[{"_id":"14768","year":"2023","ec_funded":1,"date_created":"2024-01-09T16:20:09Z","article_processing_charge":"No","oa_version":"Preprint","quality_controlled":"1","abstract":[{"text":"In all state-of-the-art sketching and coreset techniques for clustering, as well as in the best known fixed-parameter tractable approximation algorithms, randomness plays a key role. For the classic k-median and k-means problems, there are no known deterministic dimensionality reduction procedure or coreset construction that avoid an exponential dependency on the input dimension d, the precision parameter $\\varepsilon^{-1}$ or k. Furthermore, there is no coreset construction that succeeds with probability $1-1/n$ and whose size does not depend on the number of input points, n. This has led researchers in the area to ask what is the power of randomness for clustering sketches [Feldman WIREs Data Mining Knowl. Discov’20].Similarly, the best approximation ratio achievable deterministically without a complexity exponential in the dimension are $1+\\sqrt{2}$ for k-median [Cohen-Addad, Esfandiari, Mirrokni, Narayanan, STOC’22] and 6.12903 for k-means [Grandoni, Ostrovsky, Rabani, Schulman, Venkat, Inf. Process. Lett.’22]. Those are the best results, even when allowing a complexity FPT in the number of clusters k: this stands in sharp contrast with the $(1+\\varepsilon)$-approximation achievable in that case, when allowing randomization.In this paper, we provide deterministic sketches constructions for clustering, whose size bounds are close to the best-known randomized ones. We show how to compute a dimension reduction onto $\\varepsilon^{-O(1)} \\log k$ dimensions in time $k^{O\\left(\\varepsilon^{-O(1)}+\\log \\log k\\right)}$ poly $(n d)$, and how to build a coreset of size $O\\left(k^{2} \\log ^{3} k \\varepsilon^{-O(1)}\\right)$ in time $2^{\\varepsilon^{O(1)} k \\log ^{3} k}+k^{O\\left(\\varepsilon^{-O(1)}+\\log \\log k\\right)}$ poly $(n d)$. In the case where k is small, this answers an open question of [Feldman WIDM’20] and [Munteanu and Schwiegelshohn, Künstliche Intell. ’18] on whether it is possible to efficiently compute coresets deterministically.We also construct a deterministic algorithm for computing $(1+$ $\\varepsilon)$-approximation to k-median and k-means in high dimensional Euclidean spaces in time $2^{k^{2} \\log ^{3} k / \\varepsilon^{O(1)}}$ poly $(n d)$, close to the best randomized complexity of $2^{(k / \\varepsilon)^{O(1)}}$ nd (see [Kumar, Sabharwal, Sen, JACM 10] and [Bhattacharya, Jaiswal, Kumar, TCS’18]).Furthermore, our new insights on sketches also yield a randomized coreset construction that uses uniform sampling, that immediately improves over the recent results of [Braverman et al. FOCS ’22] by a factor k.","lang":"eng"}],"publication_status":"published","oa":1,"publication":"2023 IEEE 64th Annual Symposium on Foundations of Computer Science","publication_identifier":{"eisbn":["9798350318944"]},"day":"22","citation":{"short":"V. Cohen-Addad, D. Saulpic, C. Schwiegelshohn, in:, 2023 IEEE 64th Annual Symposium on Foundations of Computer Science, IEEE, 2023, pp. 1105–1130.","chicago":"Cohen-Addad, Vincent, David Saulpic, and Chris Schwiegelshohn. “Deterministic Clustering in High Dimensional Spaces: Sketches and Approximation.” In <i>2023 IEEE 64th Annual Symposium on Foundations of Computer Science</i>, 1105–30. IEEE, 2023. <a href=\"https://doi.org/10.1109/focs57990.2023.00066\">https://doi.org/10.1109/focs57990.2023.00066</a>.","ista":"Cohen-Addad V, Saulpic D, Schwiegelshohn C. 2023. Deterministic clustering in high dimensional spaces: Sketches and approximation. 2023 IEEE 64th Annual Symposium on Foundations of Computer Science. FOCS: Symposium on Foundations of Computer Science, 1105–1130.","mla":"Cohen-Addad, Vincent, et al. “Deterministic Clustering in High Dimensional Spaces: Sketches and Approximation.” <i>2023 IEEE 64th Annual Symposium on Foundations of Computer Science</i>, IEEE, 2023, pp. 1105–30, doi:<a href=\"https://doi.org/10.1109/focs57990.2023.00066\">10.1109/focs57990.2023.00066</a>.","apa":"Cohen-Addad, V., Saulpic, D., &#38; Schwiegelshohn, C. (2023). Deterministic clustering in high dimensional spaces: Sketches and approximation. In <i>2023 IEEE 64th Annual Symposium on Foundations of Computer Science</i> (pp. 1105–1130). Santa Cruz, CA, United States: IEEE. <a href=\"https://doi.org/10.1109/focs57990.2023.00066\">https://doi.org/10.1109/focs57990.2023.00066</a>","ama":"Cohen-Addad V, Saulpic D, Schwiegelshohn C. Deterministic clustering in high dimensional spaces: Sketches and approximation. In: <i>2023 IEEE 64th Annual Symposium on Foundations of Computer Science</i>. IEEE; 2023:1105-1130. doi:<a href=\"https://doi.org/10.1109/focs57990.2023.00066\">10.1109/focs57990.2023.00066</a>","ieee":"V. Cohen-Addad, D. Saulpic, and C. Schwiegelshohn, “Deterministic clustering in high dimensional spaces: Sketches and approximation,” in <i>2023 IEEE 64th Annual Symposium on Foundations of Computer Science</i>, Santa Cruz, CA, United States, 2023, pp. 1105–1130."},"date_updated":"2024-01-16T07:28:06Z","author":[{"full_name":"Cohen-Addad, Vincent","first_name":"Vincent","last_name":"Cohen-Addad"},{"first_name":"David","last_name":"Saulpic","id":"f8e48cf0-b0ff-11ed-b0e9-b4c35598f964","full_name":"Saulpic, David"},{"first_name":"Chris","last_name":"Schwiegelshohn","full_name":"Schwiegelshohn, Chris"}],"title":"Deterministic clustering in high dimensional spaces: Sketches and approximation","external_id":{"arxiv":["2310.04076"]},"project":[{"name":"IST-BRIDGE: International postdoctoral program","call_identifier":"H2020","_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c","grant_number":"101034413"},{"call_identifier":"H2020","grant_number":"101019564","_id":"bd9ca328-d553-11ed-ba76-dc4f890cfe62","name":"The design and evaluation of modern fully dynamic data structures"}],"scopus_import":"1","acknowledgement":"D. Sauplic has received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement No 101034413, and Grant agreement No. 101019564 “The Design of Modern Fully Dynamic Data Structures (MoDynStruct)”.\r\nC. Schwiegelshohn acknowledges the support of the Independent Research Fund Denmark (DFF) under a Sapere Aude Research Leader grant No 1051-00106B.","conference":{"location":"Santa Cruz, CA, United States","name":"FOCS: Symposium on Foundations of Computer Science","start_date":"2023-11-06","end_date":"2023-11-09"},"page":"1105-1130","arxiv":1,"main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2310.04076","open_access":"1"}],"month":"12","publisher":"IEEE","department":[{"_id":"MoHe"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"conference","status":"public","language":[{"iso":"eng"}],"date_published":"2023-12-22T00:00:00Z","doi":"10.1109/focs57990.2023.00066"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"journal_article","volume":20,"intvolume":"        20","doi":"10.1038/s41592-023-01937-5","date_published":"2023-08-01T00:00:00Z","language":[{"iso":"eng"}],"status":"public","scopus_import":"1","page":"1141-1142","isi":1,"publisher":"Springer Nature","department":[{"_id":"JoDa"}],"month":"08","day":"01","publication":"Nature Methods","publication_identifier":{"eissn":["1548-7105"],"issn":["1548-7091"]},"author":[{"full_name":"Danzl, Johann G","id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8559-3973","first_name":"Johann G","last_name":"Danzl"},{"last_name":"Velicky","first_name":"Philipp","orcid":"0000-0002-2340-7431","full_name":"Velicky, Philipp","id":"39BDC62C-F248-11E8-B48F-1D18A9856A87"}],"citation":{"short":"J.G. Danzl, P. Velicky, Nature Methods 20 (2023) 1141–1142.","chicago":"Danzl, Johann G, and Philipp Velicky. “LIONESS Enables 4D Nanoscale Reconstruction of Living Brain Tissue.” <i>Nature Methods</i>. Springer Nature, 2023. <a href=\"https://doi.org/10.1038/s41592-023-01937-5\">https://doi.org/10.1038/s41592-023-01937-5</a>.","ista":"Danzl JG, Velicky P. 2023. LIONESS enables 4D nanoscale reconstruction of living brain tissue. Nature Methods. 20(8), 1141–1142.","mla":"Danzl, Johann G., and Philipp Velicky. “LIONESS Enables 4D Nanoscale Reconstruction of Living Brain Tissue.” <i>Nature Methods</i>, vol. 20, no. 8, Springer Nature, 2023, pp. 1141–42, doi:<a href=\"https://doi.org/10.1038/s41592-023-01937-5\">10.1038/s41592-023-01937-5</a>.","ama":"Danzl JG, Velicky P. LIONESS enables 4D nanoscale reconstruction of living brain tissue. <i>Nature Methods</i>. 2023;20(8):1141-1142. doi:<a href=\"https://doi.org/10.1038/s41592-023-01937-5\">10.1038/s41592-023-01937-5</a>","apa":"Danzl, J. G., &#38; Velicky, P. (2023). LIONESS enables 4D nanoscale reconstruction of living brain tissue. <i>Nature Methods</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41592-023-01937-5\">https://doi.org/10.1038/s41592-023-01937-5</a>","ieee":"J. G. Danzl and P. Velicky, “LIONESS enables 4D nanoscale reconstruction of living brain tissue,” <i>Nature Methods</i>, vol. 20, no. 8. Springer Nature, pp. 1141–1142, 2023."},"date_updated":"2024-01-10T08:37:48Z","issue":"8","title":"LIONESS enables 4D nanoscale reconstruction of living brain tissue","external_id":{"isi":["001025621500002"]},"date_created":"2024-01-10T08:07:15Z","year":"2023","_id":"14770","quality_controlled":"1","oa_version":"None","article_processing_charge":"No","keyword":["Cell Biology","Molecular Biology","Biochemistry","Biotechnology"],"related_material":{"record":[{"status":"public","id":"13267","relation":"extended_version"}]},"publication_status":"published","article_type":"letter_note","abstract":[{"text":"We developed LIONESS, a technology that leverages improvements to optical super-resolution microscopy and prior information on sample structure via machine learning to overcome the limitations (in 3D-resolution, signal-to-noise ratio and light exposure) of optical microscopy of living biological specimens. LIONESS enables dense reconstruction of living brain tissue and morphodynamics visualization at the nanoscale.","lang":"eng"}]},{"date_created":"2024-01-10T08:42:40Z","ec_funded":1,"year":"2023","_id":"14771","quality_controlled":"1","oa_version":"Preprint","article_processing_charge":"No","related_material":{"link":[{"url":"https://github.com/IST-DASLab/pruned-vision-model-bias","relation":"software"}]},"publication_status":"published","abstract":[{"lang":"eng","text":"Pruning—that is, setting a significant subset of the parameters of a neural network to zero—is one of the most popular methods of model compression. Yet, several recent works have raised the issue that pruning may induce or exacerbate bias in the output of the compressed model. Despite existing evidence for this phenomenon, the relationship between neural network pruning and induced bias is not well-understood. In this work, we systematically investigate and characterize this phenomenon in Convolutional Neural Networks for computer vision. First, we show that it is in fact possible to obtain highly-sparse models, e.g. with less than 10% remaining weights, which do not decrease in accuracy nor substantially increase in bias when compared to dense models. At the same time, we also find that, at higher sparsities, pruned models exhibit higher uncertainty in their outputs, as well as increased correlations, which we directly link to increased bias. We propose easy-to-use criteria which, based only on the uncompressed model, establish whether bias will increase with pruning, and identify the samples most susceptible to biased predictions post-compression. Our code can be found at https://github.com/IST-DASLab/pruned-vision-model-bias."}],"day":"22","publication":"2023 IEEE/CVF Conference on Computer Vision and Pattern Recognition","publication_identifier":{"eissn":["2575-7075"],"eisbn":["9798350301298"]},"oa":1,"author":[{"last_name":"Iofinova","first_name":"Eugenia B","orcid":"0000-0002-7778-3221","id":"f9a17499-f6e0-11ea-865d-fdf9a3f77117","full_name":"Iofinova, Eugenia B"},{"first_name":"Elena-Alexandra","last_name":"Peste","id":"32D78294-F248-11E8-B48F-1D18A9856A87","full_name":"Peste, Elena-Alexandra"},{"orcid":"0000-0003-3650-940X","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","full_name":"Alistarh, Dan-Adrian","last_name":"Alistarh","first_name":"Dan-Adrian"}],"date_updated":"2024-01-10T08:59:26Z","citation":{"short":"E.B. Iofinova, E.-A. Peste, D.-A. Alistarh, in:, 2023 IEEE/CVF Conference on Computer Vision and Pattern Recognition, IEEE, 2023, pp. 24364–24373.","ama":"Iofinova EB, Peste E-A, Alistarh D-A. Bias in pruned vision models: In-depth analysis and countermeasures. In: <i>2023 IEEE/CVF Conference on Computer Vision and Pattern Recognition</i>. IEEE; 2023:24364-24373. doi:<a href=\"https://doi.org/10.1109/cvpr52729.2023.02334\">10.1109/cvpr52729.2023.02334</a>","ieee":"E. B. Iofinova, E.-A. Peste, and D.-A. Alistarh, “Bias in pruned vision models: In-depth analysis and countermeasures,” in <i>2023 IEEE/CVF Conference on Computer Vision and Pattern Recognition</i>, Vancouver, BC, Canada, 2023, pp. 24364–24373.","apa":"Iofinova, E. B., Peste, E.-A., &#38; Alistarh, D.-A. (2023). Bias in pruned vision models: In-depth analysis and countermeasures. In <i>2023 IEEE/CVF Conference on Computer Vision and Pattern Recognition</i> (pp. 24364–24373). Vancouver, BC, Canada: IEEE. <a href=\"https://doi.org/10.1109/cvpr52729.2023.02334\">https://doi.org/10.1109/cvpr52729.2023.02334</a>","mla":"Iofinova, Eugenia B., et al. “Bias in Pruned Vision Models: In-Depth Analysis and Countermeasures.” <i>2023 IEEE/CVF Conference on Computer Vision and Pattern Recognition</i>, IEEE, 2023, pp. 24364–73, doi:<a href=\"https://doi.org/10.1109/cvpr52729.2023.02334\">10.1109/cvpr52729.2023.02334</a>.","ista":"Iofinova EB, Peste E-A, Alistarh D-A. 2023. Bias in pruned vision models: In-depth analysis and countermeasures. 2023 IEEE/CVF Conference on Computer Vision and Pattern Recognition. CVPR: Conference on Computer Vision and Pattern Recognition, 24364–24373.","chicago":"Iofinova, Eugenia B, Elena-Alexandra Peste, and Dan-Adrian Alistarh. “Bias in Pruned Vision Models: In-Depth Analysis and Countermeasures.” In <i>2023 IEEE/CVF Conference on Computer Vision and Pattern Recognition</i>, 24364–73. IEEE, 2023. <a href=\"https://doi.org/10.1109/cvpr52729.2023.02334\">https://doi.org/10.1109/cvpr52729.2023.02334</a>."},"project":[{"name":"Vienna Graduate School on Computational Optimization","_id":"9B9290DE-BA93-11EA-9121-9846C619BF3A","grant_number":" W1260-N35"},{"name":"Elastic Coordination for Scalable Machine Learning","_id":"268A44D6-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"805223"}],"title":"Bias in pruned vision models: In-depth analysis and countermeasures","external_id":{"isi":["001062531308068"],"arxiv":["2304.12622"]},"acknowledgement":"The authors would like to sincerely thank Sara Hooker for her feedback during the development of this work. EI was supported in part by the FWF DK VGSCO, grant agreement number W1260-N35. AP and DA acknowledge generous ERC support, via Starting Grant 805223 ScaleML.","arxiv":1,"page":"24364-24373","conference":{"start_date":"2023-06-17","name":"CVPR: Conference on Computer Vision and Pattern Recognition","location":"Vancouver, BC, Canada","end_date":"2023-06-24"},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2304.12622"}],"isi":1,"publisher":"IEEE","department":[{"_id":"DaAl"},{"_id":"ChLa"}],"month":"08","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"conference","doi":"10.1109/cvpr52729.2023.02334","date_published":"2023-08-22T00:00:00Z","language":[{"iso":"eng"}],"status":"public"},{"has_accepted_license":"1","issue":"11","article_number":"110146","external_id":{"isi":["001081809000001"],"arxiv":["2108.01962"]},"title":"Maximal Lp-regularity and H∞-calculus for block operator matrices and applications","day":"01","publication_identifier":{"issn":["0022-1236"]},"publication":"Journal of Functional Analysis","oa":1,"date_updated":"2024-01-10T11:24:56Z","citation":{"chicago":"Agresti, Antonio, and Amru Hussein. “Maximal Lp-Regularity and H∞-Calculus for Block Operator Matrices and Applications.” <i>Journal of Functional Analysis</i>. Elsevier, 2023. <a href=\"https://doi.org/10.1016/j.jfa.2023.110146\">https://doi.org/10.1016/j.jfa.2023.110146</a>.","ista":"Agresti A, Hussein A. 2023. Maximal Lp-regularity and H∞-calculus for block operator matrices and applications. Journal of Functional Analysis. 285(11), 110146.","mla":"Agresti, Antonio, and Amru Hussein. “Maximal Lp-Regularity and H∞-Calculus for Block Operator Matrices and Applications.” <i>Journal of Functional Analysis</i>, vol. 285, no. 11, 110146, Elsevier, 2023, doi:<a href=\"https://doi.org/10.1016/j.jfa.2023.110146\">10.1016/j.jfa.2023.110146</a>.","ieee":"A. Agresti and A. Hussein, “Maximal Lp-regularity and H∞-calculus for block operator matrices and applications,” <i>Journal of Functional Analysis</i>, vol. 285, no. 11. Elsevier, 2023.","apa":"Agresti, A., &#38; Hussein, A. (2023). Maximal Lp-regularity and H∞-calculus for block operator matrices and applications. <i>Journal of Functional Analysis</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.jfa.2023.110146\">https://doi.org/10.1016/j.jfa.2023.110146</a>","ama":"Agresti A, Hussein A. Maximal Lp-regularity and H∞-calculus for block operator matrices and applications. <i>Journal of Functional Analysis</i>. 2023;285(11). doi:<a href=\"https://doi.org/10.1016/j.jfa.2023.110146\">10.1016/j.jfa.2023.110146</a>","short":"A. Agresti, A. Hussein, Journal of Functional Analysis 285 (2023)."},"author":[{"full_name":"Agresti, Antonio","id":"673cd0cc-9b9a-11eb-b144-88f30e1fbb72","orcid":"0000-0002-9573-2962","first_name":"Antonio","last_name":"Agresti"},{"full_name":"Hussein, Amru","last_name":"Hussein","first_name":"Amru"}],"quality_controlled":"1","oa_version":"Published Version","article_processing_charge":"Yes (in subscription journal)","keyword":["Analysis"],"article_type":"original","publication_status":"published","file":[{"checksum":"eda98ca2aa73da91bd074baed34c2b3c","content_type":"application/pdf","file_size":1120592,"creator":"dernst","access_level":"open_access","file_name":"2023_JourFunctionalAnalysis_Agresti.pdf","date_created":"2024-01-10T11:23:57Z","relation":"main_file","success":1,"file_id":"14789","date_updated":"2024-01-10T11:23:57Z"}],"abstract":[{"text":"Many coupled evolution equations can be described via 2×2-block operator matrices of the form A=[ \r\nA\tB\r\nC\tD\r\n ] in a product space X=X1×X2 with possibly unbounded entries. Here, the case of diagonally dominant block operator matrices is considered, that is, the case where the full operator A can be seen as a relatively bounded perturbation of its diagonal part with D(A)=D(A)×D(D) though with possibly large relative bound. For such operators the properties of sectoriality, R-sectoriality and the boundedness of the H∞-calculus are studied, and for these properties perturbation results for possibly large but structured perturbations are derived. Thereby, the time dependent parabolic problem associated with A can be analyzed in maximal Lpt\r\n-regularity spaces, and this is applied to a wide range of problems such as different theories for liquid crystals, an artificial Stokes system, strongly damped wave and plate equations, and a Keller-Segel model.","lang":"eng"}],"date_created":"2024-01-10T09:15:18Z","year":"2023","_id":"14772","ddc":["510"],"intvolume":"       285","doi":"10.1016/j.jfa.2023.110146","date_published":"2023-12-01T00:00:00Z","language":[{"iso":"eng"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"status":"public","file_date_updated":"2024-01-10T11:23:57Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"journal_article","volume":285,"license":"https://creativecommons.org/licenses/by/4.0/","isi":1,"publisher":"Elsevier","department":[{"_id":"JuFi"}],"month":"12","acknowledgement":"We would like to thank Tim Binz, Emiel Lorist and Mark Veraar for valuable discussions. We also thank the anonymous referees for their helpful comments and suggestions, and for the very accurate reading of the manuscript.\r\nThe first author has been supported partially by the Nachwuchsring – Network for the promotion of young scientists – at TU Kaiserslautern. Both authors have been supported by MathApp – Mathematics Applied to Real-World Problems - part of the Research Initiative of the Federal State of Rhineland-Palatinate, Germany.","scopus_import":"1","arxiv":1},{"issue":"5","article_number":"28","external_id":{"isi":["000984516100007"]},"title":"The cloud dynamics of convective storm systems","day":"01","oa":1,"publication":"Physics Today","publication_identifier":{"eissn":["1945-0699"],"issn":["0031-9228"]},"citation":{"chicago":"Muller, Caroline J, and Sophie Abramian. “The Cloud Dynamics of Convective Storm Systems.” <i>Physics Today</i>. AIP Publishing, 2023. <a href=\"https://doi.org/10.1063/pt.3.5234\">https://doi.org/10.1063/pt.3.5234</a>.","ista":"Muller CJ, Abramian S. 2023. The cloud dynamics of convective storm systems. Physics Today. 76(5), 28.","mla":"Muller, Caroline J., and Sophie Abramian. “The Cloud Dynamics of Convective Storm Systems.” <i>Physics Today</i>, vol. 76, no. 5, 28, AIP Publishing, 2023, doi:<a href=\"https://doi.org/10.1063/pt.3.5234\">10.1063/pt.3.5234</a>.","apa":"Muller, C. J., &#38; Abramian, S. (2023). The cloud dynamics of convective storm systems. <i>Physics Today</i>. AIP Publishing. <a href=\"https://doi.org/10.1063/pt.3.5234\">https://doi.org/10.1063/pt.3.5234</a>","ieee":"C. J. Muller and S. Abramian, “The cloud dynamics of convective storm systems,” <i>Physics Today</i>, vol. 76, no. 5. AIP Publishing, 2023.","ama":"Muller CJ, Abramian S. The cloud dynamics of convective storm systems. <i>Physics Today</i>. 2023;76(5). doi:<a href=\"https://doi.org/10.1063/pt.3.5234\">10.1063/pt.3.5234</a>","short":"C.J. Muller, S. Abramian, Physics Today 76 (2023)."},"date_updated":"2024-01-10T12:38:02Z","author":[{"orcid":"0000-0001-5836-5350","full_name":"Muller, Caroline J","id":"f978ccb0-3f7f-11eb-b193-b0e2bd13182b","last_name":"Muller","first_name":"Caroline J"},{"first_name":"Sophie","last_name":"Abramian","full_name":"Abramian, Sophie"}],"quality_controlled":"1","article_processing_charge":"No","keyword":["General Physics and Astronomy"],"oa_version":"Published Version","publication_status":"published","article_type":"original","abstract":[{"text":"Through a combination of idealized simulations and real-world data, researchers are uncovering how internal feedbacks and large-scale motions influence cloud dynamics.","lang":"eng"}],"date_created":"2024-01-10T09:18:04Z","_id":"14773","year":"2023","intvolume":"        76","date_published":"2023-05-01T00:00:00Z","doi":"10.1063/pt.3.5234","status":"public","language":[{"iso":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"journal_article","volume":76,"isi":1,"main_file_link":[{"open_access":"1","url":"https://www.lmd.ens.fr/muller/Pubs/2023-MullerAbramianPhysToday.pdf"}],"month":"05","department":[{"_id":"CaMu"}],"publisher":"AIP Publishing"},{"language":[{"iso":"eng"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"status":"public","doi":"10.1242/dev.201559","date_published":"2023-10-01T00:00:00Z","intvolume":"       150","ddc":["570"],"volume":150,"type":"journal_article","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file_date_updated":"2024-01-10T12:41:13Z","department":[{"_id":"AnKi"}],"publisher":"The Company of Biologists","month":"10","isi":1,"acknowledgement":"We thank members of the Brand lab, as well as Justina Stark (Ivo Sbalzarini group, Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany) for project-related discussions; Darren Gilmour (University of Zurich), Karuna Sampath (University of Warwick) and Gokul Kesavan (Vowels Lifesciences Private Limited, Bangalore) for comments on the manuscript; personnel of the CMCB technology platform, TU Dresden for imaging and image analysis-related support; and Maurizio Abbate (Technical support, Arivis) for help with image analysis. We are also grateful to Stapornwongkul and Briscoe for commenting on a preprint version of our work (Stapornwongkul and Briscoe, 2022).\r\nThis work was supported by the Deutsche Forschungsgemeinschaft (BR 1746/6-2, BR 1746/11-1 and BR 1746/3 to M.B.), by a Cluster of Excellence ‘Physics of Life’ seed grant and by institutional funds from Technische Universitat Dresden (to M.B.). Open Access funding provided by Technische Universitat Dresden. Deposited in PMC for immediate release.","external_id":{"isi":["001097449100002"],"pmid":["37665167"]},"title":"Real-time monitoring of an endogenous Fgf8a gradient attests to its role as a morphogen during zebrafish gastrulation","article_number":"dev201559","issue":"19","has_accepted_license":"1","citation":{"short":"R.K. Harish, M. Gupta, D. Zöller, H. Hartmann, A. Gheisari, A. Machate, S. Hans, M. Brand, Development 150 (2023).","mla":"Harish, Rohit K., et al. “Real-Time Monitoring of an Endogenous Fgf8a Gradient Attests to Its Role as a Morphogen during Zebrafish Gastrulation.” <i>Development</i>, vol. 150, no. 19, dev201559, The Company of Biologists, 2023, doi:<a href=\"https://doi.org/10.1242/dev.201559\">10.1242/dev.201559</a>.","apa":"Harish, R. K., Gupta, M., Zöller, D., Hartmann, H., Gheisari, A., Machate, A., … Brand, M. (2023). Real-time monitoring of an endogenous Fgf8a gradient attests to its role as a morphogen during zebrafish gastrulation. <i>Development</i>. The Company of Biologists. <a href=\"https://doi.org/10.1242/dev.201559\">https://doi.org/10.1242/dev.201559</a>","ieee":"R. K. Harish <i>et al.</i>, “Real-time monitoring of an endogenous Fgf8a gradient attests to its role as a morphogen during zebrafish gastrulation,” <i>Development</i>, vol. 150, no. 19. The Company of Biologists, 2023.","ama":"Harish RK, Gupta M, Zöller D, et al. Real-time monitoring of an endogenous Fgf8a gradient attests to its role as a morphogen during zebrafish gastrulation. <i>Development</i>. 2023;150(19). doi:<a href=\"https://doi.org/10.1242/dev.201559\">10.1242/dev.201559</a>","chicago":"Harish, Rohit K, Mansi Gupta, Daniela Zöller, Hella Hartmann, Ali Gheisari, Anja Machate, Stefan Hans, and Michael Brand. “Real-Time Monitoring of an Endogenous Fgf8a Gradient Attests to Its Role as a Morphogen during Zebrafish Gastrulation.” <i>Development</i>. The Company of Biologists, 2023. <a href=\"https://doi.org/10.1242/dev.201559\">https://doi.org/10.1242/dev.201559</a>.","ista":"Harish RK, Gupta M, Zöller D, Hartmann H, Gheisari A, Machate A, Hans S, Brand M. 2023. Real-time monitoring of an endogenous Fgf8a gradient attests to its role as a morphogen during zebrafish gastrulation. Development. 150(19), dev201559."},"date_updated":"2024-01-10T12:45:25Z","author":[{"full_name":"Harish, Rohit K","id":"1bae78aa-ee0e-11ec-9b76-bc42990f409d","first_name":"Rohit K","last_name":"Harish"},{"full_name":"Gupta, Mansi","first_name":"Mansi","last_name":"Gupta"},{"full_name":"Zöller, Daniela","first_name":"Daniela","last_name":"Zöller"},{"full_name":"Hartmann, Hella","last_name":"Hartmann","first_name":"Hella"},{"first_name":"Ali","last_name":"Gheisari","full_name":"Gheisari, Ali"},{"first_name":"Anja","last_name":"Machate","full_name":"Machate, Anja"},{"full_name":"Hans, Stefan","last_name":"Hans","first_name":"Stefan"},{"full_name":"Brand, Michael","last_name":"Brand","first_name":"Michael"}],"publication":"Development","publication_identifier":{"issn":["0950-1991"],"eissn":["1477-9129"]},"oa":1,"day":"01","file":[{"creator":"dernst","access_level":"open_access","file_size":12836306,"content_type":"application/pdf","checksum":"2d6f52dc33260a9b2352b8f28374ba5f","date_updated":"2024-01-10T12:41:13Z","relation":"main_file","success":1,"date_created":"2024-01-10T12:41:13Z","file_id":"14790","file_name":"2023_Development_Harish.pdf"}],"abstract":[{"text":"Morphogen gradients impart positional information to cells in a homogenous tissue field. Fgf8a, a highly conserved growth factor, has been proposed to act as a morphogen during zebrafish gastrulation. However, technical limitations have so far prevented direct visualization of the endogenous Fgf8a gradient and confirmation of its morphogenic activity. Here, we monitor Fgf8a propagation in the developing neural plate using a CRISPR/Cas9-mediated EGFP knock-in at the endogenous fgf8a locus. By combining sensitive imaging with single-molecule fluorescence correlation spectroscopy, we demonstrate that Fgf8a, which is produced at the embryonic margin, propagates by diffusion through the extracellular space and forms a graded distribution towards the animal pole. Overlaying the Fgf8a gradient curve with expression profiles of its downstream targets determines the precise input-output relationship of Fgf8a-mediated patterning. Manipulation of the extracellular Fgf8a levels alters the signaling outcome, thus establishing Fgf8a as a bona fide morphogen during zebrafish gastrulation. Furthermore, by hindering Fgf8a diffusion, we demonstrate that extracellular diffusion of the protein from the source is crucial for it to achieve its morphogenic potential.","lang":"eng"}],"publication_status":"published","article_type":"original","oa_version":"Published Version","article_processing_charge":"Yes (via OA deal)","keyword":["Developmental Biology","Molecular Biology"],"quality_controlled":"1","year":"2023","_id":"14774","pmid":1,"date_created":"2024-01-10T09:18:54Z"},{"author":[{"last_name":"Schnelli","first_name":"Kevin","orcid":"0000-0003-0954-3231","full_name":"Schnelli, Kevin","id":"434AD0AE-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Xu, Yuanyuan","id":"7902bdb1-a2a4-11eb-a164-c9216f71aea3","orcid":"0000-0003-1559-1205","first_name":"Yuanyuan","last_name":"Xu"}],"citation":{"apa":"Schnelli, K., &#38; Xu, Y. (2023). Convergence rate to the Tracy–Widom laws for the largest eigenvalue of sample covariance matrices. <i>The Annals of Applied Probability</i>. Institute of Mathematical Statistics. <a href=\"https://doi.org/10.1214/22-aap1826\">https://doi.org/10.1214/22-aap1826</a>","ama":"Schnelli K, Xu Y. Convergence rate to the Tracy–Widom laws for the largest eigenvalue of sample covariance matrices. <i>The Annals of Applied Probability</i>. 2023;33(1):677-725. doi:<a href=\"https://doi.org/10.1214/22-aap1826\">10.1214/22-aap1826</a>","ieee":"K. Schnelli and Y. Xu, “Convergence rate to the Tracy–Widom laws for the largest eigenvalue of sample covariance matrices,” <i>The Annals of Applied Probability</i>, vol. 33, no. 1. Institute of Mathematical Statistics, pp. 677–725, 2023.","mla":"Schnelli, Kevin, and Yuanyuan Xu. “Convergence Rate to the Tracy–Widom Laws for the Largest Eigenvalue of Sample Covariance Matrices.” <i>The Annals of Applied Probability</i>, vol. 33, no. 1, Institute of Mathematical Statistics, 2023, pp. 677–725, doi:<a href=\"https://doi.org/10.1214/22-aap1826\">10.1214/22-aap1826</a>.","ista":"Schnelli K, Xu Y. 2023. Convergence rate to the Tracy–Widom laws for the largest eigenvalue of sample covariance matrices. The Annals of Applied Probability. 33(1), 677–725.","chicago":"Schnelli, Kevin, and Yuanyuan Xu. “Convergence Rate to the Tracy–Widom Laws for the Largest Eigenvalue of Sample Covariance Matrices.” <i>The Annals of Applied Probability</i>. Institute of Mathematical Statistics, 2023. <a href=\"https://doi.org/10.1214/22-aap1826\">https://doi.org/10.1214/22-aap1826</a>.","short":"K. Schnelli, Y. Xu, The Annals of Applied Probability 33 (2023) 677–725."},"date_updated":"2024-01-10T13:31:46Z","day":"01","publication":"The Annals of Applied Probability","publication_identifier":{"issn":["1050-5164"]},"oa":1,"project":[{"call_identifier":"H2020","_id":"62796744-2b32-11ec-9570-940b20777f1d","grant_number":"101020331","name":"Random matrices beyond Wigner-Dyson-Mehta"}],"external_id":{"isi":["000946432400021"],"arxiv":["2108.02728"]},"title":"Convergence rate to the Tracy–Widom laws for the largest eigenvalue of sample covariance matrices","issue":"1","date_created":"2024-01-10T09:23:31Z","ec_funded":1,"year":"2023","_id":"14775","article_type":"original","publication_status":"published","abstract":[{"text":"We establish a quantitative version of the Tracy–Widom law for the largest eigenvalue of high-dimensional sample covariance matrices. To be precise, we show that the fluctuations of the largest eigenvalue of a sample covariance matrix X∗X converge to its Tracy–Widom limit at a rate nearly N−1/3, where X is an M×N random matrix whose entries are independent real or complex random variables, assuming that both M and N tend to infinity at a constant rate. This result improves the previous estimate N−2/9 obtained by Wang (2019). Our proof relies on a Green function comparison method (Adv. Math. 229 (2012) 1435–1515) using iterative cumulant expansions, the local laws for the Green function and asymptotic properties of the correlation kernel of the white Wishart ensemble.","lang":"eng"}],"quality_controlled":"1","oa_version":"Preprint","keyword":["Statistics","Probability and Uncertainty","Statistics and Probability"],"article_processing_charge":"No","type":"journal_article","volume":33,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","doi":"10.1214/22-aap1826","date_published":"2023-02-01T00:00:00Z","language":[{"iso":"eng"}],"status":"public","intvolume":"        33","arxiv":1,"page":"677-725","acknowledgement":"K. Schnelli was supported by the Swedish Research Council Grants VR-2017-05195, and the Knut and Alice Wallenberg Foundation. Y. Xu was supported by the Swedish Research Council Grant VR-2017-05195 and the ERC Advanced Grant “RMTBeyond” No. 101020331.","scopus_import":"1","department":[{"_id":"LaEr"}],"publisher":"Institute of Mathematical Statistics","month":"02","isi":1,"main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2108.02728","open_access":"1"}]},{"acknowledgement":"We thank C.U.T. Hellen for critically reading the manuscript. The MALDI MS facility and CLSM became available to us in the framework of Moscow State University Development Programs PNG 5.13 and PNR 5.13.\r\nThis work was funded by the Russian Science Foundation, grant numbers 19-14-00010 and 22-14-00071.","month":"11","department":[{"_id":"JiFr"}],"publisher":"MDPI","isi":1,"type":"journal_article","volume":24,"file_date_updated":"2024-01-10T13:39:42Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2023-11-01T00:00:00Z","doi":"10.3390/ijms242216527","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"language":[{"iso":"eng"}],"ddc":["580"],"intvolume":"        24","pmid":1,"date_created":"2024-01-10T09:24:35Z","_id":"14776","year":"2023","publication_status":"published","article_type":"original","abstract":[{"text":"Soluble chaperones residing in the endoplasmic reticulum (ER) play vitally important roles in folding and quality control of newly synthesized proteins that transiently pass through the ER en route to their final destinations. These soluble residents of the ER are themselves endowed with an ER retrieval signal that enables the cell to bring the escaped residents back from the Golgi. Here, by using purified proteins, we showed that Nicotiana tabacum phytaspase, a plant aspartate-specific protease, introduces two breaks at the C-terminus of the N. tabacum ER resident calreticulin-3. These cleavages resulted in removal of either a dipeptide or a hexapeptide from the C-terminus of calreticulin-3 encompassing part or all of the ER retrieval signal. Consistently, expression of the calreticulin-3 derivative mimicking the phytaspase cleavage product in Nicotiana benthamiana cells demonstrated loss of the ER accumulation of the protein. Notably, upon its escape from the ER, calreticulin-3 was further processed by an unknown protease(s) to generate the free N-terminal (N) domain of calreticulin-3, which was ultimately secreted into the apoplast. Our study thus identified a specific proteolytic enzyme capable of precise detachment of the ER retrieval signal from a plant ER resident protein, with implications for the further fate of the escaped resident.","lang":"eng"}],"file":[{"date_updated":"2024-01-10T13:39:42Z","file_name":"2023_IJMS_Teplova.pdf","success":1,"relation":"main_file","date_created":"2024-01-10T13:39:42Z","file_id":"14791","creator":"dernst","access_level":"open_access","checksum":"4df7d206ba022b7f54eff1f0aec1659a","content_type":"application/pdf","file_size":2637784}],"quality_controlled":"1","article_processing_charge":"Yes","keyword":["Inorganic Chemistry","Organic Chemistry","Physical and Theoretical Chemistry","Computer Science Applications","Spectroscopy","Molecular Biology","General Medicine","Catalysis"],"oa_version":"Published Version","author":[{"id":"e3736151-106c-11ec-b916-c2558e2762c6","full_name":"Teplova, Anastasiia","last_name":"Teplova","first_name":"Anastasiia"},{"full_name":"Pigidanov, Artemii A.","first_name":"Artemii A.","last_name":"Pigidanov"},{"first_name":"Marina V.","last_name":"Serebryakova","full_name":"Serebryakova, Marina V."},{"first_name":"Sergei A.","last_name":"Golyshev","full_name":"Golyshev, Sergei A."},{"last_name":"Galiullina","first_name":"Raisa A.","full_name":"Galiullina, Raisa A."},{"full_name":"Chichkova, Nina V.","first_name":"Nina V.","last_name":"Chichkova"},{"full_name":"Vartapetian, Andrey B.","first_name":"Andrey B.","last_name":"Vartapetian"}],"citation":{"mla":"Teplova, Anastasiia, et al. “Phytaspase Is Capable of Detaching the Endoplasmic Reticulum Retrieval Signal from Tobacco Calreticulin-3.” <i>International Journal of Molecular Sciences</i>, vol. 24, no. 22, 16527, MDPI, 2023, doi:<a href=\"https://doi.org/10.3390/ijms242216527\">10.3390/ijms242216527</a>.","apa":"Teplova, A., Pigidanov, A. A., Serebryakova, M. V., Golyshev, S. A., Galiullina, R. A., Chichkova, N. V., &#38; Vartapetian, A. B. (2023). Phytaspase Is capable of detaching the endoplasmic reticulum retrieval signal from tobacco calreticulin-3. <i>International Journal of Molecular Sciences</i>. MDPI. <a href=\"https://doi.org/10.3390/ijms242216527\">https://doi.org/10.3390/ijms242216527</a>","ieee":"A. Teplova <i>et al.</i>, “Phytaspase Is capable of detaching the endoplasmic reticulum retrieval signal from tobacco calreticulin-3,” <i>International Journal of Molecular Sciences</i>, vol. 24, no. 22. MDPI, 2023.","ama":"Teplova A, Pigidanov AA, Serebryakova MV, et al. Phytaspase Is capable of detaching the endoplasmic reticulum retrieval signal from tobacco calreticulin-3. <i>International Journal of Molecular Sciences</i>. 2023;24(22). doi:<a href=\"https://doi.org/10.3390/ijms242216527\">10.3390/ijms242216527</a>","chicago":"Teplova, Anastasiia, Artemii A. Pigidanov, Marina V. Serebryakova, Sergei A. Golyshev, Raisa A. Galiullina, Nina V. Chichkova, and Andrey B. Vartapetian. “Phytaspase Is Capable of Detaching the Endoplasmic Reticulum Retrieval Signal from Tobacco Calreticulin-3.” <i>International Journal of Molecular Sciences</i>. MDPI, 2023. <a href=\"https://doi.org/10.3390/ijms242216527\">https://doi.org/10.3390/ijms242216527</a>.","ista":"Teplova A, Pigidanov AA, Serebryakova MV, Golyshev SA, Galiullina RA, Chichkova NV, Vartapetian AB. 2023. Phytaspase Is capable of detaching the endoplasmic reticulum retrieval signal from tobacco calreticulin-3. International Journal of Molecular Sciences. 24(22), 16527.","short":"A. Teplova, A.A. Pigidanov, M.V. Serebryakova, S.A. Golyshev, R.A. Galiullina, N.V. Chichkova, A.B. Vartapetian, International Journal of Molecular Sciences 24 (2023)."},"date_updated":"2024-01-10T13:41:10Z","day":"01","oa":1,"publication":"International Journal of Molecular Sciences","publication_identifier":{"issn":["1422-0067"]},"external_id":{"isi":["001113792600001"],"pmid":["38003717"]},"title":"Phytaspase Is capable of detaching the endoplasmic reticulum retrieval signal from tobacco calreticulin-3","has_accepted_license":"1","article_number":"16527","issue":"22"},{"year":"2023","_id":"14777","date_created":"2024-01-10T09:26:08Z","file":[{"file_id":"14792","success":1,"relation":"main_file","date_created":"2024-01-10T13:47:31Z","file_name":"2023_AIPAdvances_Sato.pdf","date_updated":"2024-01-10T13:47:31Z","file_size":9676071,"content_type":"application/pdf","checksum":"a7098388b8ff822b47f5ddd37ed3bdbc","access_level":"open_access","creator":"dernst"}],"abstract":[{"lang":"eng","text":"The effects of the partial V-substitution for Ag on the thermoelectric (TE) properties are investigated for a flexible semiconducting compound Ag2S0.55Se0.45. Density functional theory calculations predict that such a partial V-substitution constructively modifies the electronic structure near the bottom of the conduction band to improve the TE performance. The synthesized Ag1.97V0.03S0.55Se0.45 is found to possess a TE dimensionless figure-of-merit (ZT) of 0.71 at 350 K with maintaining its flexible nature. This ZT value is relatively high in comparison with those reported for flexible TE materials below 360 K. The increase in the ZT value is caused by the enhanced absolute value of the Seebeck coefficient with less significant variation in electrical resistivity. The high ZT value with the flexible nature naturally allows us to employ the Ag1.97V0.03S0.55Se0.45 as a component of flexible TE generators."}],"publication_status":"published","article_type":"original","oa_version":"Published Version","article_processing_charge":"Yes","keyword":["General Physics and Astronomy"],"quality_controlled":"1","author":[{"full_name":"Sato, Kosuke","last_name":"Sato","first_name":"Kosuke"},{"last_name":"Singh","first_name":"Saurabh","full_name":"Singh, Saurabh","id":"12d625da-9cb3-11ed-9667-af09d37d3f0a","orcid":"0000-0003-2209-5269"},{"full_name":"Yamazaki, Itsuki","last_name":"Yamazaki","first_name":"Itsuki"},{"last_name":"Hirata","first_name":"Keisuke","full_name":"Hirata, Keisuke"},{"full_name":"Ang, Artoni Kevin R.","first_name":"Artoni Kevin R.","last_name":"Ang"},{"full_name":"Matsunami, Masaharu","last_name":"Matsunami","first_name":"Masaharu"},{"full_name":"Takeuchi, Tsunehiro","first_name":"Tsunehiro","last_name":"Takeuchi"}],"citation":{"ista":"Sato K, Singh S, Yamazaki I, Hirata K, Ang AKR, Matsunami M, Takeuchi T. 2023. Improvement of thermoelectric performance of flexible compound Ag2S0.55Se0.45 by means of partial V-substitution for Ag. AIP Advances. 13(12), 125206.","chicago":"Sato, Kosuke, Saurabh Singh, Itsuki Yamazaki, Keisuke Hirata, Artoni Kevin R. Ang, Masaharu Matsunami, and Tsunehiro Takeuchi. “Improvement of Thermoelectric Performance of Flexible Compound Ag2S0.55Se0.45 by Means of Partial V-Substitution for Ag.” <i>AIP Advances</i>. AIP Publishing, 2023. <a href=\"https://doi.org/10.1063/5.0171888\">https://doi.org/10.1063/5.0171888</a>.","ama":"Sato K, Singh S, Yamazaki I, et al. Improvement of thermoelectric performance of flexible compound Ag2S0.55Se0.45 by means of partial V-substitution for Ag. <i>AIP Advances</i>. 2023;13(12). doi:<a href=\"https://doi.org/10.1063/5.0171888\">10.1063/5.0171888</a>","apa":"Sato, K., Singh, S., Yamazaki, I., Hirata, K., Ang, A. K. R., Matsunami, M., &#38; Takeuchi, T. (2023). Improvement of thermoelectric performance of flexible compound Ag2S0.55Se0.45 by means of partial V-substitution for Ag. <i>AIP Advances</i>. AIP Publishing. <a href=\"https://doi.org/10.1063/5.0171888\">https://doi.org/10.1063/5.0171888</a>","ieee":"K. Sato <i>et al.</i>, “Improvement of thermoelectric performance of flexible compound Ag2S0.55Se0.45 by means of partial V-substitution for Ag,” <i>AIP Advances</i>, vol. 13, no. 12. AIP Publishing, 2023.","mla":"Sato, Kosuke, et al. “Improvement of Thermoelectric Performance of Flexible Compound Ag2S0.55Se0.45 by Means of Partial V-Substitution for Ag.” <i>AIP Advances</i>, vol. 13, no. 12, 125206, AIP Publishing, 2023, doi:<a href=\"https://doi.org/10.1063/5.0171888\">10.1063/5.0171888</a>.","short":"K. Sato, S. Singh, I. Yamazaki, K. Hirata, A.K.R. Ang, M. Matsunami, T. Takeuchi, AIP Advances 13 (2023)."},"date_updated":"2024-01-10T13:49:09Z","publication":"AIP Advances","publication_identifier":{"eissn":["2158-3226"]},"oa":1,"day":"01","external_id":{"isi":["001114917200005"]},"title":"Improvement of thermoelectric performance of flexible compound Ag2S0.55Se0.45 by means of partial V-substitution for Ag","article_number":"125206","issue":"12","has_accepted_license":"1","acknowledgement":"This work received financial support partially from Japan Science and Technology Agency (JST) CREST Grant No. JPMJCR18I2, Japan. The powder-XRD experiments were conducted at BL5S2 of Aichi Synchrotron Radiation Center, Aichi Science & Technology Foundation, Aichi, Japan (Proposal No. 202301057).","department":[{"_id":"MaIb"}],"publisher":"AIP Publishing","month":"12","isi":1,"volume":13,"type":"journal_article","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file_date_updated":"2024-01-10T13:47:31Z","language":[{"iso":"eng"}],"status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"doi":"10.1063/5.0171888","date_published":"2023-12-01T00:00:00Z","ddc":["540"],"intvolume":"        13"},{"month":"06","department":[{"_id":"KrCh"}],"publisher":"Association for Computing Machinery","acknowledgement":"This research was partially supported by the ERC CoG (grant no. 863818; ForM-SMArt), the Czech Science Foundation (grant no. GA21-24711S), and the European Union’s Horizon 2020 research and innovation program under the Marie Skłodowska-Curie Grant Agreement No. 665385.","arxiv":1,"intvolume":"        35","ddc":["000"],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"status":"public","language":[{"iso":"eng"}],"date_published":"2023-06-23T00:00:00Z","doi":"10.1145/3585391","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file_date_updated":"2024-01-16T08:11:24Z","volume":35,"type":"journal_article","keyword":["Theoretical Computer Science","Software"],"article_processing_charge":"Yes (via OA deal)","oa_version":"Published Version","quality_controlled":"1","abstract":[{"lang":"eng","text":"We consider the almost-sure (a.s.) termination problem for probabilistic programs, which are a stochastic extension of classical imperative programs. Lexicographic ranking functions provide a sound and practical approach for termination of non-probabilistic programs, and their extension to probabilistic programs is achieved via lexicographic ranking supermartingales (LexRSMs). However, LexRSMs introduced in the previous work have a limitation that impedes their automation: all of their components have to be non-negative in all reachable states. This might result in a LexRSM not existing even for simple terminating programs. Our contributions are twofold. First, we introduce a generalization of LexRSMs that allows for some components to be negative. This standard feature of non-probabilistic termination proofs was hitherto not known to be sound in the probabilistic setting, as the soundness proof requires a careful analysis of the underlying stochastic process. Second, we present polynomial-time algorithms using our generalized LexRSMs for proving a.s. termination in broad classes of linear-arithmetic programs."}],"file":[{"date_updated":"2024-01-16T08:11:24Z","file_id":"14804","success":1,"date_created":"2024-01-16T08:11:24Z","relation":"main_file","file_name":"2023_FormalAspectsComputing_Chatterjee.pdf","access_level":"open_access","creator":"dernst","file_size":502522,"content_type":"application/pdf","checksum":"3bb133eeb27ec01649a9a36445d952d9"}],"related_material":{"record":[{"status":"public","id":"10414","relation":"earlier_version"}]},"article_type":"original","publication_status":"published","_id":"14778","year":"2023","ec_funded":1,"date_created":"2024-01-10T09:27:43Z","issue":"2","article_number":"11","has_accepted_license":"1","external_id":{"arxiv":["2108.02188"]},"title":"On lexicographic proof rules for probabilistic termination","project":[{"call_identifier":"H2020","grant_number":"863818","_id":"0599E47C-7A3F-11EA-A408-12923DDC885E","name":"Formal Methods for Stochastic Models: Algorithms and Applications"},{"grant_number":"665385","call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","name":"International IST Doctoral Program"}],"oa":1,"publication_identifier":{"eissn":["1433-299X"],"issn":["0934-5043"]},"publication":"Formal Aspects of Computing","day":"23","author":[{"orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee","first_name":"Krishnendu"},{"first_name":"Ehsan","last_name":"Kafshdar Goharshady","full_name":"Kafshdar Goharshady, Ehsan"},{"full_name":"Novotný, Petr","id":"3CC3B868-F248-11E8-B48F-1D18A9856A87","last_name":"Novotný","first_name":"Petr"},{"first_name":"Jiří","last_name":"Zárevúcky","full_name":"Zárevúcky, Jiří"},{"id":"294AA7A6-F248-11E8-B48F-1D18A9856A87","full_name":"Zikelic, Dorde","orcid":"0000-0002-4681-1699","last_name":"Zikelic","first_name":"Dorde"}],"date_updated":"2025-07-14T09:10:10Z","citation":{"short":"K. Chatterjee, E. Kafshdar Goharshady, P. Novotný, J. Zárevúcky, D. Zikelic, Formal Aspects of Computing 35 (2023).","mla":"Chatterjee, Krishnendu, et al. “On Lexicographic Proof Rules for Probabilistic Termination.” <i>Formal Aspects of Computing</i>, vol. 35, no. 2, 11, Association for Computing Machinery, 2023, doi:<a href=\"https://doi.org/10.1145/3585391\">10.1145/3585391</a>.","ama":"Chatterjee K, Kafshdar Goharshady E, Novotný P, Zárevúcky J, Zikelic D. On lexicographic proof rules for probabilistic termination. <i>Formal Aspects of Computing</i>. 2023;35(2). doi:<a href=\"https://doi.org/10.1145/3585391\">10.1145/3585391</a>","apa":"Chatterjee, K., Kafshdar Goharshady, E., Novotný, P., Zárevúcky, J., &#38; Zikelic, D. (2023). On lexicographic proof rules for probabilistic termination. <i>Formal Aspects of Computing</i>. Association for Computing Machinery. <a href=\"https://doi.org/10.1145/3585391\">https://doi.org/10.1145/3585391</a>","ieee":"K. Chatterjee, E. Kafshdar Goharshady, P. Novotný, J. Zárevúcky, and D. Zikelic, “On lexicographic proof rules for probabilistic termination,” <i>Formal Aspects of Computing</i>, vol. 35, no. 2. Association for Computing Machinery, 2023.","chicago":"Chatterjee, Krishnendu, Ehsan Kafshdar Goharshady, Petr Novotný, Jiří Zárevúcky, and Dorde Zikelic. “On Lexicographic Proof Rules for Probabilistic Termination.” <i>Formal Aspects of Computing</i>. Association for Computing Machinery, 2023. <a href=\"https://doi.org/10.1145/3585391\">https://doi.org/10.1145/3585391</a>.","ista":"Chatterjee K, Kafshdar Goharshady E, Novotný P, Zárevúcky J, Zikelic D. 2023. On lexicographic proof rules for probabilistic termination. Formal Aspects of Computing. 35(2), 11."}},{"month":"06","department":[{"_id":"FrPe"}],"publisher":"American Geophysical Union","isi":1,"acknowledgement":"This work was funded by the EU Horizon 2020 Marie Skłodowska-Curie Actions Grant 101026058. The authors acknowl-edge the dedicated collection of field data by many parties since 2001, including those acknowledged for the cited works on Arolla Glacier. The authors would like to thank Fabienne Meier, Alice Zaugg, Raphael Willi, Maria Grundmann, and Marta Corrà for assistance in the field for the summers of 2021 and 2022. Off-glacier data provided by Grand Dixence SA (Arolla) and MeteoSwiss are kindly acknowledged. Simone Fatichi is thanked for the provision and support in the use of the Tethys-Chloris model. We thank Editor Mathieu Morlighem and two anonymous reviewers whose comments have helped to improve the quality of the manuscript.","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"language":[{"iso":"eng"}],"date_published":"2023-06-16T00:00:00Z","doi":"10.1029/2023gl103043","ddc":["550"],"intvolume":"        50","volume":50,"type":"journal_article","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file_date_updated":"2024-01-16T08:35:02Z","abstract":[{"text":"The presence of a developed boundary layer decouples a glacier's response from ambient conditions, suggesting that sensitivity to climate change is increased by glacier retreat. To test this hypothesis, we explore six years of distributed meteorological data on a small Swiss glacier in the period 2001–2022. Large glacier fragmentation has occurred since 2001 (−35% area change up to 2022) coinciding with notable frontal retreat, an observed switch from down‐glacier katabatic to up‐glacier valley winds and an increased sensitivity (ratio) of on‐glacier to off‐glacier temperature. As the glacier ceases to develop density‐driven katabatic winds, sensible heat fluxes on the glacier are increasingly determined by the conditions occurring outside the boundary layer of the glacier, sealing the glacier's demise as the climate continues to warm and experience an increased frequency of extreme summers.","lang":"eng"}],"file":[{"date_updated":"2024-01-16T08:35:02Z","file_name":"2023_GeophysicalResearchLetter_Shaw.pdf","file_id":"14805","success":1,"date_created":"2024-01-16T08:35:02Z","relation":"main_file","access_level":"open_access","creator":"dernst","checksum":"391a3005c95340a0ae129ce4fbdf2bae","content_type":"application/pdf","file_size":2529327}],"publication_status":"published","article_type":"original","keyword":["General Earth and Planetary Sciences","Geophysics"],"article_processing_charge":"No","oa_version":"Published Version","quality_controlled":"1","_id":"14779","year":"2023","date_created":"2024-01-10T09:28:34Z","external_id":{"isi":["000999436400001"]},"title":"The decaying near‐surface boundary layer of a retreating alpine glacier","article_number":"e2023GL103043","issue":"11","has_accepted_license":"1","author":[{"first_name":"Thomas E.","last_name":"Shaw","full_name":"Shaw, Thomas E."},{"full_name":"Buri, Pascal","last_name":"Buri","first_name":"Pascal"},{"last_name":"McCarthy","first_name":"Michael","full_name":"McCarthy, Michael"},{"full_name":"Miles, Evan S.","first_name":"Evan S.","last_name":"Miles"},{"first_name":"Álvaro","last_name":"Ayala","full_name":"Ayala, Álvaro"},{"first_name":"Francesca","last_name":"Pellicciotti","full_name":"Pellicciotti, Francesca","id":"b28f055a-81ea-11ed-b70c-a9fe7f7b0e70","orcid":"0000-0002-5554-8087"}],"citation":{"ista":"Shaw TE, Buri P, McCarthy M, Miles ES, Ayala Á, Pellicciotti F. 2023. The decaying near‐surface boundary layer of a retreating alpine glacier. Geophysical Research Letters. 50(11), e2023GL103043.","chicago":"Shaw, Thomas E., Pascal Buri, Michael McCarthy, Evan S. Miles, Álvaro Ayala, and Francesca Pellicciotti. “The Decaying Near‐surface Boundary Layer of a Retreating Alpine Glacier.” <i>Geophysical Research Letters</i>. American Geophysical Union, 2023. <a href=\"https://doi.org/10.1029/2023gl103043\">https://doi.org/10.1029/2023gl103043</a>.","ieee":"T. E. Shaw, P. Buri, M. McCarthy, E. S. Miles, Á. Ayala, and F. Pellicciotti, “The decaying near‐surface boundary layer of a retreating alpine glacier,” <i>Geophysical Research Letters</i>, vol. 50, no. 11. American Geophysical Union, 2023.","ama":"Shaw TE, Buri P, McCarthy M, Miles ES, Ayala Á, Pellicciotti F. The decaying near‐surface boundary layer of a retreating alpine glacier. <i>Geophysical Research Letters</i>. 2023;50(11). doi:<a href=\"https://doi.org/10.1029/2023gl103043\">10.1029/2023gl103043</a>","apa":"Shaw, T. E., Buri, P., McCarthy, M., Miles, E. S., Ayala, Á., &#38; Pellicciotti, F. (2023). The decaying near‐surface boundary layer of a retreating alpine glacier. <i>Geophysical Research Letters</i>. American Geophysical Union. <a href=\"https://doi.org/10.1029/2023gl103043\">https://doi.org/10.1029/2023gl103043</a>","mla":"Shaw, Thomas E., et al. “The Decaying Near‐surface Boundary Layer of a Retreating Alpine Glacier.” <i>Geophysical Research Letters</i>, vol. 50, no. 11, e2023GL103043, American Geophysical Union, 2023, doi:<a href=\"https://doi.org/10.1029/2023gl103043\">10.1029/2023gl103043</a>.","short":"T.E. Shaw, P. Buri, M. McCarthy, E.S. Miles, Á. Ayala, F. Pellicciotti, Geophysical Research Letters 50 (2023)."},"date_updated":"2024-01-16T08:42:36Z","oa":1,"publication":"Geophysical Research Letters","publication_identifier":{"issn":["0094-8276"],"eissn":["1944-8007"]},"day":"16"},{"quality_controlled":"1","article_processing_charge":"Yes (in subscription journal)","keyword":["Applied Mathematics","Modeling and Simulation","Statistics and Probability"],"oa_version":"Published Version","article_type":"original","publication_status":"published","abstract":[{"lang":"eng","text":"In this paper, we study the eigenvalues and eigenvectors of the spiked invariant multiplicative models when the randomness is from Haar matrices. We establish the limits of the outlier eigenvalues λˆi and the generalized components (⟨v,uˆi⟩ for any deterministic vector v) of the outlier eigenvectors uˆi with optimal convergence rates. Moreover, we prove that the non-outlier eigenvalues stick with those of the unspiked matrices and the non-outlier eigenvectors are delocalized. The results also hold near the so-called BBP transition and for degenerate spikes. On one hand, our results can be regarded as a refinement of the counterparts of [12] under additional regularity conditions. On the other hand, they can be viewed as an analog of [34] by replacing the random matrix with i.i.d. entries with Haar random matrix."}],"file":[{"creator":"dernst","access_level":"open_access","checksum":"46a708b0cd5569a73d0f3d6c3e0a44dc","file_size":1870349,"content_type":"application/pdf","date_updated":"2024-01-16T08:47:31Z","file_name":"2023_StochasticProcAppl_Ding.pdf","relation":"main_file","date_created":"2024-01-16T08:47:31Z","success":1,"file_id":"14806"}],"ec_funded":1,"date_created":"2024-01-10T09:29:25Z","_id":"14780","year":"2023","has_accepted_license":"1","title":"Spiked multiplicative random matrices and principal components","external_id":{"arxiv":["2302.13502"],"isi":["001113615900001"]},"project":[{"name":"Random matrices beyond Wigner-Dyson-Mehta","call_identifier":"H2020","grant_number":"101020331","_id":"62796744-2b32-11ec-9570-940b20777f1d"}],"day":"01","oa":1,"publication_identifier":{"eissn":["1879-209X"],"issn":["0304-4149"]},"publication":"Stochastic Processes and their Applications","date_updated":"2024-01-16T08:49:51Z","author":[{"last_name":"Ding","first_name":"Xiucai","full_name":"Ding, Xiucai"},{"last_name":"Ji","first_name":"Hong Chang","full_name":"Ji, Hong Chang","id":"dd216c0a-c1f9-11eb-beaf-e9ea9d2de76d"}],"citation":{"short":"X. Ding, H.C. Ji, Stochastic Processes and Their Applications 163 (2023) 25–60.","chicago":"Ding, Xiucai, and Hong Chang Ji. “Spiked Multiplicative Random Matrices and Principal Components.” <i>Stochastic Processes and Their Applications</i>. Elsevier, 2023. <a href=\"https://doi.org/10.1016/j.spa.2023.05.009\">https://doi.org/10.1016/j.spa.2023.05.009</a>.","ista":"Ding X, Ji HC. 2023. Spiked multiplicative random matrices and principal components. Stochastic Processes and their Applications. 163, 25–60.","mla":"Ding, Xiucai, and Hong Chang Ji. “Spiked Multiplicative Random Matrices and Principal Components.” <i>Stochastic Processes and Their Applications</i>, vol. 163, Elsevier, 2023, pp. 25–60, doi:<a href=\"https://doi.org/10.1016/j.spa.2023.05.009\">10.1016/j.spa.2023.05.009</a>.","ieee":"X. Ding and H. C. Ji, “Spiked multiplicative random matrices and principal components,” <i>Stochastic Processes and their Applications</i>, vol. 163. Elsevier, pp. 25–60, 2023.","apa":"Ding, X., &#38; Ji, H. C. (2023). Spiked multiplicative random matrices and principal components. <i>Stochastic Processes and Their Applications</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.spa.2023.05.009\">https://doi.org/10.1016/j.spa.2023.05.009</a>","ama":"Ding X, Ji HC. Spiked multiplicative random matrices and principal components. <i>Stochastic Processes and their Applications</i>. 2023;163:25-60. doi:<a href=\"https://doi.org/10.1016/j.spa.2023.05.009\">10.1016/j.spa.2023.05.009</a>"},"isi":1,"month":"09","publisher":"Elsevier","department":[{"_id":"LaEr"}],"acknowledgement":"The authors would like to thank the editor, the associated editor and two anonymous referees for their many critical suggestions which have significantly improved the paper. The authors are also grateful to Zhigang Bao and Ji Oon Lee for many helpful discussions. The first author also wants to thank Hari Bercovici for many useful comments. The first author is partially supported by National Science Foundation DMS-2113489 and the second author is supported by ERC Advanced Grant “RMTBeyond” No. 101020331.","arxiv":1,"page":"25-60","intvolume":"       163","ddc":["510"],"date_published":"2023-09-01T00:00:00Z","doi":"10.1016/j.spa.2023.05.009","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"language":[{"iso":"eng"}],"file_date_updated":"2024-01-16T08:47:31Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"journal_article","volume":163},{"_id":"14782","year":"2023","pmid":1,"date_created":"2024-01-10T09:45:48Z","article_processing_charge":"Yes (in subscription journal)","keyword":["Biophysics"],"oa_version":"Published Version","quality_controlled":"1","abstract":[{"text":"The actin cortex is a complex cytoskeletal machinery that drives and responds to changes in cell shape. It must generate or adapt to plasma membrane curvature to facilitate diverse functions such as cell division, migration, and phagocytosis. Due to the complex molecular makeup of the actin cortex, it remains unclear whether actin networks are inherently able to sense and generate membrane curvature, or whether they rely on their diverse binding partners to accomplish this. Here, we show that curvature sensing is an inherent capability of branched actin networks nucleated by Arp2/3 and VCA. We develop a robust method to encapsulate actin inside giant unilamellar vesicles (GUVs) and assemble an actin cortex at the inner surface of the GUV membrane. We show that actin forms a uniform and thin cortical layer when present at high concentration and distinct patches associated with negative membrane curvature at low concentration. Serendipitously, we find that the GUV production method also produces dumbbell-shaped GUVs, which we explain using mathematical modeling in terms of membrane hemifusion of nested GUVs. We find that branched actin networks preferentially assemble at the neck of the dumbbells, which possess a micrometer-range convex curvature comparable with the curvature of the actin patches found in spherical GUVs. Minimal branched actin networks can thus sense membrane curvature, which may help mammalian cells to robustly recruit actin to curved membranes to facilitate diverse cellular functions such as cytokinesis and migration.","lang":"eng"}],"file":[{"checksum":"70566e54cd95ea6df340909ad44c5cd5","content_type":"application/pdf","file_size":3285810,"creator":"dernst","access_level":"open_access","file_name":"2023_BiophysicalJournal_Baldauf.pdf","success":1,"date_created":"2024-01-16T09:09:29Z","relation":"main_file","file_id":"14807","date_updated":"2024-01-16T09:09:29Z"}],"related_material":{"link":[{"relation":"software","url":"https://github.com/BioSoftMatterGroup/actin-curvature-sensing"}]},"article_type":"original","publication_status":"published","oa":1,"publication":"Biophysical Journal","publication_identifier":{"issn":["0006-3495"]},"day":"06","citation":{"chicago":"Baldauf, Lucia, Felix F Frey, Marcos Arribas Perez, Timon Idema, and Gijsje H. Koenderink. “Branched Actin Cortices Reconstituted in Vesicles Sense Membrane Curvature.” <i>Biophysical Journal</i>. Elsevier, 2023. <a href=\"https://doi.org/10.1016/j.bpj.2023.02.018\">https://doi.org/10.1016/j.bpj.2023.02.018</a>.","ista":"Baldauf L, Frey FF, Arribas Perez M, Idema T, Koenderink GH. 2023. Branched actin cortices reconstituted in vesicles sense membrane curvature. Biophysical Journal. 122(11), 2311–2324.","mla":"Baldauf, Lucia, et al. “Branched Actin Cortices Reconstituted in Vesicles Sense Membrane Curvature.” <i>Biophysical Journal</i>, vol. 122, no. 11, Elsevier, 2023, pp. 2311–24, doi:<a href=\"https://doi.org/10.1016/j.bpj.2023.02.018\">10.1016/j.bpj.2023.02.018</a>.","apa":"Baldauf, L., Frey, F. F., Arribas Perez, M., Idema, T., &#38; Koenderink, G. H. (2023). Branched actin cortices reconstituted in vesicles sense membrane curvature. <i>Biophysical Journal</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.bpj.2023.02.018\">https://doi.org/10.1016/j.bpj.2023.02.018</a>","ieee":"L. Baldauf, F. F. Frey, M. Arribas Perez, T. Idema, and G. H. Koenderink, “Branched actin cortices reconstituted in vesicles sense membrane curvature,” <i>Biophysical Journal</i>, vol. 122, no. 11. Elsevier, pp. 2311–2324, 2023.","ama":"Baldauf L, Frey FF, Arribas Perez M, Idema T, Koenderink GH. Branched actin cortices reconstituted in vesicles sense membrane curvature. <i>Biophysical Journal</i>. 2023;122(11):2311-2324. doi:<a href=\"https://doi.org/10.1016/j.bpj.2023.02.018\">10.1016/j.bpj.2023.02.018</a>","short":"L. Baldauf, F.F. Frey, M. Arribas Perez, T. Idema, G.H. Koenderink, Biophysical Journal 122 (2023) 2311–2324."},"date_updated":"2024-01-16T09:20:03Z","author":[{"full_name":"Baldauf, Lucia","last_name":"Baldauf","first_name":"Lucia"},{"full_name":"Frey, Felix F","id":"a0270b37-8f1a-11ec-95c7-8e710c59a4f3","first_name":"Felix F","last_name":"Frey"},{"first_name":"Marcos","last_name":"Arribas Perez","full_name":"Arribas Perez, Marcos"},{"full_name":"Idema, Timon","last_name":"Idema","first_name":"Timon"},{"full_name":"Koenderink, Gijsje H.","first_name":"Gijsje H.","last_name":"Koenderink"}],"issue":"11","has_accepted_license":"1","external_id":{"isi":["001016792600001"],"pmid":["36806830"]},"title":"Branched actin cortices reconstituted in vesicles sense membrane curvature","acknowledgement":"We thank Jeffrey den Haan for protein purification, Kristina Ganzinger (AMOLF) for providing the 10xHis VCA construct, David Kovar (University of Chicago) for the CP constructs, and Michael Way (Crick Institute) for providing purified human Arp2/3 proteins. We are grateful to Iris Lambert for early actin encapsulation experiments that formed the basis for establishing the eDICE method, to Federico Fanalista for acquiring images of dumbbell-shaped GUVs in samples produced by cDICE, and to Tom Aarts for images of dumbbell-shaped GUVs produced by gel-assisted swelling. Lennard van Buren is thanked for his help with image analysis to quantify actin concentrations in GUVs. We thank Kristina Ganzinger (AMOLF) for hosting us to perform pyrene assays in her lab, and Balász Antalicz (AMOLF) for technical assistance with the spectrophotometer. The authors also thank Matthieu Piel and Daniel Fletcher for insightful and inspiring discussions. We acknowledge financial support from The Netherlands Organization of Scientific Research (NWO/OCW) Gravitation program Building a Synthetic Cell (BaSyC) (024.003.019). F.F. gratefully acknowledges funding from the Kavli Synergy program of the Kavli Institute of Nanoscience Delft.","page":"2311-2324","isi":1,"license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","month":"06","department":[{"_id":"AnSa"}],"publisher":"Elsevier","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file_date_updated":"2024-01-16T09:09:29Z","volume":122,"type":"journal_article","ddc":["570"],"intvolume":"       122","tmp":{"image":"/images/cc_by_nc_nd.png","short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode"},"status":"public","language":[{"iso":"eng"}],"date_published":"2023-06-06T00:00:00Z","doi":"10.1016/j.bpj.2023.02.018"},{"title":"Astroglial connexin 43 regulates synaptic vesicle release at hippocampal synapses","external_id":{"isi":["000977445700001"],"pmid":["37190042"]},"has_accepted_license":"1","issue":"8","article_number":"1133","author":[{"first_name":"Giselle T","last_name":"Cheung","orcid":"0000-0001-8457-2572","id":"471195F6-F248-11E8-B48F-1D18A9856A87","full_name":"Cheung, Giselle T"},{"first_name":"Oana","last_name":"Chever","full_name":"Chever, Oana"},{"full_name":"Rollenhagen, Astrid","first_name":"Astrid","last_name":"Rollenhagen"},{"first_name":"Nicole","last_name":"Quenech’du","full_name":"Quenech’du, Nicole"},{"last_name":"Ezan","first_name":"Pascal","full_name":"Ezan, Pascal"},{"full_name":"Lübke, Joachim H. R.","last_name":"Lübke","first_name":"Joachim H. R."},{"last_name":"Rouach","first_name":"Nathalie","full_name":"Rouach, Nathalie"}],"date_updated":"2024-01-16T09:29:35Z","citation":{"short":"G.T. Cheung, O. Chever, A. Rollenhagen, N. Quenech’du, P. Ezan, J.H.R. Lübke, N. Rouach, Cells 12 (2023).","ista":"Cheung GT, Chever O, Rollenhagen A, Quenech’du N, Ezan P, Lübke JHR, Rouach N. 2023. Astroglial connexin 43 regulates synaptic vesicle release at hippocampal synapses. Cells. 12(8), 1133.","chicago":"Cheung, Giselle T, Oana Chever, Astrid Rollenhagen, Nicole Quenech’du, Pascal Ezan, Joachim H. R. Lübke, and Nathalie Rouach. “Astroglial Connexin 43 Regulates Synaptic Vesicle Release at Hippocampal Synapses.” <i>Cells</i>. MDPI, 2023. <a href=\"https://doi.org/10.3390/cells12081133\">https://doi.org/10.3390/cells12081133</a>.","ieee":"G. T. Cheung <i>et al.</i>, “Astroglial connexin 43 regulates synaptic vesicle release at hippocampal synapses,” <i>Cells</i>, vol. 12, no. 8. MDPI, 2023.","ama":"Cheung GT, Chever O, Rollenhagen A, et al. Astroglial connexin 43 regulates synaptic vesicle release at hippocampal synapses. <i>Cells</i>. 2023;12(8). doi:<a href=\"https://doi.org/10.3390/cells12081133\">10.3390/cells12081133</a>","apa":"Cheung, G. T., Chever, O., Rollenhagen, A., Quenech’du, N., Ezan, P., Lübke, J. H. R., &#38; Rouach, N. (2023). Astroglial connexin 43 regulates synaptic vesicle release at hippocampal synapses. <i>Cells</i>. MDPI. <a href=\"https://doi.org/10.3390/cells12081133\">https://doi.org/10.3390/cells12081133</a>","mla":"Cheung, Giselle T., et al. “Astroglial Connexin 43 Regulates Synaptic Vesicle Release at Hippocampal Synapses.” <i>Cells</i>, vol. 12, no. 8, 1133, MDPI, 2023, doi:<a href=\"https://doi.org/10.3390/cells12081133\">10.3390/cells12081133</a>."},"day":"11","oa":1,"publication":"Cells","publication_identifier":{"issn":["2073-4409"]},"article_type":"original","publication_status":"published","abstract":[{"text":"Connexin 43, an astroglial gap junction protein, is enriched in perisynaptic astroglial processes and plays major roles in synaptic transmission. We have previously found that astroglial Cx43 controls synaptic glutamate levels and allows for activity-dependent glutamine release to sustain physiological synaptic transmissions and cognitiogns. However, whether Cx43 is important for the release of synaptic vesicles, which is a critical component of synaptic efficacy, remains unanswered. Here, using transgenic mice with a glial conditional knockout of Cx43 (Cx43−/−), we investigate whether and how astrocytes regulate the release of synaptic vesicles from hippocampal synapses. We report that CA1 pyramidal neurons and their synapses develop normally in the absence of astroglial Cx43. However, a significant impairment in synaptic vesicle distribution and release dynamics were observed. In particular, the FM1-43 assays performed using two-photon live imaging and combined with multi-electrode array stimulation in acute hippocampal slices, revealed a slower rate of synaptic vesicle release in Cx43−/− mice. Furthermore, paired-pulse recordings showed that synaptic vesicle release probability was also reduced and is dependent on glutamine supply via Cx43 hemichannel (HC). Taken together, we have uncovered a role for Cx43 in regulating presynaptic functions by controlling the rate and probability of synaptic vesicle release. Our findings further highlight the significance of astroglial Cx43 in synaptic transmission and efficacy.","lang":"eng"}],"file":[{"file_id":"14808","success":1,"relation":"main_file","date_created":"2024-01-16T09:26:52Z","file_name":"2023_Cells_Cheung.pdf","date_updated":"2024-01-16T09:26:52Z","file_size":7931643,"content_type":"application/pdf","checksum":"6798cd75d8857976fbc58a43fd173d68","access_level":"open_access","creator":"dernst"}],"quality_controlled":"1","article_processing_charge":"Yes","keyword":["General Medicine"],"oa_version":"Published Version","date_created":"2024-01-10T09:46:35Z","pmid":1,"_id":"14783","year":"2023","date_published":"2023-04-11T00:00:00Z","doi":"10.3390/cells12081133","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"status":"public","language":[{"iso":"eng"}],"intvolume":"        12","ddc":["570"],"type":"journal_article","volume":12,"file_date_updated":"2024-01-16T09:26:52Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"04","publisher":"MDPI","department":[{"_id":"SiHi"}],"isi":1,"acknowledgement":"This research was funded by grants from the European Research Council (Consolidator grant #683154) and European Union’s Horizon 2020 research and innovation program (Marie Sklodowska-Curie Innovative Training Networks, grant #722053, EU-GliaPhD) to N.R., as well as from FP7-PEOPLE Marie Curie Intra-European Fellowship for career development (grant #622289) to G.C. We thank Elena Dossi, Grégory Ghézali, and Jérémie Teillon for support with setting up the MEA system for the two-photon microscope. We would also like to thank Tayfun Palaz for their technical assistance with the EM preparations."},{"volume":9,"type":"journal_article","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file_date_updated":"2024-01-16T09:35:28Z","language":[{"iso":"eng"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"status":"public","doi":"10.1126/sciadv.adg1610","date_published":"2023-08-25T00:00:00Z","ddc":["570"],"intvolume":"         9","acknowledgement":"This work was supported by a postdoctoral fellowship from the Swedish Society for Medical Research to J.R., a CAPES-STINT joint grant to R.G.G. and L.S.W., a PhD fellowship from Karolinska Institutet (KID) to E.D., a PhD fellowship from Fundação para a Ciência e a Tecnologia and European Social Fund to M.M.S.O., the program of fundamental research (theme 65.1) of the Institute for Biomedical Problems of the Russian Academy of Sciences (IBMP RAS) to A.A.S., S.M.S., V.A.S., O.V.K., D.D.V., K.D.O., M.P.R., and S.A.P., the Tamkeen under the NYU Abu Dhabi Research Institute Award to the NYUAD Center for Genomics and Systems Biology (ADHPG-CGSB) to P.P., the Knut and Alice Wallenberg foundation to C.K., the Swedish National Space Agency to N.V.K. and L.S.W., Swedish Research Council, Gösta Fraenckel Foundation, and Karolinska Institutet to L.S.W.","department":[{"_id":"FlSc"}],"publisher":"American Association for the Advancement of Science","month":"08","isi":1,"date_updated":"2024-01-16T09:38:58Z","author":[{"last_name":"Gallardo-Dodd","first_name":"Carlos J.","full_name":"Gallardo-Dodd, Carlos J."},{"last_name":"Oertlin","first_name":"Christian","full_name":"Oertlin, Christian"},{"full_name":"Record, Julien","first_name":"Julien","last_name":"Record"},{"full_name":"Galvani, Rômulo G.","last_name":"Galvani","first_name":"Rômulo G."},{"full_name":"Sommerauer, Christian","first_name":"Christian","last_name":"Sommerauer"},{"full_name":"Kuznetsov, Nikolai V.","last_name":"Kuznetsov","first_name":"Nikolai V."},{"last_name":"Doukoumopoulos","first_name":"Evangelos","full_name":"Doukoumopoulos, Evangelos"},{"last_name":"Ali","first_name":"Liaqat","full_name":"Ali, Liaqat"},{"last_name":"Oliveira","first_name":"Mariana M. S.","full_name":"Oliveira, Mariana M. S."},{"full_name":"Seitz, Christina","last_name":"Seitz","first_name":"Christina"},{"first_name":"Mathias","last_name":"Percipalle","full_name":"Percipalle, Mathias","id":"45adb726-eb97-11eb-a6c2-c7c3d3caabe9"},{"last_name":"Nikić","first_name":"Tijana","full_name":"Nikić, Tijana"},{"full_name":"Sadova, Anastasia A.","last_name":"Sadova","first_name":"Anastasia A."},{"full_name":"Shulgina, Sofia M.","last_name":"Shulgina","first_name":"Sofia M."},{"full_name":"Shmarov, Vjacheslav A.","last_name":"Shmarov","first_name":"Vjacheslav A."},{"last_name":"Kutko","first_name":"Olga V.","full_name":"Kutko, Olga V."},{"full_name":"Vlasova, Daria D.","first_name":"Daria D.","last_name":"Vlasova"},{"full_name":"Orlova, Kseniya D.","first_name":"Kseniya D.","last_name":"Orlova"},{"full_name":"Rykova, Marina P.","first_name":"Marina P.","last_name":"Rykova"},{"last_name":"Andersson","first_name":"John","full_name":"Andersson, John"},{"last_name":"Percipalle","first_name":"Piergiorgio","full_name":"Percipalle, Piergiorgio"},{"full_name":"Kutter, Claudia","last_name":"Kutter","first_name":"Claudia"},{"last_name":"Ponomarev","first_name":"Sergey A.","full_name":"Ponomarev, Sergey A."},{"last_name":"Westerberg","first_name":"Lisa S.","full_name":"Westerberg, Lisa S."}],"citation":{"short":"C.J. Gallardo-Dodd, C. Oertlin, J. Record, R.G. Galvani, C. Sommerauer, N.V. Kuznetsov, E. Doukoumopoulos, L. Ali, M.M.S. Oliveira, C. Seitz, M. Percipalle, T. Nikić, A.A. Sadova, S.M. Shulgina, V.A. Shmarov, O.V. Kutko, D.D. Vlasova, K.D. Orlova, M.P. Rykova, J. Andersson, P. Percipalle, C. Kutter, S.A. Ponomarev, L.S. Westerberg, Science Advances 9 (2023).","ista":"Gallardo-Dodd CJ, Oertlin C, Record J, Galvani RG, Sommerauer C, Kuznetsov NV, Doukoumopoulos E, Ali L, Oliveira MMS, Seitz C, Percipalle M, Nikić T, Sadova AA, Shulgina SM, Shmarov VA, Kutko OV, Vlasova DD, Orlova KD, Rykova MP, Andersson J, Percipalle P, Kutter C, Ponomarev SA, Westerberg LS. 2023. Exposure of volunteers to microgravity by dry immersion bed over 21 days results in gene expression changes and adaptation of T cells. Science Advances. 9(34), adg1610.","chicago":"Gallardo-Dodd, Carlos J., Christian Oertlin, Julien Record, Rômulo G. Galvani, Christian Sommerauer, Nikolai V. Kuznetsov, Evangelos Doukoumopoulos, et al. “Exposure of Volunteers to Microgravity by Dry Immersion Bed over 21 Days Results in Gene Expression Changes and Adaptation of T Cells.” <i>Science Advances</i>. American Association for the Advancement of Science, 2023. <a href=\"https://doi.org/10.1126/sciadv.adg1610\">https://doi.org/10.1126/sciadv.adg1610</a>.","ieee":"C. J. Gallardo-Dodd <i>et al.</i>, “Exposure of volunteers to microgravity by dry immersion bed over 21 days results in gene expression changes and adaptation of T cells,” <i>Science Advances</i>, vol. 9, no. 34. American Association for the Advancement of Science, 2023.","apa":"Gallardo-Dodd, C. J., Oertlin, C., Record, J., Galvani, R. G., Sommerauer, C., Kuznetsov, N. V., … Westerberg, L. S. (2023). Exposure of volunteers to microgravity by dry immersion bed over 21 days results in gene expression changes and adaptation of T cells. <i>Science Advances</i>. American Association for the Advancement of Science. <a href=\"https://doi.org/10.1126/sciadv.adg1610\">https://doi.org/10.1126/sciadv.adg1610</a>","ama":"Gallardo-Dodd CJ, Oertlin C, Record J, et al. Exposure of volunteers to microgravity by dry immersion bed over 21 days results in gene expression changes and adaptation of T cells. <i>Science Advances</i>. 2023;9(34). doi:<a href=\"https://doi.org/10.1126/sciadv.adg1610\">10.1126/sciadv.adg1610</a>","mla":"Gallardo-Dodd, Carlos J., et al. “Exposure of Volunteers to Microgravity by Dry Immersion Bed over 21 Days Results in Gene Expression Changes and Adaptation of T Cells.” <i>Science Advances</i>, vol. 9, no. 34, adg1610, American Association for the Advancement of Science, 2023, doi:<a href=\"https://doi.org/10.1126/sciadv.adg1610\">10.1126/sciadv.adg1610</a>."},"publication":"Science Advances","publication_identifier":{"issn":["2375-2548"]},"oa":1,"day":"25","external_id":{"pmid":["37624890"],"isi":["001054596800007"]},"title":"Exposure of volunteers to microgravity by dry immersion bed over 21 days results in gene expression changes and adaptation of T cells","article_number":"adg1610","issue":"34","has_accepted_license":"1","year":"2023","_id":"14784","pmid":1,"date_created":"2024-01-10T09:48:01Z","file":[{"checksum":"b9072e20e2d5d9d34d2c53319bafee41","file_size":1596639,"content_type":"application/pdf","access_level":"open_access","creator":"dernst","file_name":"2023_ScienceAdvances_GallardoDodd.pdf","file_id":"14809","success":1,"relation":"main_file","date_created":"2024-01-16T09:35:28Z","date_updated":"2024-01-16T09:35:28Z"}],"abstract":[{"text":"The next steps of deep space exploration are manned missions to Moon and Mars. For safe space missions for crew members, it is important to understand the impact of space flight on the immune system. We studied the effects of 21 days dry immersion (DI) exposure on the transcriptomes of T cells isolated from blood samples of eight healthy volunteers. Samples were collected 7 days before DI, at day 7, 14, and 21 during DI, and 7 days after DI. RNA sequencing of CD3+T cells revealed transcriptional alterations across all time points, with most changes occurring 14 days after DI exposure. At day 21, T cells showed evidence of adaptation with a transcriptional profile resembling that of 7 days before DI. At 7 days after DI, T cells again changed their transcriptional profile. These data suggest that T cells adapt by rewiring their transcriptomes in response to simulated weightlessness and that remodeling cues persist when reexposed to normal gravity.","lang":"eng"}],"article_type":"original","publication_status":"published","oa_version":"Published Version","keyword":["Multidisciplinary"],"article_processing_charge":"Yes","quality_controlled":"1"},{"month":"12","publisher":"Wiley","department":[{"_id":"MaLo"}],"isi":1,"page":"656-668","acknowledgement":"We thank the lab of Francisco Javier Florencio Bel-lido, Sevilla, Spain for supplying theSynechocystislabtype Sevilla used in this work and the lab of MartinHagemann, Rostock, Germany for supplying the pIGAplasmidusedinthiswork.WethankNilsHülterforfruitful discussions. We thank Fenna Stücker forgraphical illustrations and Katrin Schumann, FennaStücker,  and  Lidusha  Manivannan  for  technicalsupport.\r\nChilean National Agency for Research andDevelopment (ANID), Grant/Award Number:21191763; DeutscheForschungsgemeinschaft, Grant/AwardNumbers: 456882089, RTG2501; EuropeanResearch Council (ERC), Grant/AwardNumber: 101043835","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"language":[{"iso":"eng"}],"date_published":"2023-12-01T00:00:00Z","doi":"10.1111/1758-2229.13203","intvolume":"        15","ddc":["570"],"volume":15,"type":"journal_article","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file_date_updated":"2024-01-16T09:42:10Z","abstract":[{"lang":"eng","text":"Small cryptic plasmids have no clear effect on the host fitness and their functional repertoire remains obscure. The naturally competent cyanobacterium Synechocystis sp. PCC 6803 harbours several small cryptic plasmids; whether their evolution with this species is supported by horizontal transfer remains understudied. Here, we show that the small cryptic plasmid DNA is transferred in the population exclusively by natural transformation, where the transfer frequency of plasmid‐encoded genes is similar to that of chromosome‐encoded genes. Establishing a system to follow gene transfer, we compared the transfer frequency of genes encoded in cryptic plasmids pCA2.4 (2378 bp) and pCB2.4 (2345 bp) within and between populations of two <jats:italic>Synechocystis</jats:italic> sp. PCC 6803 labtypes (termed Kiel and Sevilla). Our results reveal that plasmid gene transfer frequency depends on the recipient labtype. Furthermore, gene transfer via whole plasmid uptake in the Sevilla labtype ranged among the lowest detected transfer rates in our experiments. Our study indicates that horizontal DNA transfer via natural transformation is frequent in the evolution of small cryptic plasmids that reside in naturally competent organisms. Furthermore, we suggest that the contribution of natural transformation to cryptic plasmid persistence in Synechocystis is limited."}],"file":[{"date_updated":"2024-01-16T09:42:10Z","success":1,"relation":"main_file","date_created":"2024-01-16T09:42:10Z","file_id":"14810","file_name":"2023_EnvirMicroBiolReports_Nies.pdf","creator":"dernst","access_level":"open_access","content_type":"application/pdf","file_size":1518350,"checksum":"d09ebb68fee61f4e2e09ec286c9cf1d3"}],"article_type":"original","publication_status":"published","article_processing_charge":"Yes (in subscription journal)","keyword":["Agricultural and Biological Sciences (miscellaneous)","Ecology","Evolution","Behavior and Systematics"],"oa_version":"Published Version","quality_controlled":"1","_id":"14785","year":"2023","date_created":"2024-01-10T10:41:07Z","pmid":1,"external_id":{"pmid":["37794696"],"isi":["001080203100001"]},"title":"Role of natural transformation in the evolution of small cryptic plasmids in Synechocystis sp. PCC 6803","issue":"6","has_accepted_license":"1","date_updated":"2024-01-16T09:46:12Z","citation":{"short":"F. Nies, T. Wein, D.M. Hanke, B.L. Springstein, J. Alcorta, C. Taubenheim, T. Dagan, Environmental Microbiology Reports 15 (2023) 656–668.","ista":"Nies F, Wein T, Hanke DM, Springstein BL, Alcorta J, Taubenheim C, Dagan T. 2023. Role of natural transformation in the evolution of small cryptic plasmids in Synechocystis sp. PCC 6803. Environmental Microbiology Reports. 15(6), 656–668.","chicago":"Nies, Fabian, Tanita Wein, Dustin M. Hanke, Benjamin L Springstein, Jaime Alcorta, Claudia Taubenheim, and Tal Dagan. “Role of Natural Transformation in the Evolution of Small Cryptic Plasmids in Synechocystis Sp. PCC 6803.” <i>Environmental Microbiology Reports</i>. Wiley, 2023. <a href=\"https://doi.org/10.1111/1758-2229.13203\">https://doi.org/10.1111/1758-2229.13203</a>.","ama":"Nies F, Wein T, Hanke DM, et al. Role of natural transformation in the evolution of small cryptic plasmids in Synechocystis sp. PCC 6803. <i>Environmental Microbiology Reports</i>. 2023;15(6):656-668. doi:<a href=\"https://doi.org/10.1111/1758-2229.13203\">10.1111/1758-2229.13203</a>","apa":"Nies, F., Wein, T., Hanke, D. M., Springstein, B. L., Alcorta, J., Taubenheim, C., &#38; Dagan, T. (2023). Role of natural transformation in the evolution of small cryptic plasmids in Synechocystis sp. PCC 6803. <i>Environmental Microbiology Reports</i>. Wiley. <a href=\"https://doi.org/10.1111/1758-2229.13203\">https://doi.org/10.1111/1758-2229.13203</a>","ieee":"F. Nies <i>et al.</i>, “Role of natural transformation in the evolution of small cryptic plasmids in Synechocystis sp. PCC 6803,” <i>Environmental Microbiology Reports</i>, vol. 15, no. 6. Wiley, pp. 656–668, 2023.","mla":"Nies, Fabian, et al. “Role of Natural Transformation in the Evolution of Small Cryptic Plasmids in Synechocystis Sp. PCC 6803.” <i>Environmental Microbiology Reports</i>, vol. 15, no. 6, Wiley, 2023, pp. 656–68, doi:<a href=\"https://doi.org/10.1111/1758-2229.13203\">10.1111/1758-2229.13203</a>."},"author":[{"full_name":"Nies, Fabian","last_name":"Nies","first_name":"Fabian"},{"full_name":"Wein, Tanita","first_name":"Tanita","last_name":"Wein"},{"full_name":"Hanke, Dustin M.","first_name":"Dustin M.","last_name":"Hanke"},{"full_name":"Springstein, Benjamin L","id":"b4eb62ef-ac72-11ed-9503-ed3b4d66c083","orcid":"0000-0002-3461-5391","first_name":"Benjamin L","last_name":"Springstein"},{"last_name":"Alcorta","first_name":"Jaime","full_name":"Alcorta, Jaime"},{"full_name":"Taubenheim, Claudia","last_name":"Taubenheim","first_name":"Claudia"},{"full_name":"Dagan, Tal","last_name":"Dagan","first_name":"Tal"}],"oa":1,"publication":"Environmental Microbiology Reports","publication_identifier":{"eissn":["1758-2229"]},"day":"01"},{"acknowledgement":"We thank Julian Catchen for making modifications to Stacks to aid this project. Peter L. Ralph, Thomas Nelson, Roger K. Butlin, Anja M. Westram and Nicholas H. Barton provided advice, stimulating discussion and critical feedback. The project was supported by National Science Foundation grant DEB-1258199.","page":"2041-2054","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1101/2022.01.28.478139"}],"isi":1,"month":"04","publisher":"Wiley","department":[{"_id":"NiBa"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","volume":32,"type":"journal_article","intvolume":"        32","status":"public","language":[{"iso":"eng"}],"date_published":"2023-04-01T00:00:00Z","doi":"10.1111/mec.16849","_id":"14787","year":"2023","date_created":"2024-01-10T10:44:45Z","pmid":1,"keyword":["Genetics","Ecology","Evolution","Behavior and Systematics"],"article_processing_charge":"No","oa_version":"Preprint","quality_controlled":"1","abstract":[{"lang":"eng","text":"Understanding the phenotypic and genetic architecture of reproductive isolation is a long‐standing goal of speciation research. In several systems, large‐effect loci contributing to barrier phenotypes have been characterized, but such causal connections are rarely known for more complex genetic architectures. In this study, we combine “top‐down” and “bottom‐up” approaches with demographic modelling toward an integrated understanding of speciation across a monkeyflower hybrid zone. Previous work suggests that pollinator visitation acts as a primary barrier to gene flow between two divergent red‐ and yellow‐flowered ecotypes of<jats:italic>Mimulus aurantiacus</jats:italic>. Several candidate isolating traits and anonymous single nucleotide polymorphism loci under divergent selection have been identified, but their genomic positions remain unknown. Here, we report findings from demographic analyses that indicate this hybrid zone formed by secondary contact, but that subsequent gene flow was restricted by widespread barrier loci across the genome. Using a novel, geographic cline‐based genome scan, we demonstrate that candidate barrier loci are broadly distributed across the genome, rather than mapping to one or a few “islands of speciation.” Quantitative trait locus (QTL) mapping reveals that most floral traits are highly polygenic, with little evidence that QTL colocalize, indicating that most traits are genetically independent. Finally, we find little evidence that QTL and candidate barrier loci overlap, suggesting that some loci contribute to other forms of reproductive isolation. Our findings highlight the challenges of understanding the genetic architecture of reproductive isolation and reveal that barriers to gene flow other than pollinator isolation may play an important role in this system."}],"publication_status":"published","article_type":"original","oa":1,"publication":"Molecular Ecology","publication_identifier":{"eissn":["1365-294X"],"issn":["0962-1083"]},"day":"01","author":[{"id":"43161670-5719-11EA-8025-FABC3DDC885E","full_name":"Stankowski, Sean","first_name":"Sean","last_name":"Stankowski"},{"full_name":"Chase, Madeline A.","last_name":"Chase","first_name":"Madeline A."},{"full_name":"McIntosh, Hanna","last_name":"McIntosh","first_name":"Hanna"},{"last_name":"Streisfeld","first_name":"Matthew A.","full_name":"Streisfeld, Matthew A."}],"citation":{"ista":"Stankowski S, Chase MA, McIntosh H, Streisfeld MA. 2023. Integrating top‐down and bottom‐up approaches to understand the genetic architecture of speciation across a monkeyflower hybrid zone. Molecular Ecology. 32(8), 2041–2054.","chicago":"Stankowski, Sean, Madeline A. Chase, Hanna McIntosh, and Matthew A. Streisfeld. “Integrating Top‐down and Bottom‐up Approaches to Understand the Genetic Architecture of Speciation across a Monkeyflower Hybrid Zone.” <i>Molecular Ecology</i>. Wiley, 2023. <a href=\"https://doi.org/10.1111/mec.16849\">https://doi.org/10.1111/mec.16849</a>.","apa":"Stankowski, S., Chase, M. A., McIntosh, H., &#38; Streisfeld, M. A. (2023). Integrating top‐down and bottom‐up approaches to understand the genetic architecture of speciation across a monkeyflower hybrid zone. <i>Molecular Ecology</i>. Wiley. <a href=\"https://doi.org/10.1111/mec.16849\">https://doi.org/10.1111/mec.16849</a>","ieee":"S. Stankowski, M. A. Chase, H. McIntosh, and M. A. Streisfeld, “Integrating top‐down and bottom‐up approaches to understand the genetic architecture of speciation across a monkeyflower hybrid zone,” <i>Molecular Ecology</i>, vol. 32, no. 8. Wiley, pp. 2041–2054, 2023.","ama":"Stankowski S, Chase MA, McIntosh H, Streisfeld MA. Integrating top‐down and bottom‐up approaches to understand the genetic architecture of speciation across a monkeyflower hybrid zone. <i>Molecular Ecology</i>. 2023;32(8):2041-2054. doi:<a href=\"https://doi.org/10.1111/mec.16849\">10.1111/mec.16849</a>","mla":"Stankowski, Sean, et al. “Integrating Top‐down and Bottom‐up Approaches to Understand the Genetic Architecture of Speciation across a Monkeyflower Hybrid Zone.” <i>Molecular Ecology</i>, vol. 32, no. 8, Wiley, 2023, pp. 2041–54, doi:<a href=\"https://doi.org/10.1111/mec.16849\">10.1111/mec.16849</a>.","short":"S. Stankowski, M.A. Chase, H. McIntosh, M.A. Streisfeld, Molecular Ecology 32 (2023) 2041–2054."},"date_updated":"2024-01-16T10:10:00Z","issue":"8","title":"Integrating top‐down and bottom‐up approaches to understand the genetic architecture of speciation across a monkeyflower hybrid zone","external_id":{"pmid":["36651268"],"isi":["000919244600001"]}},{"has_accepted_license":"1","article_number":"e202206038","issue":"3","external_id":{"isi":["000978065000001"],"pmid":["36734980"]},"title":"Clathrin coats partially preassemble and subsequently bend during endocytosis","day":"03","oa":1,"publication":"Journal of Cell Biology","publication_identifier":{"issn":["0021-9525"],"eissn":["1540-8140"]},"date_updated":"2024-01-16T10:17:05Z","citation":{"short":"M. Mund, A. Tschanz, Y.-L. Wu, F.F. Frey, J.L. Mehl, M. Kaksonen, O. Avinoam, U.S. Schwarz, J. Ries, Journal of Cell Biology 222 (2023).","mla":"Mund, Markus, et al. “Clathrin Coats Partially Preassemble and Subsequently Bend during Endocytosis.” <i>Journal of Cell Biology</i>, vol. 222, no. 3, e202206038, Rockefeller University Press, 2023, doi:<a href=\"https://doi.org/10.1083/jcb.202206038\">10.1083/jcb.202206038</a>.","ieee":"M. Mund <i>et al.</i>, “Clathrin coats partially preassemble and subsequently bend during endocytosis,” <i>Journal of Cell Biology</i>, vol. 222, no. 3. Rockefeller University Press, 2023.","ama":"Mund M, Tschanz A, Wu Y-L, et al. Clathrin coats partially preassemble and subsequently bend during endocytosis. <i>Journal of Cell Biology</i>. 2023;222(3). doi:<a href=\"https://doi.org/10.1083/jcb.202206038\">10.1083/jcb.202206038</a>","apa":"Mund, M., Tschanz, A., Wu, Y.-L., Frey, F. F., Mehl, J. L., Kaksonen, M., … Ries, J. (2023). Clathrin coats partially preassemble and subsequently bend during endocytosis. <i>Journal of Cell Biology</i>. Rockefeller University Press. <a href=\"https://doi.org/10.1083/jcb.202206038\">https://doi.org/10.1083/jcb.202206038</a>","chicago":"Mund, Markus, Aline Tschanz, Yu-Le Wu, Felix F Frey, Johanna L. Mehl, Marko Kaksonen, Ori Avinoam, Ulrich S. Schwarz, and Jonas Ries. “Clathrin Coats Partially Preassemble and Subsequently Bend during Endocytosis.” <i>Journal of Cell Biology</i>. Rockefeller University Press, 2023. <a href=\"https://doi.org/10.1083/jcb.202206038\">https://doi.org/10.1083/jcb.202206038</a>.","ista":"Mund M, Tschanz A, Wu Y-L, Frey FF, Mehl JL, Kaksonen M, Avinoam O, Schwarz US, Ries J. 2023. Clathrin coats partially preassemble and subsequently bend during endocytosis. Journal of Cell Biology. 222(3), e202206038."},"author":[{"last_name":"Mund","first_name":"Markus","full_name":"Mund, Markus"},{"full_name":"Tschanz, Aline","first_name":"Aline","last_name":"Tschanz"},{"full_name":"Wu, Yu-Le","last_name":"Wu","first_name":"Yu-Le"},{"orcid":"0000-0001-8501-6017","id":"a0270b37-8f1a-11ec-95c7-8e710c59a4f3","full_name":"Frey, Felix F","first_name":"Felix F","last_name":"Frey"},{"last_name":"Mehl","first_name":"Johanna L.","full_name":"Mehl, Johanna L."},{"first_name":"Marko","last_name":"Kaksonen","full_name":"Kaksonen, Marko"},{"first_name":"Ori","last_name":"Avinoam","full_name":"Avinoam, Ori"},{"full_name":"Schwarz, Ulrich S.","first_name":"Ulrich S.","last_name":"Schwarz"},{"first_name":"Jonas","last_name":"Ries","full_name":"Ries, Jonas"}],"quality_controlled":"1","keyword":["Cell Biology"],"article_processing_charge":"No","oa_version":"Published Version","article_type":"original","publication_status":"published","abstract":[{"lang":"eng","text":"Eukaryotic cells use clathrin-mediated endocytosis to take up a large range of extracellular cargo. During endocytosis, a clathrin coat forms on the plasma membrane, but it remains controversial when and how it is remodeled into a spherical vesicle.\r\nHere, we use 3D superresolution microscopy to determine the precise geometry of the clathrin coat at large numbers of endocytic sites. Through pseudo-temporal sorting, we determine the average trajectory of clathrin remodeling during endocytosis. We find that clathrin coats assemble first on flat membranes to 50% of the coat area before they become rapidly and continuously bent, and this mechanism is confirmed in three cell lines. We introduce the cooperative curvature model, which is based on positive feedback for curvature generation. It accurately describes the measured shapes and dynamics of the clathrin coat and could represent a general mechanism for clathrin coat remodeling on the plasma membrane."}],"file":[{"access_level":"open_access","creator":"dernst","content_type":"application/pdf","file_size":5678069,"checksum":"505d5cac36c14b073b68c7fed1a92bd3","date_updated":"2024-01-16T10:15:09Z","file_id":"14811","relation":"main_file","date_created":"2024-01-16T10:15:09Z","success":1,"file_name":"2023_JCB_Mund.pdf"}],"date_created":"2024-01-10T10:45:55Z","pmid":1,"_id":"14788","year":"2023","intvolume":"       222","ddc":["570"],"date_published":"2023-02-03T00:00:00Z","doi":"10.1083/jcb.202206038","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"status":"public","language":[{"iso":"eng"}],"file_date_updated":"2024-01-16T10:15:09Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"journal_article","volume":222,"isi":1,"month":"02","department":[{"_id":"AnSa"}],"publisher":"Rockefeller University Press","acknowledgement":"We thank the entire Ries and Kaksonen labs for fruitful discussions and support. This work was supported by the European Research Council (ERC CoG-724489 to J. Ries), the National Institutes of Health Common Fund 4D Nucleome Program (Grant U01 to J. Ries), the Human Frontier Science Program (RGY0065/2017 to J. Ries), the EMBL Interdisciplinary Postdoc Programme (EIPOD) under Marie Curie Actions COFUND (Grant 229597 to O. Avinoam), the European Molecular Biology Laboratory (M. Mund, A. Tschanz, Y.-L. Wu and J. Ries), and the Swiss National Science Foundation (grant 310030B_182825 and NCCR Chemical Biology to M. Kaksonen). O. Avinoam is an incumbent of the Miriam Berman Presidential Development Chair."},{"has_accepted_license":"1","article_number":"90","project":[{"name":"Perception-Aware Appearance Fabrication","grant_number":"M03319","_id":"eb901961-77a9-11ec-83b8-f5c883a62027"}],"title":"The effect of display capabilities on the gloss consistency between real and virtual objects","day":"10","publication":"Proceedings of the SIGGRAPH Asia 2023 Conference","publication_identifier":{"isbn":["9798400703157"]},"oa":1,"citation":{"short":"B. Chen, A. Jindal, M. Piovarci, C. Wang, H.P. Seidel, P. Didyk, K. Myszkowski, A. Serrano, R.K. Mantiuk, in:, Proceedings of the SIGGRAPH Asia 2023 Conference, Association for Computing Machinery, 2023.","apa":"Chen, B., Jindal, A., Piovarci, M., Wang, C., Seidel, H. P., Didyk, P., … Mantiuk, R. K. (2023). The effect of display capabilities on the gloss consistency between real and virtual objects. In <i>Proceedings of the SIGGRAPH Asia 2023 Conference</i>. Sydney, Australia: Association for Computing Machinery. <a href=\"https://doi.org/10.1145/3610548.3618226\">https://doi.org/10.1145/3610548.3618226</a>","ieee":"B. Chen <i>et al.</i>, “The effect of display capabilities on the gloss consistency between real and virtual objects,” in <i>Proceedings of the SIGGRAPH Asia 2023 Conference</i>, Sydney, Australia, 2023.","ama":"Chen B, Jindal A, Piovarci M, et al. The effect of display capabilities on the gloss consistency between real and virtual objects. In: <i>Proceedings of the SIGGRAPH Asia 2023 Conference</i>. Association for Computing Machinery; 2023. doi:<a href=\"https://doi.org/10.1145/3610548.3618226\">10.1145/3610548.3618226</a>","mla":"Chen, Bin, et al. “The Effect of Display Capabilities on the Gloss Consistency between Real and Virtual Objects.” <i>Proceedings of the SIGGRAPH Asia 2023 Conference</i>, 90, Association for Computing Machinery, 2023, doi:<a href=\"https://doi.org/10.1145/3610548.3618226\">10.1145/3610548.3618226</a>.","ista":"Chen B, Jindal A, Piovarci M, Wang C, Seidel HP, Didyk P, Myszkowski K, Serrano A, Mantiuk RK. 2023. The effect of display capabilities on the gloss consistency between real and virtual objects. Proceedings of the SIGGRAPH Asia 2023 Conference. SIGGRAPH: Computer Graphics and Interactive Techniques Conference, 90.","chicago":"Chen, Bin, Akshay Jindal, Michael Piovarci, Chao Wang, Hans Peter Seidel, Piotr Didyk, Karol Myszkowski, Ana Serrano, and Rafał K. Mantiuk. “The Effect of Display Capabilities on the Gloss Consistency between Real and Virtual Objects.” In <i>Proceedings of the SIGGRAPH Asia 2023 Conference</i>. Association for Computing Machinery, 2023. <a href=\"https://doi.org/10.1145/3610548.3618226\">https://doi.org/10.1145/3610548.3618226</a>."},"date_updated":"2024-01-17T08:38:35Z","author":[{"last_name":"Chen","first_name":"Bin","full_name":"Chen, Bin"},{"full_name":"Jindal, Akshay","first_name":"Akshay","last_name":"Jindal"},{"orcid":"0000-0002-5062-4474","id":"62E473F4-5C99-11EA-A40E-AF823DDC885E","full_name":"Piovarci, Michael","last_name":"Piovarci","first_name":"Michael"},{"full_name":"Wang, Chao","last_name":"Wang","first_name":"Chao"},{"full_name":"Seidel, Hans Peter","last_name":"Seidel","first_name":"Hans Peter"},{"full_name":"Didyk, Piotr","last_name":"Didyk","first_name":"Piotr"},{"last_name":"Myszkowski","first_name":"Karol","full_name":"Myszkowski, Karol"},{"last_name":"Serrano","first_name":"Ana","full_name":"Serrano, Ana"},{"full_name":"Mantiuk, Rafał K.","last_name":"Mantiuk","first_name":"Rafał K."}],"quality_controlled":"1","oa_version":"Published Version","article_processing_charge":"Yes (in subscription journal)","publication_status":"published","file":[{"date_updated":"2024-01-17T08:33:06Z","success":1,"relation":"main_file","date_created":"2024-01-17T08:33:06Z","file_id":"14823","file_name":"2023_SA_Chen.pdf","creator":"dernst","access_level":"open_access","content_type":"application/pdf","file_size":95967451,"checksum":"8abe27432ed222b50d1af9b3388db1b0"}],"abstract":[{"text":"A faithful reproduction of gloss is inherently difficult because of the limited dynamic range, peak luminance, and 3D capabilities of display devices. This work investigates how the display capabilities affect gloss appearance with respect to a real-world reference object. To this end, we employ an accurate imaging pipeline to achieve a perceptual gloss match between a virtual and real object presented side-by-side on an augmented-reality high-dynamic-range (HDR) stereoscopic display, which has not been previously attained to this extent. Based on this precise gloss reproduction, we conduct a series of gloss matching experiments to study how gloss perception degrades based on individual factors: object albedo, display luminance, dynamic range, stereopsis, and tone mapping. We support the study with a detailed analysis of individual factors, followed by an in-depth discussion on the observed perceptual effects. Our experiments demonstrate that stereoscopic presentation has a limited effect on the gloss matching task on our HDR display. However, both reduced luminance and dynamic range of the display reduce the perceived gloss. This means that the visual system cannot compensate for the changes in gloss appearance across luminance (lack of gloss constancy), and the tone mapping operator should be carefully selected when reproducing gloss on a low dynamic range (LDR) display.","lang":"eng"}],"date_created":"2024-01-14T23:00:57Z","year":"2023","_id":"14798","ddc":["000"],"doi":"10.1145/3610548.3618226","date_published":"2023-12-10T00:00:00Z","language":[{"iso":"eng"}],"status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"file_date_updated":"2024-01-17T08:33:06Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"conference","department":[{"_id":"BeBi"}],"publisher":"Association for Computing Machinery","month":"12","acknowledgement":"This work is supported by FWF Lise Meitner (Grant M 3319), Spanish Agencia Estatal de Investigación (project PID2022-141539NBI00), European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement\r\nN◦ 725253–EyeCode), Swiss National Science Foundation (Grant no. 200502), and academic gifts from Meta. We thank Dmitry Lubyako and Ali Özgür Yöntem for building the turntable for our experiment.","scopus_import":"1","conference":{"end_date":"2023-12-15","location":"Sydney, Australia","start_date":"2023-12-12","name":"SIGGRAPH: Computer Graphics and Interactive Techniques Conference"}},{"month":"09","department":[{"_id":"NiBa"}],"related_material":{"record":[{"status":"for_moderation","id":"14796","relation":"used_in_publication"}]},"publisher":"Zenodo","abstract":[{"text":"This repository contains the code and VCF files needed to conduct the analyses in our MS. Each folder contains a readMe document explaining the nature of each file and dataset and the results and analyses that they relate to. The same anlaysis code (but not VCF files) is also available at https://github.com/seanstankowski/Littorina_reproductive_mode","lang":"eng"}],"main_file_link":[{"open_access":"1","url":"https://doi.org/10.5281/zenodo.8318995"}],"article_processing_charge":"No","oa_version":"Published Version","date_created":"2024-01-16T10:23:01Z","_id":"14812","year":"2023","date_published":"2023-09-05T00:00:00Z","doi":"10.5281/ZENODO.8318995","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"title":"Data and code for: The genetic architecture of a recent transition to live-bearing in marine snails","has_accepted_license":"1","ddc":["570"],"author":[{"last_name":"Stankowski","first_name":"Sean","id":"43161670-5719-11EA-8025-FABC3DDC885E","full_name":"Stankowski, Sean"}],"type":"research_data_reference","date_updated":"2025-08-12T09:04:30Z","citation":{"mla":"Stankowski, Sean. <i>Data and Code for: The Genetic Architecture of a Recent Transition to Live-Bearing in Marine Snails</i>. Zenodo, 2023, doi:<a href=\"https://doi.org/10.5281/ZENODO.8318995\">10.5281/ZENODO.8318995</a>.","ieee":"S. Stankowski, “Data and code for: The genetic architecture of a recent transition to live-bearing in marine snails.” Zenodo, 2023.","ama":"Stankowski S. Data and code for: The genetic architecture of a recent transition to live-bearing in marine snails. 2023. doi:<a href=\"https://doi.org/10.5281/ZENODO.8318995\">10.5281/ZENODO.8318995</a>","apa":"Stankowski, S. (2023). Data and code for: The genetic architecture of a recent transition to live-bearing in marine snails. Zenodo. <a href=\"https://doi.org/10.5281/ZENODO.8318995\">https://doi.org/10.5281/ZENODO.8318995</a>","chicago":"Stankowski, Sean. “Data and Code for: The Genetic Architecture of a Recent Transition to Live-Bearing in Marine Snails.” Zenodo, 2023. <a href=\"https://doi.org/10.5281/ZENODO.8318995\">https://doi.org/10.5281/ZENODO.8318995</a>.","ista":"Stankowski S. 2023. Data and code for: The genetic architecture of a recent transition to live-bearing in marine snails, Zenodo, <a href=\"https://doi.org/10.5281/ZENODO.8318995\">10.5281/ZENODO.8318995</a>.","short":"S. Stankowski, (2023)."},"contributor":[{"last_name":"Zagrodzka","first_name":"Zusanna"},{"first_name":"Martin","last_name":"Garlovsky"},{"orcid":"0000-0002-4530-8469","id":"6AAB2240-CA9A-11E9-9C1A-D9D1E5697425","last_name":"Pal","first_name":"Arka"},{"first_name":"Daria","last_name":"Shipilina","orcid":"0000-0002-1145-9226","id":"428A94B0-F248-11E8-B48F-1D18A9856A87"},{"id":"ae681a14-dc74-11ea-a0a7-c6ef18161701","last_name":"Garcia Castillo","first_name":"Diego Fernando"},{"first_name":"Hila","last_name":"Lifchitz","id":"d6ab5470-2fb3-11ed-8633-986a9b84edac"},{"last_name":"Le Moan","first_name":"Alan"},{"first_name":"Erica","last_name":"Leder"},{"first_name":"James","last_name":"Reeve"},{"first_name":"Kerstin","last_name":"Johannesson"},{"last_name":"Westram","first_name":"Anja M","id":"3C147470-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1050-4969"},{"first_name":"Roger","last_name":"Butlin"}],"day":"05","oa":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"}]