[{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"keyword":["Multidisciplinary"],"date_updated":"2025-04-23T08:56:48Z","author":[{"full_name":"Zavadakova, Anna","first_name":"Anna","last_name":"Zavadakova"},{"full_name":"Vistejnova, Lucie","first_name":"Lucie","last_name":"Vistejnova"},{"id":"0bf89b6a-d28b-11eb-8bd6-f43768e4d368","last_name":"Belinova","first_name":"Tereza","full_name":"Belinova, Tereza"},{"last_name":"Tichanek","first_name":"Filip","full_name":"Tichanek, Filip"},{"full_name":"Bilikova, Dagmar","first_name":"Dagmar","last_name":"Bilikova"},{"last_name":"Mouton","first_name":"Peter R.","full_name":"Mouton, Peter R."}],"title":"Novel stereological method for estimation of cell counts in 3D collagen scaffolds","article_type":"original","acknowledgement":"The study was supported by Project No. CZ.02.1.01/0.0/0.0/16_019/0000787 “Fighting INfectious Diseases”, awarded by the MEYS CR, financed from EFRR, by the Cooperatio Program, research area DIAG and research area MED/DIAG, by the profiBONE project (TO01000309) benefitting from a € (1.433.000) grant from Iceland, Liechtenstein and Norway through the EEA Grants and the Technology Agency of the Czech Republic and by a Grant (#1926990) to PRM and SRC Biosciences from the National Science Foundation (U.S. Public Health Service). The authors acknowledge the invaluable assistance provided by Iveta Paurova via her support in terms of the provision of laboratory services.","day":"17","department":[{"_id":"Bio"}],"date_published":"2023-05-17T00:00:00Z","publication_identifier":{"issn":["2045-2322"]},"external_id":{"pmid":["37198326"],"isi":["000995271600104"]},"oa":1,"oa_version":"Published Version","article_number":"7959","date_created":"2023-05-19T11:12:25Z","pmid":1,"_id":"13033","publication":"Scientific Reports","file":[{"creator":"dernst","file_name":"2023_ScientificReports_Zavadakova.pdf","relation":"main_file","file_size":3055077,"checksum":"8c1b769693ff4288df8376e59ad1176d","date_created":"2023-05-22T07:57:37Z","success":1,"content_type":"application/pdf","date_updated":"2023-05-22T07:57:37Z","access_level":"open_access","file_id":"13047"}],"quality_controlled":"1","year":"2023","ddc":["570"],"language":[{"iso":"eng"}],"volume":13,"article_processing_charge":"No","isi":1,"month":"05","issue":"1","file_date_updated":"2023-05-22T07:57:37Z","scopus_import":"1","related_material":{"link":[{"url":"https://doi.org/10.1038/s41598-023-37265-z","relation":"erratum"}]},"doi":"10.1038/s41598-023-35162-z","citation":{"apa":"Zavadakova, A., Vistejnova, L., Belinova, T., Tichanek, F., Bilikova, D., &#38; Mouton, P. R. (2023). Novel stereological method for estimation of cell counts in 3D collagen scaffolds. <i>Scientific Reports</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41598-023-35162-z\">https://doi.org/10.1038/s41598-023-35162-z</a>","mla":"Zavadakova, Anna, et al. “Novel Stereological Method for Estimation of Cell Counts in 3D Collagen Scaffolds.” <i>Scientific Reports</i>, vol. 13, no. 1, 7959, Springer Nature, 2023, doi:<a href=\"https://doi.org/10.1038/s41598-023-35162-z\">10.1038/s41598-023-35162-z</a>.","ama":"Zavadakova A, Vistejnova L, Belinova T, Tichanek F, Bilikova D, Mouton PR. Novel stereological method for estimation of cell counts in 3D collagen scaffolds. <i>Scientific Reports</i>. 2023;13(1). doi:<a href=\"https://doi.org/10.1038/s41598-023-35162-z\">10.1038/s41598-023-35162-z</a>","short":"A. Zavadakova, L. Vistejnova, T. Belinova, F. Tichanek, D. Bilikova, P.R. Mouton, Scientific Reports 13 (2023).","ieee":"A. Zavadakova, L. Vistejnova, T. Belinova, F. Tichanek, D. Bilikova, and P. R. Mouton, “Novel stereological method for estimation of cell counts in 3D collagen scaffolds,” <i>Scientific Reports</i>, vol. 13, no. 1. Springer Nature, 2023.","ista":"Zavadakova A, Vistejnova L, Belinova T, Tichanek F, Bilikova D, Mouton PR. 2023. Novel stereological method for estimation of cell counts in 3D collagen scaffolds. Scientific Reports. 13(1), 7959.","chicago":"Zavadakova, Anna, Lucie Vistejnova, Tereza Belinova, Filip Tichanek, Dagmar Bilikova, and Peter R. Mouton. “Novel Stereological Method for Estimation of Cell Counts in 3D Collagen Scaffolds.” <i>Scientific Reports</i>. Springer Nature, 2023. <a href=\"https://doi.org/10.1038/s41598-023-35162-z\">https://doi.org/10.1038/s41598-023-35162-z</a>."},"abstract":[{"text":"Current methods for assessing cell proliferation in 3D scaffolds rely on changes in metabolic activity or total DNA, however, direct quantification of cell number in 3D scaffolds remains a challenge. To address this issue, we developed an unbiased stereology approach that uses systematic-random sampling and thin focal-plane optical sectioning of the scaffolds followed by estimation of total cell number (StereoCount). This approach was validated against an indirect method for measuring the total DNA (DNA content); and the Bürker counting chamber, the current reference method for quantifying cell number. We assessed the total cell number for cell seeding density (cells per unit volume) across four values and compared the methods in terms of accuracy, ease-of-use and time demands. The accuracy of StereoCount markedly outperformed the DNA content for cases with ~ 10,000 and ~ 125,000 cells/scaffold. For cases with ~ 250,000 and ~ 375,000 cells/scaffold both StereoCount and DNA content showed lower accuracy than the Bürker but did not differ from each other. In terms of ease-of-use, there was a strong advantage for the StereoCount due to output in terms of absolute cell numbers along with the possibility for an overview of cell distribution and future use of automation for high throughput analysis. Taking together, the StereoCount method is an efficient approach for direct cell quantification in 3D collagen scaffolds. Its major benefit is that automated StereoCount could accelerate research using 3D scaffolds focused on drug discovery for a wide variety of human diseases.","lang":"eng"}],"publication_status":"published","type":"journal_article","publisher":"Springer Nature","has_accepted_license":"1","intvolume":"        13"},{"external_id":{"isi":["000985051300001"],"pmid":["36970847"]},"oa":1,"date_published":"2023-07-06T00:00:00Z","publication_identifier":{"issn":["1864-5631"],"eissn":["1864-564X"]},"publication":"ChemSusChem","file":[{"file_name":"2023_ChemSusChem_Farag.pdf","creator":"dernst","date_created":"2023-11-14T11:27:16Z","checksum":"efa0713289995af83a2147b3e8e1d6a6","file_size":1168683,"relation":"main_file","access_level":"open_access","date_updated":"2023-11-14T11:27:16Z","content_type":"application/pdf","success":1,"file_id":"14532"}],"oa_version":"Published Version","article_number":"e202300128","date_created":"2023-05-21T22:01:05Z","pmid":1,"_id":"13041","status":"public","tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"date_updated":"2023-11-14T11:28:23Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_type":"original","acknowledgement":"The authors (N.L.F and R.B.J) would like to acknowledge the funding contributions of Shell and the EPRSC via I–Case studentships (grants no. EP/V519662/1 and EP/R511870/1 respectively). T.I would like to thank the ERC advanced Investigator Grant for CPG (EC H2020 835073). Thank you to Zhen Wang from the University of Cambridge for measuring GPC, the Yusuf Hamied Department of Chemistry's mass spectrometry service for MS measurements and analysis and Dr Andrew Bond from the University of Cambridge for XRD measurement and analysis.","day":"06","department":[{"_id":"StFr"}],"author":[{"full_name":"Farag, Nadia L.","last_name":"Farag","first_name":"Nadia L."},{"id":"4cc538d5-803f-11ed-ab7e-8139573aad8f","full_name":"Jethwa, Rajesh B","orcid":"0000-0002-0404-4356","first_name":"Rajesh B","last_name":"Jethwa"},{"full_name":"Beardmore, Alice E.","last_name":"Beardmore","first_name":"Alice E."},{"full_name":"Insinna, Teresa","last_name":"Insinna","first_name":"Teresa"},{"last_name":"O'Keefe","first_name":"Christopher A.","full_name":"O'Keefe, Christopher A."},{"last_name":"Klusener","first_name":"Peter A.A.","full_name":"Klusener, Peter A.A."},{"first_name":"Clare P.","last_name":"Grey","full_name":"Grey, Clare P."},{"first_name":"Dominic S.","last_name":"Wright","full_name":"Wright, Dominic S."}],"title":"Triarylamines as catholytes in aqueous organic redox flow batteries","citation":{"ama":"Farag NL, Jethwa RB, Beardmore AE, et al. Triarylamines as catholytes in aqueous organic redox flow batteries. <i>ChemSusChem</i>. 2023;16(13). doi:<a href=\"https://doi.org/10.1002/cssc.202300128\">10.1002/cssc.202300128</a>","short":"N.L. Farag, R.B. Jethwa, A.E. Beardmore, T. Insinna, C.A. O’Keefe, P.A.A. Klusener, C.P. Grey, D.S. Wright, ChemSusChem 16 (2023).","ista":"Farag NL, Jethwa RB, Beardmore AE, Insinna T, O’Keefe CA, Klusener PAA, Grey CP, Wright DS. 2023. Triarylamines as catholytes in aqueous organic redox flow batteries. ChemSusChem. 16(13), e202300128.","chicago":"Farag, Nadia L., Rajesh B Jethwa, Alice E. Beardmore, Teresa Insinna, Christopher A. O’Keefe, Peter A.A. Klusener, Clare P. Grey, and Dominic S. Wright. “Triarylamines as Catholytes in Aqueous Organic Redox Flow Batteries.” <i>ChemSusChem</i>. Wiley, 2023. <a href=\"https://doi.org/10.1002/cssc.202300128\">https://doi.org/10.1002/cssc.202300128</a>.","ieee":"N. L. Farag <i>et al.</i>, “Triarylamines as catholytes in aqueous organic redox flow batteries,” <i>ChemSusChem</i>, vol. 16, no. 13. Wiley, 2023.","mla":"Farag, Nadia L., et al. “Triarylamines as Catholytes in Aqueous Organic Redox Flow Batteries.” <i>ChemSusChem</i>, vol. 16, no. 13, e202300128, Wiley, 2023, doi:<a href=\"https://doi.org/10.1002/cssc.202300128\">10.1002/cssc.202300128</a>.","apa":"Farag, N. L., Jethwa, R. B., Beardmore, A. E., Insinna, T., O’Keefe, C. A., Klusener, P. A. A., … Wright, D. S. (2023). Triarylamines as catholytes in aqueous organic redox flow batteries. <i>ChemSusChem</i>. Wiley. <a href=\"https://doi.org/10.1002/cssc.202300128\">https://doi.org/10.1002/cssc.202300128</a>"},"abstract":[{"text":"A series of triarylamines was synthesised and screened for their suitability as catholytes in redox flow batteries using cyclic voltammetry (CV). Tris(4-aminophenyl)amine was found to be the strongest candidate. Solubility and initial electrochemical performance were promising; however, polymerisation was observed during electrochemical cycling leading to rapid capacity fade prescribed to a loss of accessible active material and the limitation of ion transport processes within the cell. A mixed electrolyte system of H3PO4 and HCl was found to inhibit polymerisation producing oligomers that consumed less active material reducing rates of degradation in the redox flow battery. Under these conditions Coulombic efficiency improved by over 4 %, the maximum number of cycles more than quadrupled and an additional theoretical capacity of 20 % was accessed. This paper is, to our knowledge, the first example of triarylamines as catholytes in all-aqueous redox flow batteries and emphasises the impact supporting electrolytes can have on electrochemical performance.","lang":"eng"}],"scopus_import":"1","doi":"10.1002/cssc.202300128","has_accepted_license":"1","intvolume":"        16","publication_status":"published","publisher":"Wiley","type":"journal_article","language":[{"iso":"eng"}],"volume":16,"quality_controlled":"1","year":"2023","ddc":["540"],"month":"07","issue":"13","file_date_updated":"2023-11-14T11:27:16Z","article_processing_charge":"Yes (in subscription journal)","isi":1},{"scopus_import":"1","doi":"10.37236/11471","citation":{"ama":"Anastos M. A note on long cycles in sparse random graphs. <i>Electronic Journal of Combinatorics</i>. 2023;30(2). doi:<a href=\"https://doi.org/10.37236/11471\">10.37236/11471</a>","short":"M. Anastos, Electronic Journal of Combinatorics 30 (2023).","ieee":"M. Anastos, “A note on long cycles in sparse random graphs,” <i>Electronic Journal of Combinatorics</i>, vol. 30, no. 2. Electronic Journal of Combinatorics, 2023.","chicago":"Anastos, Michael. “A Note on Long Cycles in Sparse Random Graphs.” <i>Electronic Journal of Combinatorics</i>. Electronic Journal of Combinatorics, 2023. <a href=\"https://doi.org/10.37236/11471\">https://doi.org/10.37236/11471</a>.","ista":"Anastos M. 2023. A note on long cycles in sparse random graphs. Electronic Journal of Combinatorics. 30(2), P2.21.","mla":"Anastos, Michael. “A Note on Long Cycles in Sparse Random Graphs.” <i>Electronic Journal of Combinatorics</i>, vol. 30, no. 2, P2.21, Electronic Journal of Combinatorics, 2023, doi:<a href=\"https://doi.org/10.37236/11471\">10.37236/11471</a>.","apa":"Anastos, M. (2023). A note on long cycles in sparse random graphs. <i>Electronic Journal of Combinatorics</i>. Electronic Journal of Combinatorics. <a href=\"https://doi.org/10.37236/11471\">https://doi.org/10.37236/11471</a>"},"abstract":[{"lang":"eng","text":"Let Lc,n denote the size of the longest cycle in G(n, c/n),c >1 constant.  We show that there exists a continuous function f(c) such that Lc,n/n→f(c) a.s.  for c>20,  thus  extending  a  result  of  Frieze  and  the  author  to  smaller  values  of c. Thereafter,  for c>20,  we  determine  the  limit  of  the  probability  that G(n, c/n)contains  cycles  of  every  length  between  the  length  of  its  shortest  and  its  longest cycles as n→∞."}],"publication_status":"published","corr_author":"1","type":"journal_article","publisher":"Electronic Journal of Combinatorics","has_accepted_license":"1","intvolume":"        30","quality_controlled":"1","ddc":["510"],"year":"2023","language":[{"iso":"eng"}],"volume":30,"article_processing_charge":"No","isi":1,"month":"05","issue":"2","file_date_updated":"2023-05-22T07:43:19Z","date_published":"2023-05-05T00:00:00Z","publication_identifier":{"eissn":["1077-8926"]},"arxiv":1,"external_id":{"arxiv":["2105.13828"],"isi":["000988285500001"]},"oa":1,"article_number":"P2.21","oa_version":"Published Version","date_created":"2023-05-21T22:01:05Z","_id":"13042","publication":"Electronic Journal of Combinatorics","file":[{"access_level":"open_access","content_type":"application/pdf","success":1,"date_updated":"2023-05-22T07:43:19Z","file_id":"13046","file_name":"2023_JourCombinatorics_Anastos.pdf","creator":"dernst","file_size":448736,"checksum":"6269ed3b3eded6536d3d9d6baad2d5b9","date_created":"2023-05-22T07:43:19Z","relation":"main_file"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","status":"public","tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"date_updated":"2024-10-09T21:05:26Z","title":"A note on long cycles in sparse random graphs","author":[{"id":"0b2a4358-bb35-11ec-b7b9-e3279b593dbb","first_name":"Michael","last_name":"Anastos","full_name":"Anastos, Michael"}],"article_type":"original","acknowledgement":"We would like to thank the reviewers for their helpful comments and remarks.","department":[{"_id":"MaKw"}],"day":"05"},{"scopus_import":"1","related_material":{"record":[{"status":"public","id":"10013","relation":"earlier_version"}]},"doi":"10.4171/IFB/484","citation":{"ieee":"S. Hensel and T. Laux, “Weak-strong uniqueness for the mean curvature flow of double bubbles,” <i>Interfaces and Free Boundaries</i>, vol. 25, no. 1. EMS Press, pp. 37–107, 2023.","chicago":"Hensel, Sebastian, and Tim Laux. “Weak-Strong Uniqueness for the Mean Curvature Flow of Double Bubbles.” <i>Interfaces and Free Boundaries</i>. EMS Press, 2023. <a href=\"https://doi.org/10.4171/IFB/484\">https://doi.org/10.4171/IFB/484</a>.","ista":"Hensel S, Laux T. 2023. Weak-strong uniqueness for the mean curvature flow of double bubbles. Interfaces and Free Boundaries. 25(1), 37–107.","short":"S. Hensel, T. Laux, Interfaces and Free Boundaries 25 (2023) 37–107.","ama":"Hensel S, Laux T. Weak-strong uniqueness for the mean curvature flow of double bubbles. <i>Interfaces and Free Boundaries</i>. 2023;25(1):37-107. doi:<a href=\"https://doi.org/10.4171/IFB/484\">10.4171/IFB/484</a>","apa":"Hensel, S., &#38; Laux, T. (2023). Weak-strong uniqueness for the mean curvature flow of double bubbles. <i>Interfaces and Free Boundaries</i>. EMS Press. <a href=\"https://doi.org/10.4171/IFB/484\">https://doi.org/10.4171/IFB/484</a>","mla":"Hensel, Sebastian, and Tim Laux. “Weak-Strong Uniqueness for the Mean Curvature Flow of Double Bubbles.” <i>Interfaces and Free Boundaries</i>, vol. 25, no. 1, EMS Press, 2023, pp. 37–107, doi:<a href=\"https://doi.org/10.4171/IFB/484\">10.4171/IFB/484</a>."},"abstract":[{"text":"We derive a weak-strong uniqueness principle for BV solutions to multiphase mean curvature flow of triple line clusters in three dimensions. Our proof is based on the explicit construction\r\nof a gradient flow calibration in the sense of the recent work of Fischer et al. (2020) for any such\r\ncluster. This extends the two-dimensional construction to the three-dimensional case of surfaces\r\nmeeting along triple junctions.","lang":"eng"}],"publication_status":"published","publisher":"EMS Press","type":"journal_article","corr_author":"1","has_accepted_license":"1","intvolume":"        25","quality_controlled":"1","year":"2023","ddc":["510"],"language":[{"iso":"eng"}],"volume":25,"article_processing_charge":"No","isi":1,"month":"04","issue":"1","page":"37-107","file_date_updated":"2023-05-22T07:24:13Z","date_published":"2023-04-20T00:00:00Z","publication_identifier":{"issn":["1463-9963"],"eissn":["1463-9971"]},"arxiv":1,"external_id":{"isi":["000975817300002"],"arxiv":["2108.01733"]},"oa":1,"oa_version":"Published Version","date_created":"2023-05-21T22:01:06Z","project":[{"grant_number":"948819","_id":"0aa76401-070f-11eb-9043-b5bb049fa26d","call_identifier":"H2020","name":"Bridging Scales in Random Materials"}],"_id":"13043","publication":"Interfaces and Free Boundaries","file":[{"file_id":"13045","access_level":"open_access","success":1,"content_type":"application/pdf","date_updated":"2023-05-22T07:24:13Z","file_size":867876,"checksum":"622422484810441e48f613e968c7e7a4","date_created":"2023-05-22T07:24:13Z","relation":"main_file","file_name":"2023_Interfaces_Hensel.pdf","creator":"dernst"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","status":"public","tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"date_updated":"2025-04-14T09:35:57Z","title":"Weak-strong uniqueness for the mean curvature flow of double bubbles","author":[{"first_name":"Sebastian","last_name":"Hensel","full_name":"Hensel, Sebastian","orcid":"0000-0001-7252-8072","id":"4D23B7DA-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Laux","first_name":"Tim","full_name":"Laux, Tim"}],"article_type":"original","acknowledgement":"This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement no. 948819), and from the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) under Germany’s Excellence Strategy – EXC-2047/1 – 390685813.","day":"20","department":[{"_id":"JuFi"}],"ec_funded":1},{"doi":"10.1145/3564246.3585113","scopus_import":"1","abstract":[{"lang":"eng","text":"In this paper we introduce a pruning of the medial axis called the (λ,α)-medial axis (axλα). We prove that the (λ,α)-medial axis of a set K is stable in a Gromov-Hausdorff sense under weak assumptions. More formally we prove that if K and K′ are close in the Hausdorff (dH) sense then the (λ,α)-medial axes of K and K′ are close as metric spaces, that is the Gromov-Hausdorff distance (dGH) between the two is 1/4-Hölder in the sense that dGH (axλα(K),axλα(K′)) ≲ dH(K,K′)1/4. The Hausdorff distance between the two medial axes is also bounded, by dH (axλα(K),λα(K′)) ≲ dH(K,K′)1/2. These quantified stability results provide guarantees for practical computations of medial axes from approximations. Moreover, they provide key ingredients for studying the computability of the medial axis in the context of computable analysis."}],"citation":{"ista":"Lieutier A, Wintraecken M. 2023. Hausdorff and Gromov-Hausdorff stable subsets of the medial axis. Proceedings of the 55th Annual ACM Symposium on Theory of Computing. STOC: Symposium on Theory of Computing, 1768–1776.","ieee":"A. Lieutier and M. Wintraecken, “Hausdorff and Gromov-Hausdorff stable subsets of the medial axis,” in <i>Proceedings of the 55th Annual ACM Symposium on Theory of Computing</i>, Orlando, FL, United States, 2023, pp. 1768–1776.","chicago":"Lieutier, André, and Mathijs Wintraecken. “Hausdorff and Gromov-Hausdorff Stable Subsets of the Medial Axis.” In <i>Proceedings of the 55th Annual ACM Symposium on Theory of Computing</i>, 1768–76. Association for Computing Machinery, 2023. <a href=\"https://doi.org/10.1145/3564246.3585113\">https://doi.org/10.1145/3564246.3585113</a>.","ama":"Lieutier A, Wintraecken M. Hausdorff and Gromov-Hausdorff stable subsets of the medial axis. In: <i>Proceedings of the 55th Annual ACM Symposium on Theory of Computing</i>. Association for Computing Machinery; 2023:1768-1776. doi:<a href=\"https://doi.org/10.1145/3564246.3585113\">10.1145/3564246.3585113</a>","short":"A. Lieutier, M. Wintraecken, in:, Proceedings of the 55th Annual ACM Symposium on Theory of Computing, Association for Computing Machinery, 2023, pp. 1768–1776.","mla":"Lieutier, André, and Mathijs Wintraecken. “Hausdorff and Gromov-Hausdorff Stable Subsets of the Medial Axis.” <i>Proceedings of the 55th Annual ACM Symposium on Theory of Computing</i>, Association for Computing Machinery, 2023, pp. 1768–76, doi:<a href=\"https://doi.org/10.1145/3564246.3585113\">10.1145/3564246.3585113</a>.","apa":"Lieutier, A., &#38; Wintraecken, M. (2023). Hausdorff and Gromov-Hausdorff stable subsets of the medial axis. In <i>Proceedings of the 55th Annual ACM Symposium on Theory of Computing</i> (pp. 1768–1776). Orlando, FL, United States: Association for Computing Machinery. <a href=\"https://doi.org/10.1145/3564246.3585113\">https://doi.org/10.1145/3564246.3585113</a>"},"corr_author":"1","type":"conference","publisher":"Association for Computing Machinery","publication_status":"published","year":"2023","conference":{"start_date":"2023-06-20","location":"Orlando, FL, United States","name":"STOC: Symposium on Theory of Computing","end_date":"2023-06-23"},"quality_controlled":"1","language":[{"iso":"eng"}],"isi":1,"article_processing_charge":"No","page":"1768-1776","month":"06","arxiv":1,"publication_identifier":{"isbn":["9781450399135"]},"date_published":"2023-06-02T00:00:00Z","oa":1,"external_id":{"arxiv":["2303.04014"],"isi":["001064640700143"]},"_id":"13048","project":[{"_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411","call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships"},{"grant_number":"M03073","_id":"fc390959-9c52-11eb-aca3-afa58bd282b2","name":"Learning and triangulating manifolds via collapses"}],"date_created":"2023-05-22T08:02:02Z","oa_version":"Preprint","publication":"Proceedings of the 55th Annual ACM Symposium on Theory of Computing","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_updated":"2025-09-09T12:26:49Z","status":"public","main_file_link":[{"url":"https://arxiv.org/abs/2303.04014","open_access":"1"}],"author":[{"full_name":"Lieutier, André","last_name":"Lieutier","first_name":"André"},{"orcid":"0000-0002-7472-2220","full_name":"Wintraecken, Mathijs","last_name":"Wintraecken","first_name":"Mathijs","id":"307CFBC8-F248-11E8-B48F-1D18A9856A87"}],"title":"Hausdorff and Gromov-Hausdorff stable subsets of the medial axis","ec_funded":1,"department":[{"_id":"HeEd"}],"day":"02","acknowledgement":"We are greatly indebted to Erin Chambers for posing a number of questions that eventually led to this paper. We would also like to thank the other organizers of the workshop on ‘Algorithms\r\nfor the medial axis’. We are also indebted to Tatiana Ezubova for helping with the search for and translation of Russian literature. The second author thanks all members of the Edelsbrunner and Datashape groups for the atmosphere in which the research was conducted.\r\nThe research leading to these results has received funding from the European Research Council (ERC) under the European Union’s Seventh Framework Programme (FP/2007-2013) / ERC Grant Agreement No. 339025 GUDHI (Algorithmic Foundations of Geometry Understanding in Higher Dimensions). Supported by the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement No. 754411. The Austrian science fund (FWF) M-3073."},{"intvolume":"      2654","publication_status":"published","publisher":"Springer Nature","type":"book_chapter","place":"New York, NY","citation":{"chicago":"Leithner, Alexander F, Jack Merrin, and Michael K Sixt. “En-Face Imaging of T Cell-Dendritic Cell Immunological Synapses.” In <i>The Immune Synapse</i>, edited by Cosima Baldari and Michael Dustin, 2654:137–47. MIMB. New York, NY: Springer Nature, 2023. <a href=\"https://doi.org/10.1007/978-1-0716-3135-5_9\">https://doi.org/10.1007/978-1-0716-3135-5_9</a>.","ieee":"A. F. Leithner, J. Merrin, and M. K. Sixt, “En-Face Imaging of T Cell-Dendritic Cell Immunological Synapses,” in <i>The Immune Synapse</i>, vol. 2654, C. Baldari and M. Dustin, Eds. New York, NY: Springer Nature, 2023, pp. 137–147.","ista":"Leithner AF, Merrin J, Sixt MK. 2023.En-Face Imaging of T Cell-Dendritic Cell Immunological Synapses. In: The Immune Synapse. Methods in Molecular Biology, vol. 2654, 137–147.","ama":"Leithner AF, Merrin J, Sixt MK. En-Face Imaging of T Cell-Dendritic Cell Immunological Synapses. In: Baldari C, Dustin M, eds. <i>The Immune Synapse</i>. Vol 2654. MIMB. New York, NY: Springer Nature; 2023:137-147. doi:<a href=\"https://doi.org/10.1007/978-1-0716-3135-5_9\">10.1007/978-1-0716-3135-5_9</a>","short":"A.F. Leithner, J. Merrin, M.K. Sixt, in:, C. Baldari, M. Dustin (Eds.), The Immune Synapse, Springer Nature, New York, NY, 2023, pp. 137–147.","mla":"Leithner, Alexander F., et al. “En-Face Imaging of T Cell-Dendritic Cell Immunological Synapses.” <i>The Immune Synapse</i>, edited by Cosima Baldari and Michael Dustin, vol. 2654, Springer Nature, 2023, pp. 137–47, doi:<a href=\"https://doi.org/10.1007/978-1-0716-3135-5_9\">10.1007/978-1-0716-3135-5_9</a>.","apa":"Leithner, A. F., Merrin, J., &#38; Sixt, M. K. (2023). En-Face Imaging of T Cell-Dendritic Cell Immunological Synapses. In C. Baldari &#38; M. Dustin (Eds.), <i>The Immune Synapse</i> (Vol. 2654, pp. 137–147). New York, NY: Springer Nature. <a href=\"https://doi.org/10.1007/978-1-0716-3135-5_9\">https://doi.org/10.1007/978-1-0716-3135-5_9</a>"},"abstract":[{"text":"Imaging of the immunological synapse (IS) between dendritic cells (DCs) and T cells in suspension is hampered by suboptimal alignment of cell-cell contacts along the vertical imaging plane. This requires optical sectioning that often results in unsatisfactory resolution in time and space. Here, we present a workflow where DCs and T cells are confined between a layer of glass and polydimethylsiloxane (PDMS) that orients the cells along one, horizontal imaging plane, allowing for fast en-face-imaging of the DC-T cell IS.","lang":"eng"}],"scopus_import":"1","doi":"10.1007/978-1-0716-3135-5_9","month":"04","series_title":"MIMB","page":"137-147","editor":[{"full_name":"Baldari, Cosima","last_name":"Baldari","first_name":"Cosima"},{"first_name":"Michael","last_name":"Dustin","full_name":"Dustin, Michael"}],"article_processing_charge":"No","language":[{"iso":"eng"}],"volume":2654,"acknowledged_ssus":[{"_id":"Bio"},{"_id":"NanoFab"},{"_id":"M-Shop"}],"quality_controlled":"1","year":"2023","publication":"The Immune Synapse","date_created":"2023-05-22T08:41:48Z","oa_version":"None","_id":"13052","pmid":1,"project":[{"name":"Cellular Navigation Along Spatial Gradients","call_identifier":"H2020","grant_number":"724373","_id":"25FE9508-B435-11E9-9278-68D0E5697425"}],"external_id":{"pmid":["37106180"]},"date_published":"2023-04-28T00:00:00Z","publication_identifier":{"issn":["1064-3745"],"eissn":["1940-6029"],"eisbn":["9781071631355"],"isbn":["9781071631348"]},"acknowledgement":"A.L. was funded by an Erwin Schrödinger postdoctoral fellowship of the Austrian Science Fund (FWF, project number: J4542-B) and is an EMBO non-stipendiary postdoctoral fellow. This work was supported by a European Research Council grant ERC-CoG-72437 to M.S. We thank the Imaging & Optics facility, the Nanofabrication facility, and the Miba Machine Shop of ISTA for their excellent support.","ec_funded":1,"department":[{"_id":"MiSi"},{"_id":"NanoFab"}],"day":"28","title":"En-Face Imaging of T Cell-Dendritic Cell Immunological Synapses","author":[{"orcid":"0000-0002-1073-744X","full_name":"Leithner, Alexander F","last_name":"Leithner","first_name":"Alexander F","id":"3B1B77E4-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Jack","last_name":"Merrin","full_name":"Merrin, Jack","orcid":"0000-0001-5145-4609","id":"4515C308-F248-11E8-B48F-1D18A9856A87"},{"id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","full_name":"Sixt, Michael K","orcid":"0000-0002-6620-9179","first_name":"Michael K","last_name":"Sixt"}],"alternative_title":["Methods in Molecular Biology"],"status":"public","date_updated":"2025-04-14T07:42:07Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"citation":{"ieee":"A. Krumes, A. Vladu, E. Kurtic, C. Lampert, and D.-A. Alistarh, “CrAM: A Compression-Aware Minimizer,” in <i>11th International Conference on Learning Representations </i>, Kigali, Rwanda , 2023.","ista":"Krumes A, Vladu A, Kurtic E, Lampert C, Alistarh D-A. 2023. CrAM: A Compression-Aware Minimizer. 11th International Conference on Learning Representations . ICLR: International Conference on Learning Representations.","chicago":"Krumes, Alexandra, Adrian Vladu, Eldar Kurtic, Christoph Lampert, and Dan-Adrian Alistarh. “CrAM: A Compression-Aware Minimizer.” In <i>11th International Conference on Learning Representations </i>. OpenReview, 2023.","ama":"Krumes A, Vladu A, Kurtic E, Lampert C, Alistarh D-A. CrAM: A Compression-Aware Minimizer. In: <i>11th International Conference on Learning Representations </i>. OpenReview; 2023.","short":"A. Krumes, A. Vladu, E. Kurtic, C. Lampert, D.-A. Alistarh, in:, 11th International Conference on Learning Representations , OpenReview, 2023.","mla":"Krumes, Alexandra, et al. “CrAM: A Compression-Aware Minimizer.” <i>11th International Conference on Learning Representations </i>, OpenReview, 2023.","apa":"Krumes, A., Vladu, A., Kurtic, E., Lampert, C., &#38; Alistarh, D.-A. (2023). CrAM: A Compression-Aware Minimizer. In <i>11th International Conference on Learning Representations </i>. Kigali, Rwanda : OpenReview."},"abstract":[{"lang":"eng","text":"Deep neural networks (DNNs) often have to be compressed, via pruning and/or quantization, before they can be deployed in practical settings. In this work we propose a new compression-aware minimizer dubbed CrAM that modifies the optimization step in a principled way, in order to produce models whose local loss behavior is stable under compression operations such as pruning. Thus, dense models trained via CrAM should be compressible post-training, in a single step, without significant accuracy loss. Experimental results on standard benchmarks, such as residual networks for ImageNet classification and BERT models for language modelling, show that CrAM produces dense models that can be more accurate than the standard SGD/Adam-based baselines, but which are stable under weight pruning: specifically, we can prune models in one-shot to 70-80% sparsity with almost no accuracy loss, and to 90% with reasonable (∼1%) accuracy loss, which is competitive with gradual compression methods. Additionally, CrAM can produce sparse models which perform well for transfer learning, and it also works for semi-structured 2:4 pruning patterns supported by GPU hardware. The code for reproducing the results is available at this https URL ."}],"related_material":{"link":[{"url":"https://github.com/IST-DASLab/CrAM","relation":"software"}],"record":[{"relation":"dissertation_contains","id":"13074","status":"public"}]},"has_accepted_license":"1","publication_status":"published","type":"conference","corr_author":"1","publisher":"OpenReview","language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"ScienComp"}],"quality_controlled":"1","year":"2023","conference":{"start_date":"2023-05-01","location":"Kigali, Rwanda ","end_date":"2023-05-05","name":"ICLR: International Conference on Learning Representations"},"ddc":["000"],"month":"05","file_date_updated":"2024-07-22T09:09:45Z","article_processing_charge":"No","oa":1,"external_id":{"arxiv":["2207.14200"]},"date_published":"2023-05-01T00:00:00Z","arxiv":1,"publication":"11th International Conference on Learning Representations ","file":[{"file_size":458201,"checksum":"a6eec897e13a91cdc3eeaf309801752c","date_created":"2024-07-22T09:09:45Z","relation":"main_file","file_name":"2023_ICLR_Peste.pdf","creator":"dernst","file_id":"17294","access_level":"open_access","success":1,"content_type":"application/pdf","date_updated":"2024-07-22T09:09:45Z"}],"date_created":"2023-05-23T11:36:18Z","oa_version":"Published Version","_id":"13053","project":[{"_id":"268A44D6-B435-11E9-9278-68D0E5697425","grant_number":"805223","call_identifier":"H2020","name":"Elastic Coordination for Scalable Machine Learning"}],"status":"public","date_updated":"2026-04-07T13:30:19Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","acknowledgement":"AP, EK, DA received funding from the European Research Council (ERC) under the European\r\nUnion’s Horizon 2020 research and innovation programme (grant agreement No 805223 ScaleML). AV acknowledges the support of the French Agence Nationale de la Recherche (ANR), under grant ANR-21-CE48-0016 (project COMCOPT). We further acknowledge the support from the Scientific Service Units (SSU) of ISTA through resources provided by Scientific Computing (SciComp).","ec_funded":1,"day":"01","department":[{"_id":"GradSch"},{"_id":"DaAl"},{"_id":"ChLa"}],"author":[{"id":"32D78294-F248-11E8-B48F-1D18A9856A87","first_name":"Elena-Alexandra","last_name":"Peste","full_name":"Peste, Elena-Alexandra"},{"full_name":"Vladu, Adrian","last_name":"Vladu","first_name":"Adrian"},{"id":"47beb3a5-07b5-11eb-9b87-b108ec578218","first_name":"Eldar","last_name":"Kurtic","full_name":"Kurtic, Eldar"},{"full_name":"Lampert, Christoph","orcid":"0000-0001-8622-7887","first_name":"Christoph","last_name":"Lampert","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Alistarh","first_name":"Dan-Adrian","full_name":"Alistarh, Dan-Adrian","orcid":"0000-0003-3650-940X","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87"}],"main_file_link":[{"open_access":"1","url":"https://openreview.net/pdf?id=_eTZBs-yedr"}],"title":"CrAM: A Compression-Aware Minimizer"},{"article_processing_charge":"No","isi":1,"month":"05","file_date_updated":"2023-05-30T07:38:44Z","issue":"19","page":"23380–23389","quality_controlled":"1","year":"2023","ddc":["540"],"language":[{"iso":"eng"}],"volume":15,"publication_status":"published","publisher":"American Chemical Society","corr_author":"1","type":"journal_article","has_accepted_license":"1","intvolume":"        15","scopus_import":"1","doi":"10.1021/acsami.3c00625","citation":{"ama":"Nan B, Song X, Chang C, et al. Bottom-up synthesis of SnTe-based thermoelectric composites. <i>ACS Applied Materials and Interfaces</i>. 2023;15(19):23380–23389. doi:<a href=\"https://doi.org/10.1021/acsami.3c00625\">10.1021/acsami.3c00625</a>","short":"B. Nan, X. Song, C. Chang, K. Xiao, Y. Zhang, L. Yang, S. Horta, J. Li, K.H. Lim, M. Ibáñez, A. Cabot, ACS Applied Materials and Interfaces 15 (2023) 23380–23389.","ieee":"B. Nan <i>et al.</i>, “Bottom-up synthesis of SnTe-based thermoelectric composites,” <i>ACS Applied Materials and Interfaces</i>, vol. 15, no. 19. American Chemical Society, pp. 23380–23389, 2023.","chicago":"Nan, Bingfei, Xuan Song, Cheng Chang, Ke Xiao, Yu Zhang, Linlin Yang, Sharona Horta, et al. “Bottom-up Synthesis of SnTe-Based Thermoelectric Composites.” <i>ACS Applied Materials and Interfaces</i>. American Chemical Society, 2023. <a href=\"https://doi.org/10.1021/acsami.3c00625\">https://doi.org/10.1021/acsami.3c00625</a>.","ista":"Nan B, Song X, Chang C, Xiao K, Zhang Y, Yang L, Horta S, Li J, Lim KH, Ibáñez M, Cabot A. 2023. Bottom-up synthesis of SnTe-based thermoelectric composites. ACS Applied Materials and Interfaces. 15(19), 23380–23389.","apa":"Nan, B., Song, X., Chang, C., Xiao, K., Zhang, Y., Yang, L., … Cabot, A. (2023). Bottom-up synthesis of SnTe-based thermoelectric composites. <i>ACS Applied Materials and Interfaces</i>. American Chemical Society. <a href=\"https://doi.org/10.1021/acsami.3c00625\">https://doi.org/10.1021/acsami.3c00625</a>","mla":"Nan, Bingfei, et al. “Bottom-up Synthesis of SnTe-Based Thermoelectric Composites.” <i>ACS Applied Materials and Interfaces</i>, vol. 15, no. 19, American Chemical Society, 2023, pp. 23380–23389, doi:<a href=\"https://doi.org/10.1021/acsami.3c00625\">10.1021/acsami.3c00625</a>."},"abstract":[{"text":"There is a need for the development of lead-free thermoelectric materials for medium-/high-temperature applications. Here, we report a thiol-free tin telluride (SnTe) precursor that can be thermally decomposed to produce SnTe crystals with sizes ranging from tens to several hundreds of nanometers. We further engineer SnTe–Cu2SnTe3 nanocomposites with a homogeneous phase distribution by decomposing the liquid SnTe precursor containing a dispersion of Cu1.5Te colloidal nanoparticles. The presence of Cu within the SnTe and the segregated semimetallic Cu2SnTe3 phase effectively improves the electrical conductivity of SnTe while simultaneously reducing the lattice thermal conductivity without compromising the Seebeck coefficient. Overall, power factors up to 3.63 mW m–1 K–2 and thermoelectric figures of merit up to 1.04 are obtained at 823 K, which represent a 167% enhancement compared with pristine SnTe.","lang":"eng"}],"title":"Bottom-up synthesis of SnTe-based thermoelectric composites","author":[{"last_name":"Nan","first_name":"Bingfei","full_name":"Nan, Bingfei"},{"full_name":"Song, Xuan","first_name":"Xuan","last_name":"Song"},{"last_name":"Chang","first_name":"Cheng","orcid":"0000-0002-9515-4277","full_name":"Chang, Cheng","id":"9E331C2E-9F27-11E9-AE48-5033E6697425"},{"full_name":"Xiao, Ke","last_name":"Xiao","first_name":"Ke"},{"full_name":"Zhang, Yu","first_name":"Yu","last_name":"Zhang"},{"first_name":"Linlin","last_name":"Yang","full_name":"Yang, Linlin"},{"id":"03a7e858-01b1-11ec-8b71-99ae6c4a05bc","full_name":"Horta, Sharona","first_name":"Sharona","last_name":"Horta"},{"last_name":"Li","first_name":"Junshan","full_name":"Li, Junshan"},{"last_name":"Lim","first_name":"Khak Ho","full_name":"Lim, Khak Ho"},{"orcid":"0000-0001-5013-2843","full_name":"Ibáñez, Maria","first_name":"Maria","last_name":"Ibáñez","id":"43C61214-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Cabot, Andreu","last_name":"Cabot","first_name":"Andreu"}],"acknowledgement":"Open Access is funded by the Austrian Science Fund (FWF). We thank Generalitat de Catalunya AGAUR─2021 SGR 01581 for financial support. B.F.N., K.X., and L.L.Y. thank the China Scholarship Council (CSC) for the scholarship support. C.C. acknowledges funding from the FWF “Lise Meitner Fellowship” grant agreement M 2889-N. J.S.L is grateful to the Science and Technology Department of Sichuan Province for the project no. 22NSFSC0966. K.H.L. was supported by the Institute of Zhejiang University-Quzhou (IZQ2021RCZX003). M.I. acknowledges the financial support from IST Austria.","article_type":"original","day":"04","department":[{"_id":"MaIb"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","status":"public","date_updated":"2025-04-14T09:29:33Z","tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"date_created":"2023-05-28T22:01:03Z","oa_version":"Published Version","_id":"13092","pmid":1,"project":[{"name":"Bottom-up Engineering for Thermoelectric Applications","grant_number":"M02889","_id":"9B8804FC-BA93-11EA-9121-9846C619BF3A"}],"publication":"ACS Applied Materials and Interfaces","file":[{"file_id":"13099","access_level":"open_access","content_type":"application/pdf","success":1,"date_updated":"2023-05-30T07:38:44Z","file_size":5640829,"date_created":"2023-05-30T07:38:44Z","checksum":"23893be46763c4c78daacddd019de821","relation":"main_file","file_name":"2023_ACSAppliedMaterials_Nan.pdf","creator":"dernst"}],"date_published":"2023-05-04T00:00:00Z","publication_identifier":{"issn":["1944-8244"],"eissn":["1944-8252"]},"oa":1,"external_id":{"pmid":["37141543"],"isi":["000985497900001"]}},{"intvolume":"        23","has_accepted_license":"1","type":"journal_article","publisher":"American Chemical Society","publication_status":"published","abstract":[{"text":"Endocytosis is a key cellular process involved in the uptake of nutrients, pathogens, or the therapy of diseases. Most studies have focused on spherical objects, whereas biologically relevant shapes can be highly anisotropic. In this letter, we use an experimental model system based on Giant Unilamellar Vesicles (GUVs) and dumbbell-shaped colloidal particles to mimic and investigate the first stage of the passive endocytic process: engulfment of an anisotropic object by the membrane. Our model has specific ligand–receptor interactions realized by mobile receptors on the vesicles and immobile ligands on the particles. Through a series of experiments, theory, and molecular dynamics simulations, we quantify the wrapping process of anisotropic dumbbells by GUVs and identify distinct stages of the wrapping pathway. We find that the strong curvature variation in the neck of the dumbbell as well as membrane tension are crucial in determining both the speed of wrapping and the final states.","lang":"eng"}],"citation":{"mla":"Azadbakht, Ali, et al. “Wrapping Pathways of Anisotropic Dumbbell Particles by Giant Unilamellar Vesicles.” <i>Nano Letters</i>, vol. 23, no. 10, American Chemical Society, 2023, pp. 4267–4273, doi:<a href=\"https://doi.org/10.1021/acs.nanolett.3c00375\">10.1021/acs.nanolett.3c00375</a>.","apa":"Azadbakht, A., Meadowcroft, B., Varkevisser, T., Šarić, A., &#38; Kraft, D. J. (2023). Wrapping pathways of anisotropic dumbbell particles by Giant Unilamellar Vesicles. <i>Nano Letters</i>. American Chemical Society. <a href=\"https://doi.org/10.1021/acs.nanolett.3c00375\">https://doi.org/10.1021/acs.nanolett.3c00375</a>","ieee":"A. Azadbakht, B. Meadowcroft, T. Varkevisser, A. Šarić, and D. J. Kraft, “Wrapping pathways of anisotropic dumbbell particles by Giant Unilamellar Vesicles,” <i>Nano Letters</i>, vol. 23, no. 10. American Chemical Society, pp. 4267–4273, 2023.","chicago":"Azadbakht, Ali, Billie Meadowcroft, Thijs Varkevisser, Anđela Šarić, and Daniela J. Kraft. “Wrapping Pathways of Anisotropic Dumbbell Particles by Giant Unilamellar Vesicles.” <i>Nano Letters</i>. American Chemical Society, 2023. <a href=\"https://doi.org/10.1021/acs.nanolett.3c00375\">https://doi.org/10.1021/acs.nanolett.3c00375</a>.","ista":"Azadbakht A, Meadowcroft B, Varkevisser T, Šarić A, Kraft DJ. 2023. Wrapping pathways of anisotropic dumbbell particles by Giant Unilamellar Vesicles. Nano Letters. 23(10), 4267–4273.","ama":"Azadbakht A, Meadowcroft B, Varkevisser T, Šarić A, Kraft DJ. Wrapping pathways of anisotropic dumbbell particles by Giant Unilamellar Vesicles. <i>Nano Letters</i>. 2023;23(10):4267–4273. doi:<a href=\"https://doi.org/10.1021/acs.nanolett.3c00375\">10.1021/acs.nanolett.3c00375</a>","short":"A. Azadbakht, B. Meadowcroft, T. Varkevisser, A. Šarić, D.J. Kraft, Nano Letters 23 (2023) 4267–4273."},"doi":"10.1021/acs.nanolett.3c00375","scopus_import":"1","issue":"10","page":"4267–4273","file_date_updated":"2023-05-30T07:55:31Z","month":"05","isi":1,"article_processing_charge":"No","volume":23,"language":[{"iso":"eng"}],"ddc":["540"],"year":"2023","quality_controlled":"1","file":[{"file_name":"2023_NanoLetters_Azadbakht.pdf","creator":"dernst","file_size":3654910,"date_created":"2023-05-30T07:55:31Z","checksum":"9734d4c617bab3578ef62916b764547a","relation":"main_file","access_level":"open_access","success":1,"content_type":"application/pdf","date_updated":"2023-05-30T07:55:31Z","file_id":"13100"}],"publication":"Nano Letters","pmid":1,"project":[{"grant_number":"802960","_id":"eba2549b-77a9-11ec-83b8-a81e493eae4e","call_identifier":"H2020","name":"Non-Equilibrium Protein Assembly: from Building Blocks to Biological Machines"}],"_id":"13094","oa_version":"Published Version","date_created":"2023-05-28T22:01:03Z","external_id":{"isi":["000985481400001"],"pmid":["37141427"]},"oa":1,"publication_identifier":{"eissn":["1530-6992"],"issn":["1530-6984"]},"date_published":"2023-05-04T00:00:00Z","department":[{"_id":"AnSa"}],"day":"04","ec_funded":1,"article_type":"letter_note","acknowledgement":"We sincerely thank Casper van der Wel for providing open-source packages for tracking, as well as Yogesh Shelke for his assistance with PAA coverslip preparation and Rachel Doherty for her assistance with particle functionalization. We are grateful to Felix Frey for useful discussions on the theory of membrane wrapping. B.M. and A.Š. acknowledge funding by the European Union’s Horizon 2020 research and innovation programme (ERC Starting Grant No. 802960).","title":"Wrapping pathways of anisotropic dumbbell particles by Giant Unilamellar Vesicles","author":[{"last_name":"Azadbakht","first_name":"Ali","full_name":"Azadbakht, Ali"},{"id":"a4725fd6-932b-11ed-81e2-c098c7f37ae1","last_name":"Meadowcroft","first_name":"Billie","full_name":"Meadowcroft, Billie","orcid":"0000-0003-3441-1337"},{"first_name":"Thijs","last_name":"Varkevisser","full_name":"Varkevisser, Thijs"},{"id":"bf63d406-f056-11eb-b41d-f263a6566d8b","last_name":"Šarić","first_name":"Anđela","full_name":"Šarić, Anđela","orcid":"0000-0002-7854-2139"},{"full_name":"Kraft, Daniela J.","first_name":"Daniela J.","last_name":"Kraft"}],"tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"date_updated":"2025-04-14T07:59:30Z","status":"public","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8"},{"intvolume":"       145","has_accepted_license":"1","corr_author":"1","type":"journal_article","publisher":"American Chemical Society","publication_status":"published","abstract":[{"text":"Disulfide bond formation is fundamentally important for protein structure and constitutes a key mechanism by which cells regulate the intracellular oxidation state. Peroxiredoxins (PRDXs) eliminate reactive oxygen species such as hydrogen peroxide through a catalytic cycle of Cys oxidation and reduction. Additionally, upon Cys oxidation PRDXs undergo extensive conformational rearrangements that may underlie their presently structurally poorly defined functions as molecular chaperones. Rearrangements include high molecular-weight oligomerization, the dynamics of which are, however, poorly understood, as is the impact of disulfide bond formation on these properties. Here we show that formation of disulfide bonds along the catalytic cycle induces extensive μs time scale dynamics, as monitored by magic-angle spinning NMR of the 216 kDa-large Tsa1 decameric assembly and solution-NMR of a designed dimeric mutant. We ascribe the conformational dynamics to structural frustration, resulting from conflicts between the disulfide-constrained reduction of mobility and the desire to fulfill other favorable contacts.","lang":"eng"}],"citation":{"mla":"Troussicot, Laura, et al. “Disulfide-Bond-Induced Structural Frustration and Dynamic Disorder in a Peroxiredoxin from MAS NMR.” <i>Journal of the American Chemical Society</i>, vol. 145, no. 19, American Chemical Society, 2023, pp. 10700–10711, doi:<a href=\"https://doi.org/10.1021/jacs.3c01200\">10.1021/jacs.3c01200</a>.","apa":"Troussicot, L., Vallet, A., Molin, M., Burmann, B. M., &#38; Schanda, P. (2023). Disulfide-bond-induced structural frustration and dynamic disorder in a peroxiredoxin from MAS NMR. <i>Journal of the American Chemical Society</i>. American Chemical Society. <a href=\"https://doi.org/10.1021/jacs.3c01200\">https://doi.org/10.1021/jacs.3c01200</a>","short":"L. Troussicot, A. Vallet, M. Molin, B.M. Burmann, P. Schanda, Journal of the American Chemical Society 145 (2023) 10700–10711.","ama":"Troussicot L, Vallet A, Molin M, Burmann BM, Schanda P. Disulfide-bond-induced structural frustration and dynamic disorder in a peroxiredoxin from MAS NMR. <i>Journal of the American Chemical Society</i>. 2023;145(19):10700–10711. doi:<a href=\"https://doi.org/10.1021/jacs.3c01200\">10.1021/jacs.3c01200</a>","chicago":"Troussicot, Laura, Alicia Vallet, Mikael Molin, Björn M. Burmann, and Paul Schanda. “Disulfide-Bond-Induced Structural Frustration and Dynamic Disorder in a Peroxiredoxin from MAS NMR.” <i>Journal of the American Chemical Society</i>. American Chemical Society, 2023. <a href=\"https://doi.org/10.1021/jacs.3c01200\">https://doi.org/10.1021/jacs.3c01200</a>.","ista":"Troussicot L, Vallet A, Molin M, Burmann BM, Schanda P. 2023. Disulfide-bond-induced structural frustration and dynamic disorder in a peroxiredoxin from MAS NMR. Journal of the American Chemical Society. 145(19), 10700–10711.","ieee":"L. Troussicot, A. Vallet, M. Molin, B. M. Burmann, and P. Schanda, “Disulfide-bond-induced structural frustration and dynamic disorder in a peroxiredoxin from MAS NMR,” <i>Journal of the American Chemical Society</i>, vol. 145, no. 19. American Chemical Society, pp. 10700–10711, 2023."},"related_material":{"record":[{"relation":"research_data","id":"12820","status":"public"}]},"doi":"10.1021/jacs.3c01200","scopus_import":"1","issue":"19","page":"10700–10711","file_date_updated":"2023-05-30T07:05:28Z","month":"05","isi":1,"article_processing_charge":"No","volume":145,"language":[{"iso":"eng"}],"year":"2023","ddc":["540"],"quality_controlled":"1","file":[{"content_type":"application/pdf","success":1,"date_updated":"2023-05-30T07:05:28Z","access_level":"open_access","file_id":"13098","creator":"dernst","file_name":"2023_JACS_Troussicot.pdf","relation":"main_file","file_size":6719299,"date_created":"2023-05-30T07:05:28Z","checksum":"0758a930ef21c62fc91b14e657479f83"}],"publication":"Journal of the American Chemical Society","pmid":1,"_id":"13095","oa_version":"Published Version","date_created":"2023-05-28T22:01:04Z","external_id":{"pmid":["37140345"],"isi":["000985907400001"]},"oa":1,"publication_identifier":{"eissn":["1520-5126"],"issn":["0002-7863"]},"date_published":"2023-05-04T00:00:00Z","day":"04","department":[{"_id":"PaSc"}],"article_type":"original","acknowledgement":"We thank Albert A. Smith (Univ. Leipzig) for discussions and help with detectors analyses, Undina Guillerm (IST Austria) for gel electrophoresis experiments (Figure S7), and Jens\r\nLidman (Univ. Gothenburg) for a 3Q relaxation analysis script. Intramural funding from Institute of Science and Technology Austria is acknowledged. This work also used the platforms of\r\nthe Grenoble Instruct-ERIC center (ISBG; UMS 3518 CNRSCEA-UJF-EMBL) within the Grenoble Partnership for Structural Biology (PSB), as well as the Swedish NMR Centre\r\nof the University of Gothenburg. Both platforms provided excellent research infrastructures. B.M.B. gratefully acknowledges funding from the Swedish Research Council (Starting grant 2016-04721), the Swedish Cancer Foundation (2019-0415), and the Knut och Alice Wallenberg Foundation through a Wallenberg Academy Fellowship (2016.0163) as well as through the Wallenberg Centre for Molecular and Translational Medicine, University of Gothenburg, Sweden. ","title":"Disulfide-bond-induced structural frustration and dynamic disorder in a peroxiredoxin from MAS NMR","author":[{"id":"3d9cac31-413c-11eb-9514-d1ec2a7fb7f3","orcid":"0000-0001-8297-8886","full_name":"Troussicot, Laura","first_name":"Laura","last_name":"Troussicot"},{"last_name":"Vallet","first_name":"Alicia","full_name":"Vallet, Alicia"},{"full_name":"Molin, Mikael","first_name":"Mikael","last_name":"Molin"},{"full_name":"Burmann, Björn M.","last_name":"Burmann","first_name":"Björn M."},{"orcid":"0000-0002-9350-7606","full_name":"Schanda, Paul","first_name":"Paul","last_name":"Schanda","id":"7B541462-FAF6-11E9-A490-E8DFE5697425"}],"tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"date_updated":"2024-10-09T21:05:30Z","status":"public","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8"},{"oa":1,"external_id":{"isi":["000991386800011"],"pmid":["37198476"]},"publication_identifier":{"eissn":["1476-4687"],"issn":["0028-0836"]},"date_published":"2023-06-29T00:00:00Z","file":[{"file_id":"14533","date_updated":"2023-11-14T11:48:18Z","content_type":"application/pdf","success":1,"access_level":"open_access","relation":"main_file","checksum":"0fab69252453bff1de7f0e2eceb76d34","date_created":"2023-11-14T11:48:18Z","file_size":12292188,"creator":"dernst","file_name":"2023_Nature_Degen.pdf"}],"publication":"Nature","_id":"13096","pmid":1,"date_created":"2023-05-28T22:01:04Z","oa_version":"Published Version","date_updated":"2025-04-23T08:57:12Z","tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"PaSc"}],"day":"29","acknowledgement":"This work was supported by the Deutsche Forschungsgemeinschaft under Germany’s Excellence Strategy EXC 2075–390740016 and the Stuttgart Center for Simulation Science (SC SimTech) to K.P., by ERC-CoG 770988 (InflamCellDeath) and SNF Project funding (310030B_198005, 310030B_192523) to P.B., by the Swiss Nanoscience Institute and the Swiss National Science Foundation via the NCCR AntiResist (180541) to S.H. and the NCCR Molecular Systems Engineering (51NF40-205608) to D.J.M., by the Helmholtz Young Investigator Program of the Helmholtz Association to C.S., by the SNF Professorship funding (PP00P3_198903) to C.P., EMBO postdoctoral fellowship ALTF 27-2022 to E.H. and by the Scientific Service Units of IST Austria through resources provided by the NMR and Life Science Facilities to P.S. Molecular dynamics simulations were performed on the HoreKa supercomputer funded by the Ministry of Science, Research and the Arts Baden-Württemberg and by the Federal Ministry of Education and Research. The authors thank the BioEM Lab of the Biozentrum, University of Basel for support; V. Mack, K. Shkarina and J. Fricke for technical support; D. Ricklin and S. Vogt for peptide synthesis; P. Pelczar for support with animals; S.-J. Marrink and P. Telles de Souza for supply with Martini3 parameters and scripts; and P. Radler und M. Loose for help with QCM. Fig. 4g and Extended Data Fig. 1a were in part created with BioRender.com.\r\nOpen access funding provided by University of Basel.","article_type":"original","title":"Structural basis of NINJ1-mediated plasma membrane rupture in cell death","author":[{"full_name":"Degen, Morris","last_name":"Degen","first_name":"Morris"},{"full_name":"Santos, José Carlos","first_name":"José Carlos","last_name":"Santos"},{"full_name":"Pluhackova, Kristyna","last_name":"Pluhackova","first_name":"Kristyna"},{"full_name":"Cebrero, Gonzalo","last_name":"Cebrero","first_name":"Gonzalo"},{"first_name":"Saray","last_name":"Ramos","full_name":"Ramos, Saray"},{"first_name":"Gytis","last_name":"Jankevicius","full_name":"Jankevicius, Gytis"},{"full_name":"Hartenian, Ella","last_name":"Hartenian","first_name":"Ella"},{"id":"bb74f472-ae54-11eb-9835-bc9c22fb1183","last_name":"Guillerm","first_name":"Undina","full_name":"Guillerm, Undina"},{"full_name":"Mari, Stefania A.","first_name":"Stefania A.","last_name":"Mari"},{"full_name":"Kohl, Bastian","first_name":"Bastian","last_name":"Kohl"},{"full_name":"Müller, Daniel J.","first_name":"Daniel J.","last_name":"Müller"},{"id":"7B541462-FAF6-11E9-A490-E8DFE5697425","full_name":"Schanda, Paul","orcid":"0000-0002-9350-7606","first_name":"Paul","last_name":"Schanda"},{"full_name":"Maier, Timm","last_name":"Maier","first_name":"Timm"},{"full_name":"Perez, Camilo","first_name":"Camilo","last_name":"Perez"},{"last_name":"Sieben","first_name":"Christian","full_name":"Sieben, Christian"},{"full_name":"Broz, Petr","first_name":"Petr","last_name":"Broz"},{"full_name":"Hiller, Sebastian","last_name":"Hiller","first_name":"Sebastian"}],"abstract":[{"lang":"eng","text":"Eukaryotic cells can undergo different forms of programmed cell death, many of which culminate in plasma membrane rupture as the defining terminal event1,2,3,4,5,6,7. Plasma membrane rupture was long thought to be driven by osmotic pressure, but it has recently been shown to be in many cases an active process, mediated by the protein ninjurin-18 (NINJ1). Here we resolve the structure of NINJ1 and the mechanism by which it ruptures membranes. Super-resolution microscopy reveals that NINJ1 clusters into structurally diverse assemblies in the membranes of dying cells, in particular large, filamentous assemblies with branched morphology. A cryo-electron microscopy structure of NINJ1 filaments shows a tightly packed fence-like array of transmembrane α-helices. Filament directionality and stability is defined by two amphipathic α-helices that interlink adjacent filament subunits. The NINJ1 filament features a hydrophilic side and a hydrophobic side, and molecular dynamics simulations show that it can stably cap membrane edges. The function of the resulting supramolecular arrangement was validated by site-directed mutagenesis. Our data thus suggest that, during lytic cell death, the extracellular α-helices of NINJ1 insert into the plasma membrane to polymerize NINJ1 monomers into amphipathic filaments that rupture the plasma membrane. The membrane protein NINJ1 is therefore an interactive component of the eukaryotic cell membrane that functions as an in-built breaking point in response to activation of cell death."}],"citation":{"apa":"Degen, M., Santos, J. C., Pluhackova, K., Cebrero, G., Ramos, S., Jankevicius, G., … Hiller, S. (2023). Structural basis of NINJ1-mediated plasma membrane rupture in cell death. <i>Nature</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41586-023-05991-z\">https://doi.org/10.1038/s41586-023-05991-z</a>","mla":"Degen, Morris, et al. “Structural Basis of NINJ1-Mediated Plasma Membrane Rupture in Cell Death.” <i>Nature</i>, vol. 618, Springer Nature, 2023, pp. 1065–71, doi:<a href=\"https://doi.org/10.1038/s41586-023-05991-z\">10.1038/s41586-023-05991-z</a>.","short":"M. Degen, J.C. Santos, K. Pluhackova, G. Cebrero, S. Ramos, G. Jankevicius, E. Hartenian, U. Guillerm, S.A. Mari, B. Kohl, D.J. Müller, P. Schanda, T. Maier, C. Perez, C. Sieben, P. Broz, S. Hiller, Nature 618 (2023) 1065–1071.","ama":"Degen M, Santos JC, Pluhackova K, et al. Structural basis of NINJ1-mediated plasma membrane rupture in cell death. <i>Nature</i>. 2023;618:1065-1071. doi:<a href=\"https://doi.org/10.1038/s41586-023-05991-z\">10.1038/s41586-023-05991-z</a>","ista":"Degen M, Santos JC, Pluhackova K, Cebrero G, Ramos S, Jankevicius G, Hartenian E, Guillerm U, Mari SA, Kohl B, Müller DJ, Schanda P, Maier T, Perez C, Sieben C, Broz P, Hiller S. 2023. Structural basis of NINJ1-mediated plasma membrane rupture in cell death. Nature. 618, 1065–1071.","chicago":"Degen, Morris, José Carlos Santos, Kristyna Pluhackova, Gonzalo Cebrero, Saray Ramos, Gytis Jankevicius, Ella Hartenian, et al. “Structural Basis of NINJ1-Mediated Plasma Membrane Rupture in Cell Death.” <i>Nature</i>. Springer Nature, 2023. <a href=\"https://doi.org/10.1038/s41586-023-05991-z\">https://doi.org/10.1038/s41586-023-05991-z</a>.","ieee":"M. Degen <i>et al.</i>, “Structural basis of NINJ1-mediated plasma membrane rupture in cell death,” <i>Nature</i>, vol. 618. Springer Nature, pp. 1065–1071, 2023."},"doi":"10.1038/s41586-023-05991-z","scopus_import":"1","intvolume":"       618","has_accepted_license":"1","publisher":"Springer Nature","type":"journal_article","publication_status":"published","volume":618,"language":[{"iso":"eng"}],"year":"2023","ddc":["570"],"acknowledged_ssus":[{"_id":"NMR"},{"_id":"LifeSc"}],"quality_controlled":"1","file_date_updated":"2023-11-14T11:48:18Z","page":"1065-1071","month":"06","isi":1,"article_processing_charge":"Yes (via OA deal)"},{"date_created":"2023-05-31T11:39:24Z","oa_version":"Preprint","_id":"13106","project":[{"grant_number":"758053","_id":"26336814-B435-11E9-9278-68D0E5697425","name":"A Fiber Optic Transceiver for Superconducting Qubits","call_identifier":"H2020"},{"grant_number":"899354","_id":"9B868D20-BA93-11EA-9121-9846C619BF3A","name":"Quantum Local Area Networks with Superconducting Qubits","call_identifier":"H2020"},{"grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships"},{"name":"Quantum readout techniques and technologies","call_identifier":"H2020","grant_number":"862644","_id":"237CBA6C-32DE-11EA-91FC-C7463DDC885E"},{"_id":"2671EB66-B435-11E9-9278-68D0E5697425","name":"Coherent on-chip conversion of superconducting qubit signals from microwaves to optical frequencies"},{"name":"QUANTUM INFORMATION SYSTEMS BEYOND CLASSICAL CAPABILITIES / P5- Integration of Superconducting Quantum Circuits","grant_number":"F07105","_id":"bdb108fd-d553-11ed-ba76-83dc74a9864f"}],"pmid":1,"publication":"Science","date_published":"2023-05-18T00:00:00Z","arxiv":1,"publication_identifier":{"issn":["0036-8075"],"eissn":["1095-9203"]},"oa":1,"external_id":{"isi":["000996515200004"],"pmid":["37200415"],"arxiv":["2301.03315"]},"title":"Entangling microwaves with light","author":[{"id":"47D26E34-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6264-2162","full_name":"Sahu, Rishabh","last_name":"Sahu","first_name":"Rishabh"},{"orcid":"0000-0003-4345-4267","full_name":"Qiu, Liu","first_name":"Liu","last_name":"Qiu","id":"45e99c0d-1eb1-11eb-9b96-ed8ab2983cac"},{"id":"29705398-F248-11E8-B48F-1D18A9856A87","last_name":"Hease","first_name":"William J","full_name":"Hease, William J","orcid":"0000-0001-9868-2166"},{"id":"3770C838-F248-11E8-B48F-1D18A9856A87","full_name":"Arnold, Georg M","orcid":"0000-0003-1397-7876","first_name":"Georg M","last_name":"Arnold"},{"first_name":"Y.","last_name":"Minoguchi","full_name":"Minoguchi, Y."},{"full_name":"Rabl, P.","last_name":"Rabl","first_name":"P."},{"id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","last_name":"Fink","first_name":"Johannes M","full_name":"Fink, Johannes M","orcid":"0000-0001-8112-028X"}],"main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2301.03315"}],"acknowledgement":"This work was supported by the European Research Council (grant no. 758053, ERC StG QUNNECT) and the European Union’s Horizon 2020 Research and Innovation Program (grant no. 899354, FETopen SuperQuLAN). L.Q. acknowledges generous support from the ISTFELLOW program. W.H. is the recipient of an ISTplus postdoctoral fellowship with funding from the European Union’s Horizon 2020 Research and Innovation Program (Marie Sklodowska-Curie grant no. 754411). G.A. is the recipient of a DOC fellowship of the Austrian Academy of Sciences at IST Austria. J.M.F. acknowledges support from the Austrian Science Fund (FWF) through BeyondC (grant no. F7105) and the European Union’s Horizon 2020 Research and Innovation Program (grant no. 862644, FETopen QUARTET).","article_type":"original","ec_funded":1,"day":"18","department":[{"_id":"JoFi"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","keyword":["Multidisciplinary"],"date_updated":"2026-04-15T06:39:33Z","publication_status":"published","corr_author":"1","type":"journal_article","publisher":"American Association for the Advancement of Science","intvolume":"       380","scopus_import":"1","doi":"10.1126/science.adg3812","related_material":{"record":[{"status":"public","id":"13122","relation":"research_data"}],"link":[{"relation":"press_release","url":"https://ista.ac.at/en/news/wiring-up-quantum-circuits-with-light/","description":"News on ISTA Website"}]},"citation":{"apa":"Sahu, R., Qiu, L., Hease, W. J., Arnold, G. M., Minoguchi, Y., Rabl, P., &#38; Fink, J. M. (2023). Entangling microwaves with light. <i>Science</i>. American Association for the Advancement of Science. <a href=\"https://doi.org/10.1126/science.adg3812\">https://doi.org/10.1126/science.adg3812</a>","mla":"Sahu, Rishabh, et al. “Entangling Microwaves with Light.” <i>Science</i>, vol. 380, no. 6646, American Association for the Advancement of Science, 2023, pp. 718–21, doi:<a href=\"https://doi.org/10.1126/science.adg3812\">10.1126/science.adg3812</a>.","chicago":"Sahu, Rishabh, Liu Qiu, William J Hease, Georg M Arnold, Y. Minoguchi, P. Rabl, and Johannes M Fink. “Entangling Microwaves with Light.” <i>Science</i>. American Association for the Advancement of Science, 2023. <a href=\"https://doi.org/10.1126/science.adg3812\">https://doi.org/10.1126/science.adg3812</a>.","ieee":"R. Sahu <i>et al.</i>, “Entangling microwaves with light,” <i>Science</i>, vol. 380, no. 6646. American Association for the Advancement of Science, pp. 718–721, 2023.","ista":"Sahu R, Qiu L, Hease WJ, Arnold GM, Minoguchi Y, Rabl P, Fink JM. 2023. Entangling microwaves with light. Science. 380(6646), 718–721.","short":"R. Sahu, L. Qiu, W.J. Hease, G.M. Arnold, Y. Minoguchi, P. Rabl, J.M. Fink, Science 380 (2023) 718–721.","ama":"Sahu R, Qiu L, Hease WJ, et al. Entangling microwaves with light. <i>Science</i>. 2023;380(6646):718-721. doi:<a href=\"https://doi.org/10.1126/science.adg3812\">10.1126/science.adg3812</a>"},"abstract":[{"text":"Quantum entanglement is a key resource in currently developed quantum technologies. Sharing this fragile property between superconducting microwave circuits and optical or atomic systems would enable new functionalities, but this has been hindered by an energy scale mismatch of >104 and the resulting mutually imposed loss and noise. In this work, we created and verified entanglement between microwave and optical fields in a millikelvin environment. Using an optically pulsed superconducting electro-optical device, we show entanglement between propagating microwave and optical fields in the continuous variable domain. This achievement not only paves the way for entanglement between superconducting circuits and telecom wavelength light, but also has wide-ranging implications for hybrid quantum networks in the context of modularization, scaling, sensing, and cross-platform verification.","lang":"eng"}],"article_processing_charge":"No","isi":1,"month":"05","page":"718-721","issue":"6646","quality_controlled":"1","year":"2023","language":[{"iso":"eng"}],"volume":380},{"abstract":[{"text":"Within the human body, the brain exhibits the highest rate of energy consumption amongst all organs, with the majority of generated ATP being utilized to sustain neuronal activity. Therefore, the metabolism of the mature cerebral cortex is geared towards preserving metabolic homeostasis whilst generating significant amounts of energy. This requires a precise interplay between diverse metabolic pathways, spanning from a tissue-wide scale to the level of individual neurons. Disturbances to this delicate metabolic equilibrium, such as those resulting from maternal malnutrition\r\nor mutations affecting metabolic enzymes, often result in neuropathological variants of neurodevelopment. For instance, mutations in SLC7A5, a transporter of metabolically essential large neutral amino acids (LNAAs), have been associated with autism and microcephaly. However, despite recent progress in the field, the extent of metabolic restructuring that occurs within the developing brain and the corresponding alterations in nutrient demands during various critical periods remain largely unknown. To investigate this, we performed metabolomic profiling of the murine cerebral cortex to characterize the metabolic state of the forebrain at different developmental stages. We found that the developing cortex undergoes substantial metabolic reprogramming, with specific sets of metabolites displaying stage-specific changes. According to our observations, we determined a distinct temporal period in postnatal development during which the cortex displays heightened reliance on LNAAs. Hence, using a conditional knock-out mouse model, we deleted Slc7a5 in neural cells, allowing us to monitor the impact of a perturbed neuronal metabolic state across multiple developmental stages of corticogenesis. We found that manipulating the levels of essential LNAAs in cortical neurons in vivo affects one particular perinatal developmental period critical for cortical network refinement. Abnormally low intracellular LNAA levels result in cell-autonomous alterations in neuronal lipid metabolism, excitability, and survival during this particular time window. Although most of the effects of Slc7a5 deletion on neuronal physiology are transient, derailment of these processes during this brief but crucial window leads to long-term circuit dysfunction in mice. In conclusion, out data indicate that the cerebral cortex undergoes significant metabolic reorganization during development. This process involves the intricate integration of multiple metabolic pathways to ensure optimal neuronal function throughout different developmental stages. Our findings offer a paradigm for understanding how neurons synchronize the expression of nutrient-related genes with their activity to allow proper brain maturation. Further, our results demonstrate that disruptions in these precisely calibrated metabolic processes during critical periods of brain development may result in neuropathological outcomes in mice and in humans.","lang":"eng"}],"citation":{"short":"L. Knaus, The Metabolism of the Developing Brain : How Large Neutral Amino Acids Modulate Perinatal Neuronal Excitability and Survival, Institute of Science and Technology Austria, 2023.","ama":"Knaus L. The metabolism of the developing brain : How large neutral amino acids modulate perinatal neuronal excitability and survival. 2023. doi:<a href=\"https://doi.org/10.15479/at:ista:13107\">10.15479/at:ista:13107</a>","ista":"Knaus L. 2023. The metabolism of the developing brain : How large neutral amino acids modulate perinatal neuronal excitability and survival. Institute of Science and Technology Austria.","ieee":"L. Knaus, “The metabolism of the developing brain : How large neutral amino acids modulate perinatal neuronal excitability and survival,” Institute of Science and Technology Austria, 2023.","chicago":"Knaus, Lisa. “The Metabolism of the Developing Brain : How Large Neutral Amino Acids Modulate Perinatal Neuronal Excitability and Survival.” Institute of Science and Technology Austria, 2023. <a href=\"https://doi.org/10.15479/at:ista:13107\">https://doi.org/10.15479/at:ista:13107</a>.","mla":"Knaus, Lisa. <i>The Metabolism of the Developing Brain : How Large Neutral Amino Acids Modulate Perinatal Neuronal Excitability and Survival</i>. Institute of Science and Technology Austria, 2023, doi:<a href=\"https://doi.org/10.15479/at:ista:13107\">10.15479/at:ista:13107</a>.","apa":"Knaus, L. (2023). <i>The metabolism of the developing brain : How large neutral amino acids modulate perinatal neuronal excitability and survival</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:13107\">https://doi.org/10.15479/at:ista:13107</a>"},"related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"12802"}]},"doi":"10.15479/at:ista:13107","has_accepted_license":"1","supervisor":[{"full_name":"Novarino, Gaia","orcid":"0000-0002-7673-7178","last_name":"Novarino","first_name":"Gaia","id":"3E57A680-F248-11E8-B48F-1D18A9856A87"}],"type":"dissertation","publisher":"Institute of Science and Technology Austria","corr_author":"1","publication_status":"published","language":[{"iso":"eng"}],"ddc":["570"],"year":"2023","acknowledged_ssus":[{"_id":"PreCl"},{"_id":"Bio"},{"_id":"EM-Fac"}],"page":"147","file_date_updated":"2023-06-07T08:41:49Z","month":"05","article_processing_charge":"No","oa":1,"publication_identifier":{"issn":["2663-337X"]},"date_published":"2023-05-31T00:00:00Z","file":[{"date_updated":"2023-06-01T13:48:41Z","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","access_level":"closed","file_id":"13112","creator":"lknaus","file_name":"Thesis_Lisa Knaus_approved_final.docx","relation":"source_file","date_created":"2023-06-01T13:48:41Z","checksum":"4b69a4ac0bbf4163d59c0b58dcb4f2c3","file_size":12991551},{"creator":"lknaus","file_name":"Thesis_Lisa Knaus_approved_final_pdfa2b.pdf","relation":"main_file","checksum":"6903d152aa01181d87a696085af31c83","date_created":"2023-06-02T09:47:29Z","file_size":9309015,"date_updated":"2023-06-07T08:41:49Z","content_type":"application/pdf","access_level":"open_access","file_id":"13114"}],"project":[{"_id":"25444568-B435-11E9-9278-68D0E5697425","grant_number":"715508","call_identifier":"H2020","name":"Probing the Reversibility of Autism Spectrum Disorders by Employing in vivo and in vitro Models"},{"grant_number":"W1232","_id":"2548AE96-B435-11E9-9278-68D0E5697425","name":"Molecular Drug Targets","call_identifier":"FWF"}],"_id":"13107","oa_version":"Published Version","date_created":"2023-06-01T09:05:24Z","date_updated":"2026-04-14T08:34:36Z","status":"public","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","department":[{"_id":"GradSch"},{"_id":"GaNo"}],"day":"31","ec_funded":1,"OA_place":"publisher","degree_awarded":"PhD","alternative_title":["ISTA Thesis"],"author":[{"id":"3B2ABCF4-F248-11E8-B48F-1D18A9856A87","last_name":"Knaus","first_name":"Lisa","full_name":"Knaus, Lisa"}],"title":"The metabolism of the developing brain : How large neutral amino acids modulate perinatal neuronal excitability and survival"},{"acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"ddc":["539"],"year":"2023","month":"07","file_date_updated":"2023-08-08T11:17:28Z","article_processing_charge":"No","citation":{"apa":"Dunajova, Z., Prats Mateu, B., Radler, P., Lim, K., Brandis, D., Velicky, P., … Loose, M. (2023). Chiral and nematic phases of flexible active filaments. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:13116\">https://doi.org/10.15479/AT:ISTA:13116</a>","mla":"Dunajova, Zuzana, et al. <i>Chiral and Nematic Phases of Flexible Active Filaments</i>. Institute of Science and Technology Austria, 2023, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:13116\">10.15479/AT:ISTA:13116</a>.","ista":"Dunajova Z, Prats Mateu B, Radler P, Lim K, Brandis D, Velicky P, Danzl JG, Wong RW, Elgeti J, Hannezo EB, Loose M. 2023. Chiral and nematic phases of flexible active filaments, Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:13116\">10.15479/AT:ISTA:13116</a>.","ieee":"Z. Dunajova <i>et al.</i>, “Chiral and nematic phases of flexible active filaments.” Institute of Science and Technology Austria, 2023.","chicago":"Dunajova, Zuzana, Batirtze Prats Mateu, Philipp Radler, Keesiang Lim, Dörte Brandis, Philipp Velicky, Johann G Danzl, et al. “Chiral and Nematic Phases of Flexible Active Filaments.” Institute of Science and Technology Austria, 2023. <a href=\"https://doi.org/10.15479/AT:ISTA:13116\">https://doi.org/10.15479/AT:ISTA:13116</a>.","ama":"Dunajova Z, Prats Mateu B, Radler P, et al. Chiral and nematic phases of flexible active filaments. 2023. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:13116\">10.15479/AT:ISTA:13116</a>","short":"Z. Dunajova, B. Prats Mateu, P. Radler, K. Lim, D. Brandis, P. Velicky, J.G. Danzl, R.W. Wong, J. Elgeti, E.B. Hannezo, M. Loose, (2023)."},"abstract":[{"lang":"eng","text":"The emergence of large-scale order in self-organized systems relies on local interactions between individual components. During bacterial cell division, FtsZ -- a prokaryotic homologue of the eukaryotic protein tubulin -- polymerizes into treadmilling filaments that further organize into a cytoskeletal ring. In vitro, FtsZ filaments can form dynamic chiral assemblies. However, how the active and passive properties of individual filaments relate to these large-scale self-organized structures remains poorly understood. Here, we connect single filament properties with the mesoscopic scale by combining minimal active matter simulations and biochemical reconstitution experiments. We show that density and flexibility of active chiral filaments define their global order. At intermediate densities, curved, flexible filaments organize into chiral rings and polar bands. An effectively nematic organization dominates for high densities and for straight, mutant filaments with increased rigidity. Our predicted phase diagram captures these features quantitatively, demonstrating how the flexibility, density and chirality of active filaments affect their collective behaviour. Our findings shed light on the fundamental properties of active chiral matter and explain how treadmilling FtsZ filaments organize during bacterial cell division. 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Z.D. has received funding from Doctoral Programme of the Austrian Academy of Sciences (OeAW): Grant agreement 26360. We thank Jan Brugues (MPI CBG, Dresden, Germany), Andela Saric (ISTA, Klosterneuburg, Austria), Daniel Pearce (Uni Geneva, Switzerland) for valuable scientific input and comments on the manuscript. We are also thankful for the support by the Scientific Service Units (SSU) of IST Austria through resources provided by the Imaging and Optics Facility (IOF) and the Lab Support Facility (LSF). 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Donner and T. Esslinger. We thank G. del Pace and T. Bühler for their assistance in the final stages of the experiment. We acknowledge funding from the European Research Council under the European Union Horizon 2020 Research and Innovation Programme (Grant no. 714309) and the Swiss National Science Foundation (Grant no. 184654). F.M. acknowledges financial support from the Austrian Science Fund (Stand-Alone Project P 35891-N).","article_type":"original","department":[{"_id":"GeKa"}],"day":"22","title":"Density-wave ordering in a unitary Fermi gas with photon-mediated interactions","author":[{"full_name":"Helson, Victor","first_name":"Victor","last_name":"Helson"},{"full_name":"Zwettler, Timo","last_name":"Zwettler","first_name":"Timo"},{"last_name":"Mivehvar","first_name":"Farokh","full_name":"Mivehvar, Farokh"},{"last_name":"Colella","first_name":"Elvia","full_name":"Colella, Elvia"},{"id":"53f93ea2-803f-11ed-ab7e-b283135794ef","full_name":"Roux, Kevin Etienne Robert","last_name":"Roux","first_name":"Kevin Etienne Robert"},{"last_name":"Konishi","first_name":"Hideki","full_name":"Konishi, Hideki"},{"full_name":"Ritsch, Helmut","last_name":"Ritsch","first_name":"Helmut"},{"first_name":"Jean Philippe","last_name":"Brantut","full_name":"Brantut, Jean Philippe"}],"status":"public","date_updated":"2025-04-23T08:58:21Z","tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","has_accepted_license":"1","intvolume":"       618","publication_status":"published","type":"journal_article","publisher":"Springer Nature","citation":{"ama":"Helson V, Zwettler T, Mivehvar F, et al. Density-wave ordering in a unitary Fermi gas with photon-mediated interactions. <i>Nature</i>. 2023;618:716-720. doi:<a href=\"https://doi.org/10.1038/s41586-023-06018-3\">10.1038/s41586-023-06018-3</a>","short":"V. Helson, T. Zwettler, F. Mivehvar, E. Colella, K.E.R. Roux, H. Konishi, H. Ritsch, J.P. Brantut, Nature 618 (2023) 716–720.","ista":"Helson V, Zwettler T, Mivehvar F, Colella E, Roux KER, Konishi H, Ritsch H, Brantut JP. 2023. Density-wave ordering in a unitary Fermi gas with photon-mediated interactions. Nature. 618, 716–720.","ieee":"V. Helson <i>et al.</i>, “Density-wave ordering in a unitary Fermi gas with photon-mediated interactions,” <i>Nature</i>, vol. 618. Springer Nature, pp. 716–720, 2023.","chicago":"Helson, Victor, Timo Zwettler, Farokh Mivehvar, Elvia Colella, Kevin Etienne Robert Roux, Hideki Konishi, Helmut Ritsch, and Jean Philippe Brantut. “Density-Wave Ordering in a Unitary Fermi Gas with Photon-Mediated Interactions.” <i>Nature</i>. Springer Nature, 2023. <a href=\"https://doi.org/10.1038/s41586-023-06018-3\">https://doi.org/10.1038/s41586-023-06018-3</a>.","mla":"Helson, Victor, et al. “Density-Wave Ordering in a Unitary Fermi Gas with Photon-Mediated Interactions.” <i>Nature</i>, vol. 618, Springer Nature, 2023, pp. 716–20, doi:<a href=\"https://doi.org/10.1038/s41586-023-06018-3\">10.1038/s41586-023-06018-3</a>.","apa":"Helson, V., Zwettler, T., Mivehvar, F., Colella, E., Roux, K. E. R., Konishi, H., … Brantut, J. P. (2023). Density-wave ordering in a unitary Fermi gas with photon-mediated interactions. <i>Nature</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41586-023-06018-3\">https://doi.org/10.1038/s41586-023-06018-3</a>"},"abstract":[{"lang":"eng","text":"A density wave (DW) is a fundamental type of long-range order in quantum matter tied to self-organization into a crystalline structure. The interplay of DW order with superfluidity can lead to complex scenarios that pose a great challenge to theoretical analysis. In the past decades, tunable quantum Fermi gases have served as model systems for exploring the physics of strongly interacting fermions, including most notably magnetic ordering1, pairing and superfluidity2, and the crossover from a Bardeen–Cooper–Schrieffer superfluid to a Bose–Einstein condensate3. Here, we realize a Fermi gas featuring both strong, tunable contact interactions and photon-mediated, spatially structured long-range interactions in a transversely driven high-finesse optical cavity. Above a critical long-range interaction strength, DW order is stabilized in the system, which we identify via its superradiant light-scattering properties. We quantitatively measure the variation of the onset of DW order as the contact interaction is varied across the Bardeen–Cooper–Schrieffer superfluid and Bose–Einstein condensate crossover, in qualitative agreement with a mean-field theory. The atomic DW susceptibility varies over an order of magnitude upon tuning the strength and the sign of the long-range interactions below the self-ordering threshold, demonstrating independent and simultaneous control over the contact and long-range interactions. Therefore, our experimental setup provides a fully tunable and microscopically controllable platform for the experimental study of the interplay of superfluidity and DW order."}],"scopus_import":"1","doi":"10.1038/s41586-023-06018-3","month":"06","file_date_updated":"2023-11-14T13:00:19Z","page":"716-720","article_processing_charge":"Yes (via OA deal)","isi":1,"language":[{"iso":"eng"}],"volume":618,"quality_controlled":"1","year":"2023","ddc":["530"]},{"title":"Entangling microwaves with light","author":[{"id":"47D26E34-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6264-2162","full_name":"Sahu, Rishabh","last_name":"Sahu","first_name":"Rishabh"}],"main_file_link":[{"open_access":"1","url":"https://doi.org/10.5281/zenodo.7789418"}],"article_processing_charge":"No","day":"31","department":[{"_id":"JoFi"}],"month":"03","year":"2023","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"date_updated":"2026-04-15T06:39:32Z","status":"public","_id":"13122","corr_author":"1","publisher":"Zenodo","type":"research_data_reference","oa_version":"Published Version","date_created":"2023-06-06T06:46:16Z","related_material":{"record":[{"status":"public","id":"13106","relation":"used_in_publication"}]},"doi":"10.5281/ZENODO.7789417","date_published":"2023-03-31T00:00:00Z","abstract":[{"lang":"eng","text":"Data for submitted article \"Entangling microwaves with light\" at arXiv:2301.03315v1"}],"citation":{"apa":"Sahu, R. (2023). Entangling microwaves with light. Zenodo. <a href=\"https://doi.org/10.5281/ZENODO.7789417\">https://doi.org/10.5281/ZENODO.7789417</a>","mla":"Sahu, Rishabh. <i>Entangling Microwaves with Light</i>. Zenodo, 2023, doi:<a href=\"https://doi.org/10.5281/ZENODO.7789417\">10.5281/ZENODO.7789417</a>.","ista":"Sahu R. 2023. Entangling microwaves with light, Zenodo, <a href=\"https://doi.org/10.5281/ZENODO.7789417\">10.5281/ZENODO.7789417</a>.","chicago":"Sahu, Rishabh. “Entangling Microwaves with Light.” Zenodo, 2023. <a href=\"https://doi.org/10.5281/ZENODO.7789417\">https://doi.org/10.5281/ZENODO.7789417</a>.","ieee":"R. Sahu, “Entangling microwaves with light.” Zenodo, 2023.","ama":"Sahu R. Entangling microwaves with light. 2023. doi:<a href=\"https://doi.org/10.5281/ZENODO.7789417\">10.5281/ZENODO.7789417</a>","short":"R. Sahu, (2023)."},"oa":1},{"year":"2023","ddc":["530"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2026-06-03T07:16:05Z","tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"status":"public","author":[{"first_name":"Elena","last_name":"Redchenko","full_name":"Redchenko, Elena","id":"2C21D6E8-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Poshakinskiy, Alexander","first_name":"Alexander","last_name":"Poshakinskiy"},{"first_name":"Riya","last_name":"Sett","full_name":"Sett, Riya","orcid":"0000-0001-7641-8348","id":"2E6D040E-F248-11E8-B48F-1D18A9856A87"},{"id":"2DCF8DE6-F248-11E8-B48F-1D18A9856A87","first_name":"Martin","last_name":"Zemlicka","orcid":"0009-0005-0878-3032","full_name":"Zemlicka, Martin"},{"first_name":"Alexander","last_name":"Poddubny","full_name":"Poddubny, Alexander"},{"id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8112-028X","full_name":"Fink, Johannes M","first_name":"Johannes M","last_name":"Fink"}],"main_file_link":[{"open_access":"1","url":"https://doi.org/10.5281/zenodo.7858567"}],"title":"Tunable directional photon scattering from a pair of superconducting qubits","article_processing_charge":"No","department":[{"_id":"JoFi"}],"day":"28","month":"04","doi":"10.5281/ZENODO.7858567","related_material":{"record":[{"status":"public","id":"13117","relation":"used_in_publication"}]},"date_published":"2023-04-28T00:00:00Z","abstract":[{"text":"This dataset comprises all data shown in the figures of the submitted article \"Tunable directional photon scattering from a pair of superconducting qubits\" at arXiv:2205.03293. Additional raw data are available from the corresponding author on reasonable request.","lang":"eng"}],"oa":1,"citation":{"chicago":"Redchenko, Elena, Alexander Poshakinskiy, Riya Sett, Martin Zemlicka, Alexander Poddubny, and Johannes M Fink. “Tunable Directional Photon Scattering from a Pair of Superconducting Qubits.” Zenodo, 2023. <a href=\"https://doi.org/10.5281/ZENODO.7858567\">https://doi.org/10.5281/ZENODO.7858567</a>.","ieee":"E. Redchenko, A. Poshakinskiy, R. Sett, M. Zemlicka, A. Poddubny, and J. M. Fink, “Tunable directional photon scattering from a pair of superconducting qubits.” Zenodo, 2023.","ista":"Redchenko E, Poshakinskiy A, Sett R, Zemlicka M, Poddubny A, Fink JM. 2023. Tunable directional photon scattering from a pair of superconducting qubits, Zenodo, <a href=\"https://doi.org/10.5281/ZENODO.7858567\">10.5281/ZENODO.7858567</a>.","short":"E. Redchenko, A. Poshakinskiy, R. Sett, M. Zemlicka, A. Poddubny, J.M. Fink, (2023).","ama":"Redchenko E, Poshakinskiy A, Sett R, Zemlicka M, Poddubny A, Fink JM. Tunable directional photon scattering from a pair of superconducting qubits. 2023. doi:<a href=\"https://doi.org/10.5281/ZENODO.7858567\">10.5281/ZENODO.7858567</a>","apa":"Redchenko, E., Poshakinskiy, A., Sett, R., Zemlicka, M., Poddubny, A., &#38; Fink, J. M. (2023). Tunable directional photon scattering from a pair of superconducting qubits. Zenodo. <a href=\"https://doi.org/10.5281/ZENODO.7858567\">https://doi.org/10.5281/ZENODO.7858567</a>","mla":"Redchenko, Elena, et al. <i>Tunable Directional Photon Scattering from a Pair of Superconducting Qubits</i>. Zenodo, 2023, doi:<a href=\"https://doi.org/10.5281/ZENODO.7858567\">10.5281/ZENODO.7858567</a>."},"_id":"13124","corr_author":"1","type":"research_data_reference","publisher":"Zenodo","date_created":"2023-06-06T07:36:50Z","oa_version":"Published Version"},{"citation":{"mla":"Danzl, Johann G. <i>Research Data for the Publication “Imaging Brain Tissue Architecture across Millimeter to Nanometer Scales.”</i> Institute of Science and Technology Austria, 2023, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:13126\">10.15479/AT:ISTA:13126</a>.","apa":"Danzl, J. G. (2023). Research data for the publication “Imaging brain tissue architecture across millimeter to nanometer scales.” Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:13126\">https://doi.org/10.15479/AT:ISTA:13126</a>","short":"J.G. Danzl, (2023).","ama":"Danzl JG. Research data for the publication “Imaging brain tissue architecture across millimeter to nanometer scales.” 2023. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:13126\">10.15479/AT:ISTA:13126</a>","ista":"Danzl JG. 2023. Research data for the publication ‘Imaging brain tissue architecture across millimeter to nanometer scales’, Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:13126\">10.15479/AT:ISTA:13126</a>.","ieee":"J. G. Danzl, “Research data for the publication ‘Imaging brain tissue architecture across millimeter to nanometer scales.’” Institute of Science and Technology Austria, 2023.","chicago":"Danzl, Johann G. “Research Data for the Publication ‘Imaging Brain Tissue Architecture across Millimeter to Nanometer Scales.’” Institute of Science and Technology Austria, 2023. <a href=\"https://doi.org/10.15479/AT:ISTA:13126\">https://doi.org/10.15479/AT:ISTA:13126</a>."},"abstract":[{"lang":"eng","text":"Mapping the complex and dense arrangement of cells and their connectivity in brain tissue demands nanoscale spatial resolution imaging. Super-resolution optical microscopy excels at visualizing specific molecules and individual cells but fails to provide tissue context. Here, we developed Comprehensive Analysis of Tissues across Scales (CATS), a technology to densely map brain tissue architecture from millimeter regional to nanometer synaptic scales in diverse chemically fixed brain preparations, including rodent and human. CATS uses fixation-compatible extracellular labeling and optical imaging, including stimulated emission depletion or expansion microscopy, to comprehensively delineate cellular structures. It enables three-dimensional reconstruction of single synapses and mapping of synaptic connectivity by identification and analysis of putative synaptic cleft regions. Applying CATS to the mouse hippocampal mossy fiber circuitry, we reconstructed and quantified the synaptic input and output structure of identified neurons. We furthermore demonstrate applicability to clinically derived human tissue samples, including formalin-fixed paraffin-embedded routine diagnostic specimens, for visualizing the cellular architecture of brain tissue in health and disease."}],"related_material":{"record":[{"status":"public","id":"14257","relation":"used_in_publication"}],"link":[{"url":"https://pub.ista.ac.at/group_danzl/data/CATS/","relation":"research_data","description":"Original data for Fig. 5d, Fig. 5d (N2V) and Fig. 5f-i, provided via an external link due to the large size (>10GB) of the datasets. 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We gratefully acknowledge Eder Miguel for setting up webKnossos and Marek Šuplata for computational support and hardware control. We are grateful to Ryuichi Shigemoto and Bernd Bickel for generous support, and Michael Sixt and Scott Boyd (Stanford University) for discussions and critical reading of the manuscript. PSD95-HaloTag mice were kindly provided by Seth Grant (University of Edinburgh). We acknowledge expert support by IST Austria’s scientific computing, imaging and optics, preclinical, and lab support facilities, and by the Library and Miba machine shop.\r\nWe gratefully acknowledge funding by the following sources: \r\nAustrian Science Fund (FWF) grant I3600-B27 (JGD)\r\nAustrian Science Fund (FWF) grant DK W1232 (JGD, JMM)\r\nAustrian Science Fund (FWF) grant Z 312-B27, Wittgenstein award (PJ)\r\nAustrian Science Funds (FWF) projects I4685-B, I6565-B (SYNABS) and DOC 33-B27 (RH)\r\nGesellschaft für Forschungsförderung NÖ (NFB) grant LSC18-022 (JGD)\r\nEuropean Union’s Horizon 2020 research and innovation programme, European Research Council (ERC) grant 715508 – REVERSEAUTISM (GN)\r\nEuropean Union’s Horizon 2020 research and innovation programme, European Research Council (ERC) grant 692692 – GIANTSYN (PJ)\r\nMarie Skłodowska-Curie Actions Fellowship GA no. 665385 under the EU Horizon 2020 program (JMM, JL)\r\nMarie Skłodowska-Curie Actions Individual Fellowship 101026635 under the EU Horizon 2020 program (JFW)","day":"04","department":[{"_id":"JoDa"},{"_id":"SaSi"},{"_id":"GaNo"},{"_id":"PeJo"},{"_id":"Bio"},{"_id":"RySh"}],"contributor":[{"first_name":"Julia M","last_name":"Michalska","id":"443DB6DE-F248-11E8-B48F-1D18A9856A87"},{"id":"46E28B80-F248-11E8-B48F-1D18A9856A87","first_name":"Julia","last_name":"Lyudchik"},{"first_name":"Philipp","last_name":"Velicky","orcid":"0000-0002-2340-7431","id":"39BDC62C-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Stefanickova","first_name":"Hana","id":"ee3cb6ca-ec98-11ea-ae11-ff703e2254ed"},{"orcid":"0000-0002-8698-3823","last_name":"Watson","first_name":"Jake","id":"63836096-4690-11EA-BD4E-32803DDC885E"},{"id":"9ac8f577-2357-11eb-997a-e566c5550886","first_name":"Alban","last_name":"Cenameri"},{"id":"4DF26D8C-F248-11E8-B48F-1D18A9856A87","first_name":"Christoph M","last_name":"Sommer","orcid":"0000-0003-1216-9105"},{"orcid":"0000-0002-3183-8207","last_name":"Amberg","first_name":"Nicole","id":"4CD6AAC6-F248-11E8-B48F-1D18A9856A87"},{"id":"41CB84B2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2356-9403","last_name":"Venturino","first_name":"Alessandro"},{"first_name":"Karl","last_name":"Roessler"},{"first_name":"Thomas","last_name":"Czech"},{"first_name":"Romana","last_name":"Höftberger"},{"orcid":"0000-0001-8635-0877","first_name":"Sandra","last_name":"Siegert","id":"36ACD32E-F248-11E8-B48F-1D18A9856A87"},{"id":"3E57A680-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7673-7178","last_name":"Novarino","first_name":"Gaia"},{"id":"353C1B58-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5001-4804","last_name":"Jonas","first_name":"Peter M"}],"ec_funded":1,"title":"Research data for the publication \"Imaging brain tissue architecture across millimeter to nanometer scales\"","author":[{"first_name":"Johann G","last_name":"Danzl","full_name":"Danzl, Johann G","orcid":"0000-0001-8559-3973","id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87"}]},{"date_created":"2023-06-11T22:00:40Z","oa_version":"Published Version","article_number":"3232","_id":"13127","pmid":1,"project":[{"grant_number":"771402","_id":"2649B4DE-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Epidemics in ant societies on a chip"},{"grant_number":"RGP0065/2012","_id":"255008E4-B435-11E9-9278-68D0E5697425","name":"Information processing and computation in fish groups"}],"publication":"Nature Communications","file":[{"file_size":2358167,"checksum":"4af0393e3ed47b3fc46e68b81c3c1007","date_created":"2023-06-13T08:05:46Z","relation":"main_file","file_name":"2023_NatureComm_CasillasPerez.pdf","creator":"dernst","file_id":"13132","access_level":"open_access","content_type":"application/pdf","success":1,"date_updated":"2023-06-13T08:05:46Z"}],"date_published":"2023-06-03T00:00:00Z","publication_identifier":{"eissn":["2041-1723"]},"oa":1,"external_id":{"isi":["001002562700005"],"pmid":["37270641"]},"author":[{"first_name":"Barbara E","last_name":"Casillas Perez","full_name":"Casillas Perez, Barbara E","id":"351ED2AA-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0002-7214-0171","full_name":"Bod'Ová, Katarína","first_name":"Katarína","last_name":"Bod'Ová","id":"2BA24EA0-F248-11E8-B48F-1D18A9856A87"},{"id":"406F989C-F248-11E8-B48F-1D18A9856A87","full_name":"Grasse, Anna V","first_name":"Anna V","last_name":"Grasse"},{"id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6699-1455","full_name":"Tkačik, Gašper","last_name":"Tkačik","first_name":"Gašper"},{"id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","last_name":"Cremer","first_name":"Sylvia","orcid":"0000-0002-2193-3868","full_name":"Cremer, Sylvia"}],"title":"Dynamic pathogen detection and social feedback shape collective hygiene in ants","acknowledgement":"We thank Mike Bidochka for the fungal strains, the ISTA Social Immunity Team for ant collection, Hanna Leitner for experimental and molecular support, Jennifer Robb and Lukas Lindorfer for microscopy, and the LabSupport Facility at ISTA for general laboratory support. We further thank Victor Mireles, Iain Couzin, Fabian Theis and the Social Immunity Team for continued feedback throughout, and Michael Sixt, Yuko Ulrich, Koos Boomsma, Erika Dawson, Megan Kutzer and Hinrich Schulenburg for comments on the manuscript. This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (Grant No. 771402; EPIDEMICSonCHIP) to SC, from the Scientific Grant Agency of the Slovak Republic (Grant No. 1/0521/20) to KB, and the Human Frontier Science Program (Grant No. RGP0065/2012) to GT.","article_type":"original","ec_funded":1,"day":"03","department":[{"_id":"SyCr"},{"_id":"GaTk"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","date_updated":"2025-04-14T07:47:53Z","tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"publication_status":"published","publisher":"Springer Nature","type":"journal_article","corr_author":"1","has_accepted_license":"1","intvolume":"        14","scopus_import":"1","doi":"10.1038/s41467-023-38947-y","related_material":{"record":[{"relation":"research_data","id":"12945","status":"public"}]},"citation":{"mla":"Casillas Perez, Barbara E., et al. “Dynamic Pathogen Detection and Social Feedback Shape Collective Hygiene in Ants.” <i>Nature Communications</i>, vol. 14, 3232, Springer Nature, 2023, doi:<a href=\"https://doi.org/10.1038/s41467-023-38947-y\">10.1038/s41467-023-38947-y</a>.","apa":"Casillas Perez, B. E., Bodova, K., Grasse, A. V., Tkačik, G., &#38; Cremer, S. (2023). Dynamic pathogen detection and social feedback shape collective hygiene in ants. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-023-38947-y\">https://doi.org/10.1038/s41467-023-38947-y</a>","ama":"Casillas Perez BE, Bodova K, Grasse AV, Tkačik G, Cremer S. Dynamic pathogen detection and social feedback shape collective hygiene in ants. <i>Nature Communications</i>. 2023;14. doi:<a href=\"https://doi.org/10.1038/s41467-023-38947-y\">10.1038/s41467-023-38947-y</a>","short":"B.E. Casillas Perez, K. Bodova, A.V. Grasse, G. Tkačik, S. Cremer, Nature Communications 14 (2023).","ieee":"B. E. Casillas Perez, K. Bodova, A. V. Grasse, G. Tkačik, and S. Cremer, “Dynamic pathogen detection and social feedback shape collective hygiene in ants,” <i>Nature Communications</i>, vol. 14. Springer Nature, 2023.","ista":"Casillas Perez BE, Bodova K, Grasse AV, Tkačik G, Cremer S. 2023. Dynamic pathogen detection and social feedback shape collective hygiene in ants. Nature Communications. 14, 3232.","chicago":"Casillas Perez, Barbara E, Katarina Bodova, Anna V Grasse, Gašper Tkačik, and Sylvia Cremer. “Dynamic Pathogen Detection and Social Feedback Shape Collective Hygiene in Ants.” <i>Nature Communications</i>. Springer Nature, 2023. <a href=\"https://doi.org/10.1038/s41467-023-38947-y\">https://doi.org/10.1038/s41467-023-38947-y</a>."},"abstract":[{"lang":"eng","text":"Cooperative disease defense emerges as group-level collective behavior, yet how group members make the underlying individual decisions is poorly understood. Using garden ants and fungal pathogens as an experimental model, we derive the rules governing individual ant grooming choices and show how they produce colony-level hygiene. Time-resolved behavioral analysis, pathogen quantification, and probabilistic modeling reveal that ants increase grooming and preferentially target highly-infectious individuals when perceiving high pathogen load, but transiently suppress grooming after having been groomed by nestmates. Ants thus react to both, the infectivity of others and the social feedback they receive on their own contagiousness. While inferred solely from momentary ant decisions, these behavioral rules quantitatively predict hour-long experimental dynamics, and synergistically combine into efficient colony-wide pathogen removal. Our analyses show that noisy individual decisions based on only local, incomplete, yet dynamically-updated information on pathogen threat and social feedback can lead to potent collective disease defense."}],"article_processing_charge":"Yes","isi":1,"month":"06","file_date_updated":"2023-06-13T08:05:46Z","acknowledged_ssus":[{"_id":"LifeSc"}],"quality_controlled":"1","year":"2023","ddc":["570"],"language":[{"iso":"eng"}],"volume":14},{"publication":"Canadian Mathematical Bulletin","oa_version":"Preprint","date_created":"2023-06-11T22:00:40Z","_id":"13128","external_id":{"isi":["001011963000001"],"arxiv":["2106.07328"]},"oa":1,"date_published":"2023-12-01T00:00:00Z","publication_identifier":{"issn":["0008-4395"],"eissn":["1496-4287"]},"arxiv":1,"article_type":"original","day":"01","department":[{"_id":"GradSch"}],"title":"An energy decomposition theorem for matrices and related questions","main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2106.07328","open_access":"1"}],"author":[{"last_name":"Mohammadi","first_name":"Ali","full_name":"Mohammadi, Ali"},{"last_name":"Pham","first_name":"Thang","full_name":"Pham, Thang"},{"id":"1917d194-076e-11ed-97cd-837255f88785","last_name":"Wang","first_name":"Yiting","full_name":"Wang, Yiting","orcid":"0000-0002-2856-767X"}],"status":"public","date_updated":"2026-04-08T13:04:49Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":"        66","publication_status":"published","publisher":"Cambridge University Press","type":"journal_article","citation":{"chicago":"Mohammadi, Ali, Thang Pham, and Yiting Wang. “An Energy Decomposition Theorem for Matrices and Related Questions.” <i>Canadian Mathematical Bulletin</i>. Cambridge University Press, 2023. <a href=\"https://doi.org/10.4153/S000843952300036X\">https://doi.org/10.4153/S000843952300036X</a>.","ieee":"A. Mohammadi, T. Pham, and Y. Wang, “An energy decomposition theorem for matrices and related questions,” <i>Canadian Mathematical Bulletin</i>, vol. 66, no. 4. Cambridge University Press, pp. 1280–1295, 2023.","ista":"Mohammadi A, Pham T, Wang Y. 2023. An energy decomposition theorem for matrices and related questions. Canadian Mathematical Bulletin. 66(4), 1280–1295.","short":"A. Mohammadi, T. Pham, Y. Wang, Canadian Mathematical Bulletin 66 (2023) 1280–1295.","ama":"Mohammadi A, Pham T, Wang Y. An energy decomposition theorem for matrices and related questions. <i>Canadian Mathematical Bulletin</i>. 2023;66(4):1280-1295. doi:<a href=\"https://doi.org/10.4153/S000843952300036X\">10.4153/S000843952300036X</a>","mla":"Mohammadi, Ali, et al. “An Energy Decomposition Theorem for Matrices and Related Questions.” <i>Canadian Mathematical Bulletin</i>, vol. 66, no. 4, Cambridge University Press, 2023, pp. 1280–95, doi:<a href=\"https://doi.org/10.4153/S000843952300036X\">10.4153/S000843952300036X</a>.","apa":"Mohammadi, A., Pham, T., &#38; Wang, Y. (2023). An energy decomposition theorem for matrices and related questions. <i>Canadian Mathematical Bulletin</i>. Cambridge University Press. <a href=\"https://doi.org/10.4153/S000843952300036X\">https://doi.org/10.4153/S000843952300036X</a>"},"abstract":[{"lang":"eng","text":"Given 𝐴 ⊆𝐺⁡𝐿2⁡(𝔽𝑞), we prove that there exist disjoint subsets 𝐵,𝐶 ⊆𝐴 such that 𝐴 =𝐵 ⊔𝐶 and their additive and multiplicative energies satisfying\r\nmax⁡{𝐸+⁡(𝐵),𝐸×⁡(𝐶)}≪|𝐴|3/𝑀⁡(|𝐴|), where\r\n𝑀⁡(|𝐴|)=min⁡{𝑞4/3/|𝐴|1/3⁢(log⁡|𝐴|)2/3, |𝐴|4/5/𝑞13/5⁢(log⁡|𝐴|)27/10}.\r\n \r\nWe also study some related questions on moderate expanders over matrix rings, namely, for 𝐴,𝐵,𝐶 ⊆𝐺⁡𝐿2⁡(𝔽𝑞), we have\r\n|𝐴⁢𝐵+𝐶|, |(𝐴+𝐵)⁢𝐶|≫𝑞4,\r\n whenever |𝐴|⁢|𝐵|⁢|𝐶| ≫𝑞10+1/2. These improve earlier results due to Karabulut, Koh, Pham, Shen, and Vinh ([2019], Expanding phenomena over matrix rings, 𝐹⁡𝑜⁢𝑟⁢𝑢⁢𝑚⁢𝑀⁢𝑎⁢𝑡⁢ℎ., 31, 951–970)."}],"scopus_import":"1","doi":"10.4153/S000843952300036X","month":"12","page":"1280-1295","issue":"4","article_processing_charge":"No","isi":1,"language":[{"iso":"eng"}],"volume":66,"quality_controlled":"1","year":"2023"}]