[{"date_created":"2024-12-22T23:01:47Z","article_type":"original","year":"2025","doi":"10.1016/j.matlet.2024.137869","publication_status":"published","intvolume":"       382","author":[{"first_name":"Neelima","last_name":"Mahato","full_name":"Mahato, Neelima"},{"full_name":"Singh, Saurabh","id":"12d625da-9cb3-11ed-9667-af09d37d3f0a","orcid":"0000-0003-2209-5269","first_name":"Saurabh","last_name":"Singh"},{"last_name":"Sreekanth","first_name":"T. V.M.","full_name":"Sreekanth, T. V.M."},{"full_name":"Yoo, Kisoo","first_name":"Kisoo","last_name":"Yoo"},{"first_name":"Jonghoon","last_name":"Kim","full_name":"Kim, Jonghoon"}],"language":[{"iso":"eng"}],"department":[{"_id":"MaIb"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"18701","publication":"Materials Letters","day":"01","title":"In-situ engineered highly-crystalline Polythiophene empowered electrochemical capacitor-II: Anomalous electrochemical charge storage behavior of Polythiophene-rGO composite","acknowledgement":"This work was partly supported by the Institute of Information & Communications Technology Planning & Evaluation (IITP) grant funded by the Korea government (MSIT) (No.RS-2021-II210077) and Korea Institute of Energy Technology Evaluation and Planning (KETEP) grant funded by the Korea government (MOTIE)(RS-2024-00398346, ESS BigData-Based O&M and Asset Management Technical Manpower Training).","isi":1,"date_published":"2025-03-01T00:00:00Z","article_processing_charge":"No","volume":382,"month":"03","external_id":{"isi":["001433664000001"]},"quality_controlled":"1","date_updated":"2025-05-19T14:05:22Z","publisher":"Elsevier","oa_version":"None","citation":{"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.","short":"N. Mahato, S. Singh, T.V.M. Sreekanth, K. Yoo, J. Kim, Materials Letters 382 (2025).","mla":"Mahato, Neelima, et al. “In-Situ Engineered Highly-Crystalline Polythiophene Empowered Electrochemical Capacitor-II: Anomalous Electrochemical Charge Storage Behavior of Polythiophene-RGO Composite.” <i>Materials Letters</i>, vol. 382, 137869, Elsevier, 2025, doi:<a href=\"https://doi.org/10.1016/j.matlet.2024.137869\">10.1016/j.matlet.2024.137869</a>.","chicago":"Mahato, Neelima, Saurabh Singh, T. V.M. Sreekanth, Kisoo Yoo, and Jonghoon Kim. “In-Situ Engineered Highly-Crystalline Polythiophene Empowered Electrochemical Capacitor-II: Anomalous Electrochemical Charge Storage Behavior of Polythiophene-RGO Composite.” <i>Materials Letters</i>. Elsevier, 2025. <a href=\"https://doi.org/10.1016/j.matlet.2024.137869\">https://doi.org/10.1016/j.matlet.2024.137869</a>.","apa":"Mahato, N., Singh, S., Sreekanth, T. V. M., Yoo, K., &#38; Kim, J. (2025). In-situ engineered highly-crystalline Polythiophene empowered electrochemical capacitor-II: Anomalous electrochemical charge storage behavior of Polythiophene-rGO composite. <i>Materials Letters</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.matlet.2024.137869\">https://doi.org/10.1016/j.matlet.2024.137869</a>","ama":"Mahato N, Singh S, Sreekanth TVM, Yoo K, Kim J. In-situ engineered highly-crystalline Polythiophene empowered electrochemical capacitor-II: Anomalous electrochemical charge storage behavior of Polythiophene-rGO composite. <i>Materials Letters</i>. 2025;382. doi:<a href=\"https://doi.org/10.1016/j.matlet.2024.137869\">10.1016/j.matlet.2024.137869</a>","ieee":"N. Mahato, S. Singh, T. V. M. Sreekanth, K. Yoo, and J. Kim, “In-situ engineered highly-crystalline Polythiophene empowered electrochemical capacitor-II: Anomalous electrochemical charge storage behavior of Polythiophene-rGO composite,” <i>Materials Letters</i>, vol. 382. Elsevier, 2025."},"article_number":"137869","scopus_import":"1","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."}],"publication_identifier":{"eissn":["1873-4979"],"issn":["0167-577X"]},"type":"journal_article","status":"public","OA_type":"closed access"},{"oa_version":"None","citation":{"ista":"Shu H, Zhao M, Lu S, Wan S, Genç A, Huang L, Ibáñez M, Lim KH, Hong M, Liu Y. 2025. Influence of surface engineering on the transport properties of lead sulfide nanomaterials. Journal of Colloid and Interface Science. 683, 703–712.","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.","mla":"Shu, Haibo, et al. “Influence of Surface Engineering on the Transport Properties of Lead Sulfide Nanomaterials.” <i>Journal of Colloid and Interface Science</i>, vol. 683, Elsevier, 2025, pp. 703–12, doi:<a href=\"https://doi.org/10.1016/j.jcis.2024.12.067\">10.1016/j.jcis.2024.12.067</a>.","chicago":"Shu, Haibo, Mingjun Zhao, Shaoqing Lu, Shanhong Wan, Aziz Genç, Lulu Huang, Maria Ibáñez, Khak Ho Lim, Min Hong, and Yu Liu. “Influence of Surface Engineering on the Transport Properties of Lead Sulfide Nanomaterials.” <i>Journal of Colloid and Interface Science</i>. Elsevier, 2025. <a href=\"https://doi.org/10.1016/j.jcis.2024.12.067\">https://doi.org/10.1016/j.jcis.2024.12.067</a>.","apa":"Shu, H., Zhao, M., Lu, S., Wan, S., Genç, A., Huang, L., … Liu, Y. (2025). Influence of surface engineering on the transport properties of lead sulfide nanomaterials. <i>Journal of Colloid and Interface Science</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.jcis.2024.12.067\">https://doi.org/10.1016/j.jcis.2024.12.067</a>","ama":"Shu H, Zhao M, Lu S, et al. Influence of surface engineering on the transport properties of lead sulfide nanomaterials. <i>Journal of Colloid and Interface Science</i>. 2025;683:703-712. doi:<a href=\"https://doi.org/10.1016/j.jcis.2024.12.067\">10.1016/j.jcis.2024.12.067</a>","ieee":"H. Shu <i>et al.</i>, “Influence of surface engineering on the transport properties of lead sulfide nanomaterials,” <i>Journal of Colloid and Interface Science</i>, vol. 683. Elsevier, pp. 703–712, 2025."},"scopus_import":"1","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."}],"publisher":"Elsevier","OA_type":"closed access","status":"public","publication_identifier":{"eissn":["1095-7103"],"issn":["0021-9797"]},"type":"journal_article","volume":683,"isi":1,"acknowledgement":"Y.L. acknowledges funding from the National Natural Science Foundation of China (NSFC) (Grants No. 22209034), the Innovation and Entrepreneurship Project of Overseas Returnees in Anhui Province (Grant No. 2022LCX002) and the Fundamental Research Funds for the Central Universities (JZ2024HGTB0239). M.I. acknowledges financial support from ISTA and the Werner Siemens Foundation. K.H.L. acknowledges financial support from the National Natural Science Foundation of China (NSFC) (Grant No. 22208293). M.H acknowledges funding from Australian Research Council (FT230100316 and IH200100035) and iLAuNCH, Trailblazer Universities Program. L. H. and S. W. acknowledge the Fundamental Research Funds for the Central Universities (JZ2023HGTA0179, JZ2024HGTA0170).","date_published":"2025-04-01T00:00:00Z","article_processing_charge":"No","title":"Influence of surface engineering on the transport properties of lead sulfide nanomaterials","quality_controlled":"1","date_updated":"2025-05-19T14:03:54Z","external_id":{"isi":["001393340800001"],"pmid":["39706089"]},"month":"04","pmid":1,"department":[{"_id":"MaIb"}],"_id":"18707","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","page":"703-712","day":"01","publication":"Journal of Colloid and Interface Science","year":"2025","article_type":"original","date_created":"2024-12-29T23:01:56Z","author":[{"full_name":"Shu, Haibo","last_name":"Shu","first_name":"Haibo"},{"first_name":"Mingjun","last_name":"Zhao","full_name":"Zhao, Mingjun"},{"full_name":"Lu, Shaoqing","last_name":"Lu","first_name":"Shaoqing"},{"full_name":"Wan, Shanhong","last_name":"Wan","first_name":"Shanhong"},{"full_name":"Genç, Aziz","last_name":"Genç","first_name":"Aziz"},{"full_name":"Huang, Lulu","first_name":"Lulu","last_name":"Huang"},{"orcid":"0000-0001-5013-2843","first_name":"Maria","last_name":"Ibáñez","full_name":"Ibáñez, Maria","id":"43C61214-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Khak Ho","last_name":"Lim","full_name":"Lim, Khak Ho"},{"full_name":"Hong, Min","first_name":"Min","last_name":"Hong"},{"id":"2A70014E-F248-11E8-B48F-1D18A9856A87","full_name":"Liu, Yu","first_name":"Yu","last_name":"Liu","orcid":"0000-0001-7313-6740"}],"language":[{"iso":"eng"}],"intvolume":"       683","project":[{"name":"HighTE: The Werner Siemens Laboratory for the High Throughput Discovery of Semiconductors for Waste Heat Recovery","_id":"9B8F7476-BA93-11EA-9121-9846C619BF3A"}],"doi":"10.1016/j.jcis.2024.12.067","publication_status":"published"},{"publisher":"Royal Society of Chemistry","scopus_import":"1","abstract":[{"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.","lang":"eng"}],"citation":{"ieee":"M. Hrast, M. Ljubotina, and M. Zitnik, “Ab initio Auger spectrum of the ultrafast dissociating 2p3/2−1σ* resonance in HCl,” <i>Physical Chemistry Chemical Physics</i>, vol. 27, no. 3. Royal Society of Chemistry, pp. 1473–1482, 2025.","ama":"Hrast M, Ljubotina M, Zitnik M. Ab initio Auger spectrum of the ultrafast dissociating 2p3/2−1σ* resonance in HCl. <i>Physical Chemistry Chemical Physics</i>. 2025;27(3):1473-1482. doi:<a href=\"https://doi.org/10.1039/d4cp03727h\">10.1039/d4cp03727h</a>","apa":"Hrast, M., Ljubotina, M., &#38; Zitnik, M. (2025). Ab initio Auger spectrum of the ultrafast dissociating 2p3/2−1σ* resonance in HCl. <i>Physical Chemistry Chemical Physics</i>. Royal Society of Chemistry. <a href=\"https://doi.org/10.1039/d4cp03727h\">https://doi.org/10.1039/d4cp03727h</a>","chicago":"Hrast, Mateja, Marko Ljubotina, and Matjaz Zitnik. “Ab Initio Auger Spectrum of the Ultrafast Dissociating 2p3/2−1σ* Resonance in HCl.” <i>Physical Chemistry Chemical Physics</i>. Royal Society of Chemistry, 2025. <a href=\"https://doi.org/10.1039/d4cp03727h\">https://doi.org/10.1039/d4cp03727h</a>.","mla":"Hrast, Mateja, et al. “Ab Initio Auger Spectrum of the Ultrafast Dissociating 2p3/2−1σ* Resonance in HCl.” <i>Physical Chemistry Chemical Physics</i>, vol. 27, no. 3, Royal Society of Chemistry, 2025, pp. 1473–82, doi:<a href=\"https://doi.org/10.1039/d4cp03727h\">10.1039/d4cp03727h</a>.","short":"M. Hrast, M. Ljubotina, M. Zitnik, Physical Chemistry Chemical Physics 27 (2025) 1473–1482.","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."},"oa_version":"Published Version","status":"public","type":"journal_article","publication_identifier":{"issn":["1463-9076"]},"related_material":{"record":[{"id":"18716","relation":"research_data","status":"public"}]},"OA_type":"hybrid","article_processing_charge":"Yes (via OA deal)","date_published":"2025-01-21T00:00:00Z","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.","isi":1,"title":"Ab initio Auger spectrum of the ultrafast dissociating 2p3/2−1σ* resonance in HCl","volume":27,"month":"01","date_updated":"2025-05-19T14:03:19Z","quality_controlled":"1","external_id":{"isi":["001379819100001"],"pmid":["39698879"]},"tmp":{"short":"CC BY-NC (3.0)","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)"},"has_accepted_license":"1","page":"1473-1482","pmid":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"18710","department":[{"_id":"MiLe"},{"_id":"MaSe"}],"ec_funded":1,"issue":"3","publication":"Physical Chemistry Chemical Physics","OA_place":"publisher","corr_author":"1","day":"21","article_type":"original","date_created":"2024-12-29T23:01:58Z","year":"2025","intvolume":"        27","oa":1,"publication_status":"published","file":[{"date_updated":"2025-04-16T09:46:45Z","content_type":"application/pdf","relation":"main_file","file_size":1270582,"access_level":"open_access","file_name":"2025_PCCP_Hrast.pdf","creator":"dernst","checksum":"d035683179547b41b811107a8649aab0","file_id":"19581","success":1,"date_created":"2025-04-16T09:46:45Z"}],"doi":"10.1039/d4cp03727h","project":[{"name":"Angulon: physics and applications of a new quasiparticle","call_identifier":"H2020","_id":"2688CF98-B435-11E9-9278-68D0E5697425","grant_number":"801770"}],"language":[{"iso":"eng"}],"ddc":["530"],"author":[{"last_name":"Hrast","first_name":"Mateja","id":"48dbb294-2a9c-11ef-905d-f56be71f0e5d","full_name":"Hrast, Mateja"},{"id":"F75EE9BE-5C90-11EA-905D-16643DDC885E","full_name":"Ljubotina, Marko","first_name":"Marko","last_name":"Ljubotina","orcid":"0000-0003-0038-7068"},{"last_name":"Zitnik","first_name":"Matjaz","full_name":"Zitnik, Matjaz"}],"file_date_updated":"2025-04-16T09:46:45Z"},{"month":"01","file":[{"file_id":"18722","success":1,"date_created":"2025-01-02T12:30:27Z","access_level":"open_access","file_name":"Codes.zip","checksum":"9c5f91876014706990a0728c3675cd2a","creator":"psurendr","date_updated":"2025-01-02T12:30:27Z","relation":"main_file","content_type":"application/zip","file_size":326835},{"file_size":620,"relation":"main_file","content_type":"text/plain","date_updated":"2025-01-02T12:30:39Z","creator":"psurendr","checksum":"47fe98b7cc526e634e42de58f5eae288","access_level":"open_access","file_name":"ReadMe.txt","date_created":"2025-01-02T12:30:39Z","file_id":"18723","success":1}],"doi":"10.15479/AT:ISTA:17344","oa":1,"file_date_updated":"2025-01-02T12:30:39Z","date_updated":"2025-12-30T08:44:12Z","author":[{"full_name":"Surendranadh, Parvathy","id":"455235B8-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6395-386X","last_name":"Surendranadh","first_name":"Parvathy"},{"first_name":"Himani","last_name":"Sachdeva","full_name":"Sachdeva, Himani"}],"ddc":["576"],"date_created":"2025-01-01T15:28:27Z","title":"Mathematica notebook and Fortran code for 'Effect of assortative mating and sexual selection on polygenic barriers to gene flow'","article_processing_charge":"No","date_published":"2025-01-07T00:00:00Z","acknowledged_ssus":[{"_id":"ScienComp"}],"year":"2025","corr_author":"1","type":"research_data","status":"public","related_material":{"record":[{"status":"public","relation":"used_in_publication","id":"19876"}]},"day":"07","publisher":"Institute of Science and Technology Austria","has_accepted_license":"1","tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"department":[{"_id":"GradSch"},{"_id":"NiBa"}],"_id":"18712","user_id":"9947682f-b9fa-11ee-9c4a-b3ffaafe6614","oa_version":"Published Version","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'. "}],"citation":{"apa":"Surendranadh, P., &#38; Sachdeva, H. (2025). Mathematica notebook and Fortran code for “Effect of assortative mating and sexual selection on polygenic barriers to gene flow.” Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:17344\">https://doi.org/10.15479/AT:ISTA:17344</a>","chicago":"Surendranadh, Parvathy, and Himani Sachdeva. “Mathematica Notebook and Fortran Code for ‘Effect of Assortative Mating and Sexual Selection on Polygenic Barriers to Gene Flow.’” Institute of Science and Technology Austria, 2025. <a href=\"https://doi.org/10.15479/AT:ISTA:17344\">https://doi.org/10.15479/AT:ISTA:17344</a>.","mla":"Surendranadh, Parvathy, and Himani Sachdeva. <i>Mathematica Notebook and Fortran Code for “Effect of Assortative Mating and Sexual Selection on Polygenic Barriers to Gene Flow.”</i> Institute of Science and Technology Austria, 2025, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:17344\">10.15479/AT:ISTA:17344</a>.","short":"P. Surendranadh, H. Sachdeva, (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, <a href=\"https://doi.org/10.15479/AT:ISTA:17344\">10.15479/AT:ISTA:17344</a>.","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.","ama":"Surendranadh P, Sachdeva H. Mathematica notebook and Fortran code for “Effect of assortative mating and sexual selection on polygenic barriers to gene flow.” 2025. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:17344\">10.15479/AT:ISTA:17344</a>"}},{"oa":1,"publication_status":"published","file":[{"date_updated":"2025-04-16T09:16:25Z","content_type":"application/pdf","relation":"main_file","file_size":1110657,"file_name":"2025_EuropJournCombinatorics_Carbonero.pdf","access_level":"open_access","creator":"dernst","checksum":"2c75f78f40ebb93d16fe3765bda2905a","success":1,"file_id":"19577","date_created":"2025-04-16T09:16:25Z"}],"project":[{"name":"Randomness and structure in combinatorics","grant_number":"101076777","_id":"bd95085b-d553-11ed-ba76-e55d3349be45"}],"doi":"10.1016/j.ejc.2024.104104","intvolume":"       125","file_date_updated":"2025-04-16T09:16:25Z","ddc":["510"],"language":[{"iso":"eng"}],"author":[{"first_name":"Alvaro","last_name":"Carbonero","full_name":"Carbonero, Alvaro"},{"first_name":"Hidde","last_name":"Koerts","full_name":"Koerts, Hidde"},{"full_name":"Moore, Benjamin","id":"6dc1a1be-bf1c-11ed-8d2b-d044840f49d6","first_name":"Benjamin","last_name":"Moore"},{"full_name":"Spirkl, Sophie","last_name":"Spirkl","first_name":"Sophie"}],"date_created":"2025-01-05T23:01:55Z","article_type":"original","year":"2025","OA_place":"publisher","corr_author":"1","publication":"European Journal of Combinatorics","day":"01","tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"has_accepted_license":"1","_id":"18753","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"MaKw"}],"month":"03","external_id":{"isi":["001400113700001"],"arxiv":["2306.04710"]},"quality_controlled":"1","date_updated":"2025-05-19T14:06:00Z","title":"On heroes in digraphs with forbidden induced forests","arxiv":1,"date_published":"2025-03-01T00:00:00Z","article_processing_charge":"Yes (in subscription journal)","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 .","isi":1,"volume":125,"type":"journal_article","publication_identifier":{"issn":["0195-6698"]},"status":"public","OA_type":"hybrid","publisher":"Elsevier","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."}],"scopus_import":"1","article_number":"104104","citation":{"ieee":"A. Carbonero, H. Koerts, B. Moore, and S. Spirkl, “On heroes in digraphs with forbidden induced forests,” <i>European Journal of Combinatorics</i>, vol. 125. Elsevier, 2025.","ama":"Carbonero A, Koerts H, Moore B, Spirkl S. On heroes in digraphs with forbidden induced forests. <i>European Journal of Combinatorics</i>. 2025;125. doi:<a href=\"https://doi.org/10.1016/j.ejc.2024.104104\">10.1016/j.ejc.2024.104104</a>","chicago":"Carbonero, Alvaro, Hidde Koerts, Benjamin Moore, and Sophie Spirkl. “On Heroes in Digraphs with Forbidden Induced Forests.” <i>European Journal of Combinatorics</i>. Elsevier, 2025. <a href=\"https://doi.org/10.1016/j.ejc.2024.104104\">https://doi.org/10.1016/j.ejc.2024.104104</a>.","apa":"Carbonero, A., Koerts, H., Moore, B., &#38; Spirkl, S. (2025). On heroes in digraphs with forbidden induced forests. <i>European Journal of Combinatorics</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.ejc.2024.104104\">https://doi.org/10.1016/j.ejc.2024.104104</a>","ista":"Carbonero A, Koerts H, Moore B, Spirkl S. 2025. On heroes in digraphs with forbidden induced forests. European Journal of Combinatorics. 125, 104104.","short":"A. Carbonero, H. Koerts, B. Moore, S. Spirkl, European Journal of Combinatorics 125 (2025).","mla":"Carbonero, Alvaro, et al. “On Heroes in Digraphs with Forbidden Induced Forests.” <i>European Journal of Combinatorics</i>, vol. 125, 104104, Elsevier, 2025, doi:<a href=\"https://doi.org/10.1016/j.ejc.2024.104104\">10.1016/j.ejc.2024.104104</a>."},"oa_version":"Published Version"},{"article_type":"original","date_created":"2025-01-05T23:01:56Z","year":"2025","intvolume":"       112","file":[{"date_updated":"2025-01-08T09:26:42Z","relation":"main_file","content_type":"application/pdf","file_size":2266488,"file_id":"18776","success":1,"date_created":"2025-01-08T09:26:42Z","access_level":"open_access","file_name":"2025_AJHG_Smith.pdf","checksum":"891d120554f07da2c35d38388c29a690","creator":"dernst"}],"doi":"10.1016/j.ajhg.2024.11.012","oa":1,"publication_status":"published","author":[{"first_name":"Hannah M.","last_name":"Smith","full_name":"Smith, Hannah M."},{"full_name":"Ng, Hong Kiat","first_name":"Hong Kiat","last_name":"Ng"},{"full_name":"Moodie, Joanna E.","last_name":"Moodie","first_name":"Joanna E."},{"last_name":"Gadd","first_name":"Danni A.","full_name":"Gadd, Danni A."},{"first_name":"Daniel L.","last_name":"Mccartney","full_name":"Mccartney, Daniel L."},{"full_name":"Bernabeu, Elena","last_name":"Bernabeu","first_name":"Elena"},{"full_name":"Campbell, Archie","first_name":"Archie","last_name":"Campbell"},{"first_name":"Paul","last_name":"Redmond","full_name":"Redmond, Paul"},{"full_name":"Taylor, Adele","last_name":"Taylor","first_name":"Adele"},{"full_name":"Page, Danielle","first_name":"Danielle","last_name":"Page"},{"full_name":"Corley, Janie","first_name":"Janie","last_name":"Corley"},{"full_name":"Harris, Sarah E.","first_name":"Sarah E.","last_name":"Harris"},{"last_name":"Tay","first_name":"Darwin","full_name":"Tay, Darwin"},{"full_name":"Deary, Ian J.","last_name":"Deary","first_name":"Ian J."},{"first_name":"Kathryn L.","last_name":"Evans","full_name":"Evans, Kathryn L."},{"id":"E5D42276-F5DA-11E9-8E24-6303E6697425","full_name":"Robinson, Matthew Richard","first_name":"Matthew Richard","last_name":"Robinson","orcid":"0000-0001-8982-8813"},{"last_name":"Chambers","first_name":"John C.","full_name":"Chambers, John C."},{"first_name":"Marie","last_name":"Loh","full_name":"Loh, Marie"},{"last_name":"Cox","first_name":"Simon R.","full_name":"Cox, Simon R."},{"full_name":"Marioni, Riccardo E.","last_name":"Marioni","first_name":"Riccardo E."},{"last_name":"Hillary","first_name":"Robert F.","full_name":"Hillary, Robert F."}],"ddc":["570"],"language":[{"iso":"eng"}],"file_date_updated":"2025-01-08T09:26:42Z","has_accepted_license":"1","tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"page":"106-115","pmid":1,"department":[{"_id":"MaRo"}],"issue":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"18754","publication":"American Journal of Human Genetics","OA_place":"publisher","day":"02","isi":1,"date_published":"2025-01-02T00:00:00Z","article_processing_charge":"No","title":"DNA methylation-based predictors of metabolic traits in Scottish and Singaporean cohorts","volume":112,"month":"01","date_updated":"2025-02-27T12:38:23Z","quality_controlled":"1","external_id":{"pmid":["39706196"],"isi":["001412498600001"]},"publisher":"Elsevier","oa_version":"Published Version","citation":{"ama":"Smith HM, Ng HK, Moodie JE, et al. DNA methylation-based predictors of metabolic traits in Scottish and Singaporean cohorts. <i>American Journal of Human Genetics</i>. 2025;112(1):106-115. doi:<a href=\"https://doi.org/10.1016/j.ajhg.2024.11.012\">10.1016/j.ajhg.2024.11.012</a>","ieee":"H. M. Smith <i>et al.</i>, “DNA methylation-based predictors of metabolic traits in Scottish and Singaporean cohorts,” <i>American Journal of Human Genetics</i>, vol. 112, no. 1. Elsevier, pp. 106–115, 2025.","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.","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.","mla":"Smith, Hannah M., et al. “DNA Methylation-Based Predictors of Metabolic Traits in Scottish and Singaporean Cohorts.” <i>American Journal of Human Genetics</i>, vol. 112, no. 1, Elsevier, 2025, pp. 106–15, doi:<a href=\"https://doi.org/10.1016/j.ajhg.2024.11.012\">10.1016/j.ajhg.2024.11.012</a>.","chicago":"Smith, Hannah M., Hong Kiat Ng, Joanna E. Moodie, Danni A. Gadd, Daniel L. Mccartney, Elena Bernabeu, Archie Campbell, et al. “DNA Methylation-Based Predictors of Metabolic Traits in Scottish and Singaporean Cohorts.” <i>American Journal of Human Genetics</i>. Elsevier, 2025. <a href=\"https://doi.org/10.1016/j.ajhg.2024.11.012\">https://doi.org/10.1016/j.ajhg.2024.11.012</a>.","apa":"Smith, H. M., Ng, H. K., Moodie, J. E., Gadd, D. A., Mccartney, D. L., Bernabeu, E., … Hillary, R. F. (2025). DNA methylation-based predictors of metabolic traits in Scottish and Singaporean cohorts. <i>American Journal of Human Genetics</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.ajhg.2024.11.012\">https://doi.org/10.1016/j.ajhg.2024.11.012</a>"},"scopus_import":"1","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."}],"status":"public","publication_identifier":{"eissn":["1537-6605"],"issn":["0002-9297"]},"type":"journal_article","related_material":{"link":[{"relation":"software","url":"https://github.com/marioni-group/Metabolic_trait"}]},"OA_type":"hybrid"},{"day":"03","publication":"Lineage Tracing","corr_author":"1","pmid":1,"_id":"18765","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ec_funded":1,"department":[{"_id":"SiHi"}],"page":"139-151","language":[{"iso":"eng"}],"author":[{"first_name":"Giselle T","last_name":"Cheung","orcid":"0000-0001-8457-2572","id":"471195F6-F248-11E8-B48F-1D18A9856A87","full_name":"Cheung, Giselle T"},{"id":"48EA0138-F248-11E8-B48F-1D18A9856A87","full_name":"Pauler, Florian","first_name":"Florian","last_name":"Pauler","orcid":"0000-0002-7462-0048"},{"orcid":"0000-0003-2279-1061","last_name":"Hippenmeyer","first_name":"Simon","full_name":"Hippenmeyer, Simon","id":"37B36620-F248-11E8-B48F-1D18A9856A87"}],"intvolume":"      2886","series_title":"MIMB","publication_status":"published","project":[{"name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411"}],"doi":"10.1007/978-1-0716-4310-5_7","year":"2025","alternative_title":["Methods in Molecular Biology"],"place":"New York, NY","date_created":"2025-01-07T08:36:47Z","OA_type":"closed access","status":"public","type":"book_chapter","publication_identifier":{"eissn":["1940-6029"],"issn":["1064-3745"],"eisbn":["9781071643105"],"isbn":["9781071643099"]},"scopus_import":"1","abstract":[{"text":"Mosaic Analysis with Double Markers (MADM) represents a mouse genetic approach coupling differential fluorescent labeling to genetic manipulations in dividing cells and their lineages. MADM uniquely enables the generation and visualization of individual control or homozygous mutant cells in a heterozygous genetic environment. Among its diverse applications, MADM has been used to dissect cell-autonomous gene functions important for cortical development and neural development in general. The high cellular resolution offered by MADM also permits the analysis of transcriptomic changes of individual cells upon genetic manipulations. In this chapter, we describe an experimental protocol combining the generation and isolation of MADM-labeled cells with downstream single-cell RNA-sequencing technologies to probe cell-type specific phenotypes due to genetic mutations at single-cell resolution.","lang":"eng"}],"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. <i>Lineage Tracing</i>. Vol 2886. MIMB. New York, NY: Springer Nature; 2025:139-151. doi:<a href=\"https://doi.org/10.1007/978-1-0716-4310-5_7\">10.1007/978-1-0716-4310-5_7</a>","ieee":"G. T. Cheung, F. Pauler, and S. Hippenmeyer, “Probing Cell-Type Specificity of Mutant Phenotype at Transcriptomic Level Using Mosaic Analysis with Double Markers (MADM),” in <i>Lineage Tracing</i>, vol. 2886, J. Garcia-Marques and T. Lee, Eds. New York, NY: Springer Nature, 2025, pp. 139–151.","mla":"Cheung, Giselle T., et al. “Probing Cell-Type Specificity of Mutant Phenotype at Transcriptomic Level Using Mosaic Analysis with Double Markers (MADM).” <i>Lineage Tracing</i>, edited by Jorge Garcia-Marques and Tzumin Lee, vol. 2886, Springer Nature, 2025, pp. 139–51, doi:<a href=\"https://doi.org/10.1007/978-1-0716-4310-5_7\">10.1007/978-1-0716-4310-5_7</a>.","ista":"Cheung GT, Pauler F, Hippenmeyer S. 2025.Probing Cell-Type Specificity of Mutant Phenotype at Transcriptomic Level Using Mosaic Analysis with Double Markers (MADM). In: Lineage Tracing. Methods in Molecular Biology, vol. 2886, 139–151.","short":"G.T. Cheung, F. Pauler, S. Hippenmeyer, in:, J. Garcia-Marques, T. Lee (Eds.), Lineage Tracing, Springer Nature, New York, NY, 2025, pp. 139–151.","apa":"Cheung, G. T., Pauler, F., &#38; Hippenmeyer, S. (2025). Probing Cell-Type Specificity of Mutant Phenotype at Transcriptomic Level Using Mosaic Analysis with Double Markers (MADM). In J. Garcia-Marques &#38; T. Lee (Eds.), <i>Lineage Tracing</i> (Vol. 2886, pp. 139–151). New York, NY: Springer Nature. <a href=\"https://doi.org/10.1007/978-1-0716-4310-5_7\">https://doi.org/10.1007/978-1-0716-4310-5_7</a>","chicago":"Cheung, Giselle T, Florian Pauler, and Simon Hippenmeyer. “Probing Cell-Type Specificity of Mutant Phenotype at Transcriptomic Level Using Mosaic Analysis with Double Markers (MADM).” In <i>Lineage Tracing</i>, edited by Jorge Garcia-Marques and Tzumin Lee, 2886:139–51. MIMB. New York, NY: Springer Nature, 2025. <a href=\"https://doi.org/10.1007/978-1-0716-4310-5_7\">https://doi.org/10.1007/978-1-0716-4310-5_7</a>."},"oa_version":"None","publisher":"Springer Nature","quality_controlled":"1","date_updated":"2025-04-14T07:43:46Z","external_id":{"pmid":["39745639"]},"month":"01","volume":2886,"acknowledged_ssus":[{"_id":"Bio"}],"date_published":"2025-01-03T00:00:00Z","article_processing_charge":"No","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.","editor":[{"full_name":"Garcia-Marques, Jorge","first_name":"Jorge","last_name":"Garcia-Marques"},{"full_name":"Lee, Tzumin","last_name":"Lee","first_name":"Tzumin"}],"title":"Probing Cell-Type Specificity of Mutant Phenotype at Transcriptomic Level Using Mosaic Analysis with Double Markers (MADM)"},{"OA_place":"publisher","corr_author":"1","publication":"Nature Structural & Molecular Biology","day":"01","page":"607-612","tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"has_accepted_license":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"18778","department":[{"_id":"CaBe"}],"pmid":1,"publication_status":"published","oa":1,"file":[{"relation":"main_file","date_updated":"2025-04-16T08:17:27Z","content_type":"application/pdf","file_size":9306639,"access_level":"open_access","file_name":"2025_NatureStrucMolBiol_Tluckova.pdf","creator":"dernst","checksum":"2919b30b271f395888e880076a680d73","file_id":"19573","success":1,"date_created":"2025-04-16T08:17:27Z"}],"project":[{"name":"Regulation of mammalian transcription by noncoding RNA","grant_number":"P34185","_id":"c08a6700-5a5b-11eb-8a69-82a722b2bc30"}],"doi":"10.1038/s41594-024-01448-7","intvolume":"        32","APC_amount":"12348 EUR","file_date_updated":"2025-04-16T08:17:27Z","language":[{"iso":"eng"}],"ddc":["570"],"author":[{"full_name":"Tluckova, Katarina","id":"4AC7D980-F248-11E8-B48F-1D18A9856A87","first_name":"Katarina","last_name":"Tluckova"},{"last_name":"Kaczmarek","first_name":"Beata M","id":"36FA4AFA-F248-11E8-B48F-1D18A9856A87","full_name":"Kaczmarek, Beata M"},{"id":"41F1F098-F248-11E8-B48F-1D18A9856A87","full_name":"Testa Salmazo, Anita P","last_name":"Testa Salmazo","first_name":"Anita P"},{"full_name":"Bernecky, Carrie A","id":"2CB9DFE2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-0893-7036","first_name":"Carrie A","last_name":"Bernecky"}],"date_created":"2025-01-08T11:20:20Z","article_type":"original","year":"2025","type":"journal_article","publication_identifier":{"issn":["1545-9993"],"eissn":["1545-9985"]},"status":"public","OA_type":"hybrid","related_material":{"record":[{"status":"public","id":"14644","relation":"earlier_version"}]},"publisher":"Springer Nature","citation":{"mla":"Tluckova, Katarina, et al. “Mechanism of Mammalian Transcriptional Repression by Noncoding RNA.” <i>Nature Structural &#38; Molecular Biology</i>, vol. 32, Springer Nature, 2025, pp. 607–12, doi:<a href=\"https://doi.org/10.1038/s41594-024-01448-7\">10.1038/s41594-024-01448-7</a>.","ista":"Tluckova K, Kaczmarek BM, Testa Salmazo AP, Bernecky C. 2025. Mechanism of mammalian transcriptional repression by noncoding RNA. Nature Structural &#38; Molecular Biology. 32, 607–612.","short":"K. Tluckova, B.M. Kaczmarek, A.P. Testa Salmazo, C. Bernecky, Nature Structural &#38; Molecular Biology 32 (2025) 607–612.","apa":"Tluckova, K., Kaczmarek, B. M., Testa Salmazo, A. P., &#38; Bernecky, C. (2025). Mechanism of mammalian transcriptional repression by noncoding RNA. <i>Nature Structural &#38; Molecular Biology</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41594-024-01448-7\">https://doi.org/10.1038/s41594-024-01448-7</a>","chicago":"Tluckova, Katarina, Beata M Kaczmarek, Anita P Testa Salmazo, and Carrie Bernecky. “Mechanism of Mammalian Transcriptional Repression by Noncoding RNA.” <i>Nature Structural &#38; Molecular Biology</i>. Springer Nature, 2025. <a href=\"https://doi.org/10.1038/s41594-024-01448-7\">https://doi.org/10.1038/s41594-024-01448-7</a>.","ama":"Tluckova K, Kaczmarek BM, Testa Salmazo AP, Bernecky C. Mechanism of mammalian transcriptional repression by noncoding RNA. <i>Nature Structural &#38; Molecular Biology</i>. 2025;32:607-612. doi:<a href=\"https://doi.org/10.1038/s41594-024-01448-7\">10.1038/s41594-024-01448-7</a>","ieee":"K. Tluckova, B. M. Kaczmarek, A. P. Testa Salmazo, and C. Bernecky, “Mechanism of mammalian transcriptional repression by noncoding RNA,” <i>Nature Structural &#38; Molecular Biology</i>, vol. 32. Springer Nature, pp. 607–612, 2025."},"scopus_import":"1","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."}],"oa_version":"Published Version","month":"04","external_id":{"pmid":["39762629"],"isi":["001390268000001"]},"quality_controlled":"1","date_updated":"2025-11-20T10:28:36Z","title":"Mechanism of mammalian transcriptional repression by noncoding RNA","article_processing_charge":"Yes (in subscription journal)","date_published":"2025-04-01T00:00:00Z","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.","isi":1,"volume":32,"acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"EM-Fac"},{"_id":"ScienComp"},{"_id":"PreCl"}]},{"issue":"1","department":[{"_id":"MiLe"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"18821","day":"03","publication":"Physical Review A","OA_place":"repository","year":"2025","article_type":"original","date_created":"2025-01-12T23:04:00Z","author":[{"full_name":"Brauneis, Fabian","first_name":"Fabian","last_name":"Brauneis"},{"last_name":"Hammer","first_name":"Hans Werner","full_name":"Hammer, Hans Werner"},{"last_name":"Reimann","first_name":"Stephanie M.","full_name":"Reimann, Stephanie M."},{"id":"37D278BC-F248-11E8-B48F-1D18A9856A87","full_name":"Volosniev, Artem","last_name":"Volosniev","first_name":"Artem","orcid":"0000-0003-0393-5525"}],"language":[{"iso":"eng"}],"intvolume":"       111","doi":"10.1103/PhysRevA.111.013303","publication_status":"published","oa":1,"oa_version":"Preprint","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."}],"scopus_import":"1","article_number":"013303","citation":{"apa":"Brauneis, F., Hammer, H. W., Reimann, S. M., &#38; Volosniev, A. (2025). Comparison of renormalized interactions using one-dimensional few-body systems as a testbed. <i>Physical Review A</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevA.111.013303\">https://doi.org/10.1103/PhysRevA.111.013303</a>","chicago":"Brauneis, Fabian, Hans Werner Hammer, Stephanie M. Reimann, and Artem Volosniev. “Comparison of Renormalized Interactions Using One-Dimensional Few-Body Systems as a Testbed.” <i>Physical Review A</i>. American Physical Society, 2025. <a href=\"https://doi.org/10.1103/PhysRevA.111.013303\">https://doi.org/10.1103/PhysRevA.111.013303</a>.","mla":"Brauneis, Fabian, et al. “Comparison of Renormalized Interactions Using One-Dimensional Few-Body Systems as a Testbed.” <i>Physical Review A</i>, vol. 111, no. 1, 013303, American Physical Society, 2025, doi:<a href=\"https://doi.org/10.1103/PhysRevA.111.013303\">10.1103/PhysRevA.111.013303</a>.","ista":"Brauneis F, Hammer HW, Reimann SM, Volosniev A. 2025. Comparison of renormalized interactions using one-dimensional few-body systems as a testbed. Physical Review A. 111(1), 013303.","short":"F. Brauneis, H.W. Hammer, S.M. Reimann, A. Volosniev, Physical Review A 111 (2025).","ieee":"F. Brauneis, H. W. Hammer, S. M. Reimann, and A. Volosniev, “Comparison of renormalized interactions using one-dimensional few-body systems as a testbed,” <i>Physical Review A</i>, vol. 111, no. 1. American Physical Society, 2025.","ama":"Brauneis F, Hammer HW, Reimann SM, Volosniev A. Comparison of renormalized interactions using one-dimensional few-body systems as a testbed. <i>Physical Review A</i>. 2025;111(1). doi:<a href=\"https://doi.org/10.1103/PhysRevA.111.013303\">10.1103/PhysRevA.111.013303</a>"},"main_file_link":[{"url":" https://doi.org/10.48550/arXiv.2408.10052","open_access":"1"}],"publisher":"American Physical Society","OA_type":"green","status":"public","publication_identifier":{"issn":["2469-9926"],"eissn":["2469-9934"]},"type":"journal_article","volume":111,"isi":1,"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).","date_published":"2025-01-03T00:00:00Z","article_processing_charge":"No","arxiv":1,"title":"Comparison of renormalized interactions using one-dimensional few-body systems as a testbed","quality_controlled":"1","date_updated":"2025-02-27T12:41:58Z","external_id":{"arxiv":["2408.10052"],"isi":["001398791400004"]},"month":"01"},{"tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"has_accepted_license":"1","pmid":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"18823","issue":"1","department":[{"_id":"XiFe"}],"publication":"Plant Physiology","corr_author":"1","OA_place":"publisher","day":"01","article_type":"original","date_created":"2025-01-12T23:04:02Z","year":"2025","intvolume":"       197","oa":1,"publication_status":"published","file":[{"access_level":"open_access","file_name":"2025_PlantPhysiology_Cao.pdf","creator":"dernst","checksum":"a9b2a12d7bc6174f27e28413e9c77a9c","file_id":"20023","success":1,"date_created":"2025-07-15T08:17:25Z","relation":"main_file","date_updated":"2025-07-15T08:17:25Z","content_type":"application/pdf","file_size":1214018}],"doi":"10.1093/plphys/kiae651","ddc":["580"],"language":[{"iso":"eng"}],"author":[{"full_name":"Cao, Dechang","last_name":"Cao","first_name":"Dechang"},{"id":"26bd38d3-c59a-11ee-a1af-d7a988cafcc5","full_name":"De Jaeger-Braet, Joke G","last_name":"De Jaeger-Braet","first_name":"Joke G"}],"file_date_updated":"2025-07-15T08:17:25Z","publisher":"Oxford University Press","scopus_import":"1","citation":{"ama":"Cao D, De Jaeger-Braet JG. Memory of maternal temperatures: DNA methylation alterations across generations. <i>Plant Physiology</i>. 2025;197(1). doi:<a href=\"https://doi.org/10.1093/plphys/kiae651\">10.1093/plphys/kiae651</a>","ieee":"D. Cao and J. G. De Jaeger-Braet, “Memory of maternal temperatures: DNA methylation alterations across generations,” <i>Plant Physiology</i>, vol. 197, no. 1. Oxford University Press, 2025.","ista":"Cao D, De Jaeger-Braet JG. 2025. Memory of maternal temperatures: DNA methylation alterations across generations. Plant Physiology. 197(1), kiae651.","short":"D. Cao, J.G. De Jaeger-Braet, Plant Physiology 197 (2025).","mla":"Cao, Dechang, and Joke G. De Jaeger-Braet. “Memory of Maternal Temperatures: DNA Methylation Alterations across Generations.” <i>Plant Physiology</i>, vol. 197, no. 1, kiae651, Oxford University Press, 2025, doi:<a href=\"https://doi.org/10.1093/plphys/kiae651\">10.1093/plphys/kiae651</a>.","chicago":"Cao, Dechang, and Joke G De Jaeger-Braet. “Memory of Maternal Temperatures: DNA Methylation Alterations across Generations.” <i>Plant Physiology</i>. Oxford University Press, 2025. <a href=\"https://doi.org/10.1093/plphys/kiae651\">https://doi.org/10.1093/plphys/kiae651</a>.","apa":"Cao, D., &#38; De Jaeger-Braet, J. G. (2025). Memory of maternal temperatures: DNA methylation alterations across generations. <i>Plant Physiology</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/plphys/kiae651\">https://doi.org/10.1093/plphys/kiae651</a>"},"article_number":"kiae651","oa_version":"Published Version","status":"public","type":"journal_article","publication_identifier":{"eissn":["1532-2548"]},"OA_type":"hybrid","article_processing_charge":"Yes (in subscription journal)","date_published":"2025-01-01T00:00:00Z","isi":1,"title":"Memory of maternal temperatures: DNA methylation alterations across generations","volume":197,"month":"01","date_updated":"2025-07-15T08:18:19Z","quality_controlled":"1","external_id":{"isi":["001382979900001"],"pmid":["39691053"]}},{"has_accepted_license":"1","tmp":{"name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","image":"/images/cc_by_nc.png","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","short":"CC BY-NC (4.0)"},"publisher":"Institute of Science and Technology Austria","oa_version":"Published Version","abstract":[{"text":"Super-resolution methods provide far better spatial resolution than the optical diffraction limit of about half the wavelength of light (∼200-300 nm). Nevertheless, they have yet to attain widespread use in plants, largely due to plants’ challenging optical properties. Expansion microscopy improves effective resolution by isotropically increasing the physical distances between sample structures while preserving relative spatial arrangements and clearing the sample. However, its application to plants has been hindered by the rigid, mechanically cohesive structure of plant tissues. Here, we report on whole-mount expansion microscopy of thale cress (Arabidopsis thaliana) root tissues (PlantEx), achieving a four-fold resolution increase over conventional microscopy. Our results highlight the microtubule cytoskeleton organization and interaction between molecularly defined cellular constituents. Combining PlantEx with stimulated emission depletion (STED) microscopy, we increase nanoscale resolution and visualize the complex organization of subcellular organelles from intact tissues by example of the densely packed COPI-coated vesicles associated with the Golgi apparatus and put these into a cellular structural context. Our results show that expansion microscopy can be applied to increase effective imaging resolution in Arabidopsis root specimens.","lang":"eng"}],"citation":{"short":"J.G. Danzl, C. Kreuzinger, (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, <a href=\"https://doi.org/10.15479/AT:ISTA:18837\">10.15479/AT:ISTA:18837</a>.","mla":"Danzl, Johann G., and Caroline Kreuzinger. <i>Research Data for the Publication “Super-Resolution Expansion Microscopy in Plant Roots.”</i> Institute of Science and Technology Austria, 2025, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:18837\">10.15479/AT:ISTA:18837</a>.","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. <a href=\"https://doi.org/10.15479/AT:ISTA:18837\">https://doi.org/10.15479/AT:ISTA:18837</a>.","apa":"Danzl, J. G., &#38; Kreuzinger, C. (2025). Research Data for the publication “Super-resolution expansion microscopy in plant roots.” Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:18837\">https://doi.org/10.15479/AT:ISTA:18837</a>","ama":"Danzl JG, Kreuzinger C. Research Data for the publication “Super-resolution expansion microscopy in plant roots.” 2025. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:18837\">10.15479/AT:ISTA:18837</a>","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."},"department":[{"_id":"JoDa"}],"_id":"18837","user_id":"68b8ca59-c5b3-11ee-8790-cd641c68093d","status":"public","corr_author":"1","type":"research_data","contributor":[{"orcid":"0000-0003-1286-7368","last_name":"Gallei","first_name":"Michelle C","contributor_type":"researcher","id":"35A03822-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Truckenbrodt","first_name":"Sven 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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.","lang":"eng"}],"scopus_import":"1","citation":{"ieee":"R. F. Ocampo <i>et al.</i>, “DNA targeting by compact Cas9d and its resurrected ancestor,” <i>Nature Communications</i>, vol. 16. Springer Nature, 2025.","ama":"Ocampo RF, Bravo JPK, Dangerfield TL, et al. DNA targeting by compact Cas9d and its resurrected ancestor. <i>Nature Communications</i>. 2025;16. doi:<a href=\"https://doi.org/10.1038/s41467-024-55573-4\">10.1038/s41467-024-55573-4</a>","apa":"Ocampo, R. F., Bravo, J. P. K., Dangerfield, T. L., Nocedal, I., Jirde, S. A., Alexander, L. M., … Taylor, D. W. (2025). DNA targeting by compact Cas9d and its resurrected ancestor. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-024-55573-4\">https://doi.org/10.1038/s41467-024-55573-4</a>","chicago":"Ocampo, Rodrigo Fregoso, Jack Peter Kelly Bravo, Tyler L. Dangerfield, Isabel Nocedal, Samatar A. Jirde, Lisa M. Alexander, Nicole C. Thomas, et al. “DNA Targeting by Compact Cas9d and Its Resurrected Ancestor.” <i>Nature Communications</i>. Springer Nature, 2025. <a href=\"https://doi.org/10.1038/s41467-024-55573-4\">https://doi.org/10.1038/s41467-024-55573-4</a>.","mla":"Ocampo, Rodrigo Fregoso, et al. “DNA Targeting by Compact Cas9d and Its Resurrected Ancestor.” <i>Nature Communications</i>, vol. 16, 457, Springer Nature, 2025, doi:<a href=\"https://doi.org/10.1038/s41467-024-55573-4\">10.1038/s41467-024-55573-4</a>.","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).","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."},"article_number":"457","publisher":"Springer Nature","quality_controlled":"1","date_updated":"2025-07-03T11:58:22Z","external_id":{"pmid":["39774105"]},"month":"01","volume":16,"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_processing_charge":"Yes","date_published":"2025-01-07T00:00:00Z","title":"DNA targeting by compact Cas9d and its resurrected ancestor","day":"07","publication":"Nature Communications","OA_place":"publisher","pmid":1,"department":[{"_id":"JaBr"}],"_id":"18848","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","has_accepted_license":"1","tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"author":[{"full_name":"Ocampo, Rodrigo Fregoso","first_name":"Rodrigo Fregoso","last_name":"Ocampo"},{"first_name":"Jack Peter Kelly","last_name":"Bravo","orcid":"0000-0003-0456-0753","id":"96aecfa5-8931-11ee-af30-aa6a5d6eee0e","full_name":"Bravo, Jack Peter 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W."}],"language":[{"iso":"eng"}],"ddc":["570"],"file_date_updated":"2025-01-22T14:35:22Z","intvolume":"        16","doi":"10.1038/s41467-024-55573-4","file":[{"date_created":"2025-01-22T14:35:22Z","success":1,"file_id":"18869","creator":"dernst","checksum":"885e96690620790d5c9f188a1587b4cd","file_name":"2025_NatureComm_Ocampo.pdf","access_level":"open_access","file_size":5450660,"relation":"main_file","date_updated":"2025-01-22T14:35:22Z","content_type":"application/pdf"}],"publication_status":"published","oa":1,"DOAJ_listed":"1","year":"2025","article_type":"original","date_created":"2025-01-19T23:01:50Z"},{"corr_author":"1","OA_place":"publisher","publication":"Proceedings of the National Academy of Sciences","day":"07","has_accepted_license":"1","tmp":{"short":"CC BY-NC-ND (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC 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performance?","_id":"2665AAFE-B435-11E9-9278-68D0E5697425","grant_number":"RGP0034/2018"}],"oa":1,"publication_status":"published","intvolume":"       122","file_date_updated":"2025-01-20T10:10:04Z","author":[{"last_name":"Sokolowski","first_name":"Thomas R","orcid":"0000-0002-1287-3779","id":"3E999752-F248-11E8-B48F-1D18A9856A87","full_name":"Sokolowski, Thomas R"},{"last_name":"Gregor","first_name":"Thomas","full_name":"Gregor, Thomas"},{"first_name":"William","last_name":"Bialek","full_name":"Bialek, William"},{"id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","full_name":"Tkačik, Gašper","first_name":"Gašper","last_name":"Tkačik","orcid":"0000-0002-6699-1455"}],"language":[{"iso":"eng"}],"ddc":["570"],"date_created":"2025-01-19T23:01:50Z","article_type":"original","year":"2025","publication_identifier":{"eissn":["1091-6490"],"issn":["0027-8424"]},"type":"journal_article","status":"public","OA_type":"hybrid","publisher":"National Academy of Sciences","oa_version":"Published Version","scopus_import":"1","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."}],"article_number":"e2402925121","citation":{"mla":"Sokolowski, Thomas R., et al. “Deriving a Genetic Regulatory Network from an Optimization Principle.” <i>Proceedings of the National Academy of Sciences</i>, vol. 122, no. 1, e2402925121, National Academy of Sciences, 2025, doi:<a href=\"https://doi.org/10.1073/pnas.2402925121\">10.1073/pnas.2402925121</a>.","short":"T.R. Sokolowski, T. Gregor, W. Bialek, G. Tkačik, Proceedings of the National Academy of Sciences 122 (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.","apa":"Sokolowski, T. R., Gregor, T., Bialek, W., &#38; Tkačik, G. (2025). Deriving a genetic regulatory network from an optimization principle. <i>Proceedings of the National Academy of Sciences</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.2402925121\">https://doi.org/10.1073/pnas.2402925121</a>","chicago":"Sokolowski, Thomas R, Thomas Gregor, William Bialek, and Gašper Tkačik. “Deriving a Genetic Regulatory Network from an Optimization Principle.” <i>Proceedings of the National Academy of Sciences</i>. National Academy of Sciences, 2025. <a href=\"https://doi.org/10.1073/pnas.2402925121\">https://doi.org/10.1073/pnas.2402925121</a>.","ama":"Sokolowski TR, Gregor T, Bialek W, Tkačik G. Deriving a genetic regulatory network from an optimization principle. <i>Proceedings of the National Academy of Sciences</i>. 2025;122(1). doi:<a href=\"https://doi.org/10.1073/pnas.2402925121\">10.1073/pnas.2402925121</a>","ieee":"T. R. Sokolowski, T. Gregor, W. Bialek, and G. Tkačik, “Deriving a genetic regulatory network from an optimization principle,” <i>Proceedings of the National Academy of Sciences</i>, vol. 122, no. 1. National Academy of Sciences, 2025."},"month":"01","external_id":{"isi":["001392772400001"],"pmid":["39752518"]},"date_updated":"2026-02-16T12:26:51Z","quality_controlled":"1","title":"Deriving a genetic regulatory network from an optimization principle","isi":1,"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).","date_published":"2025-01-07T00:00:00Z","article_processing_charge":"Yes (in subscription journal)","volume":122},{"tmp":{"short":"CC BY-NC-ND (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)"},"has_accepted_license":"1","_id":"18850","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","issue":"1","department":[{"_id":"GaTk"}],"pmid":1,"corr_author":"1","OA_place":"publisher","publication":"Proceedings of the National Academy of Sciences","day":"07","date_created":"2025-01-19T23:01:51Z","article_type":"original","year":"2025","oa":1,"publication_status":"published","file":[{"file_name":"2025_PNAS_Perkins.pdf","access_level":"open_access","creator":"dernst","checksum":"86a8d25a6e282aeb4128f1d0b86ff911","success":1,"file_id":"18859","date_created":"2025-01-20T09:38:32Z","content_type":"application/pdf","relation":"main_file","date_updated":"2025-01-20T09:38:32Z","file_size":30943709}],"project":[{"grant_number":"101118866","_id":"7bfe6a29-9f16-11ee-852c-c0da5e2045d9","name":"Transcription in 4D: the dynamic interplay between chromatin architecture and gene expression in developing pseudo-embryos"}],"doi":"10.1073/pnas.2411887121","intvolume":"       122","APC_amount":"3261,23 EUR","file_date_updated":"2025-01-20T09:38:32Z","language":[{"iso":"eng"}],"ddc":["570"],"author":[{"first_name":"Mindy Liu","last_name":"Perkins","full_name":"Perkins, Mindy Liu"},{"full_name":"Crocker, Justin","last_name":"Crocker","first_name":"Justin"},{"full_name":"Tkačik, Gašper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6699-1455","first_name":"Gašper","last_name":"Tkačik"}],"publisher":"National Academy of Sciences","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."}],"citation":{"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.","short":"M.L. Perkins, J. Crocker, G. Tkačik, Proceedings of the National Academy of Sciences 122 (2025).","mla":"Perkins, Mindy Liu, et al. “Chromatin Enables Precise and Scalable Gene Regulation with Factors of Limited Specificity.” <i>Proceedings of the National Academy of Sciences</i>, vol. 122, no. 1, e2411887121, National Academy of Sciences, 2025, doi:<a href=\"https://doi.org/10.1073/pnas.2411887121\">10.1073/pnas.2411887121</a>.","chicago":"Perkins, Mindy Liu, Justin Crocker, and Gašper Tkačik. “Chromatin Enables Precise and Scalable Gene Regulation with Factors of Limited Specificity.” <i>Proceedings of the National Academy of Sciences</i>. National Academy of Sciences, 2025. <a href=\"https://doi.org/10.1073/pnas.2411887121\">https://doi.org/10.1073/pnas.2411887121</a>.","apa":"Perkins, M. L., Crocker, J., &#38; Tkačik, G. (2025). Chromatin enables precise and scalable gene regulation with factors of limited specificity. <i>Proceedings of the National Academy of Sciences</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.2411887121\">https://doi.org/10.1073/pnas.2411887121</a>","ama":"Perkins ML, Crocker J, Tkačik G. Chromatin enables precise and scalable gene regulation with factors of limited specificity. <i>Proceedings of the National Academy of Sciences</i>. 2025;122(1). doi:<a href=\"https://doi.org/10.1073/pnas.2411887121\">10.1073/pnas.2411887121</a>","ieee":"M. L. Perkins, J. Crocker, and G. Tkačik, “Chromatin enables precise and scalable gene regulation with factors of limited specificity,” <i>Proceedings of the National Academy of Sciences</i>, vol. 122, no. 1. National Academy of Sciences, 2025."},"scopus_import":"1","article_number":"e2411887121","oa_version":"Published Version","type":"journal_article","publication_identifier":{"issn":["0027-8424"],"eissn":["1091-6490"]},"status":"public","OA_type":"hybrid","related_material":{"link":[{"url":"https://github.com/officerredshirt/network_crosstalk","relation":"software"}]},"title":"Chromatin enables precise and scalable gene regulation with factors of limited specificity","article_processing_charge":"No","date_published":"2025-01-07T00:00:00Z","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.","isi":1,"volume":122,"month":"01","external_id":{"isi":["001392765300001"],"pmid":["39793086"]},"date_updated":"2026-05-06T12:43:59Z","quality_controlled":"1"},{"intvolume":"       137","oa":1,"publication_status":"published","doi":"10.1088/1538-3873/ada185","file":[{"file_size":5155631,"date_updated":"2025-01-20T09:52:34Z","content_type":"application/pdf","relation":"main_file","date_created":"2025-01-20T09:52:34Z","file_id":"18860","success":1,"creator":"dernst","checksum":"02a9be04a6704fc272ed5a976e5fa8c5","access_level":"open_access","file_name":"2025_PASP_Rodriguez.pdf"}],"language":[{"iso":"eng"}],"ddc":["520"],"author":[{"full_name":"Rodriguez, Antonio C.","first_name":"Antonio C.","last_name":"Rodriguez"},{"last_name":"El-Badry","first_name":"Kareem","full_name":"El-Badry, Kareem"},{"last_name":"Suleimanov","first_name":"Valery","full_name":"Suleimanov, Valery"},{"full_name":"Pala, Anna F.","first_name":"Anna F.","last_name":"Pala"},{"full_name":"Kulkarni, Shrinivas R.","last_name":"Kulkarni","first_name":"Shrinivas R."},{"last_name":"Gaensicke","first_name":"Boris","full_name":"Gaensicke, Boris"},{"first_name":"Kaya","last_name":"Mori","full_name":"Mori, Kaya"},{"first_name":"R. Michael","last_name":"Rich","full_name":"Rich, R. Michael"},{"first_name":"Arnab","last_name":"Sarkar","full_name":"Sarkar, Arnab"},{"first_name":"Tong","last_name":"Bao","full_name":"Bao, Tong"},{"last_name":"De Oliveira","first_name":"Raimundo Lopes","full_name":"De Oliveira, Raimundo Lopes"},{"first_name":"Gavin","last_name":"Ramsay","full_name":"Ramsay, Gavin"},{"first_name":"Paula","last_name":"Szkody","full_name":"Szkody, Paula"},{"full_name":"Graham, Matthew","last_name":"Graham","first_name":"Matthew"},{"full_name":"Prince, Thomas A.","last_name":"Prince","first_name":"Thomas A."},{"id":"8ae5b6e7-2a03-11ee-914d-b58ed7a3b47d","full_name":"Caiazzo, Ilaria","last_name":"Caiazzo","first_name":"Ilaria","orcid":"0000-0002-4770-5388"},{"first_name":"Zachary P.","last_name":"Vanderbosch","full_name":"Vanderbosch, Zachary P."},{"first_name":"Jan Van","last_name":"Roestel","full_name":"Roestel, Jan Van"},{"full_name":"Das, Kaustav K.","last_name":"Das","first_name":"Kaustav K."},{"full_name":"Qin, Yu Jing","first_name":"Yu Jing","last_name":"Qin"},{"first_name":"Mansi M.","last_name":"Kasliwal","full_name":"Kasliwal, Mansi M."},{"full_name":"Wold, Avery","last_name":"Wold","first_name":"Avery"},{"first_name":"Steven L.","last_name":"Groom","full_name":"Groom, Steven L."},{"full_name":"Reiley, Daniel","first_name":"Daniel","last_name":"Reiley"},{"full_name":"Riddle, Reed","last_name":"Riddle","first_name":"Reed"}],"file_date_updated":"2025-01-20T09:52:34Z","article_type":"original","date_created":"2025-01-19T23:01:51Z","year":"2025","publication":"Publications of the Astronomical Society of the Pacific","OA_place":"publisher","day":"01","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)"},"has_accepted_license":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"18851","department":[{"_id":"IlCa"}],"issue":"1","month":"01","date_updated":"2025-02-27T12:46:32Z","quality_controlled":"1","external_id":{"arxiv":["2408.16053"],"isi":["001393204700001"]},"arxiv":1,"article_processing_charge":"No","date_published":"2025-01-01T00:00:00Z","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).","isi":1,"title":"Cataclysmic variables and AM CVn binaries in SRG/eROSITA + Gaia: Volume limited samples, X-ray luminosity functions, and space densities","volume":137,"status":"public","type":"journal_article","publication_identifier":{"issn":["0004-6280"]},"OA_type":"hybrid","publisher":"IOP Publishing","abstract":[{"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.","lang":"eng"}],"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. <i>Publications of the Astronomical Society of the Pacific</i>. 2025;137(1). doi:<a href=\"https://doi.org/10.1088/1538-3873/ada185\">10.1088/1538-3873/ada185</a>","ieee":"A. C. Rodriguez <i>et al.</i>, “Cataclysmic variables and AM CVn binaries in SRG/eROSITA + Gaia: Volume limited samples, X-ray luminosity functions, and space densities,” <i>Publications of the Astronomical Society of the Pacific</i>, vol. 137, no. 1. IOP Publishing, 2025.","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).","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.” <i>Publications of the Astronomical Society of the Pacific</i>, vol. 137, no. 1, 014201, IOP Publishing, 2025, doi:<a href=\"https://doi.org/10.1088/1538-3873/ada185\">10.1088/1538-3873/ada185</a>.","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.” <i>Publications of the Astronomical Society of the Pacific</i>. IOP Publishing, 2025. <a href=\"https://doi.org/10.1088/1538-3873/ada185\">https://doi.org/10.1088/1538-3873/ada185</a>.","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. <i>Publications of the Astronomical Society of the Pacific</i>. IOP Publishing. <a href=\"https://doi.org/10.1088/1538-3873/ada185\">https://doi.org/10.1088/1538-3873/ada185</a>"},"scopus_import":"1","article_number":"014201","oa_version":"Published Version"},{"OA_place":"publisher","publication":"Astronomy & Astrophysics","day":"07","has_accepted_license":"1","tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"issue":"1","department":[{"_id":"IlCa"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"18852","doi":"10.1051/0004-6361/202451371","file":[{"date_created":"2025-01-20T09:57:00Z","file_id":"18861","success":1,"creator":"dernst","checksum":"e532b9c8123c29cfb0ee758e6d00453c","access_level":"open_access","file_name":"2025_AstronomyAstrophysics_Bhat.pdf","file_size":1692527,"date_updated":"2025-01-20T09:57:00Z","content_type":"application/pdf","relation":"main_file"}],"publication_status":"published","oa":1,"intvolume":"       693","file_date_updated":"2025-01-20T09:57:00Z","author":[{"first_name":"Aakash","last_name":"Bhat","full_name":"Bhat, Aakash"},{"first_name":"Evan B.","last_name":"Bauer","full_name":"Bauer, Evan B."},{"last_name":"Pakmor","first_name":"Rüdiger","full_name":"Pakmor, Rüdiger"},{"full_name":"Shen, Ken J.","last_name":"Shen","first_name":"Ken J."},{"orcid":"0000-0002-4770-5388","last_name":"Caiazzo","first_name":"Ilaria","full_name":"Caiazzo, Ilaria","id":"8ae5b6e7-2a03-11ee-914d-b58ed7a3b47d"},{"full_name":"Rajamuthukumar, Abinaya Swaruba","last_name":"Rajamuthukumar","first_name":"Abinaya Swaruba"},{"last_name":"El-Badry","first_name":"Kareem","full_name":"El-Badry, Kareem"},{"full_name":"Kerzendorf, Wolfgang E.","first_name":"Wolfgang E.","last_name":"Kerzendorf"}],"ddc":["520"],"language":[{"iso":"eng"}],"date_created":"2025-01-19T23:01:51Z","article_type":"original","year":"2025","publication_identifier":{"issn":["0004-6361"],"eissn":["1432-0746"]},"type":"journal_article","status":"public","OA_type":"diamond","publisher":"EDP Sciences","oa_version":"Published Version","abstract":[{"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.","lang":"eng"}],"citation":{"ieee":"A. Bhat <i>et al.</i>, “Supernova shocks cannot explain the inflated state of hypervelocity runaways from white dwarf binaries,” <i>Astronomy &#38; Astrophysics</i>, vol. 693, no. 1. EDP Sciences, 2025.","ama":"Bhat A, Bauer EB, Pakmor R, et al. Supernova shocks cannot explain the inflated state of hypervelocity runaways from white dwarf binaries. <i>Astronomy &#38; Astrophysics</i>. 2025;693(1). doi:<a href=\"https://doi.org/10.1051/0004-6361/202451371\">10.1051/0004-6361/202451371</a>","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. <i>Astronomy &#38; Astrophysics</i>. EDP Sciences. <a href=\"https://doi.org/10.1051/0004-6361/202451371\">https://doi.org/10.1051/0004-6361/202451371</a>","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.” <i>Astronomy &#38; Astrophysics</i>. EDP Sciences, 2025. <a href=\"https://doi.org/10.1051/0004-6361/202451371\">https://doi.org/10.1051/0004-6361/202451371</a>.","mla":"Bhat, Aakash, et al. “Supernova Shocks Cannot Explain the Inflated State of Hypervelocity Runaways from White Dwarf Binaries.” <i>Astronomy &#38; Astrophysics</i>, vol. 693, no. 1, A114, EDP Sciences, 2025, doi:<a href=\"https://doi.org/10.1051/0004-6361/202451371\">10.1051/0004-6361/202451371</a>.","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 &#38; Astrophysics. 693(1), A114.","short":"A. Bhat, E.B. Bauer, R. Pakmor, K.J. Shen, I. Caiazzo, A.S. Rajamuthukumar, K. El-Badry, W.E. Kerzendorf, Astronomy &#38; Astrophysics 693 (2025)."},"scopus_import":"1","article_number":"A114","month":"01","external_id":{"arxiv":["2407.03424"],"isi":["001406577300001"]},"quality_controlled":"1","date_updated":"2026-02-16T12:08:05Z","title":"Supernova shocks cannot explain the inflated state of hypervelocity runaways from white dwarf binaries","isi":1,"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.","date_published":"2025-01-07T00:00:00Z","article_processing_charge":"No","arxiv":1,"volume":693},{"publisher":"Royal Society of Chemistry","scopus_import":"1","citation":{"apa":"Zeng, G., Sun, Q., Horta, S., Martínez-Alanis, P. R., Wu, P., Li, J., … Cabot, A. (2025). Modulating the solvation structure to enhance amorphous solid electrolyte interface formation for ultra-stable aqueous zinc anode. <i>Energy and Environmental Science</i>. Royal Society of Chemistry. <a href=\"https://doi.org/10.1039/d4ee03750b\">https://doi.org/10.1039/d4ee03750b</a>","chicago":"Zeng, Guifang, Qing Sun, Sharona Horta, Paulina R. Martínez-Alanis, Peng Wu, Jing Li, Shang Wang, et al. “Modulating the Solvation Structure to Enhance Amorphous Solid Electrolyte Interface Formation for Ultra-Stable Aqueous Zinc Anode.” <i>Energy and Environmental Science</i>. Royal Society of Chemistry, 2025. <a href=\"https://doi.org/10.1039/d4ee03750b\">https://doi.org/10.1039/d4ee03750b</a>.","mla":"Zeng, Guifang, et al. “Modulating the Solvation Structure to Enhance Amorphous Solid Electrolyte Interface Formation for Ultra-Stable Aqueous Zinc Anode.” <i>Energy and Environmental Science</i>, vol. 18, no. 4, Royal Society of Chemistry, 2025, pp. 1683–95, doi:<a href=\"https://doi.org/10.1039/d4ee03750b\">10.1039/d4ee03750b</a>.","ista":"Zeng G, Sun Q, Horta S, Martínez-Alanis PR, Wu P, Li J, Wang S, Ibáñez M, Tian Y, Ci L, Cabot A. 2025. Modulating the solvation structure to enhance amorphous solid electrolyte interface formation for ultra-stable aqueous zinc anode. Energy and Environmental Science. 18(4), 1683–1695.","short":"G. Zeng, Q. Sun, S. Horta, P.R. Martínez-Alanis, P. Wu, J. Li, S. Wang, M. Ibáñez, Y. Tian, L. Ci, A. Cabot, Energy and Environmental Science 18 (2025) 1683–1695.","ieee":"G. Zeng <i>et al.</i>, “Modulating the solvation structure to enhance amorphous solid electrolyte interface formation for ultra-stable aqueous zinc anode,” <i>Energy and Environmental Science</i>, vol. 18, no. 4. Royal Society of Chemistry, pp. 1683–1695, 2025.","ama":"Zeng G, Sun Q, Horta S, et al. Modulating the solvation structure to enhance amorphous solid electrolyte interface formation for ultra-stable aqueous zinc anode. <i>Energy and Environmental Science</i>. 2025;18(4):1683-1695. doi:<a href=\"https://doi.org/10.1039/d4ee03750b\">10.1039/d4ee03750b</a>"},"abstract":[{"text":"Electrolyte additives are extensively validated effective in mitigating dendrite growth and parasitic reactions in aqueous zinc-ion batteries (AZIBs). Nonetheless, the mechanisms by which additives influence the formation and characteristics of the inorganic solid–electrolyte interphase (SEI) are not yet fully elucidated. Herein, we investigate how Zn(CF3COO)2 additives influence solvation structure and elucidate the mechanism by which these additives promote the dual reduction of anions. Through cryo-transmission electron microscopy analysis, we identified the SEI as a highly amorphous ZnS/ZnF2 phase. This amorphous hybrid SEI demonstrates exceptional stability, mechanical robustness, and high Zn2+ conductivity, effectively mitigating parasitic reactions and enhancing Zn plating/stripping reversibility. Even under elevated current densities, the Zn anode exhibits ultra-stable longevity and ultra-high reversibility. This study provides a comprehensive understanding of the intrinsic mechanisms governing solvation structure modulation that lead to the formation of amorphous hybrid SEI, underscoring their efficacy in enhancing the performance and durability of AZIBs.","lang":"eng"}],"oa_version":"None","type":"journal_article","publication_identifier":{"eissn":["1754-5706"],"issn":["1754-5692"]},"status":"public","OA_type":"closed access","title":"Modulating the solvation structure to enhance amorphous solid electrolyte interface formation for ultra-stable aqueous zinc anode","date_published":"2025-02-21T00:00:00Z","article_processing_charge":"No","acknowledgement":"The authors acknowledge financial support from the Joint Fund of Henan Province Science and Technology R&D Program (235200810097) and the Generalitat de Catalunya (2021SGR01581). This research was supported by the Scientific Service Units (SSU) of ISTA Austria through resources provided by the Electron Microscopy Facility (EMF) and the Nanofabrication Facility (NFF). G. Z. and J. L. thank the China Scholarship Council (CSC) for the scholarship support.","isi":1,"volume":18,"acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"NanoFab"}],"month":"02","external_id":{"isi":["001389898000001"]},"date_updated":"2025-07-10T11:51:27Z","quality_controlled":"1","page":"1683-1695","_id":"18853","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","issue":"4","department":[{"_id":"MaIb"}],"publication":"Energy and Environmental Science","day":"21","date_created":"2025-01-19T23:01:52Z","article_type":"original","year":"2025","publication_status":"published","doi":"10.1039/d4ee03750b","intvolume":"        18","language":[{"iso":"eng"}],"author":[{"full_name":"Zeng, Guifang","first_name":"Guifang","last_name":"Zeng"},{"first_name":"Qing","last_name":"Sun","full_name":"Sun, Qing"},{"first_name":"Sharona","last_name":"Horta","full_name":"Horta, Sharona","id":"03a7e858-01b1-11ec-8b71-99ae6c4a05bc"},{"full_name":"Martínez-Alanis, Paulina R.","last_name":"Martínez-Alanis","first_name":"Paulina R."},{"full_name":"Wu, Peng","last_name":"Wu","first_name":"Peng"},{"full_name":"Li, Jing","first_name":"Jing","last_name":"Li"},{"full_name":"Wang, Shang","last_name":"Wang","first_name":"Shang"},{"full_name":"Ibáñez, Maria","id":"43C61214-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5013-2843","first_name":"Maria","last_name":"Ibáñez"},{"full_name":"Tian, Yanhong","first_name":"Yanhong","last_name":"Tian"},{"first_name":"Lijie","last_name":"Ci","full_name":"Ci, Lijie"},{"full_name":"Cabot, Andreu","last_name":"Cabot","first_name":"Andreu"}]},{"OA_place":"publisher","publication":"Astronomy & Astrophysics","day":"06","tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"has_accepted_license":"1","_id":"18854","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"JoMa"}],"publication_status":"published","oa":1,"file":[{"file_size":4513466,"content_type":"application/pdf","date_updated":"2025-01-20T09:17:33Z","relation":"main_file","date_created":"2025-01-20T09:17:33Z","success":1,"file_id":"18858","checksum":"67a791080ade9bfb449d249de2af7456","creator":"dernst","file_name":"2025_AstronomyAstrophysics_Heintz.pdf","access_level":"open_access"}],"doi":"10.1051/0004-6361/202450243","intvolume":"       693","file_date_updated":"2025-01-20T09:17:33Z","ddc":["520"],"language":[{"iso":"eng"}],"author":[{"full_name":"Heintz, K. E.","last_name":"Heintz","first_name":"K. E."},{"full_name":"Brammer, G. B.","last_name":"Brammer","first_name":"G. B."},{"full_name":"Watson, D.","first_name":"D.","last_name":"Watson"},{"last_name":"Oesch","first_name":"P. A.","full_name":"Oesch, P. A."},{"first_name":"L. C.","last_name":"Keating","full_name":"Keating, L. C."},{"full_name":"Hayes, M. J.","first_name":"M. J.","last_name":"Hayes"},{"full_name":"Abdurro'Uf, Unknown","last_name":"Abdurro'Uf","first_name":"Unknown"},{"full_name":"Arellano-Córdova, K. Z.","first_name":"K. Z.","last_name":"Arellano-Córdova"},{"first_name":"A. C.","last_name":"Carnall","full_name":"Carnall, A. C."},{"last_name":"Christiansen","first_name":"C. R.","full_name":"Christiansen, C. R."},{"last_name":"Cullen","first_name":"F.","full_name":"Cullen, F."},{"full_name":"Davé, R.","first_name":"R.","last_name":"Davé"},{"full_name":"Dayal, P.","last_name":"Dayal","first_name":"P."},{"first_name":"A.","last_name":"Ferrara","full_name":"Ferrara, A."},{"last_name":"Finlator","first_name":"K.","full_name":"Finlator, K."},{"full_name":"Fynbo, J. P.U.","first_name":"J. P.U.","last_name":"Fynbo"},{"first_name":"S. R.","last_name":"Flury","full_name":"Flury, S. R."},{"full_name":"Gelli, V.","first_name":"V.","last_name":"Gelli"},{"full_name":"Gillman, S.","last_name":"Gillman","first_name":"S."},{"last_name":"Gottumukkala","first_name":"R.","full_name":"Gottumukkala, R."},{"full_name":"Gould, K.","first_name":"K.","last_name":"Gould"},{"full_name":"Greve, T. R.","last_name":"Greve","first_name":"T. R."},{"first_name":"S. E.","last_name":"Hardin","full_name":"Hardin, S. E."},{"first_name":"T. Y.Y.","last_name":"Hsiao","full_name":"Hsiao, T. Y.Y."},{"first_name":"A.","last_name":"Hutter","full_name":"Hutter, A."},{"full_name":"Jakobsson, P.","first_name":"P.","last_name":"Jakobsson"},{"full_name":"Killi, M.","last_name":"Killi","first_name":"M."},{"last_name":"Khosravaninezhad","first_name":"N.","full_name":"Khosravaninezhad, N."},{"last_name":"Laursen","first_name":"P.","full_name":"Laursen, P."},{"full_name":"Lee, M. M.","first_name":"M. M.","last_name":"Lee"},{"first_name":"G. E.","last_name":"Magdis","full_name":"Magdis, G. E."},{"full_name":"Matthee, Jorryt J","id":"7439a258-f3c0-11ec-9501-9df22fe06720","orcid":"0000-0003-2871-127X","first_name":"Jorryt J","last_name":"Matthee"},{"last_name":"Naidu","first_name":"R. P.","full_name":"Naidu, R. P."},{"full_name":"Narayanan, D.","first_name":"D.","last_name":"Narayanan"},{"first_name":"C.","last_name":"Pollock","full_name":"Pollock, C."},{"first_name":"M. K.M.","last_name":"Prescott","full_name":"Prescott, M. K.M."},{"full_name":"Rusakov, V.","first_name":"V.","last_name":"Rusakov"},{"first_name":"M.","last_name":"Shuntov","full_name":"Shuntov, M."},{"first_name":"A.","last_name":"Sneppen","full_name":"Sneppen, A."},{"last_name":"Smit","first_name":"R.","full_name":"Smit, R."},{"first_name":"N. R.","last_name":"Tanvir","full_name":"Tanvir, N. R."},{"first_name":"C.","last_name":"Terp","full_name":"Terp, C."},{"first_name":"S.","last_name":"Toft","full_name":"Toft, S."},{"first_name":"F.","last_name":"Valentino","full_name":"Valentino, F."},{"last_name":"Vijayan","first_name":"A. P.","full_name":"Vijayan, A. P."},{"first_name":"J. R.","last_name":"Weaver","full_name":"Weaver, J. R."},{"full_name":"Wise, J. H.","last_name":"Wise","first_name":"J. H."},{"last_name":"Witstok","first_name":"J.","full_name":"Witstok, J."}],"date_created":"2025-01-19T23:01:52Z","article_type":"original","year":"2025","type":"journal_article","publication_identifier":{"issn":["0004-6361"],"eissn":["1432-0746"]},"status":"public","OA_type":"diamond","publisher":"EDP Sciences","abstract":[{"lang":"eng","text":"Context. One of the surprising early findings with JWST has been the discovery of a strong “roll-over” or a softening of the absorption edge of Lyα in a large number of galaxies at z ≳ 6, in addition to systematic offsets from photometric redshift estimates and fundamental galaxy scaling relations. This has been interpreted as strong cumulative damped Lyα absorption (DLA) wings from high column densities of neutral atomic hydrogen (H I), signifying major gas accretion events in the formation of these galaxies.\r\nAims. To explore this new phenomenon systematically, we assembled the JWST/NIRSpec PRImordial gas Mass AssembLy (PRIMAL) legacy survey of 584 galaxies at z = 5.0 − 13.4, designed to study the physical properties and gas in and around galaxies during the reionization epoch.\r\nMethods. We characterized this benchmark sample in full and spectroscopically derived the galaxy redshifts, metallicities, star formation rates, and ultraviolet (UV) slopes. We defined a new diagnostic, the Lyα damping parameter DLyα, to measure and quantify the net effect of Lyα emission strength, the H I fraction in the intergalactic medium, or the local H I column density for each source. The JWST-PRIMAL survey is based on the spectroscopic DAWN JWST Archive (DJA-Spec). We describe DJA-Spec in this paper, detailing the reduction methods, the post-processing steps, and basic analysis tools. All the software, reduced spectra, and spectroscopically derived quantities and catalogs are made publicly available in dedicated repositories.\r\nResults. We find that the fraction of galaxies showing strong integrated DLAs with NHI > 1021 cm−2 only increases slightly from ≈60% at z ≈ 6 up to ≈65 − 90% at z > 8. Similarly, the prevalence and prominence of Lyα emission is found to increase with decreasing redshift, in qualitative agreement with previous observational results. Strong Lyα emitters (LAEs) are predominantly found to be associated with low-metallicity and UV faint galaxies. By contrast, strong DLAs are observed in galaxies with a variety of intrinsic physical properties, but predominantly at high redshifts and low metallicities.\r\nConclusions. Our results indicate that strong DLAs likely reflect a particular early assembly phase of reionization-era galaxies, at which point they are largely dominated by pristine H I gas accretion. At z = 8 − 10, this gas gradually cools and forms into stars that ionize their local surroundings, forming large ionized bubbles and producing strong observed Lyα emission at z < 8."}],"scopus_import":"1","article_number":"A60","citation":{"ieee":"K. E. Heintz <i>et al.</i>, “The JWST-PRIMAL archival survey: A JWST/NIRSpec reference sample for the physical properties and Lyman-α absorption and emission of ∼600 galaxies at z = 5.0-13.4,” <i>Astronomy &#38; Astrophysics</i>, vol. 693. EDP Sciences, 2025.","ama":"Heintz KE, Brammer GB, Watson D, et al. The JWST-PRIMAL archival survey: A JWST/NIRSpec reference sample for the physical properties and Lyman-α absorption and emission of ∼600 galaxies at z = 5.0-13.4. <i>Astronomy &#38; Astrophysics</i>. 2025;693. doi:<a href=\"https://doi.org/10.1051/0004-6361/202450243\">10.1051/0004-6361/202450243</a>","apa":"Heintz, K. E., Brammer, G. B., Watson, D., Oesch, P. A., Keating, L. C., Hayes, M. J., … Witstok, J. (2025). The JWST-PRIMAL archival survey: A JWST/NIRSpec reference sample for the physical properties and Lyman-α absorption and emission of ∼600 galaxies at z = 5.0-13.4. <i>Astronomy &#38; Astrophysics</i>. EDP Sciences. <a href=\"https://doi.org/10.1051/0004-6361/202450243\">https://doi.org/10.1051/0004-6361/202450243</a>","chicago":"Heintz, K. E., G. B. Brammer, D. Watson, P. A. Oesch, L. C. Keating, M. J. Hayes, Unknown Abdurro’Uf, et al. “The JWST-PRIMAL Archival Survey: A JWST/NIRSpec Reference Sample for the Physical Properties and Lyman-α Absorption and Emission of ∼600 Galaxies at z = 5.0-13.4.” <i>Astronomy &#38; Astrophysics</i>. EDP Sciences, 2025. <a href=\"https://doi.org/10.1051/0004-6361/202450243\">https://doi.org/10.1051/0004-6361/202450243</a>.","mla":"Heintz, K. E., et al. “The JWST-PRIMAL Archival Survey: A JWST/NIRSpec Reference Sample for the Physical Properties and Lyman-α Absorption and Emission of ∼600 Galaxies at z = 5.0-13.4.” <i>Astronomy &#38; Astrophysics</i>, vol. 693, A60, EDP Sciences, 2025, doi:<a href=\"https://doi.org/10.1051/0004-6361/202450243\">10.1051/0004-6361/202450243</a>.","ista":"Heintz KE, Brammer GB, Watson D, Oesch PA, Keating LC, Hayes MJ, Abdurro’Uf U, Arellano-Córdova KZ, Carnall AC, Christiansen CR, Cullen F, Davé R, Dayal P, Ferrara A, Finlator K, Fynbo JPU, Flury SR, Gelli V, Gillman S, Gottumukkala R, Gould K, Greve TR, Hardin SE, Hsiao TYY, Hutter A, Jakobsson P, Killi M, Khosravaninezhad N, Laursen P, Lee MM, Magdis GE, Matthee JJ, Naidu RP, Narayanan D, Pollock C, Prescott MKM, Rusakov V, Shuntov M, Sneppen A, Smit R, Tanvir NR, Terp C, Toft S, Valentino F, Vijayan AP, Weaver JR, Wise JH, Witstok J. 2025. The JWST-PRIMAL archival survey: A JWST/NIRSpec reference sample for the physical properties and Lyman-α absorption and emission of ∼600 galaxies at z = 5.0-13.4. Astronomy &#38; Astrophysics. 693, A60.","short":"K.E. Heintz, G.B. Brammer, D. Watson, P.A. Oesch, L.C. Keating, M.J. Hayes, U. Abdurro’Uf, K.Z. Arellano-Córdova, A.C. Carnall, C.R. Christiansen, F. Cullen, R. Davé, P. Dayal, A. Ferrara, K. Finlator, J.P.U. Fynbo, S.R. Flury, V. Gelli, S. Gillman, R. Gottumukkala, K. Gould, T.R. Greve, S.E. Hardin, T.Y.Y. Hsiao, A. Hutter, P. Jakobsson, M. Killi, N. Khosravaninezhad, P. Laursen, M.M. Lee, G.E. Magdis, J.J. Matthee, R.P. Naidu, D. Narayanan, C. Pollock, M.K.M. Prescott, V. Rusakov, M. Shuntov, A. Sneppen, R. Smit, N.R. Tanvir, C. Terp, S. Toft, F. Valentino, A.P. Vijayan, J.R. Weaver, J.H. Wise, J. Witstok, Astronomy &#38; Astrophysics 693 (2025)."},"oa_version":"Published Version","month":"01","external_id":{"isi":["001390856800001"]},"date_updated":"2026-02-16T12:07:37Z","quality_controlled":"1","title":"The JWST-PRIMAL archival survey: A JWST/NIRSpec reference sample for the physical properties and Lyman-α absorption and emission of ∼600 galaxies at z = 5.0-13.4","date_published":"2025-01-06T00:00:00Z","article_processing_charge":"No","isi":1,"acknowledgement":"We would like to thank the referee for a detailed and constructive report, greatly improving the presentation of the results in this work. We would like to thank Peter Jakobsen for his vision and heroic endeavor in optimally designing the JWST/NIRSpec instrument and some of its first on-sky observations and for enlightening discussions about the intricacies of the NIRSpec data. Further, we would like to thank John Chisholm for helpful clarifications and discussions related to the escape fraction of ionizing photons and Aayush Saxena for enlightening conversations on the escape and absorption of Lyman-α photons. This work has received funding from the Swiss State Secretariat for Education, Research and Innovation (SERI) under contract number MB22.00072. The Cosmic Dawn Center (DAWN) is funded by the Danish National Research Foundation under grant DNRF140. The data products presented herein were retrieved from the DAWN JWST Archive (DJA). DJA is an initiative of the Cosmic Dawn Center, which is funded by the Danish National Research Foundation under grant DNRF140. P.D. acknowledge support from the NWO grant 016.VIDI.189.162 (“ODIN\") and warmly thanks the European Commission’s and University of Groningen’s CO-FUND Rosalind Franklin program. Support from the ERC Advanced Grant INTERSTELLAR H2020/740120 is kindly acknowledged (A.F.). S.G. acknowledges financial support from the Villum Young Investigator grants 37440 and 13160 and the Cosmic Dawn Center. M.K. was supported by the ANID BASAL project FB210003. G.E.M. acknowledges financial support from the Villum Young Investigator grants 37440 and 13160 and the Cosmic Dawn Center. J.W. acknowledges support from the Science and Technology Facilities Council (STFC), by the ERC through Advanced Grant 695671 “QUENCH”, by the UKRI Frontier Research grant RISEandFALL. Support for this work was provided by NASA through the NASA Hubble Fellowship grant HST-HF2-51515.001-A awarded by the Space Telescope Science Institute, which is operated by the Association of Universities for Research in Astronomy, Incorporated, under NASA contract NAS5-26555. F.C. acknowledges support from a UKRI Frontier Research Guarantee Grant (PI Cullen; grant reference EP/X021025/1). J.H.W. acknowledges support by NSF grant AST-2108020 and NASA grants 80NSSC20K0520 and 80NSSC21K1053. NRT acknowledges support through STFC consolidated grant ST/W000857/1. M.J.H. is supported by the Swedish Research Council, VetenskapsrÅdet, and is fellow of the Knut & Alice Wallenberg foundation. This work is based in part on observations made with the NASA/ESA/CSA James Webb Space Telescope. The data were obtained from the Mikulski Archive for Space Telescopes (MAST) at the Space Telescope Science Institute, which is operated by the Association of Universities for Research in Astronomy, Inc., under NASA contract NAS 5-03127 for JWST. Software: This work made use of and acknowledge the following software: NumPy (Harris et al. 2020), Matplotlib (Hunter 2007), LMfit (Newville et al. 2014), SciPy (Virtanen et al. 2020), grizli (Brammer 2023a), Astrodrizzle (Gonzaga et al. 2012), and MsaExp (v0.3; Brammer 2023b).","volume":693},{"oa_version":"Preprint","citation":{"ama":"Harris DG, Kolmogorov V. Parameter estimation for Gibbs distributions. <i>ACM Transactions on Algorithms</i>. 2025;21(1). doi:<a href=\"https://doi.org/10.1145/3685676\">10.1145/3685676</a>","ieee":"D. G. Harris and V. Kolmogorov, “Parameter estimation for Gibbs distributions,” <i>ACM Transactions on Algorithms</i>, vol. 21, no. 1. Association for Computing Machinery, 2025.","mla":"Harris, David G., and Vladimir Kolmogorov. “Parameter Estimation for Gibbs Distributions.” <i>ACM Transactions on Algorithms</i>, vol. 21, no. 1, 3, Association for Computing Machinery, 2025, doi:<a href=\"https://doi.org/10.1145/3685676\">10.1145/3685676</a>.","ista":"Harris DG, Kolmogorov V. 2025. Parameter estimation for Gibbs distributions. ACM Transactions on Algorithms. 21(1), 3.","short":"D.G. Harris, V. Kolmogorov, ACM Transactions on Algorithms 21 (2025).","apa":"Harris, D. G., &#38; Kolmogorov, V. (2025). Parameter estimation for Gibbs distributions. <i>ACM Transactions on Algorithms</i>. Association for Computing Machinery. <a href=\"https://doi.org/10.1145/3685676\">https://doi.org/10.1145/3685676</a>","chicago":"Harris, David G., and Vladimir Kolmogorov. “Parameter Estimation for Gibbs Distributions.” <i>ACM Transactions on Algorithms</i>. Association for Computing Machinery, 2025. <a href=\"https://doi.org/10.1145/3685676\">https://doi.org/10.1145/3685676</a>."},"scopus_import":"1","abstract":[{"lang":"eng","text":"A central problem in computational statistics is to convert a procedure for sampling combinatorial objects into a procedure for counting those objects, and vice versa. We consider sampling problems which come from Gibbs distributions, which are families of probability distributions over a discrete space Ω with probability mass function of the form μ^Ω_β(ω) ∝ e^{β H(ω)} for β in an interval [β_min, β_max] and H(ω) ∈ {0} ∪ [1, n]. Two important parameters are the partition function, which is the normalization factor Z(β) = ∑_{ω ∈ Ω} e^{β H(ω)}, and the vector of pre-image counts c_x=|H^-1(x)|.\r\nWe develop black-box sampling algorithms to estimate the counts roughly Õ(n²/ε²) samples for integer-valued distributions and Õ(q/ε²) samples for general distributions, where q = (log Z(β_max))/Z(β_min)  (ignoring some second-order terms and parameters). We show this is optimal up to logarithmic factors. We illustrate with improved algorithms for counting connected subgraphs, independent sets, and perfect matchings. As a key subroutine, we estimate all values of the partition function using Õ(n²/ε²) samples for integer-valued distributions and Õ(q/ε²) samples for general distributions. This improves over a prior algorithm of Huber (2015) which computes a single point estimate Z(β_max) and which uses a slightly larger amount of samples. We show matching lower bounds, demonstrating this complexity is optimal as a function of n and q up to logarithmic terms."}],"article_number":"3","publisher":"Association for Computing Machinery","main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2007.10824","open_access":"1"}],"OA_type":"green","related_material":{"record":[{"relation":"earlier_version","id":"14084","status":"public"}]},"publication_identifier":{"eissn":["1549-6333"],"issn":["1549-6325"]},"type":"journal_article","status":"public","volume":21,"title":"Parameter estimation for Gibbs distributions","isi":1,"acknowledgement":"We thank Heng Guo for helpful explanations of algorithms for sampling connected subgraphs and matchings, and Maksym Serbyn for bringing to our attention the WL algorithm and its use in physics.\r\nThis is an extended version, which includes work under the same name from ICALP 2023, as well as the earlier work [22] appearing in COLT 2018.\r\nV. Kolmogorov was supported by the European Research Council under the European Unions Seventh Framework Programme (FP7/2007-2013)/ERC grant agreement no 616160","article_processing_charge":"No","date_published":"2025-01-01T00:00:00Z","arxiv":1,"external_id":{"arxiv":["2007.10824"],"isi":["001399998600008"]},"date_updated":"2025-07-10T11:50:44Z","quality_controlled":"1","month":"01","department":[{"_id":"VlKo"}],"ec_funded":1,"issue":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"18855","day":"01","OA_place":"repository","corr_author":"1","publication":"ACM Transactions on Algorithms","year":"2025","date_created":"2025-01-19T23:01:52Z","article_type":"original","author":[{"last_name":"Harris","first_name":"David G.","full_name":"Harris, David G."},{"first_name":"Vladimir","last_name":"Kolmogorov","id":"3D50B0BA-F248-11E8-B48F-1D18A9856A87","full_name":"Kolmogorov, Vladimir"}],"language":[{"iso":"eng"}],"doi":"10.1145/3685676","project":[{"grant_number":"616160","_id":"25FBA906-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Discrete Optimization in Computer Vision: Theory and Practice"}],"publication_status":"published","oa":1,"intvolume":"        21"},{"file_date_updated":"2025-04-16T07:13:31Z","author":[{"full_name":"Scalco, M.","last_name":"Scalco","first_name":"M."},{"first_name":"R.","last_name":"Gerasimov","full_name":"Gerasimov, R."},{"full_name":"Bedin, L. R.","last_name":"Bedin","first_name":"L. R."},{"full_name":"Vesperini, E.","last_name":"Vesperini","first_name":"E."},{"full_name":"Correnti, M.","last_name":"Correnti","first_name":"M."},{"last_name":"Nardiello","first_name":"D.","full_name":"Nardiello, D."},{"full_name":"Burgasser, A.","last_name":"Burgasser","first_name":"A."},{"first_name":"H.","last_name":"Richer","full_name":"Richer, H."},{"orcid":"0000-0002-4770-5388","first_name":"Ilaria","last_name":"Caiazzo","full_name":"Caiazzo, Ilaria","id":"8ae5b6e7-2a03-11ee-914d-b58ed7a3b47d"},{"last_name":"Heyl","first_name":"J.","full_name":"Heyl, J."},{"first_name":"M.","last_name":"Libralato","full_name":"Libralato, M."},{"full_name":"Anderson, J.","first_name":"J.","last_name":"Anderson"},{"last_name":"Griggio","first_name":"M.","full_name":"Griggio, M."}],"ddc":["520"],"language":[{"iso":"eng"}],"file":[{"date_created":"2025-04-16T07:13:31Z","file_id":"19569","success":1,"checksum":"db765ce222df60a1e7c19da1968906a8","creator":"dernst","access_level":"open_access","file_name":"2025_AstronomyAstrophysics_Scalco.pdf","file_size":18080704,"date_updated":"2025-04-16T07:13:31Z","relation":"main_file","content_type":"application/pdf"}],"doi":"10.1051/0004-6361/202452907","publication_status":"published","oa":1,"intvolume":"       694","year":"2025","date_created":"2025-01-21T15:29:36Z","article_type":"original","day":"04","OA_place":"publisher","publication":"Astronomy & Astrophysics","department":[{"_id":"IlCa"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"18866","has_accepted_license":"1","tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"external_id":{"isi":["001414753300007"],"arxiv":["2501.04446"]},"date_updated":"2025-07-10T11:51:28Z","quality_controlled":"1","month":"02","volume":694,"title":"JWST photometry and astrometry of 47 Tucanae. Discontinuity in the stellar sequence at the star--brown dwarf transition","acknowledgement":"We dedicate this paper to the memory of our colleague Prof. Harvey Richer (⋆ April 1944 —† 13 November 2023), a highly accomplished astronomer and expert in stellar populations and in particular within globular clusters, who passed away during this project. Harvey grew up in Montreal and was at least the second star man to graduate from his high school, having been preceded by William Shatner by more than a decade. He worked at the University of British Columbia for most of his career, and his focus was the late stages of stellar evolution, in particular carbon stars and white dwarfs. We thank the referee for his valuable suggestions and comments, which helped improve the paper, as well as for his prompt revision.","isi":1,"date_published":"2025-02-04T00:00:00Z","article_processing_charge":"Yes","arxiv":1,"OA_type":"diamond","publication_identifier":{"eissn":["1432-0746"],"issn":["0004-6361"]},"type":"journal_article","status":"public","oa_version":"Published Version","abstract":[{"text":"Using JWST Near Infrared Camera (NIRCam) images of the globular cluster 47,Tucanæ, (or NGC,104), taken at two epochs just 7 months apart, we derived proper-motion membership down to F322W2 ∼ 27. We identified an intriguing feature at the very low-mass end of the main sequence, around ∼ 0.08,M_⋅, at magnitudes F322W2 ∼ 24 and m_ F150W2 ∼ 25. This feature, dubbed 'kink', is characterized by a prominent discontinuity in the slope of the main sequence. A similar discontinuity is seen in theoretical isochrones with oxygen-poor chemistries, related to the rapid onset of absorption. We therefore hypothesize that the cluster hosts disproportionately more oxygen-poor stars near the bottom of the main sequence compared to the upper main sequence and the red giant branch. Our results show no strong or conclusive evidence of a rise in the brown dwarf luminosity function at faint magnitudes, in contrast to previous findings likely affected by faint red background galaxies. In our analysis, we accounted for this contamination by using proper motion membership.","lang":"eng"}],"citation":{"mla":"Scalco, M., et al. “JWST Photometry and Astrometry of 47 Tucanae. Discontinuity in the Stellar Sequence at the Star--Brown Dwarf Transition.” <i>Astronomy &#38; Astrophysics</i>, vol. 694, A68, EDP Sciences, 2025, doi:<a href=\"https://doi.org/10.1051/0004-6361/202452907\">10.1051/0004-6361/202452907</a>.","ista":"Scalco M, Gerasimov R, Bedin LR, Vesperini E, Correnti M, Nardiello D, Burgasser A, Richer H, Caiazzo I, Heyl J, Libralato M, Anderson J, Griggio M. 2025. JWST photometry and astrometry of 47 Tucanae. Discontinuity in the stellar sequence at the star--brown dwarf transition. Astronomy &#38; Astrophysics. 694, A68.","short":"M. Scalco, R. Gerasimov, L.R. Bedin, E. Vesperini, M. Correnti, D. Nardiello, A. Burgasser, H. Richer, I. Caiazzo, J. Heyl, M. Libralato, J. Anderson, M. Griggio, Astronomy &#38; Astrophysics 694 (2025).","apa":"Scalco, M., Gerasimov, R., Bedin, L. R., Vesperini, E., Correnti, M., Nardiello, D., … Griggio, M. (2025). JWST photometry and astrometry of 47 Tucanae. Discontinuity in the stellar sequence at the star--brown dwarf transition. <i>Astronomy &#38; Astrophysics</i>. EDP Sciences. <a href=\"https://doi.org/10.1051/0004-6361/202452907\">https://doi.org/10.1051/0004-6361/202452907</a>","chicago":"Scalco, M., R. Gerasimov, L. R. Bedin, E. Vesperini, M. Correnti, D. Nardiello, A. Burgasser, et al. “JWST Photometry and Astrometry of 47 Tucanae. Discontinuity in the Stellar Sequence at the Star--Brown Dwarf Transition.” <i>Astronomy &#38; Astrophysics</i>. EDP Sciences, 2025. <a href=\"https://doi.org/10.1051/0004-6361/202452907\">https://doi.org/10.1051/0004-6361/202452907</a>.","ama":"Scalco M, Gerasimov R, Bedin LR, et al. JWST photometry and astrometry of 47 Tucanae. Discontinuity in the stellar sequence at the star--brown dwarf transition. <i>Astronomy &#38; Astrophysics</i>. 2025;694. doi:<a href=\"https://doi.org/10.1051/0004-6361/202452907\">10.1051/0004-6361/202452907</a>","ieee":"M. Scalco <i>et al.</i>, “JWST photometry and astrometry of 47 Tucanae. Discontinuity in the stellar sequence at the star--brown dwarf transition,” <i>Astronomy &#38; Astrophysics</i>, vol. 694. EDP Sciences, 2025."},"scopus_import":"1","article_number":"A68","publisher":"EDP Sciences"}]