[{"OA_type":"closed access","volume":2886,"ec_funded":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","pmid":1,"corr_author":"1","date_created":"2025-01-07T08:36:47Z","external_id":{"pmid":["39745639"]},"author":[{"id":"471195F6-F248-11E8-B48F-1D18A9856A87","first_name":"Giselle T","full_name":"Cheung, Giselle T","last_name":"Cheung","orcid":"0000-0001-8457-2572"},{"id":"48EA0138-F248-11E8-B48F-1D18A9856A87","full_name":"Pauler, Florian","first_name":"Florian","last_name":"Pauler","orcid":"0000-0002-7462-0048"},{"id":"37B36620-F248-11E8-B48F-1D18A9856A87","last_name":"Hippenmeyer","orcid":"0000-0003-2279-1061","full_name":"Hippenmeyer, Simon","first_name":"Simon"}],"language":[{"iso":"eng"}],"intvolume":"      2886","status":"public","page":"139-151","title":"Probing Cell-Type Specificity of Mutant Phenotype at Transcriptomic Level Using Mosaic Analysis with Double Markers (MADM)","quality_controlled":"1","publisher":"Springer Nature","date_published":"2025-01-03T00:00:00Z","year":"2025","scopus_import":"1","abstract":[{"lang":"eng","text":"Mosaic Analysis with Double Markers (MADM) represents a mouse genetic approach coupling differential fluorescent labeling to genetic manipulations in dividing cells and their lineages. MADM uniquely enables the generation and visualization of individual control or homozygous mutant cells in a heterozygous genetic environment. Among its diverse applications, MADM has been used to dissect cell-autonomous gene functions important for cortical development and neural development in general. The high cellular resolution offered by MADM also permits the analysis of transcriptomic changes of individual cells upon genetic manipulations. In this chapter, we describe an experimental protocol combining the generation and isolation of MADM-labeled cells with downstream single-cell RNA-sequencing technologies to probe cell-type specific phenotypes due to genetic mutations at single-cell resolution."}],"alternative_title":["Methods in Molecular Biology"],"month":"01","date_updated":"2025-04-14T07:43:46Z","oa_version":"None","publication_status":"published","series_title":"MIMB","project":[{"name":"ISTplus - Postdoctoral Fellowships","_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"754411"}],"article_processing_charge":"No","department":[{"_id":"SiHi"}],"citation":{"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>.","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.","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>","ista":"Cheung GT, Pauler F, Hippenmeyer S. 2025.Probing Cell-Type Specificity of Mutant Phenotype at Transcriptomic Level Using Mosaic Analysis with Double Markers (MADM). In: Lineage Tracing. Methods in Molecular Biology, vol. 2886, 139–151.","mla":"Cheung, Giselle T., et al. “Probing Cell-Type Specificity of Mutant Phenotype at Transcriptomic Level Using Mosaic Analysis with Double Markers (MADM).” <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>.","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>","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."},"type":"book_chapter","publication_identifier":{"isbn":["9781071643099"],"eissn":["1940-6029"],"issn":["1064-3745"],"eisbn":["9781071643105"]},"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.","doi":"10.1007/978-1-0716-4310-5_7","_id":"18765","place":"New York, NY","day":"03","editor":[{"first_name":"Jorge","full_name":"Garcia-Marques, Jorge","last_name":"Garcia-Marques"},{"full_name":"Lee, Tzumin","first_name":"Tzumin","last_name":"Lee"}],"acknowledged_ssus":[{"_id":"Bio"}],"publication":"Lineage Tracing"},{"date_published":"2025-04-01T00:00:00Z","publisher":"Springer Nature","date_updated":"2025-11-20T10:28:36Z","isi":1,"month":"04","year":"2025","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."}],"scopus_import":"1","file":[{"file_id":"19573","creator":"dernst","access_level":"open_access","relation":"main_file","date_created":"2025-04-16T08:17:27Z","content_type":"application/pdf","checksum":"2919b30b271f395888e880076a680d73","file_name":"2025_NatureStrucMolBiol_Tluckova.pdf","file_size":9306639,"success":1,"date_updated":"2025-04-16T08:17:27Z"}],"oa_version":"Published Version","article_processing_charge":"Yes (in subscription journal)","project":[{"_id":"c08a6700-5a5b-11eb-8a69-82a722b2bc30","name":"Regulation of mammalian transcription by noncoding RNA","grant_number":"P34185"}],"publication_status":"published","OA_place":"publisher","citation":{"apa":"Tluckova, K., Kaczmarek, B. M., Testa Salmazo, A. P., &#38; Bernecky, C. (2025). Mechanism of mammalian transcriptional repression by noncoding RNA. <i>Nature Structural &#38; Molecular Biology</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41594-024-01448-7\">https://doi.org/10.1038/s41594-024-01448-7</a>","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.","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>","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>.","short":"K. Tluckova, B.M. Kaczmarek, A.P. Testa Salmazo, C. Bernecky, Nature Structural &#38; Molecular Biology 32 (2025) 607–612.","chicago":"Tluckova, Katarina, Beata M Kaczmarek, Anita P Testa Salmazo, and Carrie Bernecky. “Mechanism of Mammalian Transcriptional Repression by Noncoding RNA.” <i>Nature Structural &#38; Molecular Biology</i>. Springer Nature, 2025. <a href=\"https://doi.org/10.1038/s41594-024-01448-7\">https://doi.org/10.1038/s41594-024-01448-7</a>.","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."},"type":"journal_article","department":[{"_id":"CaBe"}],"oa":1,"doi":"10.1038/s41594-024-01448-7","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.","publication_identifier":{"eissn":["1545-9985"],"issn":["1545-9993"]},"_id":"18778","day":"01","publication":"Nature Structural & Molecular Biology","acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"EM-Fac"},{"_id":"ScienComp"},{"_id":"PreCl"}],"file_date_updated":"2025-04-16T08:17:27Z","OA_type":"hybrid","has_accepted_license":"1","volume":32,"related_material":{"record":[{"relation":"earlier_version","status":"public","id":"14644"}]},"pmid":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2025-01-08T11:20:20Z","ddc":["570"],"corr_author":"1","article_type":"original","language":[{"iso":"eng"}],"external_id":{"isi":["001390268000001"],"pmid":["39762629"]},"author":[{"last_name":"Tluckova","full_name":"Tluckova, Katarina","first_name":"Katarina","id":"4AC7D980-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Beata M","full_name":"Kaczmarek, Beata M","last_name":"Kaczmarek","id":"36FA4AFA-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Testa Salmazo","first_name":"Anita P","full_name":"Testa Salmazo, Anita P","id":"41F1F098-F248-11E8-B48F-1D18A9856A87"},{"id":"2CB9DFE2-F248-11E8-B48F-1D18A9856A87","first_name":"Carrie A","full_name":"Bernecky, Carrie A","orcid":"0000-0003-0893-7036","last_name":"Bernecky"}],"APC_amount":"12348 EUR","status":"public","intvolume":"        32","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"},"quality_controlled":"1","title":"Mechanism of mammalian transcriptional repression by noncoding RNA"},{"article_number":"270","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","pmid":1,"article_type":"original","date_created":"2025-01-12T23:04:00Z","ddc":["570"],"has_accepted_license":"1","OA_type":"gold","volume":16,"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png","short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)"},"DOAJ_listed":"1","quality_controlled":"1","title":"Automatic feature selection and weighting in molecular systems using Differentiable Information Imbalance","language":[{"iso":"eng"}],"author":[{"full_name":"Wild, Romina","first_name":"Romina","last_name":"Wild"},{"orcid":"0009-0000-1457-795X","last_name":"Wodaczek","first_name":"Felix","full_name":"Wodaczek, Felix","id":"8b4b6a9f-32b0-11ee-9fa8-bbe85e26258e"},{"last_name":"Del Tatto","first_name":"Vittorio","full_name":"Del Tatto, Vittorio"},{"full_name":"Cheng, Bingqing","first_name":"Bingqing","orcid":"0000-0002-3584-9632","last_name":"Cheng","id":"cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9"},{"last_name":"Laio","full_name":"Laio, Alessandro","first_name":"Alessandro"}],"external_id":{"pmid":["39747013"],"isi":["001389959100009"]},"intvolume":"        16","status":"public","file":[{"access_level":"open_access","creator":"dernst","date_created":"2025-01-14T06:59:25Z","relation":"main_file","file_id":"18846","file_size":1216738,"date_updated":"2025-01-14T06:59:25Z","success":1,"content_type":"application/pdf","file_name":"2025_NatureComm_Wild.pdf","checksum":"b3d0f3568d9a87c494cf231a5324029a"}],"oa_version":"Published Version","publication_status":"published","OA_place":"publisher","article_processing_charge":"Yes","date_published":"2025-01-02T00:00:00Z","publisher":"Springer Nature","abstract":[{"text":"Feature selection is essential in the analysis of molecular systems and many other fields, but several uncertainties remain: What is the optimal number of features for a simplified, interpretable model that retains essential information? How should features with different units be aligned, and how should their relative importance be weighted? Here, we introduce the Differentiable Information Imbalance (DII), an automated method to rank information content between sets of features. Using distances in a ground truth feature space, DII identifies a low-dimensional subset of features that best preserves these relationships. Each feature is scaled by a weight, which is optimized by minimizing the DII through gradient descent. This allows simultaneously performing unit alignment and relative importance scaling, while preserving interpretability. DII can also produce sparse solutions and determine the optimal size of the reduced feature space. We demonstrate the usefulness of this approach on two benchmark molecular problems: (1) identifying collective variables that describe conformations of a biomolecule, and (2) selecting features for training a machine-learning force field. These results show the potential of DII in addressing feature selection challenges and optimizing dimensionality in various applications. The method is available in the Python library DADApy.","lang":"eng"}],"scopus_import":"1","year":"2025","date_updated":"2025-02-27T12:41:25Z","isi":1,"month":"01","day":"02","_id":"18820","file_date_updated":"2025-01-14T06:59:25Z","publication":"Nature Communications","oa":1,"citation":{"ista":"Wild R, Wodaczek F, Del Tatto V, Cheng B, Laio A. 2025. Automatic feature selection and weighting in molecular systems using Differentiable Information Imbalance. Nature Communications. 16, 270.","apa":"Wild, R., Wodaczek, F., Del Tatto, V., Cheng, B., &#38; Laio, A. (2025). Automatic feature selection and weighting in molecular systems using Differentiable Information Imbalance. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-024-55449-7\">https://doi.org/10.1038/s41467-024-55449-7</a>","short":"R. Wild, F. Wodaczek, V. Del Tatto, B. Cheng, A. Laio, Nature Communications 16 (2025).","mla":"Wild, Romina, et al. “Automatic Feature Selection and Weighting in Molecular Systems Using Differentiable Information Imbalance.” <i>Nature Communications</i>, vol. 16, 270, Springer Nature, 2025, doi:<a href=\"https://doi.org/10.1038/s41467-024-55449-7\">10.1038/s41467-024-55449-7</a>.","ama":"Wild R, Wodaczek F, Del Tatto V, Cheng B, Laio A. Automatic feature selection and weighting in molecular systems using Differentiable Information Imbalance. <i>Nature Communications</i>. 2025;16. doi:<a href=\"https://doi.org/10.1038/s41467-024-55449-7\">10.1038/s41467-024-55449-7</a>","chicago":"Wild, Romina, Felix Wodaczek, Vittorio Del Tatto, Bingqing Cheng, and Alessandro Laio. “Automatic Feature Selection and Weighting in Molecular Systems Using Differentiable Information Imbalance.” <i>Nature Communications</i>. Springer Nature, 2025. <a href=\"https://doi.org/10.1038/s41467-024-55449-7\">https://doi.org/10.1038/s41467-024-55449-7</a>.","ieee":"R. Wild, F. Wodaczek, V. Del Tatto, B. Cheng, and A. Laio, “Automatic feature selection and weighting in molecular systems using Differentiable Information Imbalance,” <i>Nature Communications</i>, vol. 16. Springer Nature, 2025."},"department":[{"_id":"AnSa"},{"_id":"BiCh"}],"type":"journal_article","doi":"10.1038/s41467-024-55449-7","publication_identifier":{"eissn":["2041-1723"]},"acknowledgement":"The authors thank Dr. Matteo Carli for providing the CLN025 replica exchange MD trajectory and Matteo Allione for the fruitful discussions connected with the idea of the linear scaling estimator. This work was partially funded by NextGenerationEU through the Italian National Centre for HPC, Big Data, and Quantum Computing (Grant No. CN00000013 received by A.L.). A.L. also acknowledges financial support by the region Friuli Venezia Giulia (project F53C22001770002 received by A.L.)."},{"title":"Comparison of renormalized interactions using one-dimensional few-body systems as a testbed","quality_controlled":"1","author":[{"last_name":"Brauneis","full_name":"Brauneis, Fabian","first_name":"Fabian"},{"last_name":"Hammer","full_name":"Hammer, Hans Werner","first_name":"Hans Werner"},{"full_name":"Reimann, Stephanie M.","first_name":"Stephanie M.","last_name":"Reimann"},{"id":"37D278BC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-0393-5525","last_name":"Volosniev","first_name":"Artem","full_name":"Volosniev, Artem"}],"external_id":{"arxiv":["2408.10052"],"isi":["001398791400004"]},"language":[{"iso":"eng"}],"intvolume":"       111","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_number":"013303","article_type":"original","date_created":"2025-01-12T23:04:00Z","OA_type":"green","volume":111,"_id":"18821","day":"03","issue":"1","publication":"Physical Review A","oa":1,"type":"journal_article","department":[{"_id":"MiLe"}],"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>","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.","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>","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>.","short":"F. Brauneis, H.W. Hammer, S.M. Reimann, A. Volosniev, Physical Review A 111 (2025).","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>.","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."},"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).","publication_identifier":{"issn":["2469-9926"],"eissn":["2469-9934"]},"doi":"10.1103/PhysRevA.111.013303","oa_version":"Preprint","OA_place":"repository","publication_status":"published","article_processing_charge":"No","publisher":"American Physical Society","main_file_link":[{"url":" https://doi.org/10.48550/arXiv.2408.10052","open_access":"1"}],"date_published":"2025-01-03T00:00:00Z","scopus_import":"1","abstract":[{"text":"Even though the one-dimensional contact interaction requires no regularization, renormalization methods have been shown to improve the convergence of numerical calculations considerably. In this work, we compare and contrast these methods: “the running coupling constant” where the two-body ground-state energy is used as a renormalization condition, and two effective interaction approaches that include information about the ground as well as excited states. In particular, we calculate the energies and densities of few-fermion systems in a harmonic oscillator with the configuration-interaction method and compare the results based upon renormalized and bare interactions. We find that the use of the running coupling constant instead of the bare interaction improves convergence significantly. A comparison with an effective interaction, which is designed to reproduce the relative part of the energy spectrum of two particles, showed a similar improvement. The effective interaction provides an additional improvement if the center-of-mass excitations are included in the construction. Finally, we discuss the transformation of observables alongside the renormalization of the potential, and demonstrate that this might be an essential ingredient for accurate numerical calculations.","lang":"eng"}],"year":"2025","isi":1,"month":"01","arxiv":1,"date_updated":"2025-02-27T12:41:58Z"},{"has_accepted_license":"1","OA_type":"hybrid","volume":71,"ec_funded":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_number":"e70008","corr_author":"1","article_type":"original","date_created":"2025-01-12T23:04:01Z","ddc":["510"],"language":[{"iso":"eng"}],"external_id":{"isi":["001388255500001"]},"author":[{"id":"76096395-aea4-11ed-a680-ab8ebbd3f1b9","orcid":"0000-0002-0704-7026","last_name":"Wang","full_name":"Wang, Victor","first_name":"Victor"}],"intvolume":"        71","status":"public","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"},"quality_controlled":"1","title":"Diagonal cubic forms and the large sieve","date_published":"2025-01-02T00:00:00Z","publisher":"London Mathematical Society","scopus_import":"1","abstract":[{"lang":"eng","text":"Let N(X) be the number of integral zeros (mathematical equation). Works of Hooley and Heath-Brown imply (mathematical equation), if one assumes automorphy and grand Riemann hypothesis for certain Hasse–Weil L-functions. Assuming instead a natural large sieve inequality, we recover the same bound on N(X). This is part of a more general statement, for diagonal cubic forms in (mathematical equation) variables, where we allow approximations to Hasse–Weil L-functions."}],"year":"2025","date_updated":"2025-04-14T07:54:56Z","isi":1,"month":"01","oa_version":"Published Version","file":[{"date_created":"2025-01-14T06:52:09Z","relation":"main_file","access_level":"open_access","creator":"dernst","file_id":"18845","success":1,"date_updated":"2025-01-14T06:52:09Z","file_size":309893,"file_name":"2025_Mathematika_Wang.pdf","checksum":"700a8596b4bffce2320d074120962c22","content_type":"application/pdf"}],"publication_status":"published","OA_place":"publisher","project":[{"call_identifier":"H2020","grant_number":"101034413","_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c","name":"IST-BRIDGE: International postdoctoral program"}],"article_processing_charge":"Yes (via OA deal)","oa":1,"citation":{"chicago":"Wang, Victor. “Diagonal Cubic Forms and the Large Sieve.” <i>Mathematika</i>. London Mathematical Society, 2025. <a href=\"https://doi.org/10.1112/mtk.70008\">https://doi.org/10.1112/mtk.70008</a>.","ieee":"V. Wang, “Diagonal cubic forms and the large sieve,” <i>Mathematika</i>, vol. 71, no. 1. London Mathematical Society, 2025.","apa":"Wang, V. (2025). Diagonal cubic forms and the large sieve. <i>Mathematika</i>. London Mathematical Society. <a href=\"https://doi.org/10.1112/mtk.70008\">https://doi.org/10.1112/mtk.70008</a>","ista":"Wang V. 2025. Diagonal cubic forms and the large sieve. Mathematika. 71(1), e70008.","ama":"Wang V. Diagonal cubic forms and the large sieve. <i>Mathematika</i>. 2025;71(1). doi:<a href=\"https://doi.org/10.1112/mtk.70008\">10.1112/mtk.70008</a>","mla":"Wang, Victor. “Diagonal Cubic Forms and the Large Sieve.” <i>Mathematika</i>, vol. 71, no. 1, e70008, London Mathematical Society, 2025, doi:<a href=\"https://doi.org/10.1112/mtk.70008\">10.1112/mtk.70008</a>.","short":"V. Wang, Mathematika 71 (2025)."},"department":[{"_id":"TiBr"}],"type":"journal_article","doi":"10.1112/mtk.70008","publication_identifier":{"issn":["0025-5793"],"eissn":["2041-7942"]},"acknowledgement":"I thank Peter Sarnak for suggesting projects that ultimately led to the present paper. I also thank him for many encouraging discussions, helpful comments, and references. Thanks also to Tim Browning, Trevor Wooley, and Nina Zubrilina for helpful comments, and to Levent Alpöge and Will Sawin for some interesting old discussions. I thank Yang Liu, Evan O'Dorney, Ashwin Sah, and Mark Sellke for conversations illuminating the combinatorics of an older, counting version of the present Lemma 4.9. Finally, special thanks are due to the editors and referees for their patience and help with the exposition. This work was partially supported by NSF Grant DMS-1802211, and the European Union's Horizon 2020 research and innovation program under the Marie Skłodowska-Curie Grant Agreement No. 101034413.","_id":"18822","day":"02","file_date_updated":"2025-01-14T06:52:09Z","issue":"1","publication":"Mathematika"},{"quality_controlled":"1","title":"Memory of maternal temperatures: DNA methylation alterations across generations","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"},"status":"public","intvolume":"       197","language":[{"iso":"eng"}],"author":[{"full_name":"Cao, Dechang","first_name":"Dechang","last_name":"Cao"},{"id":"26bd38d3-c59a-11ee-a1af-d7a988cafcc5","first_name":"Joke G","full_name":"De Jaeger-Braet, Joke G","last_name":"De Jaeger-Braet"}],"external_id":{"isi":["001382979900001"],"pmid":["39691053"]},"date_created":"2025-01-12T23:04:02Z","ddc":["580"],"corr_author":"1","article_type":"original","pmid":1,"article_number":"kiae651","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","volume":197,"OA_type":"hybrid","has_accepted_license":"1","publication":"Plant Physiology","file_date_updated":"2025-07-15T08:17:25Z","issue":"1","_id":"18823","day":"01","doi":"10.1093/plphys/kiae651","publication_identifier":{"eissn":["1532-2548"]},"department":[{"_id":"XiFe"}],"citation":{"ista":"Cao D, De Jaeger-Braet JG. 2025. Memory of maternal temperatures: DNA methylation alterations across generations. Plant Physiology. 197(1), kiae651.","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>","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>.","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>","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>.","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."},"type":"journal_article","oa":1,"article_processing_charge":"Yes (in subscription journal)","publication_status":"published","OA_place":"publisher","file":[{"file_size":1214018,"success":1,"date_updated":"2025-07-15T08:17:25Z","content_type":"application/pdf","file_name":"2025_PlantPhysiology_Cao.pdf","checksum":"a9b2a12d7bc6174f27e28413e9c77a9c","access_level":"open_access","creator":"dernst","date_created":"2025-07-15T08:17:25Z","relation":"main_file","file_id":"20023"}],"oa_version":"Published Version","date_updated":"2025-07-15T08:18:19Z","month":"01","isi":1,"year":"2025","scopus_import":"1","date_published":"2025-01-01T00:00:00Z","publisher":"Oxford University Press"},{"article_type":"original","date_created":"2025-01-19T23:01:50Z","ddc":["570"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_number":"457","pmid":1,"volume":16,"has_accepted_license":"1","OA_type":"gold","quality_controlled":"1","title":"DNA targeting by compact Cas9d and its resurrected ancestor","DOAJ_listed":"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"},"intvolume":"        16","status":"public","language":[{"iso":"eng"}],"author":[{"first_name":"Rodrigo Fregoso","full_name":"Ocampo, Rodrigo Fregoso","last_name":"Ocampo"},{"orcid":"0000-0003-0456-0753","last_name":"Bravo","first_name":"Jack Peter Kelly","full_name":"Bravo, Jack Peter Kelly","id":"96aecfa5-8931-11ee-af30-aa6a5d6eee0e"},{"last_name":"Dangerfield","first_name":"Tyler L.","full_name":"Dangerfield, Tyler L."},{"last_name":"Nocedal","full_name":"Nocedal, Isabel","first_name":"Isabel"},{"last_name":"Jirde","full_name":"Jirde, Samatar A.","first_name":"Samatar A."},{"last_name":"Alexander","full_name":"Alexander, Lisa M.","first_name":"Lisa M."},{"full_name":"Thomas, Nicole C.","first_name":"Nicole C.","last_name":"Thomas"},{"first_name":"Anjali","full_name":"Das, Anjali","last_name":"Das"},{"last_name":"Nielson","first_name":"Sarah","full_name":"Nielson, Sarah"},{"last_name":"Johnson","first_name":"Kenneth A.","full_name":"Johnson, Kenneth A."},{"last_name":"Brown","first_name":"Christopher T.","full_name":"Brown, Christopher T."},{"first_name":"Cristina N.","full_name":"Butterfield, Cristina N.","last_name":"Butterfield"},{"last_name":"Goltsman","full_name":"Goltsman, Daniela S.A.","first_name":"Daniela S.A."},{"first_name":"David W.","full_name":"Taylor, David W.","last_name":"Taylor"}],"external_id":{"pmid":["39774105"]},"OA_place":"publisher","publication_status":"published","article_processing_charge":"Yes","file":[{"checksum":"885e96690620790d5c9f188a1587b4cd","file_name":"2025_NatureComm_Ocampo.pdf","content_type":"application/pdf","success":1,"date_updated":"2025-01-22T14:35:22Z","file_size":5450660,"file_id":"18869","relation":"main_file","date_created":"2025-01-22T14:35:22Z","creator":"dernst","access_level":"open_access"}],"oa_version":"Published Version","year":"2025","scopus_import":"1","abstract":[{"text":"Type II CRISPR endonucleases are widely used programmable genome editing tools. Recently, CRISPR-Cas systems with highly compact nucleases have been discovered, including Cas9d (a type II-D nuclease). Here, we report the cryo-EM structures of a Cas9d nuclease (747 amino acids in length) in multiple functional states, revealing a stepwise process of DNA targeting involving a conformational switch in a REC2 domain insertion. Our structures provide insights into the intricately folded guide RNA which acts as a structural scaffold to anchor small, flexible protein domains for DNA recognition. The sgRNA can be truncated by up to ~25% yet still retain activity in vivo. Using ancestral sequence reconstruction, we generated compact nucleases capable of efficient genome editing in mammalian cells. Collectively, our results provide mechanistic insights into the evolution and DNA targeting of diverse type II CRISPR-Cas systems, providing a blueprint for future re-engineering of minimal RNA-guided DNA endonucleases.","lang":"eng"}],"date_updated":"2025-07-03T11:58:22Z","month":"01","date_published":"2025-01-07T00:00:00Z","publisher":"Springer Nature","file_date_updated":"2025-01-22T14:35:22Z","publication":"Nature Communications","_id":"18848","day":"07","doi":"10.1038/s41467-024-55573-4","publication_identifier":{"eissn":["2041-1723"]},"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.).","oa":1,"type":"journal_article","citation":{"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>.","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>","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).","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>","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.","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.","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>."},"department":[{"_id":"JaBr"}]},{"oa":1,"department":[{"_id":"GaTk"}],"citation":{"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.","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>.","short":"T.R. Sokolowski, T. Gregor, W. Bialek, G. Tkačik, Proceedings of the National Academy of Sciences 122 (2025).","mla":"Sokolowski, Thomas R., et al. “Deriving a Genetic Regulatory Network from an Optimization Principle.” <i>Proceedings of the National Academy of Sciences</i>, vol. 122, no. 1, e2402925121, National Academy of Sciences, 2025, doi:<a href=\"https://doi.org/10.1073/pnas.2402925121\">10.1073/pnas.2402925121</a>.","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>","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>"},"type":"journal_article","doi":"10.1073/pnas.2402925121","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).","publication_identifier":{"eissn":["1091-6490"],"issn":["0027-8424"]},"_id":"18849","day":"07","file_date_updated":"2025-01-20T10:10:04Z","issue":"1","publication":"Proceedings of the National Academy of Sciences","date_published":"2025-01-07T00:00:00Z","publisher":"National Academy of Sciences","scopus_import":"1","year":"2025","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."}],"date_updated":"2026-02-16T12:26:51Z","isi":1,"month":"01","oa_version":"Published Version","file":[{"file_id":"18862","creator":"dernst","access_level":"open_access","relation":"main_file","date_created":"2025-01-20T10:10:04Z","content_type":"application/pdf","checksum":"8dbfc7d495413340225ebfae69b0cf9a","file_name":"2025_PNAS_Sokolowski.pdf","file_size":19073585,"date_updated":"2025-01-20T10:10:04Z","success":1}],"OA_place":"publisher","publication_status":"published","article_processing_charge":"Yes (in subscription journal)","project":[{"name":"Biophysics of information processing in gene regulation","_id":"254E9036-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"P28844-B27"},{"_id":"7bfe6a29-9f16-11ee-852c-c0da5e2045d9","name":"Transcription in 4D: the dynamic interplay between chromatin architecture and gene expression in developing pseudo-embryos","grant_number":"101118866"},{"name":"Can evolution minimize spurious signaling crosstalk to reach optimal performance?","_id":"2665AAFE-B435-11E9-9278-68D0E5697425","grant_number":"RGP0034/2018"}],"language":[{"iso":"eng"}],"external_id":{"isi":["001392772400001"],"pmid":["39752518"]},"author":[{"orcid":"0000-0002-1287-3779","last_name":"Sokolowski","full_name":"Sokolowski, Thomas R","first_name":"Thomas R","id":"3E999752-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Gregor","first_name":"Thomas","full_name":"Gregor, Thomas"},{"full_name":"Bialek, William","first_name":"William","last_name":"Bialek"},{"first_name":"Gašper","full_name":"Tkačik, Gašper","last_name":"Tkačik","orcid":"0000-0002-6699-1455","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87"}],"intvolume":"       122","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png","short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)"},"quality_controlled":"1","title":"Deriving a genetic regulatory network from an optimization principle","has_accepted_license":"1","OA_type":"hybrid","volume":122,"article_number":"e2402925121","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","pmid":1,"corr_author":"1","article_type":"original","date_created":"2025-01-19T23:01:50Z","ddc":["570"]},{"status":"public","intvolume":"       137","language":[{"iso":"eng"}],"external_id":{"isi":["001393204700001"],"arxiv":["2408.16053"]},"author":[{"full_name":"Rodriguez, Antonio C.","first_name":"Antonio C.","last_name":"Rodriguez"},{"first_name":"Kareem","full_name":"El-Badry, Kareem","last_name":"El-Badry"},{"last_name":"Suleimanov","first_name":"Valery","full_name":"Suleimanov, Valery"},{"first_name":"Anna F.","full_name":"Pala, Anna F.","last_name":"Pala"},{"last_name":"Kulkarni","first_name":"Shrinivas R.","full_name":"Kulkarni, Shrinivas R."},{"first_name":"Boris","full_name":"Gaensicke, Boris","last_name":"Gaensicke"},{"last_name":"Mori","first_name":"Kaya","full_name":"Mori, Kaya"},{"last_name":"Rich","full_name":"Rich, R. Michael","first_name":"R. Michael"},{"last_name":"Sarkar","full_name":"Sarkar, Arnab","first_name":"Arnab"},{"first_name":"Tong","full_name":"Bao, Tong","last_name":"Bao"},{"last_name":"De Oliveira","first_name":"Raimundo Lopes","full_name":"De Oliveira, Raimundo Lopes"},{"last_name":"Ramsay","full_name":"Ramsay, Gavin","first_name":"Gavin"},{"last_name":"Szkody","full_name":"Szkody, Paula","first_name":"Paula"},{"full_name":"Graham, Matthew","first_name":"Matthew","last_name":"Graham"},{"full_name":"Prince, Thomas A.","first_name":"Thomas A.","last_name":"Prince"},{"orcid":"0000-0002-4770-5388","last_name":"Caiazzo","full_name":"Caiazzo, Ilaria","first_name":"Ilaria","id":"8ae5b6e7-2a03-11ee-914d-b58ed7a3b47d"},{"full_name":"Vanderbosch, Zachary P.","first_name":"Zachary P.","last_name":"Vanderbosch"},{"last_name":"Roestel","full_name":"Roestel, Jan Van","first_name":"Jan Van"},{"last_name":"Das","first_name":"Kaustav K.","full_name":"Das, Kaustav K."},{"last_name":"Qin","full_name":"Qin, Yu Jing","first_name":"Yu Jing"},{"last_name":"Kasliwal","first_name":"Mansi M.","full_name":"Kasliwal, Mansi M."},{"last_name":"Wold","first_name":"Avery","full_name":"Wold, Avery"},{"last_name":"Groom","first_name":"Steven L.","full_name":"Groom, Steven L."},{"last_name":"Reiley","first_name":"Daniel","full_name":"Reiley, Daniel"},{"last_name":"Riddle","full_name":"Riddle, Reed","first_name":"Reed"}],"quality_controlled":"1","title":"Cataclysmic variables and AM CVn binaries in SRG/eROSITA + Gaia: Volume limited samples, X-ray luminosity functions, and space densities","license":"https://creativecommons.org/licenses/by/3.0/","tmp":{"name":"Creative Commons Attribution 3.0 Unported (CC BY 3.0)","short":"CC BY (3.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/3.0/legalcode"},"volume":137,"OA_type":"hybrid","has_accepted_license":"1","date_created":"2025-01-19T23:01:51Z","ddc":["520"],"article_type":"original","article_number":"014201","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","doi":"10.1088/1538-3873/ada185","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).","publication_identifier":{"issn":["0004-6280"]},"type":"journal_article","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>","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>.","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).","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>","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.","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.","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>."},"department":[{"_id":"IlCa"}],"oa":1,"publication":"Publications of the Astronomical Society of the Pacific","file_date_updated":"2025-01-20T09:52:34Z","issue":"1","day":"01","_id":"18851","date_updated":"2025-02-27T12:46:32Z","arxiv":1,"month":"01","isi":1,"scopus_import":"1","abstract":[{"lang":"eng","text":"We present volume-limited samples of cataclysmic variables (CVs) and AM CVn binaries jointly selected from SRG/eROSITA eRASS1 and Gaia DR3 using an X-ray + optical color–color diagram (the \"X-ray Main Sequence\"). This tool identifies all CV subtypes, including magnetic and low-accretion rate systems, in contrast to most previous surveys. We find 23 CVs, 3 of which are AM CVns, out to 150 pc in the Western Galactic Hemisphere. Our 150 pc sample is spectroscopically verified and complete down to LX = 1.3 × 1029 erg s−1 in the 0.2–2.3 keV band, and we also present CV candidates out to 300 pc and 1000 pc. We discovered two previously unknown systems in our 150 pc sample: the third nearest AM CVn and a magnetic period bouncer. We find the mean LX of CVs to be 〈LX〉 ≈ 4.6 × 1030 erg s−1, in contrast to previous surveys which yielded 〈LX〉 ∼ 1031−1032 erg s−1. We construct X-ray luminosity functions that, for the first time, flatten out at LX ∼ 1030 erg s−1. We infer average number, mass, and luminosity densities of ρN,CV = (3.7 ± 0.7) × 10−6pc−3, (math formular), and (math formular), respectively, in the solar neighborhood. Our uniform selection method also allows us to place meaningful estimates on the space density of AM CVns, ρN,AM CVn = (5.5 ± 3.7) × 10−7 pc−3. Magnetic CVs and period bouncers make up 35% and 25% of our sample, respectively. This work, through a novel discovery technique, shows that the observed number densities of CVs and AM CVns, as well as the fraction of period bouncers, are still in tension with population synthesis estimates."}],"year":"2025","date_published":"2025-01-01T00:00:00Z","publisher":"IOP Publishing","article_processing_charge":"No","OA_place":"publisher","publication_status":"published","oa_version":"Published Version","file":[{"file_id":"18860","creator":"dernst","access_level":"open_access","relation":"main_file","date_created":"2025-01-20T09:52:34Z","content_type":"application/pdf","checksum":"02a9be04a6704fc272ed5a976e5fa8c5","file_name":"2025_PASP_Rodriguez.pdf","file_size":5155631,"date_updated":"2025-01-20T09:52:34Z","success":1}]},{"file":[{"creator":"dernst","access_level":"open_access","relation":"main_file","date_created":"2025-01-20T09:57:00Z","file_id":"18861","file_size":1692527,"success":1,"date_updated":"2025-01-20T09:57:00Z","content_type":"application/pdf","checksum":"e532b9c8123c29cfb0ee758e6d00453c","file_name":"2025_AstronomyAstrophysics_Bhat.pdf"}],"oa_version":"Published Version","publication_status":"published","OA_place":"publisher","article_processing_charge":"No","date_published":"2025-01-07T00:00:00Z","publisher":"EDP Sciences","year":"2025","abstract":[{"lang":"eng","text":"Recent observations have found a growing number of hypervelocity stars with speeds of ≈1500 − 2500 km s−1 that could have only been produced through thermonuclear supernovae in white dwarf binaries. Most of the observed hypervelocity runaways in this class display a surprising inflated structure: their current radii are roughly an order of magnitude greater than they would have been as white dwarfs filling their Roche lobe. While many simulations exist studying the dynamical phase leading to supernova detonation in these systems, no detailed calculations of the long-term structure of the runaways have yet been performed. We used an existing AREPO hydrodynamical simulation of a supernova in a white dwarf binary as a starting point for the evolution of these stars with the one-dimensional stellar evolution code MESA. We show that the supernova shock is not energetic enough to inflate the white dwarf over timescales longer than a few thousand years, significantly shorter than the 105 − 6 year lifetimes inferred for observed hypervelocity runaways. Although they experience a shock from a supernova less than ≈0.02 R⊙ away, our models do not experience significant interior heating, and all contract back to radii of around 0.01 R⊙ within about 104 years. Explaining the observed inflated states requires either an additional source of significant heating or some other physics that is not yet accounted for in the subsequent evolution."}],"scopus_import":"1","date_updated":"2026-02-16T12:08:05Z","arxiv":1,"isi":1,"month":"01","day":"07","_id":"18852","file_date_updated":"2025-01-20T09:57:00Z","issue":"1","publication":"Astronomy & Astrophysics","oa":1,"department":[{"_id":"IlCa"}],"citation":{"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>","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).","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>","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>.","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>.","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."},"type":"journal_article","doi":"10.1051/0004-6361/202451371","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.","publication_identifier":{"issn":["0004-6361"],"eissn":["1432-0746"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_number":"A114","article_type":"original","date_created":"2025-01-19T23:01:51Z","ddc":["520"],"has_accepted_license":"1","OA_type":"diamond","volume":693,"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"},"quality_controlled":"1","title":"Supernova shocks cannot explain the inflated state of hypervelocity runaways from white dwarf binaries","language":[{"iso":"eng"}],"author":[{"first_name":"Aakash","full_name":"Bhat, Aakash","last_name":"Bhat"},{"last_name":"Bauer","first_name":"Evan B.","full_name":"Bauer, Evan B."},{"first_name":"Rüdiger","full_name":"Pakmor, Rüdiger","last_name":"Pakmor"},{"first_name":"Ken J.","full_name":"Shen, Ken J.","last_name":"Shen"},{"id":"8ae5b6e7-2a03-11ee-914d-b58ed7a3b47d","orcid":"0000-0002-4770-5388","last_name":"Caiazzo","full_name":"Caiazzo, Ilaria","first_name":"Ilaria"},{"last_name":"Rajamuthukumar","full_name":"Rajamuthukumar, Abinaya Swaruba","first_name":"Abinaya Swaruba"},{"last_name":"El-Badry","first_name":"Kareem","full_name":"El-Badry, Kareem"},{"first_name":"Wolfgang E.","full_name":"Kerzendorf, Wolfgang E.","last_name":"Kerzendorf"}],"external_id":{"isi":["001406577300001"],"arxiv":["2407.03424"]},"intvolume":"       693","status":"public"},{"article_processing_charge":"No","publication_status":"published","oa_version":"None","isi":1,"month":"02","date_updated":"2025-07-10T11:51:27Z","scopus_import":"1","year":"2025","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"}],"publisher":"Royal Society of Chemistry","date_published":"2025-02-21T00:00:00Z","publication":"Energy and Environmental Science","issue":"4","acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"NanoFab"}],"_id":"18853","day":"21","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.","publication_identifier":{"issn":["1754-5692"],"eissn":["1754-5706"]},"doi":"10.1039/d4ee03750b","type":"journal_article","department":[{"_id":"MaIb"}],"citation":{"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.","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>.","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>","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.","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>","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.","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>."},"date_created":"2025-01-19T23:01:52Z","article_type":"original","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","volume":18,"OA_type":"closed access","title":"Modulating the solvation structure to enhance amorphous solid electrolyte interface formation for ultra-stable aqueous zinc anode","quality_controlled":"1","page":"1683-1695","status":"public","intvolume":"        18","author":[{"last_name":"Zeng","first_name":"Guifang","full_name":"Zeng, Guifang"},{"first_name":"Qing","full_name":"Sun, Qing","last_name":"Sun"},{"first_name":"Sharona","full_name":"Horta, Sharona","last_name":"Horta","id":"03a7e858-01b1-11ec-8b71-99ae6c4a05bc"},{"last_name":"Martínez-Alanis","first_name":"Paulina R.","full_name":"Martínez-Alanis, Paulina R."},{"last_name":"Wu","full_name":"Wu, Peng","first_name":"Peng"},{"full_name":"Li, Jing","first_name":"Jing","last_name":"Li"},{"full_name":"Wang, Shang","first_name":"Shang","last_name":"Wang"},{"id":"43C61214-F248-11E8-B48F-1D18A9856A87","first_name":"Maria","full_name":"Ibáñez, Maria","orcid":"0000-0001-5013-2843","last_name":"Ibáñez"},{"last_name":"Tian","first_name":"Yanhong","full_name":"Tian, Yanhong"},{"last_name":"Ci","full_name":"Ci, Lijie","first_name":"Lijie"},{"full_name":"Cabot, Andreu","first_name":"Andreu","last_name":"Cabot"}],"external_id":{"isi":["001389898000001"]},"language":[{"iso":"eng"}]},{"doi":"10.1051/0004-6361/202450243","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).","publication_identifier":{"eissn":["1432-0746"],"issn":["0004-6361"]},"department":[{"_id":"JoMa"}],"citation":{"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>.","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.","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.","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>","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>.","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>","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)."},"type":"journal_article","oa":1,"publication":"Astronomy & Astrophysics","file_date_updated":"2025-01-20T09:17:33Z","_id":"18854","day":"06","date_updated":"2026-02-16T12:07:37Z","month":"01","isi":1,"year":"2025","scopus_import":"1","abstract":[{"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.","lang":"eng"}],"date_published":"2025-01-06T00:00:00Z","publisher":"EDP Sciences","article_processing_charge":"No","publication_status":"published","OA_place":"publisher","oa_version":"Published Version","file":[{"content_type":"application/pdf","checksum":"67a791080ade9bfb449d249de2af7456","file_name":"2025_AstronomyAstrophysics_Heintz.pdf","file_size":4513466,"success":1,"date_updated":"2025-01-20T09:17:33Z","file_id":"18858","creator":"dernst","access_level":"open_access","relation":"main_file","date_created":"2025-01-20T09:17:33Z"}],"status":"public","intvolume":"       693","language":[{"iso":"eng"}],"author":[{"first_name":"K. E.","full_name":"Heintz, K. E.","last_name":"Heintz"},{"last_name":"Brammer","full_name":"Brammer, G. B.","first_name":"G. B."},{"full_name":"Watson, D.","first_name":"D.","last_name":"Watson"},{"first_name":"P. A.","full_name":"Oesch, P. A.","last_name":"Oesch"},{"first_name":"L. C.","full_name":"Keating, L. C.","last_name":"Keating"},{"first_name":"M. J.","full_name":"Hayes, M. J.","last_name":"Hayes"},{"last_name":"Abdurro'Uf","full_name":"Abdurro'Uf, Unknown","first_name":"Unknown"},{"last_name":"Arellano-Córdova","first_name":"K. Z.","full_name":"Arellano-Córdova, K. Z."},{"full_name":"Carnall, A. C.","first_name":"A. C.","last_name":"Carnall"},{"full_name":"Christiansen, C. R.","first_name":"C. R.","last_name":"Christiansen"},{"full_name":"Cullen, F.","first_name":"F.","last_name":"Cullen"},{"last_name":"Davé","first_name":"R.","full_name":"Davé, R."},{"first_name":"P.","full_name":"Dayal, P.","last_name":"Dayal"},{"full_name":"Ferrara, A.","first_name":"A.","last_name":"Ferrara"},{"first_name":"K.","full_name":"Finlator, K.","last_name":"Finlator"},{"last_name":"Fynbo","first_name":"J. P.U.","full_name":"Fynbo, J. P.U."},{"full_name":"Flury, S. R.","first_name":"S. R.","last_name":"Flury"},{"last_name":"Gelli","first_name":"V.","full_name":"Gelli, V."},{"last_name":"Gillman","first_name":"S.","full_name":"Gillman, S."},{"last_name":"Gottumukkala","full_name":"Gottumukkala, R.","first_name":"R."},{"last_name":"Gould","first_name":"K.","full_name":"Gould, K."},{"first_name":"T. R.","full_name":"Greve, T. R.","last_name":"Greve"},{"first_name":"S. E.","full_name":"Hardin, S. E.","last_name":"Hardin"},{"full_name":"Hsiao, T. Y.Y.","first_name":"T. Y.Y.","last_name":"Hsiao"},{"last_name":"Hutter","first_name":"A.","full_name":"Hutter, A."},{"last_name":"Jakobsson","first_name":"P.","full_name":"Jakobsson, P."},{"last_name":"Killi","first_name":"M.","full_name":"Killi, M."},{"last_name":"Khosravaninezhad","first_name":"N.","full_name":"Khosravaninezhad, N."},{"last_name":"Laursen","full_name":"Laursen, P.","first_name":"P."},{"first_name":"M. M.","full_name":"Lee, M. M.","last_name":"Lee"},{"last_name":"Magdis","full_name":"Magdis, G. E.","first_name":"G. E."},{"id":"7439a258-f3c0-11ec-9501-9df22fe06720","full_name":"Matthee, Jorryt J","first_name":"Jorryt J","last_name":"Matthee","orcid":"0000-0003-2871-127X"},{"full_name":"Naidu, R. P.","first_name":"R. P.","last_name":"Naidu"},{"first_name":"D.","full_name":"Narayanan, D.","last_name":"Narayanan"},{"first_name":"C.","full_name":"Pollock, C.","last_name":"Pollock"},{"last_name":"Prescott","full_name":"Prescott, M. K.M.","first_name":"M. K.M."},{"last_name":"Rusakov","full_name":"Rusakov, V.","first_name":"V."},{"full_name":"Shuntov, M.","first_name":"M.","last_name":"Shuntov"},{"full_name":"Sneppen, A.","first_name":"A.","last_name":"Sneppen"},{"first_name":"R.","full_name":"Smit, R.","last_name":"Smit"},{"first_name":"N. R.","full_name":"Tanvir, N. R.","last_name":"Tanvir"},{"full_name":"Terp, C.","first_name":"C.","last_name":"Terp"},{"first_name":"S.","full_name":"Toft, S.","last_name":"Toft"},{"full_name":"Valentino, F.","first_name":"F.","last_name":"Valentino"},{"full_name":"Vijayan, A. P.","first_name":"A. P.","last_name":"Vijayan"},{"last_name":"Weaver","first_name":"J. R.","full_name":"Weaver, J. R."},{"last_name":"Wise","full_name":"Wise, J. H.","first_name":"J. H."},{"last_name":"Witstok","full_name":"Witstok, J.","first_name":"J."}],"external_id":{"isi":["001390856800001"]},"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","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"},"volume":693,"OA_type":"diamond","has_accepted_license":"1","date_created":"2025-01-19T23:01:52Z","ddc":["520"],"article_type":"original","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_number":"A60"},{"intvolume":"        21","status":"public","author":[{"last_name":"Harris","first_name":"David G.","full_name":"Harris, David G."},{"id":"3D50B0BA-F248-11E8-B48F-1D18A9856A87","last_name":"Kolmogorov","first_name":"Vladimir","full_name":"Kolmogorov, Vladimir"}],"external_id":{"arxiv":["2007.10824"],"isi":["001399998600008"]},"language":[{"iso":"eng"}],"title":"Parameter estimation for Gibbs distributions","quality_controlled":"1","related_material":{"record":[{"id":"14084","status":"public","relation":"earlier_version"}]},"volume":21,"ec_funded":1,"OA_type":"green","article_type":"original","corr_author":"1","date_created":"2025-01-19T23:01:52Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_number":"3","publication_identifier":{"issn":["1549-6325"],"eissn":["1549-6333"]},"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","doi":"10.1145/3685676","oa":1,"department":[{"_id":"VlKo"}],"citation":{"short":"D.G. Harris, V. Kolmogorov, ACM Transactions on Algorithms 21 (2025).","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>","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>.","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>","ista":"Harris DG, Kolmogorov V. 2025. Parameter estimation for Gibbs distributions. ACM Transactions on Algorithms. 21(1), 3.","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.","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>."},"type":"journal_article","issue":"1","publication":"ACM Transactions on Algorithms","day":"01","_id":"18855","year":"2025","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."}],"scopus_import":"1","month":"01","isi":1,"arxiv":1,"date_updated":"2025-07-10T11:50:44Z","publisher":"Association for Computing Machinery","date_published":"2025-01-01T00:00:00Z","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2007.10824"}],"publication_status":"published","OA_place":"repository","article_processing_charge":"No","project":[{"_id":"25FBA906-B435-11E9-9278-68D0E5697425","name":"Discrete Optimization in Computer Vision: Theory and Practice","grant_number":"616160","call_identifier":"FP7"}],"oa_version":"Preprint"},{"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.","publication_identifier":{"eissn":["1432-0746"],"issn":["0004-6361"]},"doi":"10.1051/0004-6361/202452907","oa":1,"department":[{"_id":"IlCa"}],"type":"journal_article","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>.","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>","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).","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.","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>","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.","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>."},"file_date_updated":"2025-04-16T07:13:31Z","publication":"Astronomy & Astrophysics","day":"04","_id":"18866","year":"2025","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"}],"scopus_import":"1","month":"02","isi":1,"date_updated":"2025-07-10T11:51:28Z","arxiv":1,"publisher":"EDP Sciences","date_published":"2025-02-04T00:00:00Z","publication_status":"published","OA_place":"publisher","article_processing_charge":"Yes","file":[{"file_id":"19569","access_level":"open_access","creator":"dernst","date_created":"2025-04-16T07:13:31Z","relation":"main_file","content_type":"application/pdf","file_name":"2025_AstronomyAstrophysics_Scalco.pdf","checksum":"db765ce222df60a1e7c19da1968906a8","file_size":18080704,"date_updated":"2025-04-16T07:13:31Z","success":1}],"oa_version":"Published Version","intvolume":"       694","status":"public","external_id":{"isi":["001414753300007"],"arxiv":["2501.04446"]},"author":[{"last_name":"Scalco","first_name":"M.","full_name":"Scalco, M."},{"full_name":"Gerasimov, R.","first_name":"R.","last_name":"Gerasimov"},{"first_name":"L. R.","full_name":"Bedin, L. R.","last_name":"Bedin"},{"first_name":"E.","full_name":"Vesperini, E.","last_name":"Vesperini"},{"last_name":"Correnti","full_name":"Correnti, M.","first_name":"M."},{"last_name":"Nardiello","full_name":"Nardiello, D.","first_name":"D."},{"first_name":"A.","full_name":"Burgasser, A.","last_name":"Burgasser"},{"full_name":"Richer, H.","first_name":"H.","last_name":"Richer"},{"id":"8ae5b6e7-2a03-11ee-914d-b58ed7a3b47d","last_name":"Caiazzo","orcid":"0000-0002-4770-5388","full_name":"Caiazzo, Ilaria","first_name":"Ilaria"},{"last_name":"Heyl","full_name":"Heyl, J.","first_name":"J."},{"first_name":"M.","full_name":"Libralato, M.","last_name":"Libralato"},{"last_name":"Anderson","full_name":"Anderson, J.","first_name":"J."},{"full_name":"Griggio, M.","first_name":"M.","last_name":"Griggio"}],"language":[{"iso":"eng"}],"title":"JWST photometry and astrometry of 47 Tucanae. Discontinuity in the stellar sequence at the star--brown dwarf transition","quality_controlled":"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"},"volume":694,"has_accepted_license":"1","OA_type":"diamond","article_type":"original","ddc":["520"],"date_created":"2025-01-21T15:29:36Z","article_number":"A68","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"language":[{"iso":"eng"}],"author":[{"last_name":"Jia","full_name":"Jia, Shiyu","first_name":"Shiyu"},{"last_name":"Qi","full_name":"Qi, Cai","first_name":"Cai"},{"id":"12ab8624-4c8a-11ec-9e11-e1ac2438f22f","last_name":"Xu","first_name":"Shengduo","full_name":"Xu, Shengduo"},{"last_name":"Yang","first_name":"Lei","full_name":"Yang, Lei"},{"first_name":"Qiang","full_name":"Sun, Qiang","last_name":"Sun"}],"external_id":{"isi":["001407204300001"]},"status":"public","intvolume":"       225","page":"212-226","quality_controlled":"1","title":"Advancements of thermoelectric nanomaterials in ROS-mediated broad-spectrum antibacterial therapies for wound healing","OA_type":"closed access","volume":225,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2025-01-26T23:01:49Z","article_type":"review","department":[{"_id":"MaIb"}],"type":"journal_article","citation":{"chicago":"Jia, Shiyu, Cai Qi, Shengduo Xu, Lei Yang, and Qiang Sun. “Advancements of Thermoelectric Nanomaterials in ROS-Mediated Broad-Spectrum Antibacterial Therapies for Wound Healing.” <i>Journal of Materials Science and Technology</i>. Elsevier, 2025. <a href=\"https://doi.org/10.1016/j.jmst.2024.11.039\">https://doi.org/10.1016/j.jmst.2024.11.039</a>.","ieee":"S. Jia, C. Qi, S. Xu, L. Yang, and Q. Sun, “Advancements of thermoelectric nanomaterials in ROS-mediated broad-spectrum antibacterial therapies for wound healing,” <i>Journal of Materials Science and Technology</i>, vol. 225, no. 08. Elsevier, pp. 212–226, 2025.","ista":"Jia S, Qi C, Xu S, Yang L, Sun Q. 2025. Advancements of thermoelectric nanomaterials in ROS-mediated broad-spectrum antibacterial therapies for wound healing. Journal of Materials Science and Technology. 225(08), 212–226.","apa":"Jia, S., Qi, C., Xu, S., Yang, L., &#38; Sun, Q. (2025). Advancements of thermoelectric nanomaterials in ROS-mediated broad-spectrum antibacterial therapies for wound healing. <i>Journal of Materials Science and Technology</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.jmst.2024.11.039\">https://doi.org/10.1016/j.jmst.2024.11.039</a>","mla":"Jia, Shiyu, et al. “Advancements of Thermoelectric Nanomaterials in ROS-Mediated Broad-Spectrum Antibacterial Therapies for Wound Healing.” <i>Journal of Materials Science and Technology</i>, vol. 225, no. 08, Elsevier, 2025, pp. 212–26, doi:<a href=\"https://doi.org/10.1016/j.jmst.2024.11.039\">10.1016/j.jmst.2024.11.039</a>.","ama":"Jia S, Qi C, Xu S, Yang L, Sun Q. Advancements of thermoelectric nanomaterials in ROS-mediated broad-spectrum antibacterial therapies for wound healing. <i>Journal of Materials Science and Technology</i>. 2025;225(08):212-226. doi:<a href=\"https://doi.org/10.1016/j.jmst.2024.11.039\">10.1016/j.jmst.2024.11.039</a>","short":"S. Jia, C. Qi, S. Xu, L. Yang, Q. Sun, Journal of Materials Science and Technology 225 (2025) 212–226."},"doi":"10.1016/j.jmst.2024.11.039","publication_identifier":{"issn":["1005-0302"]},"acknowledgement":"This work was financially supported by the Sichuan Science and Technology Program (Nos. 2023ZYD0064 and 2023YFG0220), the Fundamental Research Funds for the Central Universities (No. YJ202242), and the Research Funding from West China School/Hospital of Stomatology, Sichuan University (No. QDJF2022–2).","_id":"18878","day":"01","publication":"Journal of Materials Science and Technology","issue":"08","date_published":"2025-08-01T00:00:00Z","publisher":"Elsevier","date_updated":"2025-12-30T07:19:04Z","month":"08","isi":1,"scopus_import":"1","year":"2025","abstract":[{"lang":"eng","text":"Thermoelectric (TE) materials, with the ability to convert heat into electrical energy, can generate micro-electrical fields at electronic interfaces with biological systems, making them applicable in electric-catalyzing as nanozymes, and modulate the infected microenvironment of skin wounds. Thereby, by harnessing temperature differences in vitro or in vivo, TE nanomaterials can provide antimicrobial reactive oxygen species (ROS) by catalyzing redox reactions, thereby accelerating wound healing by suppressing infection. However, despite their promising potential, there is still a lack of comprehensive understanding of the antimicrobial mechanisms, biocompatibility, and practical applications of TE nanomaterials in wound healing, as this is a newly-emerged sub-area of energy-related biomedical applications. This review aims to address this gap by highlighting the emerging progress of TE materials in wound healing, clarifying their mechanism and advances, emphasizing their potential challenges for commercialization and clinical use, and proposing novel design strategies of TE nanomaterials for effective antibacterial performance."}],"oa_version":"None","article_processing_charge":"No","publication_status":"published"},{"article_number":"2450028","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2025-01-26T23:01:49Z","article_type":"original","OA_type":"green","volume":14,"title":"Rate of convergence in multiple SLE using random matrix theory","quality_controlled":"1","author":[{"last_name":"Campbell","first_name":"Andrew J","full_name":"Campbell, Andrew J","id":"582b06a9-1f1c-11ee-b076-82ffce00dde4"},{"first_name":"Kyle","full_name":"Luh, Kyle","last_name":"Luh"},{"last_name":"Margarint","full_name":"Margarint, Vlad","first_name":"Vlad"}],"external_id":{"arxiv":["2301.04722"],"isi":["001397136000001"]},"language":[{"iso":"eng"}],"status":"public","intvolume":"        14","oa_version":"Preprint","article_processing_charge":"No","OA_place":"repository","publication_status":"published","publisher":"World Scientific Publishing","date_published":"2025-01-01T00:00:00Z","main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2301.04722","open_access":"1"}],"month":"01","isi":1,"arxiv":1,"date_updated":"2025-07-10T11:51:29Z","abstract":[{"lang":"eng","text":"In this paper, we provide a rate of convergence for a version of the Carathéodory convergence for the multiple SLE model with a Dyson Brownian motion driver towards its hydrodynamic limit, for β=1 and β=2. The results are obtained by combining techniques from the field of Schramm–Loewner Evolutions with modern techniques from random matrices. Our approach shows how one can apply modern tools used in the proof of universality in random matrix theory to the field of Schramm–Loewner Evolutions."}],"scopus_import":"1","year":"2025","day":"01","_id":"18880","publication":"Random Matrices: Theory and Application","issue":"1","citation":{"ista":"Campbell AJ, Luh K, Margarint V. 2025. Rate of convergence in multiple SLE using random matrix theory. Random Matrices: Theory and Application. 14(1), 2450028.","apa":"Campbell, A. J., Luh, K., &#38; Margarint, V. (2025). Rate of convergence in multiple SLE using random matrix theory. <i>Random Matrices: Theory and Application</i>. World Scientific Publishing. <a href=\"https://doi.org/10.1142/S201032632450028X\">https://doi.org/10.1142/S201032632450028X</a>","short":"A.J. Campbell, K. Luh, V. Margarint, Random Matrices: Theory and Application 14 (2025).","ama":"Campbell AJ, Luh K, Margarint V. Rate of convergence in multiple SLE using random matrix theory. <i>Random Matrices: Theory and Application</i>. 2025;14(1). doi:<a href=\"https://doi.org/10.1142/S201032632450028X\">10.1142/S201032632450028X</a>","mla":"Campbell, Andrew J., et al. “Rate of Convergence in Multiple SLE Using Random Matrix Theory.” <i>Random Matrices: Theory and Application</i>, vol. 14, no. 1, 2450028, World Scientific Publishing, 2025, doi:<a href=\"https://doi.org/10.1142/S201032632450028X\">10.1142/S201032632450028X</a>.","chicago":"Campbell, Andrew J, Kyle Luh, and Vlad Margarint. “Rate of Convergence in Multiple SLE Using Random Matrix Theory.” <i>Random Matrices: Theory and Application</i>. World Scientific Publishing, 2025. <a href=\"https://doi.org/10.1142/S201032632450028X\">https://doi.org/10.1142/S201032632450028X</a>.","ieee":"A. J. Campbell, K. Luh, and V. Margarint, “Rate of convergence in multiple SLE using random matrix theory,” <i>Random Matrices: Theory and Application</i>, vol. 14, no. 1. World Scientific Publishing, 2025."},"department":[{"_id":"LaEr"}],"type":"journal_article","oa":1,"publication_identifier":{"issn":["2010-3263"],"eissn":["2010-3271"]},"doi":"10.1142/S201032632450028X"},{"OA_type":"hybrid","has_accepted_license":"1","volume":8,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_number":"e202400743","ddc":["540"],"date_created":"2025-01-26T23:01:50Z","article_type":"original","external_id":{"isi":["001402369200001"]},"author":[{"last_name":"Jiyane","first_name":"Nomnotho","full_name":"Jiyane, Nomnotho"},{"full_name":"Santana Santos, Carla","first_name":"Carla","last_name":"Santana Santos"},{"last_name":"Echevarria Poza","full_name":"Echevarria Poza, Igor","first_name":"Igor","id":"fbae1d3b-8142-11ed-8927-a8cf34feb495"},{"last_name":"Palacios Corella","full_name":"Palacios Corella, Mario","first_name":"Mario","id":"452e82c6-803f-11ed-ab7e-ca0439e73a5d"},{"full_name":"Abdillah Mahbub, Muhammad Adib","first_name":"Muhammad Adib","last_name":"Abdillah Mahbub"},{"last_name":"Marin-Tajadura","full_name":"Marin-Tajadura, Gimena","first_name":"Gimena"},{"full_name":"Quast, Thomas","first_name":"Thomas","last_name":"Quast"},{"last_name":"Ibáñez","orcid":"0000-0001-5013-2843","full_name":"Ibáñez, Maria","first_name":"Maria","id":"43C61214-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Ventosa","first_name":"Edgar","full_name":"Ventosa, Edgar"},{"last_name":"Schuhmann","first_name":"Wolfgang","full_name":"Schuhmann, Wolfgang"}],"language":[{"iso":"eng"}],"status":"public","intvolume":"         8","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png","short":"CC BY-NC (4.0)","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)"},"title":"Recessed microelectrodes as a platform to investigate the intrinsic redox process of Prussian blue analogs for energy storage application","quality_controlled":"1","publisher":"Wiley","date_published":"2025-03-01T00:00:00Z","month":"03","isi":1,"date_updated":"2026-02-16T12:15:59Z","scopus_import":"1","abstract":[{"text":"The determination of the intrinsic properties of solid active material candidates is essential for their performance optimization. However, macroscopic electrodes and related analytical techniques show challenges concerning the number of additional influencing parameters. We explore recessed microelectrodes (rME) as a platform that allows for a binder-free investigation of Prussian Blue analogues (PBA), a family of promising battery materials. The enhanced diffusion using microelectrochemical tools is indispensable to assess the intrinsic material performance, overcoming the limitation of cation diffusion from the electrolyte to the solid interface during (dis)charging cycles and allowing the investigation of limiting steps in the coupled ion-electron transfer process. The intrinsic electrochemical performance of PBAs was studied in a three-electrode configuration by means of cyclic voltammetry and galvanostatic (dis)charging in aqueous Na+-containing electrolyte. We extended the evaluation to the role of the electrolyte on the performance of cathodic and anodic processes of a Mn-based PBA. Ex-situ and operando chemical characterization were coupled to support the microelectrochemical results.","lang":"eng"}],"year":"2025","file":[{"relation":"main_file","date_created":"2025-04-16T06:47:09Z","creator":"dernst","access_level":"open_access","file_id":"19568","success":1,"date_updated":"2025-04-16T06:47:09Z","file_size":1251786,"checksum":"a9ebdb25c43dc2823cc8a1ba9154d914","file_name":"2025_Batteries_Jiyane.pdf","content_type":"application/pdf"}],"oa_version":"Published Version","article_processing_charge":"Yes (via OA deal)","publication_status":"published","OA_place":"publisher","department":[{"_id":"MaIb"}],"citation":{"apa":"Jiyane, N., Santana Santos, C., Echevarria Poza, I., Palacios Corella, M., Abdillah Mahbub, M. A., Marin-Tajadura, G., … Schuhmann, W. (2025). Recessed microelectrodes as a platform to investigate the intrinsic redox process of Prussian blue analogs for energy storage application. <i>Batteries &#38; Supercaps</i>. Wiley. <a href=\"https://doi.org/10.1002/batt.202400743\">https://doi.org/10.1002/batt.202400743</a>","ista":"Jiyane N, Santana Santos C, Echevarria Poza I, Palacios Corella M, Abdillah Mahbub MA, Marin-Tajadura G, Quast T, Ibáñez M, Ventosa E, Schuhmann W. 2025. Recessed microelectrodes as a platform to investigate the intrinsic redox process of Prussian blue analogs for energy storage application. Batteries &#38; Supercaps. 8(3), e202400743.","mla":"Jiyane, Nomnotho, et al. “Recessed Microelectrodes as a Platform to Investigate the Intrinsic Redox Process of Prussian Blue Analogs for Energy Storage Application.” <i>Batteries &#38; Supercaps</i>, vol. 8, no. 3, e202400743, Wiley, 2025, doi:<a href=\"https://doi.org/10.1002/batt.202400743\">10.1002/batt.202400743</a>.","ama":"Jiyane N, Santana Santos C, Echevarria Poza I, et al. Recessed microelectrodes as a platform to investigate the intrinsic redox process of Prussian blue analogs for energy storage application. <i>Batteries &#38; Supercaps</i>. 2025;8(3). doi:<a href=\"https://doi.org/10.1002/batt.202400743\">10.1002/batt.202400743</a>","short":"N. Jiyane, C. Santana Santos, I. Echevarria Poza, M. Palacios Corella, M.A. Abdillah Mahbub, G. Marin-Tajadura, T. Quast, M. Ibáñez, E. Ventosa, W. Schuhmann, Batteries &#38; Supercaps 8 (2025).","chicago":"Jiyane, Nomnotho, Carla Santana Santos, Igor Echevarria Poza, Mario Palacios Corella, Muhammad Adib Abdillah Mahbub, Gimena Marin-Tajadura, Thomas Quast, Maria Ibáñez, Edgar Ventosa, and Wolfgang Schuhmann. “Recessed Microelectrodes as a Platform to Investigate the Intrinsic Redox Process of Prussian Blue Analogs for Energy Storage Application.” <i>Batteries &#38; Supercaps</i>. Wiley, 2025. <a href=\"https://doi.org/10.1002/batt.202400743\">https://doi.org/10.1002/batt.202400743</a>.","ieee":"N. Jiyane <i>et al.</i>, “Recessed microelectrodes as a platform to investigate the intrinsic redox process of Prussian blue analogs for energy storage application,” <i>Batteries &#38; Supercaps</i>, vol. 8, no. 3. Wiley, 2025."},"type":"journal_article","oa":1,"acknowledgement":"The authors acknowledge funding from the European Union's Horizon Europe research and innovation programme – European Innovation Council (EIC) under the grant agreement 101046742 (MeBattery), the European Research Council (ERC) under the European Union's Horizon 2020 research and innovation programme (CasCat [833408]), and the Spanish Government (Ministerio de Ciencia e Innovación, Grants PID2021-124974OB-C22). The authors thank Martin Trautmann (RUB) and Prof. Dr. Daniel Grasseschi (Federal University of Rio de Janeiro – UFRJ) for support concerning ICP-MS and Raman measurements, respectively. Open Access funding enabled and organized by Projekt DEAL.","publication_identifier":{"eissn":["2566-6223"]},"doi":"10.1002/batt.202400743","_id":"18881","day":"01","publication":"Batteries & Supercaps","issue":"3","file_date_updated":"2025-04-16T06:47:09Z"},{"date_published":"2025-06-19T00:00:00Z","publisher":"Wiley","date_updated":"2025-12-30T07:17:39Z","month":"06","isi":1,"abstract":[{"lang":"eng","text":"Ternary liquid-like thermoelectric materials have garnered significant attention due to their ultra-low lattice thermal conductivity. Among these, Ag8SnSe6 stands out for its exceptionally low sound velocity and thermal conductivity. However, the inherent poor electrical conductivity and suboptimal thermoelectric properties of Ag8SnSe6 necessitate further improvement. Here, a novel approach is initiated to enhance the thermoelectric properties of Ag8SnSe6 by combining low-dimensionalization with intrinsic doping. For the first time, this work successfully synthesizes single-phase Ag8SnSe6 nanocrystals, ≈10 nm in size, with the correct phase and composition using a robust and reliable colloidal method. This approach represents a significant improvement over previous reports on this material. Reducing the crystal domains of Ag8SnSe6 to the nanoscale induces quantum confinement effects, increasing the density of states near the Fermi surface. It also introduces additional grain boundaries, which lower the lattice thermal conductivity and simplify structural design. Moreover, incorporating small amounts of Sn nanopowder into the Ag8SnSe6 nanocrystals before consolidation further enhances the thermoelectric performance. Sn acts as a donor dopant, increasing the electronic concentration while at the same time improving their mobility by reducing interface barriers, thus significantly improving the material transport properties. Additionally, the presence of Sn leads to the formation of point defects, dislocations, and secondary phases, which increase phonon scattering and further reduce the thermal conductivity. Through this synergistic optimization, the figure of merit  shows a significant increase across a wide temperature range. Overall, a strategy is presented for the controlled preparation of Ag8SnSe6 nanocrystals, the decoupling of their electrical and thermal transport, and the practical application of this material to thermoelectric single-leg modules."}],"year":"2025","scopus_import":"1","oa_version":"None","article_processing_charge":"No","publication_status":"published","type":"journal_article","department":[{"_id":"MaIb"},{"_id":"GradSch"}],"citation":{"chicago":"Zhao, Xueke, Mengyao Li, Mochen Jia, Christine Fiedler, Bingfei Nan, Dongwen Yang, Lei Li, et al. “Low-Dimensional Structure Modulation in Ag8SnSe6 for Enhanced Thermoelectric Performance.” <i>Advanced Functional Materials</i>. Wiley, 2025. <a href=\"https://doi.org/10.1002/adfm.202421449\">https://doi.org/10.1002/adfm.202421449</a>.","ieee":"X. Zhao <i>et al.</i>, “Low-dimensional structure modulation in Ag8SnSe6 for enhanced thermoelectric performance,” <i>Advanced Functional Materials</i>, vol. 35, no. 24. Wiley, 2025.","apa":"Zhao, X., Li, M., Jia, M., Fiedler, C., Nan, B., Yang, D., … Cabot, A. (2025). Low-dimensional structure modulation in Ag8SnSe6 for enhanced thermoelectric performance. <i>Advanced Functional Materials</i>. Wiley. <a href=\"https://doi.org/10.1002/adfm.202421449\">https://doi.org/10.1002/adfm.202421449</a>","ista":"Zhao X, Li M, Jia M, Fiedler C, Nan B, Yang D, Li L, Yuan Z, Song H, Liu Y, Ibáñez M, Wang Z, Shan C, Cabot A. 2025. Low-dimensional structure modulation in Ag8SnSe6 for enhanced thermoelectric performance. Advanced Functional Materials. 35(24), 2421449.","mla":"Zhao, Xueke, et al. “Low-Dimensional Structure Modulation in Ag8SnSe6 for Enhanced Thermoelectric Performance.” <i>Advanced Functional Materials</i>, vol. 35, no. 24, 2421449, Wiley, 2025, doi:<a href=\"https://doi.org/10.1002/adfm.202421449\">10.1002/adfm.202421449</a>.","ama":"Zhao X, Li M, Jia M, et al. Low-dimensional structure modulation in Ag8SnSe6 for enhanced thermoelectric performance. <i>Advanced Functional Materials</i>. 2025;35(24). doi:<a href=\"https://doi.org/10.1002/adfm.202421449\">10.1002/adfm.202421449</a>","short":"X. Zhao, M. Li, M. Jia, C. Fiedler, B. Nan, D. Yang, L. Li, Z. Yuan, H. Song, Y. Liu, M. Ibáñez, Z. Wang, C. Shan, A. Cabot, Advanced Functional Materials 35 (2025)."},"doi":"10.1002/adfm.202421449","publication_identifier":{"eissn":["1616-3028"],"issn":["1616-301X"]},"acknowledgement":"X.Z. and M.L. contributed equally to this work. This work was supported by the National Key R&D Program of China (No. 2024YFE0105200). Also supported by the China Postdoctoral Science Foundation under Grant Number 2023M743151. M.J. acknowledges funding from the China Postdoctoral Science Foundation (No. 2023M743221). A.C. thanks the support from the projects ENE2016-77798-C4-3-R and NANOGEN (PID2020-116093RB-C43), funded by MCIN/ AEI/10.13039/501100011033/ and by “ERDF A way of making Europe”, by the “European Union”.","day":"19","_id":"18882","publication":"Advanced Functional Materials","issue":"24","OA_type":"closed access","volume":35,"article_number":"2421449","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2025-01-26T23:01:50Z","article_type":"original","language":[{"iso":"eng"}],"external_id":{"isi":["001398067000001"]},"author":[{"full_name":"Zhao, Xueke","first_name":"Xueke","last_name":"Zhao"},{"last_name":"Li","full_name":"Li, Mengyao","first_name":"Mengyao"},{"first_name":"Mochen","full_name":"Jia, Mochen","last_name":"Jia"},{"last_name":"Fiedler","first_name":"Christine","full_name":"Fiedler, Christine","id":"bd3fceba-dc74-11ea-a0a7-c17f71817366"},{"full_name":"Nan, Bingfei","first_name":"Bingfei","last_name":"Nan"},{"full_name":"Yang, Dongwen","first_name":"Dongwen","last_name":"Yang"},{"last_name":"Li","first_name":"Lei","full_name":"Li, Lei"},{"last_name":"Yuan","first_name":"Zicheng","full_name":"Yuan, Zicheng"},{"full_name":"Song, Hongzhang","first_name":"Hongzhang","last_name":"Song"},{"orcid":"0000-0001-7313-6740","last_name":"Liu","full_name":"Liu, Yu","first_name":"Yu","id":"2A70014E-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0001-5013-2843","last_name":"Ibáñez","full_name":"Ibáñez, Maria","first_name":"Maria","id":"43C61214-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Wang","first_name":"Ziyu","full_name":"Wang, Ziyu"},{"first_name":"Chongxin","full_name":"Shan, Chongxin","last_name":"Shan"},{"last_name":"Cabot","full_name":"Cabot, Andreu","first_name":"Andreu"}],"status":"public","intvolume":"        35","quality_controlled":"1","title":"Low-dimensional structure modulation in Ag8SnSe6 for enhanced thermoelectric performance"},{"day":"01","_id":"18936","publication":"Genetics","file_date_updated":"2025-04-16T09:41:04Z","issue":"2","department":[{"_id":"CaGu"},{"_id":"GaTk"}],"type":"journal_article","citation":{"ieee":"R. Grah, C. C. Guet, G. Tkačik, and M. Lagator, “Linking molecular mechanisms to their evolutionary consequences: a primer,” <i>Genetics</i>, vol. 229, no. 2. Oxford University Press, 2025.","chicago":"Grah, Rok, Calin C Guet, Gašper Tkačik, and Mato Lagator. “Linking Molecular Mechanisms to Their Evolutionary Consequences: A Primer.” <i>Genetics</i>. Oxford University Press, 2025. <a href=\"https://doi.org/10.1093/genetics/iyae191\">https://doi.org/10.1093/genetics/iyae191</a>.","short":"R. Grah, C.C. Guet, G. Tkačik, M. Lagator, Genetics 229 (2025).","mla":"Grah, Rok, et al. “Linking Molecular Mechanisms to Their Evolutionary Consequences: A Primer.” <i>Genetics</i>, vol. 229, no. 2, iyae191, Oxford University Press, 2025, doi:<a href=\"https://doi.org/10.1093/genetics/iyae191\">10.1093/genetics/iyae191</a>.","ama":"Grah R, Guet CC, Tkačik G, Lagator M. Linking molecular mechanisms to their evolutionary consequences: a primer. <i>Genetics</i>. 2025;229(2). doi:<a href=\"https://doi.org/10.1093/genetics/iyae191\">10.1093/genetics/iyae191</a>","ista":"Grah R, Guet CC, Tkačik G, Lagator M. 2025. Linking molecular mechanisms to their evolutionary consequences: a primer. Genetics. 229(2), iyae191.","apa":"Grah, R., Guet, C. C., Tkačik, G., &#38; Lagator, M. (2025). Linking molecular mechanisms to their evolutionary consequences: a primer. <i>Genetics</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/genetics/iyae191\">https://doi.org/10.1093/genetics/iyae191</a>"},"oa":1,"doi":"10.1093/genetics/iyae191","publication_identifier":{"eissn":["1943-2631"]},"acknowledgement":"The authors thank Nick Barton, Stepan Denisov, Claudia Igler, Srdjan Sarikas, Anna Staron, and the anonymous reviewers for useful comments and discussions that helped improve our work.\r\nFunding for this work was provided by the Wellcome Trust–Royal Society Sir Henry Dale Fellowship (216779/Z/19/Z) and the Royal Society Research Grant (RG\\R2\\232522) to M.L.","oa_version":"Published Version","file":[{"date_created":"2025-04-16T09:41:04Z","relation":"main_file","access_level":"open_access","creator":"dernst","file_id":"19580","date_updated":"2025-04-16T09:41:04Z","success":1,"file_size":1511688,"file_name":"2025_Genetics_Grah.pdf","checksum":"f730e416795969449ef49d97b82ac494","content_type":"application/pdf"}],"article_processing_charge":"Yes (in subscription journal)","publication_status":"published","OA_place":"publisher","date_published":"2025-02-01T00:00:00Z","publisher":"Oxford University Press","date_updated":"2025-05-19T14:08:02Z","month":"02","isi":1,"year":"2025","scopus_import":"1","abstract":[{"lang":"eng","text":"A major obstacle to predictive understanding of evolution stems from the complexity of biological systems, which prevents detailed characterization of key evolutionary properties. Here, we highlight some of the major sources of complexity that arise when relating molecular mechanisms to their evolutionary consequences and ask whether accounting for every mechanistic detail is important to accurately predict evolutionary outcomes. To do this, we developed a mechanistic model of a bacterial promoter regulated by 2 proteins, allowing us to connect any promoter genotype to 6 phenotypes that capture the dynamics of gene expression following an environmental switch. Accounting for the mechanisms that govern how this system works enabled us to provide an in-depth picture of how regulated bacterial promoters might evolve. More importantly, we used the model to explore which factors that contribute to the complexity of this system are essential for understanding its evolution, and which can be simplified without information loss. We found that several key evolutionary properties—the distribution of phenotypic and fitness effects of mutations, the evolutionary trajectories during selection for regulation—can be accurately captured without accounting for all, or even most, parameters of the system. Our findings point to the need for a mechanistic approach to studying evolution, as it enables tackling biological complexity and in doing so improves the ability to predict evolutionary outcomes."}],"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"},"quality_controlled":"1","title":"Linking molecular mechanisms to their evolutionary consequences: a primer","language":[{"iso":"eng"}],"author":[{"orcid":"0000-0003-2539-3560","last_name":"Grah","first_name":"Rok","full_name":"Grah, Rok","id":"483E70DE-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0001-6220-2052","last_name":"Guet","full_name":"Guet, Calin C","first_name":"Calin C","id":"47F8433E-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0002-6699-1455","last_name":"Tkačik","full_name":"Tkačik, Gašper","first_name":"Gašper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87"},{"id":"345D25EC-F248-11E8-B48F-1D18A9856A87","full_name":"Lagator, Mato","first_name":"Mato","last_name":"Lagator"}],"external_id":{"isi":["001379194200001"],"pmid":["39601269"]},"status":"public","intvolume":"       229","pmid":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_number":"iyae191","date_created":"2025-01-29T08:21:35Z","ddc":["570"],"corr_author":"1","article_type":"original","OA_type":"hybrid","has_accepted_license":"1","volume":229},{"quality_controlled":"1","title":"Tissue active matter: Integrating mechanics and signaling into dynamical models","status":"public","intvolume":"        17","language":[{"iso":"eng"}],"external_id":{"pmid":["38951023"],"isi":["001456660400001"]},"author":[{"orcid":"0000-0001-7205-2975","last_name":"Brückner","first_name":"David","full_name":"Brückner, David","id":"e1e86031-6537-11eb-953a-f7ab92be508d"},{"orcid":"0000-0001-6005-1561","last_name":"Hannezo","full_name":"Hannezo, Edouard B","first_name":"Edouard B","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87"}],"date_created":"2025-01-29T13:33:47Z","corr_author":"1","article_type":"original","pmid":1,"article_number":"a041653","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ec_funded":1,"volume":17,"OA_type":"closed access","publication":"Cold Spring Harbor Perspectives in Biology","issue":"4","_id":"18960","day":"01","doi":"10.1101/cshperspect.a041653","publication_identifier":{"issn":["1943-0264"]},"acknowledgement":"We thank Fridtjof Brauns, Anna Kicheva, and Carl-Philipp Heisenberg for a critical reading of the manuscript and Claudia Flandoli for the artwork in the figures. D.B.B. was supported by the NOMIS foundation as a NOMIS Fellow and by an EMBO Postdoctoral Fellowship (ALTF 343-2022). This work received funding from the European Research Council (ERC) under the European Union\\u2019s Horizon 2020 Research and Innovation Programme Grant Agreement no. 851288.","citation":{"ieee":"D. Brückner and E. B. Hannezo, “Tissue active matter: Integrating mechanics and signaling into dynamical models,” <i>Cold Spring Harbor Perspectives in Biology</i>, vol. 17, no. 4. Cold Spring Harbor Laboratory Press, 2025.","chicago":"Brückner, David, and Edouard B Hannezo. “Tissue Active Matter: Integrating Mechanics and Signaling into Dynamical Models.” <i>Cold Spring Harbor Perspectives in Biology</i>. Cold Spring Harbor Laboratory Press, 2025. <a href=\"https://doi.org/10.1101/cshperspect.a041653\">https://doi.org/10.1101/cshperspect.a041653</a>.","mla":"Brückner, David, and Edouard B. Hannezo. “Tissue Active Matter: Integrating Mechanics and Signaling into Dynamical Models.” <i>Cold Spring Harbor Perspectives in Biology</i>, vol. 17, no. 4, a041653, Cold Spring Harbor Laboratory Press, 2025, doi:<a href=\"https://doi.org/10.1101/cshperspect.a041653\">10.1101/cshperspect.a041653</a>.","ama":"Brückner D, Hannezo EB. Tissue active matter: Integrating mechanics and signaling into dynamical models. <i>Cold Spring Harbor Perspectives in Biology</i>. 2025;17(4). doi:<a href=\"https://doi.org/10.1101/cshperspect.a041653\">10.1101/cshperspect.a041653</a>","short":"D. Brückner, E.B. Hannezo, Cold Spring Harbor Perspectives in Biology 17 (2025).","apa":"Brückner, D., &#38; Hannezo, E. B. (2025). Tissue active matter: Integrating mechanics and signaling into dynamical models. <i>Cold Spring Harbor Perspectives in Biology</i>. Cold Spring Harbor Laboratory Press. <a href=\"https://doi.org/10.1101/cshperspect.a041653\">https://doi.org/10.1101/cshperspect.a041653</a>","ista":"Brückner D, Hannezo EB. 2025. Tissue active matter: Integrating mechanics and signaling into dynamical models. Cold Spring Harbor Perspectives in Biology. 17(4), a041653."},"type":"journal_article","department":[{"_id":"EdHa"}],"project":[{"grant_number":"ALTF 343-2022","_id":"34e2a5b5-11ca-11ed-8bc3-b2265616ef0b","name":"A mechano-chemical theory for stem cell fate decisions in organoid development"},{"call_identifier":"H2020","grant_number":"851288","name":"Design Principles of Branching Morphogenesis","_id":"05943252-7A3F-11EA-A408-12923DDC885E"}],"article_processing_charge":"No","publication_status":"published","oa_version":"None","date_updated":"2025-12-30T07:08:34Z","isi":1,"month":"04","scopus_import":"1","year":"2025","abstract":[{"lang":"eng","text":"The importance of physical forces in the morphogenesis, homeostatic function, and pathological dysfunction of multicellular tissues is being increasingly characterized, both theoretically and experimentally. Analogies between biological systems and inert materials such as foams, gels, and liquid crystals have provided striking insights into the core design principles underlying multicellular organization. However, these connections can seem surprising given that a key feature of multicellular systems is their ability to constantly consume energy, providing an active origin for the forces that they produce. Key emerging questions are, therefore, to understand whether and how this activity grants tissues novel properties that do not have counterparts in classical materials, as well as their consequences for biological function. Here, we review recent discoveries at the intersection of active matter and tissue biology, with an emphasis on how modeling and experiments can be combined to understand the dynamics of multicellular systems. These approaches suggest that a number of key biological tissue-scale phenomena, such as morphogenetic shape changes, collective migration, or fate decisions, share unifying design principles that can be described by physical models of tissue active matter."}],"date_published":"2025-04-01T00:00:00Z","publisher":"Cold Spring Harbor Laboratory Press"}]