimann, Stephanie M. last_name: Reimann - first_name: Artem full_name: Volosniev, Artem id: 37D278BC-F248-11E8-B48F-1D18A9856A87 last_name: Volosniev orcid: 0000-0003-0393-5525 citation: ama: Brauneis F, Hammer HW, Reimann SM, Volosniev A. Comparison of renormalized interactions using one-dimensional few-body systems as a testbed. Physical Review A. 2025;111(1). doi:10.1103/PhysRevA.111.013303 apa: Brauneis, F., Hammer, H. W., Reimann, S. M., & Volosniev, A. (2025). Comparison of renormalized interactions using one-dimensional few-body systems as a testbed. Physical Review A. American Physical Society. https://doi.org/10.1103/PhysRevA.111.013303 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.” Physical Review A. American Physical Society, 2025. https://doi.org/10.1103/PhysRevA.111.013303. 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,” Physical Review A, vol. 111, no. 1. American Physical Society, 2025. 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. mla: Brauneis, Fabian, et al. “Comparison of Renormalized Interactions Using One-Dimensional Few-Body Systems as a Testbed.” Physical Review A, vol. 111, no. 1, 013303, American Physical Society, 2025, doi:10.1103/PhysRevA.111.013303. short: F. Brauneis, H.W. Hammer, S.M. Reimann, A. Volosniev, Physical Review A 111 (2025). date_created: 2025-01-12T23:04:00Z date_published: 2025-01-03T00:00:00Z date_updated: 2025-02-27T12:41:58Z day: '03' department: - _id: MiLe doi: 10.1103/PhysRevA.111.013303 external_id: arxiv: - '2408.10052' isi: - '001398791400004' intvolume: ' 111' isi: 1 issue: '1' language: - iso: eng main_file_link: - open_access: '1' url: ' https://doi.org/10.48550/arXiv.2408.10052' month: '01' oa: 1 oa_version: Preprint publication: Physical Review A publication_identifier: eissn: - 2469-9934 issn: - 2469-9926 publication_status: published publisher: American Physical Society quality_controlled: '1' scopus_import: '1' status: public title: Comparison of renormalized interactions using one-dimensional few-body systems as a testbed type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 111 year: '2025' ... --- OA_place: publisher OA_type: hybrid _id: '18822' 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. 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. article_number: e70008 article_processing_charge: Yes (via OA deal) article_type: original author: - first_name: Victor full_name: Wang, Victor id: 76096395-aea4-11ed-a680-ab8ebbd3f1b9 last_name: Wang orcid: 0000-0002-0704-7026 citation: ama: Wang V. Diagonal cubic forms and the large sieve. Mathematika. 2025;71(1). doi:10.1112/mtk.70008 apa: Wang, V. (2025). Diagonal cubic forms and the large sieve. Mathematika. London Mathematical Society. https://doi.org/10.1112/mtk.70008 chicago: Wang, Victor. “Diagonal Cubic Forms and the Large Sieve.” Mathematika. London Mathematical Society, 2025. https://doi.org/10.1112/mtk.70008. ieee: V. Wang, “Diagonal cubic forms and the large sieve,” Mathematika, vol. 71, no. 1. London Mathematical Society, 2025. ista: Wang V. 2025. Diagonal cubic forms and the large sieve. Mathematika. 71(1), e70008. mla: Wang, Victor. “Diagonal Cubic Forms and the Large Sieve.” Mathematika, vol. 71, no. 1, e70008, London Mathematical Society, 2025, doi:10.1112/mtk.70008. short: V. Wang, Mathematika 71 (2025). corr_author: '1' date_created: 2025-01-12T23:04:01Z date_published: 2025-01-02T00:00:00Z date_updated: 2025-04-14T07:54:56Z day: '02' ddc: - '510' department: - _id: TiBr doi: 10.1112/mtk.70008 ec_funded: 1 external_id: isi: - '001388255500001' file: - access_level: open_access checksum: 700a8596b4bffce2320d074120962c22 content_type: application/pdf creator: dernst date_created: 2025-01-14T06:52:09Z date_updated: 2025-01-14T06:52:09Z file_id: '18845' file_name: 2025_Mathematika_Wang.pdf file_size: 309893 relation: main_file success: 1 file_date_updated: 2025-01-14T06:52:09Z has_accepted_license: '1' intvolume: ' 71' isi: 1 issue: '1' language: - iso: eng month: '01' oa: 1 oa_version: Published Version project: - _id: fc2ed2f7-9c52-11eb-aca3-c01059dda49c call_identifier: H2020 grant_number: '101034413' name: 'IST-BRIDGE: International postdoctoral program' publication: Mathematika publication_identifier: eissn: - 2041-7942 issn: - 0025-5793 publication_status: published publisher: London Mathematical Society quality_controlled: '1' scopus_import: '1' status: public title: Diagonal cubic forms and the large sieve tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 71 year: '2025' ... --- OA_place: publisher OA_type: hybrid _id: '18823' article_number: kiae651 article_processing_charge: Yes (in subscription journal) article_type: original author: - first_name: Dechang full_name: Cao, Dechang last_name: Cao - first_name: Joke G full_name: De Jaeger-Braet, Joke G id: 26bd38d3-c59a-11ee-a1af-d7a988cafcc5 last_name: De Jaeger-Braet citation: ama: 'Cao D, De Jaeger-Braet JG. Memory of maternal temperatures: DNA methylation alterations across generations. Plant Physiology. 2025;197(1). doi:10.1093/plphys/kiae651' apa: 'Cao, D., & De Jaeger-Braet, J. G. (2025). Memory of maternal temperatures: DNA methylation alterations across generations. Plant Physiology. Oxford University Press. https://doi.org/10.1093/plphys/kiae651' chicago: 'Cao, Dechang, and Joke G De Jaeger-Braet. “Memory of Maternal Temperatures: DNA Methylation Alterations across Generations.” Plant Physiology. Oxford University Press, 2025. https://doi.org/10.1093/plphys/kiae651.' ieee: 'D. Cao and J. G. De Jaeger-Braet, “Memory of maternal temperatures: DNA methylation alterations across generations,” Plant Physiology, vol. 197, no. 1. Oxford University Press, 2025.' ista: 'Cao D, De Jaeger-Braet JG. 2025. Memory of maternal temperatures: DNA methylation alterations across generations. Plant Physiology. 197(1), kiae651.' mla: 'Cao, Dechang, and Joke G. De Jaeger-Braet. “Memory of Maternal Temperatures: DNA Methylation Alterations across Generations.” Plant Physiology, vol. 197, no. 1, kiae651, Oxford University Press, 2025, doi:10.1093/plphys/kiae651.' short: D. Cao, J.G. De Jaeger-Braet, Plant Physiology 197 (2025). corr_author: '1' date_created: 2025-01-12T23:04:02Z date_published: 2025-01-01T00:00:00Z date_updated: 2025-07-15T08:18:19Z day: '01' ddc: - '580' department: - _id: XiFe doi: 10.1093/plphys/kiae651 external_id: isi: - '001382979900001' pmid: - '39691053' file: - access_level: open_access checksum: a9b2a12d7bc6174f27e28413e9c77a9c content_type: application/pdf creator: dernst date_created: 2025-07-15T08:17:25Z date_updated: 2025-07-15T08:17:25Z file_id: '20023' file_name: 2025_PlantPhysiology_Cao.pdf file_size: 1214018 relation: main_file success: 1 file_date_updated: 2025-07-15T08:17:25Z has_accepted_license: '1' intvolume: ' 197' isi: 1 issue: '1' language: - iso: eng month: '01' oa: 1 oa_version: Published Version pmid: 1 publication: Plant Physiology publication_identifier: eissn: - 1532-2548 publication_status: published publisher: Oxford University Press quality_controlled: '1' scopus_import: '1' status: public title: 'Memory of maternal temperatures: DNA methylation alterations across generations' tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 197 year: '2025' ... --- _id: '18837' abstract: - lang: eng 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. article_processing_charge: No author: - first_name: Johann G full_name: Danzl, Johann G id: 42EFD3B6-F248-11E8-B48F-1D18A9856A87 last_name: Danzl orcid: 0000-0001-8559-3973 - first_name: Caroline full_name: Kreuzinger, Caroline id: 382077BA-F248-11E8-B48F-1D18A9856A87 last_name: Kreuzinger citation: ama: Danzl JG, Kreuzinger C. Research Data for the publication “Super-resolution expansion microscopy in plant roots.” 2025. doi:10.15479/AT:ISTA:18837 apa: Danzl, J. G., & Kreuzinger, C. (2025). Research Data for the publication “Super-resolution expansion microscopy in plant roots.” Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:18837 chicago: Danzl, Johann G, and Caroline Kreuzinger. “Research Data for the Publication ‘Super-Resolution Expansion Microscopy in Plant Roots.’” Institute of Science and Technology Austria, 2025. https://doi.org/10.15479/AT:ISTA:18837. ieee: J. G. Danzl and C. Kreuzinger, “Research Data for the publication ‘Super-resolution expansion microscopy in plant roots.’” Institute of Science and Technology Austria, 2025. ista: Danzl JG, Kreuzinger C. 2025. Research Data for the publication ‘Super-resolution expansion microscopy in plant roots’, Institute of Science and Technology Austria, 10.15479/AT:ISTA:18837. mla: Danzl, Johann G., and Caroline Kreuzinger. Research Data for the Publication “Super-Resolution Expansion Microscopy in Plant Roots.” Institute of Science and Technology Austria, 2025, doi:10.15479/AT:ISTA:18837. short: J.G. Danzl, C. Kreuzinger, (2025). contributor: - contributor_type: researcher first_name: Michelle C id: 35A03822-F248-11E8-B48F-1D18A9856A87 last_name: Gallei orcid: 0000-0003-1286-7368 - contributor_type: researcher first_name: Sven M id: 45812BD4-F248-11E8-B48F-1D18A9856A87 last_name: Truckenbrodt - contributor_type: researcher first_name: Caroline id: 382077BA-F248-11E8-B48F-1D18A9856A87 last_name: Kreuzinger - contributor_type: researcher first_name: Syamala id: F8660870-D756-11E9-98C5-34DFE5697425 last_name: Inumella - contributor_type: researcher first_name: Vitali id: 7e146587-8972-11ed-ae7b-d7a32ea86a81 last_name: Vistunou - contributor_type: researcher first_name: Christoph M id: 4DF26D8C-F248-11E8-B48F-1D18A9856A87 last_name: Sommer orcid: 0000-0003-1216-9105 - contributor_type: researcher first_name: Mojtaba id: 3A0A06F4-F248-11E8-B48F-1D18A9856A87 last_name: Tavakoli orcid: 0000-0002-7667-6854 - contributor_type: researcher first_name: Nathalie id: 40E7F008-F248-11E8-B48F-1D18A9856A87 last_name: Agudelo Duenas - contributor_type: researcher first_name: Jakob id: 937696FA-C996-11E9-8C7C-CF13E6697425 last_name: Vorlaufer - contributor_type: researcher first_name: Wiebke id: 425C1CE8-F248-11E8-B48F-1D18A9856A87 last_name: Jahr - contributor_type: researcher first_name: Marek id: 6ac4636d-15b2-11ec-abd3-fb8df79972ae last_name: Randuch - contributor_type: researcher first_name: Alexander J id: 46A62C3A-F248-11E8-B48F-1D18A9856A87 last_name: Johnson orcid: 0000-0002-2739-8843 - contributor_type: researcher first_name: Eva id: 38F4F166-F248-11E8-B48F-1D18A9856A87 last_name: Benková orcid: 0000-0002-8510-9739 - contributor_type: researcher first_name: Jiří id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 - contributor_type: researcher first_name: Johann G id: 42EFD3B6-F248-11E8-B48F-1D18A9856A87 last_name: Danzl orcid: 0000-0001-8559-3973 corr_author: '1' date_created: 2025-01-13T09:51:29Z date_published: 2025-04-01T00:00:00Z date_updated: 2026-06-10T08:30:20Z department: - _id: JoDa doi: 10.15479/AT:ISTA:18837 file: - access_level: open_access checksum: a522d476ca1106163abb403ee156f6d0 content_type: image/tiff creator: ckreuzin date_created: 2025-03-07T10:09:15Z date_updated: 2025-03-07T10:09:15Z file_id: '19312' file_name: Fig 1D+2D PlantEx.tif file_size: 588707932 relation: main_file success: 1 - access_level: open_access checksum: 2d0e8279e85821de946fa8dbc4ed8134 content_type: image/tiff creator: ckreuzin date_created: 2025-03-07T10:29:22Z date_updated: 2025-03-07T10:29:22Z file_id: '19313' file_name: Fig 1D+2D Pre-expansion.tif file_size: 786998434 relation: main_file success: 1 - access_level: open_access checksum: 9b965e160fb7ec9900606994fe0c3045 content_type: image/tiff creator: ckreuzin date_created: 2025-03-07T10:31:59Z date_updated: 2025-03-07T10:31:59Z file_id: '19314' file_name: Fig 1E PlantEx.tif file_size: 108411 relation: main_file success: 1 - access_level: open_access checksum: 38857ce7d0b8c4b71937ca60eef539b3 content_type: image/tiff creator: ckreuzin date_created: 2025-03-07T10:32:02Z date_updated: 2025-03-07T10:32:02Z file_id: '19315' file_name: Fig 1E Pre-expansion.tif file_size: 114825 relation: main_file success: 1 - 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id: '19003' relation: used_in_publication status: public status: public title: Research Data for the publication "Super-resolution expansion microscopy in plant roots" tmp: image: /images/cc_by_nc.png legal_code_url: https://creativecommons.org/licenses/by-nc/4.0/legalcode name: Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0) short: CC BY-NC (4.0) type: research_data user_id: 68b8ca59-c5b3-11ee-8790-cd641c68093d year: '2025' ... --- DOAJ_listed: '1' OA_place: publisher OA_type: gold _id: '18848' 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. 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.). article_number: '457' article_processing_charge: Yes article_type: original author: - first_name: Rodrigo Fregoso full_name: Ocampo, Rodrigo Fregoso last_name: Ocampo - first_name: Jack Peter Kelly full_name: Bravo, Jack Peter Kelly id: 96aecfa5-8931-11ee-af30-aa6a5d6eee0e last_name: Bravo orcid: 0000-0003-0456-0753 - first_name: Tyler L. full_name: Dangerfield, Tyler L. last_name: Dangerfield - first_name: Isabel full_name: Nocedal, Isabel last_name: Nocedal - first_name: Samatar A. full_name: Jirde, Samatar A. last_name: Jirde - first_name: Lisa M. full_name: Alexander, Lisa M. last_name: Alexander - first_name: Nicole C. full_name: Thomas, Nicole C. last_name: Thomas - first_name: Anjali full_name: Das, Anjali last_name: Das - first_name: Sarah full_name: Nielson, Sarah last_name: Nielson - first_name: Kenneth A. full_name: Johnson, Kenneth A. last_name: Johnson - first_name: Christopher T. full_name: Brown, Christopher T. last_name: Brown - first_name: Cristina N. full_name: Butterfield, Cristina N. last_name: Butterfield - first_name: Daniela S.A. full_name: Goltsman, Daniela S.A. last_name: Goltsman - first_name: David W. full_name: Taylor, David W. last_name: Taylor citation: ama: Ocampo RF, Bravo JPK, Dangerfield TL, et al. DNA targeting by compact Cas9d and its resurrected ancestor. Nature Communications. 2025;16. doi:10.1038/s41467-024-55573-4 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. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-024-55573-4 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.” Nature Communications. Springer Nature, 2025. https://doi.org/10.1038/s41467-024-55573-4. ieee: R. F. Ocampo et al., “DNA targeting by compact Cas9d and its resurrected ancestor,” Nature Communications, vol. 16. Springer Nature, 2025. 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. mla: Ocampo, Rodrigo Fregoso, et al. “DNA Targeting by Compact Cas9d and Its Resurrected Ancestor.” Nature Communications, vol. 16, 457, Springer Nature, 2025, doi:10.1038/s41467-024-55573-4. 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). date_created: 2025-01-19T23:01:50Z date_published: 2025-01-07T00:00:00Z date_updated: 2025-07-03T11:58:22Z day: '07' ddc: - '570' department: - _id: JaBr doi: 10.1038/s41467-024-55573-4 external_id: pmid: - '39774105' file: - access_level: open_access checksum: 885e96690620790d5c9f188a1587b4cd content_type: application/pdf creator: dernst date_created: 2025-01-22T14:35:22Z date_updated: 2025-01-22T14:35:22Z file_id: '18869' file_name: 2025_NatureComm_Ocampo.pdf file_size: 5450660 relation: main_file success: 1 file_date_updated: 2025-01-22T14:35:22Z has_accepted_license: '1' intvolume: ' 16' language: - iso: eng month: '01' oa: 1 oa_version: Published Version pmid: 1 publication: Nature Communications publication_identifier: eissn: - 2041-1723 publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: DNA targeting by compact Cas9d and its resurrected ancestor tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 16 year: '2025' ... --- OA_place: publisher OA_type: hybrid _id: '18849' 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. 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). article_number: e2402925121 article_processing_charge: Yes (in subscription journal) article_type: original author: - first_name: Thomas R full_name: Sokolowski, Thomas R id: 3E999752-F248-11E8-B48F-1D18A9856A87 last_name: Sokolowski orcid: 0000-0002-1287-3779 - first_name: Thomas full_name: Gregor, Thomas last_name: Gregor - first_name: William full_name: Bialek, William last_name: Bialek - first_name: Gašper full_name: Tkačik, Gašper id: 3D494DCA-F248-11E8-B48F-1D18A9856A87 last_name: Tkačik orcid: 0000-0002-6699-1455 citation: ama: Sokolowski TR, Gregor T, Bialek W, Tkačik G. Deriving a genetic regulatory network from an optimization principle. Proceedings of the National Academy of Sciences. 2025;122(1). doi:10.1073/pnas.2402925121 apa: Sokolowski, T. R., Gregor, T., Bialek, W., & Tkačik, G. (2025). Deriving a genetic regulatory network from an optimization principle. Proceedings of the National Academy of Sciences. National Academy of Sciences. https://doi.org/10.1073/pnas.2402925121 chicago: Sokolowski, Thomas R, Thomas Gregor, William Bialek, and Gašper Tkačik. “Deriving a Genetic Regulatory Network from an Optimization Principle.” Proceedings of the National Academy of Sciences. National Academy of Sciences, 2025. https://doi.org/10.1073/pnas.2402925121. ieee: T. R. Sokolowski, T. Gregor, W. Bialek, and G. Tkačik, “Deriving a genetic regulatory network from an optimization principle,” Proceedings of the National Academy of Sciences, vol. 122, no. 1. National Academy of Sciences, 2025. 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. mla: Sokolowski, Thomas R., et al. “Deriving a Genetic Regulatory Network from an Optimization Principle.” Proceedings of the National Academy of Sciences, vol. 122, no. 1, e2402925121, National Academy of Sciences, 2025, doi:10.1073/pnas.2402925121. short: T.R. Sokolowski, T. Gregor, W. Bialek, G. Tkačik, Proceedings of the National Academy of Sciences 122 (2025). corr_author: '1' date_created: 2025-01-19T23:01:50Z date_published: 2025-01-07T00:00:00Z date_updated: 2026-02-16T12:26:51Z day: '07' ddc: - '570' department: - _id: GaTk doi: 10.1073/pnas.2402925121 external_id: isi: - '001392772400001' pmid: - '39752518' file: - access_level: open_access checksum: 8dbfc7d495413340225ebfae69b0cf9a content_type: application/pdf creator: dernst date_created: 2025-01-20T10:10:04Z date_updated: 2025-01-20T10:10:04Z file_id: '18862' file_name: 2025_PNAS_Sokolowski.pdf file_size: 19073585 relation: main_file success: 1 file_date_updated: 2025-01-20T10:10:04Z has_accepted_license: '1' intvolume: ' 122' isi: 1 issue: '1' language: - iso: eng month: '01' oa: 1 oa_version: Published Version pmid: 1 project: - _id: 254E9036-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P28844-B27 name: Biophysics of information processing in gene regulation - _id: 7bfe6a29-9f16-11ee-852c-c0da5e2045d9 grant_number: '101118866' name: 'Transcription in 4D: the dynamic interplay between chromatin architecture and gene expression in developing pseudo-embryos' - _id: 2665AAFE-B435-11E9-9278-68D0E5697425 grant_number: RGP0034/2018 name: Can evolution minimize spurious signaling crosstalk to reach optimal performance? publication: Proceedings of the National Academy of Sciences publication_identifier: eissn: - 1091-6490 issn: - 0027-8424 publication_status: published publisher: National Academy of Sciences quality_controlled: '1' scopus_import: '1' status: public title: Deriving a genetic regulatory network from an optimization principle 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) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 122 year: '2025' ... --- APC_amount: 3261,23 EUR OA_place: publisher OA_type: hybrid _id: '18850' abstract: - lang: eng text: 'Biophysical constraints limit the specificity with which transcription factors (TFs) can target regulatory DNA. While individual nontarget binding events may be low affinity, the sheer number of such interactions could present a challenge for gene regulation by degrading its precision or possibly leading to an erroneous induction state. Chromatin can prevent nontarget binding by rendering DNA physically inaccessible to TFs, at the cost of energy-consuming remodeling orchestrated by pioneer factors (PFs). Under what conditions and by how much can chromatin reduce regulatory errors on a global scale? We use a theoretical approach to compare two scenarios for gene regulation: one that relies on TF binding to free DNA alone and one that uses a combination of TFs and chromatin-regulating PFs to achieve desired gene expression patterns. We find, first, that chromatin effectively silences groups of genes that should be simultaneously OFF, thereby allowing more accurate graded control of expression for the remaining ON genes. Second, chromatin buffers the deleterious consequences of nontarget binding as the number of OFF genes grows, permitting a substantial expansion in regulatory complexity. Third, chromatin-based regulation productively co-opts nontarget TF binding for ON genes in order to establish a “leaky” baseline expression level, which targeted activator or repressor binding subsequently up- or down-modulates. Thus, on a global scale, using chromatin simultaneously alleviates pressure for high specificity of regulatory interactions and enables an increase in genome size with minimal impact on global expression error.' acknowledgement: M.L.P. was supported by the European Molecular Biology Laboratory (EMBL) Interdisciplinary Postdoc Programme (EIPOD4 fellowships), cofunded by Marie SkÅ‚odowska-Curie Actions (Grant Agreement No. 847543). J.C. and M.L.P. were supported by EMBL Core Funding and Theory@EMBL. This work is supported by European Research Council Grant DynaTrans (101118866) to G.T. We would like to thank the members of the J.C. and G.T. groups, especially Natalia Misunou, Michal Hledík, and Réka Borbély, for helpful feedback and discussion. We also thank EMBL IT Services for the use of high performance computing resources. article_number: e2411887121 article_processing_charge: No article_type: original author: - first_name: Mindy Liu full_name: Perkins, Mindy Liu last_name: Perkins - first_name: Justin full_name: Crocker, Justin last_name: Crocker - first_name: Gašper full_name: Tkačik, Gašper id: 3D494DCA-F248-11E8-B48F-1D18A9856A87 last_name: Tkačik orcid: 0000-0002-6699-1455 citation: ama: Perkins ML, Crocker J, Tkačik G. Chromatin enables precise and scalable gene regulation with factors of limited specificity. Proceedings of the National Academy of Sciences. 2025;122(1). doi:10.1073/pnas.2411887121 apa: Perkins, M. L., Crocker, J., & Tkačik, G. (2025). Chromatin enables precise and scalable gene regulation with factors of limited specificity. Proceedings of the National Academy of Sciences. National Academy of Sciences. https://doi.org/10.1073/pnas.2411887121 chicago: Perkins, Mindy Liu, Justin Crocker, and Gašper Tkačik. “Chromatin Enables Precise and Scalable Gene Regulation with Factors of Limited Specificity.” Proceedings of the National Academy of Sciences. National Academy of Sciences, 2025. https://doi.org/10.1073/pnas.2411887121. ieee: M. L. Perkins, J. Crocker, and G. Tkačik, “Chromatin enables precise and scalable gene regulation with factors of limited specificity,” Proceedings of the National Academy of Sciences, vol. 122, no. 1. National Academy of Sciences, 2025. ista: Perkins ML, Crocker J, Tkačik G. 2025. Chromatin enables precise and scalable gene regulation with factors of limited specificity. Proceedings of the National Academy of Sciences. 122(1), e2411887121. mla: Perkins, Mindy Liu, et al. “Chromatin Enables Precise and Scalable Gene Regulation with Factors of Limited Specificity.” Proceedings of the National Academy of Sciences, vol. 122, no. 1, e2411887121, National Academy of Sciences, 2025, doi:10.1073/pnas.2411887121. short: M.L. Perkins, J. Crocker, G. Tkačik, Proceedings of the National Academy of Sciences 122 (2025). corr_author: '1' date_created: 2025-01-19T23:01:51Z date_published: 2025-01-07T00:00:00Z date_updated: 2026-05-06T12:43:59Z day: '07' ddc: - '570' department: - _id: GaTk doi: 10.1073/pnas.2411887121 external_id: isi: - '001392765300001' pmid: - '39793086' file: - access_level: open_access checksum: 86a8d25a6e282aeb4128f1d0b86ff911 content_type: application/pdf creator: dernst date_created: 2025-01-20T09:38:32Z date_updated: 2025-01-20T09:38:32Z file_id: '18859' file_name: 2025_PNAS_Perkins.pdf file_size: 30943709 relation: main_file success: 1 file_date_updated: 2025-01-20T09:38:32Z has_accepted_license: '1' intvolume: ' 122' isi: 1 issue: '1' language: - iso: eng month: '01' oa: 1 oa_version: Published Version pmid: 1 project: - _id: 7bfe6a29-9f16-11ee-852c-c0da5e2045d9 grant_number: '101118866' name: 'Transcription in 4D: the dynamic interplay between chromatin architecture and gene expression in developing pseudo-embryos' publication: Proceedings of the National Academy of Sciences publication_identifier: eissn: - 1091-6490 issn: - 0027-8424 publication_status: published publisher: National Academy of Sciences quality_controlled: '1' related_material: link: - relation: software url: https://github.com/officerredshirt/network_crosstalk scopus_import: '1' status: public title: Chromatin enables precise and scalable gene regulation with factors of limited specificity 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) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 122 year: '2025' ... --- OA_place: publisher OA_type: hybrid _id: '18851' abstract: - lang: eng text: 'We present volume-limited samples of cataclysmic variables (CVs) and AM CVn binaries jointly selected from SRG/eROSITA eRASS1 and Gaia DR3 using an X-ray + optical color–color diagram (the "X-ray Main Sequence"). This tool identifies all CV subtypes, including magnetic and low-accretion rate systems, in contrast to most previous surveys. We find 23 CVs, 3 of which are AM CVns, out to 150 pc in the Western Galactic Hemisphere. Our 150 pc sample is spectroscopically verified and complete down to LX = 1.3 × 1029 erg s−1 in the 0.2–2.3 keV band, and we also present CV candidates out to 300 pc and 1000 pc. We discovered two previously unknown systems in our 150 pc sample: the third nearest AM CVn and a magnetic period bouncer. We find the mean LX of CVs to be 〈LX〉 ≈ 4.6 × 1030 erg s−1, in contrast to previous surveys which yielded 〈LX〉 ∼ 1031−1032 erg s−1. We construct X-ray luminosity functions that, for the first time, flatten out at LX ∼ 1030 erg s−1. We infer average number, mass, and luminosity densities of ρN,CV = (3.7 ± 0.7) × 10−6pc−3, (math formular), and (math formular), respectively, in the solar neighborhood. Our uniform selection method also allows us to place meaningful estimates on the space density of AM CVns, ρN,AM CVn = (5.5 ± 3.7) × 10−7 pc−3. Magnetic CVs and period bouncers make up 35% and 25% of our sample, respectively. This work, through a novel discovery technique, shows that the observed number densities of CVs and AM CVns, as well as the fraction of period bouncers, are still in tension with population synthesis estimates.' acknowledgement: "We thank Roman Krivonos for insightful feedback, Kevin Burdge, Dovi Poznanski, and Jim Fuller for useful discussions, and Sunny Wong for providing AM CVn evolutionary models. A.C.R. acknowledges support from an NSF Graduate Fellowship.\r\n\r\nA.C.R. thanks the LSST-DA Data Science Fellowship Program, which is funded by LSST-DA, the Brinson Foundation, and the Moore Foundation; his participation in the program has benefited this work. RLO is a Research Fellow of the Brazilian institution CNPq (PQ-315632/2023-2).\r\n\r\nThis work is based on data from eROSITA, the soft X-ray instrument aboard SRG, a joint Russian-German science mission supported by the Russian Space Agency (Roskosmos), in the interests of the Russian Academy of Sciences represented by its Space Research Institute (IKI), and the Deutsches Zentrum für Luft- und Raumfahrt (DLR). The SRG spacecraft was built by Lavochkin Association (NPOL) and its subcontractors, and is operated by NPOL with support from the Max Planck Institute for Extraterrestrial Physics (MPE). The development and construction of the eROSITA X-ray instrument was led by MPE, with contributions from the Dr. Karl Remeis Observatory Bamberg & ECAP (FAU Erlangen-Nuernberg), the University of Hamburg Observatory, the Leibniz Institute for Astrophysics Potsdam (AIP), and the Institute for Astronomy and Astrophysics of the University of Tübingen, with the support of DLR and the Max Planck Society. The Argelander Institute for Astronomy of the University of Bonn and the Ludwig Maximilians Universität Munich also participated in the science preparation for eROSITA.\r\n\r\nThis work presents results from the European Space Agency (ESA) space mission Gaia. Gaia data are being processed by the Gaia Data Processing and Analysis Consortium (DPAC). Funding for the DPAC is provided by national institutions, in particular the institutions participating in the Gaia MultiLateral Agreement (MLA). The Gaia mission website is https://www.cosmos.esa.int/gaia. The Gaia archive website is https://archives.esac.esa.int/gaia.\r\n\r\nSome of the data presented herein were obtained at Keck Observatory, which is a private 501(c)3 non-profit organization operated as a scientific partnership among the California Institute of Technology, the University of California, and the National Aeronautics and Space Administration. The Observatory was made possible by the generous financial support of the W. M. Keck Foundation. The authors wish to recognize and acknowledge the very significant cultural role and reverence that the summit of Maunakea has always had within the Native Hawaiian community. We are most fortunate to have the opportunity to conduct observations from this mountain. We are also grateful to the staff of Palomar Observatory and that of Lick Observatory for their assistance in carrying out observations used in this work.\r\n\r\nBased on observations obtained with the Samuel Oschin Telescope 48 inch and the 60 inch Telescope at the Palomar Observatory as part of the Zwicky Transient Facility project. ZTF is supported by the National Science Foundation under grants No. AST-1440341 and AST-2034437 and a collaboration including current partners Caltech, IPAC, the Weizmann Institute of Science, the Oskar Klein Center at Stockholm University, the University of Maryland, Deutsches Elektronen-Synchrotron and Humboldt University, the TANGO Consortium of Taiwan, the University of Wisconsin at Milwaukee, Trinity College Dublin, Lawrence Livermore National Laboratories, IN2P3, University of Warwick, Ruhr University Bochum, Northwestern University and former partners the University of Washington, Los Alamos National Laboratories, and Lawrence Berkeley National Laboratories. Operations are conducted by COO, IPAC, and UW.\r\n\r\nSoftware: used: Python and the following libraries: matplotlib (Hunter 2007), scipy (Virtanen et al. 2020), astropy (Astropy Collaboration et al. 2013), numpy (van der Walt et al. 2011). PypeIt (Prochaska et al. 2020), lpipe (Perley 2019), and Tool for OPerations on Catalogues And Tables (TOPCAT) (Taylor 2005)." article_number: '014201' article_processing_charge: No article_type: original arxiv: 1 author: - first_name: Antonio C. full_name: Rodriguez, Antonio C. last_name: Rodriguez - first_name: Kareem full_name: El-Badry, Kareem last_name: El-Badry - first_name: Valery full_name: Suleimanov, Valery last_name: Suleimanov - first_name: Anna F. full_name: Pala, Anna F. last_name: Pala - first_name: Shrinivas R. full_name: Kulkarni, Shrinivas R. last_name: Kulkarni - first_name: Boris full_name: Gaensicke, Boris last_name: Gaensicke - first_name: Kaya full_name: Mori, Kaya last_name: Mori - first_name: R. Michael full_name: Rich, R. Michael last_name: Rich - first_name: Arnab full_name: Sarkar, Arnab last_name: Sarkar - first_name: Tong full_name: Bao, Tong last_name: Bao - first_name: Raimundo Lopes full_name: De Oliveira, Raimundo Lopes last_name: De Oliveira - first_name: Gavin full_name: Ramsay, Gavin last_name: Ramsay - first_name: Paula full_name: Szkody, Paula last_name: Szkody - first_name: Matthew full_name: Graham, Matthew last_name: Graham - first_name: Thomas A. full_name: Prince, Thomas A. last_name: Prince - first_name: Ilaria full_name: Caiazzo, Ilaria id: 8ae5b6e7-2a03-11ee-914d-b58ed7a3b47d last_name: Caiazzo orcid: 0000-0002-4770-5388 - first_name: Zachary P. full_name: Vanderbosch, Zachary P. last_name: Vanderbosch - first_name: Jan Van full_name: Roestel, Jan Van last_name: Roestel - first_name: Kaustav K. full_name: Das, Kaustav K. last_name: Das - first_name: Yu Jing full_name: Qin, Yu Jing last_name: Qin - first_name: Mansi M. full_name: Kasliwal, Mansi M. last_name: Kasliwal - first_name: Avery full_name: Wold, Avery last_name: Wold - first_name: Steven L. full_name: Groom, Steven L. last_name: Groom - first_name: Daniel full_name: Reiley, Daniel last_name: Reiley - first_name: Reed full_name: Riddle, Reed last_name: Riddle citation: ama: 'Rodriguez AC, El-Badry K, Suleimanov V, et al. Cataclysmic variables and AM CVn binaries in SRG/eROSITA + Gaia: Volume limited samples, X-ray luminosity functions, and space densities. Publications of the Astronomical Society of the Pacific. 2025;137(1). doi:10.1088/1538-3873/ada185' apa: 'Rodriguez, A. C., El-Badry, K., Suleimanov, V., Pala, A. F., Kulkarni, S. R., Gaensicke, B., … Riddle, R. (2025). Cataclysmic variables and AM CVn binaries in SRG/eROSITA + Gaia: Volume limited samples, X-ray luminosity functions, and space densities. Publications of the Astronomical Society of the Pacific. IOP Publishing. https://doi.org/10.1088/1538-3873/ada185' chicago: 'Rodriguez, Antonio C., Kareem El-Badry, Valery Suleimanov, Anna F. Pala, Shrinivas R. Kulkarni, Boris Gaensicke, Kaya Mori, et al. “Cataclysmic Variables and AM CVn Binaries in SRG/EROSITA + Gaia: Volume Limited Samples, X-Ray Luminosity Functions, and Space Densities.” Publications of the Astronomical Society of the Pacific. IOP Publishing, 2025. https://doi.org/10.1088/1538-3873/ada185.' ieee: 'A. C. Rodriguez et al., “Cataclysmic variables and AM CVn binaries in SRG/eROSITA + Gaia: Volume limited samples, X-ray luminosity functions, and space densities,” Publications of the Astronomical Society of the Pacific, vol. 137, no. 1. IOP Publishing, 2025.' ista: 'Rodriguez AC, El-Badry K, Suleimanov V, Pala AF, Kulkarni SR, Gaensicke B, Mori K, Rich RM, Sarkar A, Bao T, De Oliveira RL, Ramsay G, Szkody P, Graham M, Prince TA, Caiazzo I, Vanderbosch ZP, Roestel JV, Das KK, Qin YJ, Kasliwal MM, Wold A, Groom SL, Reiley D, Riddle R. 2025. Cataclysmic variables and AM CVn binaries in SRG/eROSITA + Gaia: Volume limited samples, X-ray luminosity functions, and space densities. Publications of the Astronomical Society of the Pacific. 137(1), 014201.' mla: 'Rodriguez, Antonio C., et al. “Cataclysmic Variables and AM CVn Binaries in SRG/EROSITA + Gaia: Volume Limited Samples, X-Ray Luminosity Functions, and Space Densities.” Publications of the Astronomical Society of the Pacific, vol. 137, no. 1, 014201, IOP Publishing, 2025, doi:10.1088/1538-3873/ada185.' short: A.C. Rodriguez, K. El-Badry, V. Suleimanov, A.F. Pala, S.R. Kulkarni, B. Gaensicke, K. Mori, R.M. Rich, A. Sarkar, T. Bao, R.L. De Oliveira, G. Ramsay, P. Szkody, M. Graham, T.A. Prince, I. Caiazzo, Z.P. Vanderbosch, J.V. Roestel, K.K. Das, Y.J. Qin, M.M. Kasliwal, A. Wold, S.L. Groom, D. Reiley, R. Riddle, Publications of the Astronomical Society of the Pacific 137 (2025). date_created: 2025-01-19T23:01:51Z date_published: 2025-01-01T00:00:00Z date_updated: 2025-02-27T12:46:32Z day: '01' ddc: - '520' department: - _id: IlCa doi: 10.1088/1538-3873/ada185 external_id: arxiv: - '2408.16053' isi: - '001393204700001' file: - access_level: open_access checksum: 02a9be04a6704fc272ed5a976e5fa8c5 content_type: application/pdf creator: dernst date_created: 2025-01-20T09:52:34Z date_updated: 2025-01-20T09:52:34Z file_id: '18860' file_name: 2025_PASP_Rodriguez.pdf file_size: 5155631 relation: main_file success: 1 file_date_updated: 2025-01-20T09:52:34Z has_accepted_license: '1' intvolume: ' 137' isi: 1 issue: '1' language: - iso: eng license: https://creativecommons.org/licenses/by/3.0/ month: '01' oa: 1 oa_version: Published Version publication: Publications of the Astronomical Society of the Pacific publication_identifier: issn: - 0004-6280 publication_status: published publisher: IOP Publishing quality_controlled: '1' scopus_import: '1' status: public title: 'Cataclysmic variables and AM CVn binaries in SRG/eROSITA + Gaia: Volume limited samples, X-ray luminosity functions, and space densities' tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/3.0/legalcode name: Creative Commons Attribution 3.0 Unported (CC BY 3.0) short: CC BY (3.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 137 year: '2025' ... --- OA_place: publisher OA_type: diamond _id: '18852' abstract: - lang: eng text: 'Recent observations have found a growing number of hypervelocity stars with speeds of ≈1500 − 2500 km s−1 that could have only been produced through thermonuclear supernovae in white dwarf binaries. Most of the observed hypervelocity runaways in this class display a surprising inflated structure: their current radii are roughly an order of magnitude greater than they would have been as white dwarfs filling their Roche lobe. While many simulations exist studying the dynamical phase leading to supernova detonation in these systems, no detailed calculations of the long-term structure of the runaways have yet been performed. We used an existing AREPO hydrodynamical simulation of a supernova in a white dwarf binary as a starting point for the evolution of these stars with the one-dimensional stellar evolution code MESA. We show that the supernova shock is not energetic enough to inflate the white dwarf over timescales longer than a few thousand years, significantly shorter than the 105 − 6 year lifetimes inferred for observed hypervelocity runaways. Although they experience a shock from a supernova less than ≈0.02 R⊙ away, our models do not experience significant interior heating, and all contract back to radii of around 0.01 R⊙ within about 104 years. Explaining the observed inflated states requires either an additional source of significant heating or some other physics that is not yet accounted for in the subsequent evolution.' acknowledgement: 'This project was originally started as part of the Kavli Summer Program which took place in the Max Planck Institute for Astrophysics in Garching in July 2023, supported by the Kavli Foundation. We are grateful to Stephen Justham, Selma de Mink, and Jim Fuller for enriching discussions. We would like to thank the anonymous referee for their helpful report. A.B. was supported by the Deutsche Forschungsgemeinschaft (DFG) through grant GE2506/18-1. K.J.S. was supported by NASA through the Astrophysics Theory Program (80NSSC20K0544) and by NASA/ESA Hubble Space Telescope programs #15871 and #15918. W.E.K. was supported by NSF Grants OAC-2311323, AST-2206523, and NASA/ESA HST-AR-Theory HSTAR-16613.002-A. K.E. was supported in part by HST-GO-17441.001-A. AB and ASR would like to thank Rob Farmer for his support with PyMESA.' article_number: A114 article_processing_charge: No article_type: original arxiv: 1 author: - first_name: Aakash full_name: Bhat, Aakash last_name: Bhat - first_name: Evan B. full_name: Bauer, Evan B. last_name: Bauer - first_name: Rüdiger full_name: Pakmor, Rüdiger last_name: Pakmor - first_name: Ken J. full_name: Shen, Ken J. last_name: Shen - first_name: Ilaria full_name: Caiazzo, Ilaria id: 8ae5b6e7-2a03-11ee-914d-b58ed7a3b47d last_name: Caiazzo orcid: 0000-0002-4770-5388 - first_name: Abinaya Swaruba full_name: Rajamuthukumar, Abinaya Swaruba last_name: Rajamuthukumar - first_name: Kareem full_name: El-Badry, Kareem last_name: El-Badry - first_name: Wolfgang E. full_name: Kerzendorf, Wolfgang E. last_name: Kerzendorf citation: ama: Bhat A, Bauer EB, Pakmor R, et al. Supernova shocks cannot explain the inflated state of hypervelocity runaways from white dwarf binaries. Astronomy & Astrophysics. 2025;693(1). doi:10.1051/0004-6361/202451371 apa: Bhat, A., Bauer, E. B., Pakmor, R., Shen, K. J., Caiazzo, I., Rajamuthukumar, A. S., … Kerzendorf, W. E. (2025). Supernova shocks cannot explain the inflated state of hypervelocity runaways from white dwarf binaries. Astronomy & Astrophysics. EDP Sciences. https://doi.org/10.1051/0004-6361/202451371 chicago: Bhat, Aakash, Evan B. Bauer, Rüdiger Pakmor, Ken J. Shen, Ilaria Caiazzo, Abinaya Swaruba Rajamuthukumar, Kareem El-Badry, and Wolfgang E. Kerzendorf. “Supernova Shocks Cannot Explain the Inflated State of Hypervelocity Runaways from White Dwarf Binaries.” Astronomy & Astrophysics. EDP Sciences, 2025. https://doi.org/10.1051/0004-6361/202451371. ieee: A. Bhat et al., “Supernova shocks cannot explain the inflated state of hypervelocity runaways from white dwarf binaries,” Astronomy & Astrophysics, vol. 693, no. 1. EDP Sciences, 2025. ista: Bhat A, Bauer EB, Pakmor R, Shen KJ, Caiazzo I, Rajamuthukumar AS, El-Badry K, Kerzendorf WE. 2025. Supernova shocks cannot explain the inflated state of hypervelocity runaways from white dwarf binaries. Astronomy & Astrophysics. 693(1), A114. mla: Bhat, Aakash, et al. “Supernova Shocks Cannot Explain the Inflated State of Hypervelocity Runaways from White Dwarf Binaries.” Astronomy & Astrophysics, vol. 693, no. 1, A114, EDP Sciences, 2025, doi:10.1051/0004-6361/202451371. short: A. Bhat, E.B. Bauer, R. Pakmor, K.J. Shen, I. Caiazzo, A.S. Rajamuthukumar, K. El-Badry, W.E. Kerzendorf, Astronomy & Astrophysics 693 (2025). date_created: 2025-01-19T23:01:51Z date_published: 2025-01-07T00:00:00Z date_updated: 2026-02-16T12:08:05Z day: '07' ddc: - '520' department: - _id: IlCa doi: 10.1051/0004-6361/202451371 external_id: arxiv: - '2407.03424' isi: - '001406577300001' file: - access_level: open_access checksum: e532b9c8123c29cfb0ee758e6d00453c content_type: application/pdf creator: dernst date_created: 2025-01-20T09:57:00Z date_updated: 2025-01-20T09:57:00Z file_id: '18861' file_name: 2025_AstronomyAstrophysics_Bhat.pdf file_size: 1692527 relation: main_file success: 1 file_date_updated: 2025-01-20T09:57:00Z has_accepted_license: '1' intvolume: ' 693' isi: 1 issue: '1' language: - iso: eng month: '01' oa: 1 oa_version: Published Version publication: Astronomy & Astrophysics publication_identifier: eissn: - 1432-0746 issn: - 0004-6361 publication_status: published publisher: EDP Sciences quality_controlled: '1' scopus_import: '1' status: public title: Supernova shocks cannot explain the inflated state of hypervelocity runaways from white dwarf binaries tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 693 year: '2025' ...