[{"oa_version":"Preprint","keyword":["Statistics","Probability and Uncertainty","Statistics and Probability"],"article_processing_charge":"No","quality_controlled":"1","abstract":[{"lang":"eng","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."}],"article_type":"original","publication_status":"published","year":"2023","_id":"14775","ec_funded":1,"date_created":"2024-01-10T09:23:31Z","issue":"1","project":[{"grant_number":"101020331","call_identifier":"H2020","_id":"62796744-2b32-11ec-9570-940b20777f1d","name":"Random matrices beyond Wigner-Dyson-Mehta"}],"title":"Convergence rate to the Tracy–Widom laws for the largest eigenvalue of sample covariance matrices","external_id":{"arxiv":["2108.02728"],"isi":["000946432400021"]},"publication":"The Annals of Applied Probability","publication_identifier":{"issn":["1050-5164"]},"oa":1,"day":"01","author":[{"last_name":"Schnelli","first_name":"Kevin","orcid":"0000-0003-0954-3231","full_name":"Schnelli, Kevin","id":"434AD0AE-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Xu","first_name":"Yuanyuan","id":"7902bdb1-a2a4-11eb-a164-c9216f71aea3","full_name":"Xu, Yuanyuan","orcid":"0000-0003-1559-1205"}],"citation":{"short":"K. Schnelli, Y. Xu, The Annals of Applied Probability 33 (2023) 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>.","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.","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>.","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>","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>","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."},"date_updated":"2024-01-10T13:31:46Z","main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2108.02728","open_access":"1"}],"isi":1,"publisher":"Institute of Mathematical Statistics","department":[{"_id":"LaEr"}],"month":"02","scopus_import":"1","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.","page":"677-725","arxiv":1,"intvolume":"        33","language":[{"iso":"eng"}],"status":"public","doi":"10.1214/22-aap1826","date_published":"2023-02-01T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","volume":33,"type":"journal_article"},{"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.","department":[{"_id":"JiFr"}],"publisher":"MDPI","month":"11","isi":1,"type":"journal_article","volume":24,"file_date_updated":"2024-01-10T13:39:42Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","doi":"10.3390/ijms242216527","date_published":"2023-11-01T00:00:00Z","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)"},"ddc":["580"],"intvolume":"        24","date_created":"2024-01-10T09:24:35Z","pmid":1,"year":"2023","_id":"14776","publication_status":"published","article_type":"original","file":[{"access_level":"open_access","creator":"dernst","checksum":"4df7d206ba022b7f54eff1f0aec1659a","content_type":"application/pdf","file_size":2637784,"date_updated":"2024-01-10T13:39:42Z","file_name":"2023_IJMS_Teplova.pdf","file_id":"14791","relation":"main_file","success":1,"date_created":"2024-01-10T13:39:42Z"}],"abstract":[{"lang":"eng","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."}],"quality_controlled":"1","oa_version":"Published Version","article_processing_charge":"Yes","keyword":["Inorganic Chemistry","Organic Chemistry","Physical and Theoretical Chemistry","Computer Science Applications","Spectroscopy","Molecular Biology","General Medicine","Catalysis"],"date_updated":"2024-01-10T13:41:10Z","author":[{"first_name":"Anastasiia","last_name":"Teplova","id":"e3736151-106c-11ec-b916-c2558e2762c6","full_name":"Teplova, Anastasiia"},{"full_name":"Pigidanov, Artemii A.","first_name":"Artemii A.","last_name":"Pigidanov"},{"full_name":"Serebryakova, Marina V.","last_name":"Serebryakova","first_name":"Marina V."},{"full_name":"Golyshev, Sergei A.","last_name":"Golyshev","first_name":"Sergei A."},{"full_name":"Galiullina, Raisa A.","first_name":"Raisa A.","last_name":"Galiullina"},{"full_name":"Chichkova, Nina V.","last_name":"Chichkova","first_name":"Nina V."},{"full_name":"Vartapetian, Andrey B.","last_name":"Vartapetian","first_name":"Andrey B."}],"citation":{"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>","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.","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>","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>.","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.","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>.","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)."},"day":"01","publication_identifier":{"issn":["1422-0067"]},"publication":"International Journal of Molecular Sciences","oa":1,"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","issue":"22","article_number":"16527"},{"intvolume":"        13","ddc":["540"],"doi":"10.1063/5.0171888","date_published":"2023-12-01T00:00:00Z","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":"2024-01-10T13:47:31Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"journal_article","volume":13,"isi":1,"department":[{"_id":"MaIb"}],"publisher":"AIP Publishing","month":"12","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).","has_accepted_license":"1","article_number":"125206","issue":"12","title":"Improvement of thermoelectric performance of flexible compound Ag2S0.55Se0.45 by means of partial V-substitution for Ag","external_id":{"isi":["001114917200005"]},"day":"01","publication_identifier":{"eissn":["2158-3226"]},"publication":"AIP Advances","oa":1,"author":[{"last_name":"Sato","first_name":"Kosuke","full_name":"Sato, Kosuke"},{"last_name":"Singh","first_name":"Saurabh","id":"12d625da-9cb3-11ed-9667-af09d37d3f0a","full_name":"Singh, Saurabh","orcid":"0000-0003-2209-5269"},{"full_name":"Yamazaki, Itsuki","last_name":"Yamazaki","first_name":"Itsuki"},{"full_name":"Hirata, Keisuke","last_name":"Hirata","first_name":"Keisuke"},{"full_name":"Ang, Artoni Kevin R.","first_name":"Artoni Kevin R.","last_name":"Ang"},{"full_name":"Matsunami, Masaharu","first_name":"Masaharu","last_name":"Matsunami"},{"last_name":"Takeuchi","first_name":"Tsunehiro","full_name":"Takeuchi, Tsunehiro"}],"date_updated":"2024-01-10T13:49:09Z","citation":{"short":"K. Sato, S. Singh, I. Yamazaki, K. Hirata, A.K.R. Ang, M. Matsunami, T. Takeuchi, AIP Advances 13 (2023).","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>","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.","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>","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>."},"quality_controlled":"1","oa_version":"Published Version","keyword":["General Physics and Astronomy"],"article_processing_charge":"Yes","article_type":"original","publication_status":"published","file":[{"file_size":9676071,"content_type":"application/pdf","checksum":"a7098388b8ff822b47f5ddd37ed3bdbc","creator":"dernst","access_level":"open_access","success":1,"date_created":"2024-01-10T13:47:31Z","relation":"main_file","file_id":"14792","file_name":"2023_AIPAdvances_Sato.pdf","date_updated":"2024-01-10T13:47:31Z"}],"abstract":[{"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.","lang":"eng"}],"date_created":"2024-01-10T09:26:08Z","year":"2023","_id":"14777"},{"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,"month":"06","publisher":"Association for Computing Machinery","department":[{"_id":"KrCh"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file_date_updated":"2024-01-16T08:11:24Z","volume":35,"type":"journal_article","intvolume":"        35","ddc":["000"],"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":"2023-06-23T00:00:00Z","doi":"10.1145/3585391","_id":"14778","year":"2023","ec_funded":1,"date_created":"2024-01-10T09:27:43Z","keyword":["Theoretical Computer Science","Software"],"article_processing_charge":"Yes (via OA deal)","oa_version":"Published Version","quality_controlled":"1","abstract":[{"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.","lang":"eng"}],"file":[{"date_updated":"2024-01-16T08:11:24Z","file_name":"2023_FormalAspectsComputing_Chatterjee.pdf","file_id":"14804","date_created":"2024-01-16T08:11:24Z","relation":"main_file","success":1,"access_level":"open_access","creator":"dernst","checksum":"3bb133eeb27ec01649a9a36445d952d9","content_type":"application/pdf","file_size":502522}],"related_material":{"record":[{"relation":"earlier_version","status":"public","id":"10414"}]},"article_type":"original","publication_status":"published","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","first_name":"Krishnendu","last_name":"Chatterjee"},{"full_name":"Kafshdar Goharshady, Ehsan","last_name":"Kafshdar Goharshady","first_name":"Ehsan"},{"id":"3CC3B868-F248-11E8-B48F-1D18A9856A87","full_name":"Novotný, Petr","last_name":"Novotný","first_name":"Petr"},{"full_name":"Zárevúcky, Jiří","first_name":"Jiří","last_name":"Zárevúcky"},{"full_name":"Zikelic, Dorde","id":"294AA7A6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4681-1699","first_name":"Dorde","last_name":"Zikelic"}],"citation":{"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.","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>","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>.","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.","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>.","short":"K. Chatterjee, E. Kafshdar Goharshady, P. Novotný, J. Zárevúcky, D. Zikelic, Formal Aspects of Computing 35 (2023)."},"date_updated":"2025-07-14T09:10:10Z","article_number":"11","issue":"2","has_accepted_license":"1","title":"On lexicographic proof rules for probabilistic termination","external_id":{"arxiv":["2108.02188"]},"project":[{"name":"Formal Methods for Stochastic Models: Algorithms and Applications","grant_number":"863818","_id":"0599E47C-7A3F-11EA-A408-12923DDC885E","call_identifier":"H2020"},{"grant_number":"665385","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"International IST Doctoral Program"}]},{"year":"2023","_id":"14779","date_created":"2024-01-10T09:28:34Z","file":[{"creator":"dernst","access_level":"open_access","file_size":2529327,"content_type":"application/pdf","checksum":"391a3005c95340a0ae129ce4fbdf2bae","date_updated":"2024-01-16T08:35:02Z","date_created":"2024-01-16T08:35:02Z","relation":"main_file","success":1,"file_id":"14805","file_name":"2023_GeophysicalResearchLetter_Shaw.pdf"}],"abstract":[{"lang":"eng","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."}],"article_type":"original","publication_status":"published","oa_version":"Published Version","keyword":["General Earth and Planetary Sciences","Geophysics"],"article_processing_charge":"No","quality_controlled":"1","author":[{"last_name":"Shaw","first_name":"Thomas E.","full_name":"Shaw, Thomas E."},{"last_name":"Buri","first_name":"Pascal","full_name":"Buri, Pascal"},{"last_name":"McCarthy","first_name":"Michael","full_name":"McCarthy, Michael"},{"first_name":"Evan S.","last_name":"Miles","full_name":"Miles, Evan S."},{"full_name":"Ayala, Álvaro","first_name":"Álvaro","last_name":"Ayala"},{"id":"b28f055a-81ea-11ed-b70c-a9fe7f7b0e70","full_name":"Pellicciotti, Francesca","orcid":"0000-0002-5554-8087","last_name":"Pellicciotti","first_name":"Francesca"}],"citation":{"short":"T.E. Shaw, P. Buri, M. McCarthy, E.S. Miles, Á. Ayala, F. Pellicciotti, Geophysical Research Letters 50 (2023).","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>."},"date_updated":"2024-01-16T08:42:36Z","publication_identifier":{"issn":["0094-8276"],"eissn":["1944-8007"]},"publication":"Geophysical Research Letters","oa":1,"day":"16","title":"The decaying near‐surface boundary layer of a retreating alpine glacier","external_id":{"isi":["000999436400001"]},"article_number":"e2023GL103043","issue":"11","has_accepted_license":"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.","department":[{"_id":"FrPe"}],"publisher":"American Geophysical Union","month":"06","isi":1,"volume":50,"type":"journal_article","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file_date_updated":"2024-01-16T08:35:02Z","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":"10.1029/2023gl103043","date_published":"2023-06-16T00:00:00Z","ddc":["550"],"intvolume":"        50"},{"publication_identifier":{"eissn":["1879-209X"],"issn":["0304-4149"]},"publication":"Stochastic Processes and their Applications","oa":1,"day":"01","author":[{"first_name":"Xiucai","last_name":"Ding","full_name":"Ding, Xiucai"},{"last_name":"Ji","first_name":"Hong Chang","full_name":"Ji, Hong Chang","id":"dd216c0a-c1f9-11eb-beaf-e9ea9d2de76d"}],"date_updated":"2024-01-16T08:49:51Z","citation":{"ista":"Ding X, Ji HC. 2023. Spiked multiplicative random matrices and principal components. Stochastic Processes and their Applications. 163, 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>.","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>","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>","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>.","short":"X. Ding, H.C. Ji, Stochastic Processes and Their Applications 163 (2023) 25–60."},"has_accepted_license":"1","project":[{"call_identifier":"H2020","_id":"62796744-2b32-11ec-9570-940b20777f1d","grant_number":"101020331","name":"Random matrices beyond Wigner-Dyson-Mehta"}],"title":"Spiked multiplicative random matrices and principal components","external_id":{"isi":["001113615900001"],"arxiv":["2302.13502"]},"year":"2023","_id":"14780","ec_funded":1,"date_created":"2024-01-10T09:29:25Z","oa_version":"Published Version","keyword":["Applied Mathematics","Modeling and Simulation","Statistics and Probability"],"article_processing_charge":"Yes (in subscription journal)","quality_controlled":"1","file":[{"date_updated":"2024-01-16T08:47:31Z","file_id":"14806","relation":"main_file","date_created":"2024-01-16T08:47:31Z","success":1,"file_name":"2023_StochasticProcAppl_Ding.pdf","access_level":"open_access","creator":"dernst","file_size":1870349,"content_type":"application/pdf","checksum":"46a708b0cd5569a73d0f3d6c3e0a44dc"}],"abstract":[{"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.","lang":"eng"}],"publication_status":"published","article_type":"original","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file_date_updated":"2024-01-16T08:47:31Z","volume":163,"type":"journal_article","intvolume":"       163","ddc":["510"],"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":"10.1016/j.spa.2023.05.009","date_published":"2023-09-01T00:00:00Z","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.","page":"25-60","arxiv":1,"isi":1,"publisher":"Elsevier","department":[{"_id":"LaEr"}],"month":"09"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"journal_article","volume":58,"intvolume":"        58","date_published":"2023-09-11T00:00:00Z","doi":"10.1016/j.devcel.2023.06.009","status":"public","language":[{"iso":"eng"}],"acknowledgement":"We thank Celeste Brennecka for editing and Michal Reichman-Fried for critical comments on the manuscript. We thank Ursula Jordan, Esther Messerschmidt, and Ines Sandbote for technical assistance. This work was supported by funding from the University of Münster (K.J.W., K.T., E.R., A.G., T.G.-T., J.S., and M.G.), the Max Planck Institute for Molecular Biomedicine (D.Z.), the German Research Foundation grant CRU 326 (P2) RA863/12-2 (E.R.), Baylor University (K.H. and D.R.), and the National Institutes of Health grant R35 GM 134910 (D.R.). We thank the referees for insightful comments that helped improve the manuscript.","page":"1578-1592.e5","main_file_link":[{"url":"https://www.biorxiv.org/content/10.1101/2023.07.09.548244","open_access":"1"}],"month":"09","department":[{"_id":"Bio"}],"publisher":"Elsevier","day":"11","oa":1,"publication":"Developmental Cell","publication_identifier":{"issn":["1534-5807"]},"citation":{"short":"K.J. Westerich, K. Tarbashevich, J. Schick, A. Gupta, M. Zhu, K. Hull, D. Romo, D. Zeuschner, M. Goudarzi, T. Gross-Thebing, E. Raz, Developmental Cell 58 (2023) 1578–1592.e5.","ista":"Westerich KJ, Tarbashevich K, Schick J, Gupta A, Zhu M, Hull K, Romo D, Zeuschner D, Goudarzi M, Gross-Thebing T, Raz E. 2023. Spatial organization and function of RNA molecules within phase-separated condensates in zebrafish are controlled by Dnd1. Developmental Cell. 58(17), 1578–1592.e5.","chicago":"Westerich, Kim Joana, Katsiaryna Tarbashevich, Jan Schick, Antra Gupta, Mingzhao Zhu, Kenneth Hull, Daniel Romo, et al. “Spatial Organization and Function of RNA Molecules within Phase-Separated Condensates in Zebrafish Are Controlled by Dnd1.” <i>Developmental Cell</i>. Elsevier, 2023. <a href=\"https://doi.org/10.1016/j.devcel.2023.06.009\">https://doi.org/10.1016/j.devcel.2023.06.009</a>.","ama":"Westerich KJ, Tarbashevich K, Schick J, et al. Spatial organization and function of RNA molecules within phase-separated condensates in zebrafish are controlled by Dnd1. <i>Developmental Cell</i>. 2023;58(17):1578-1592.e5. doi:<a href=\"https://doi.org/10.1016/j.devcel.2023.06.009\">10.1016/j.devcel.2023.06.009</a>","ieee":"K. J. Westerich <i>et al.</i>, “Spatial organization and function of RNA molecules within phase-separated condensates in zebrafish are controlled by Dnd1,” <i>Developmental Cell</i>, vol. 58, no. 17. Elsevier, p. 1578–1592.e5, 2023.","apa":"Westerich, K. J., Tarbashevich, K., Schick, J., Gupta, A., Zhu, M., Hull, K., … Raz, E. (2023). Spatial organization and function of RNA molecules within phase-separated condensates in zebrafish are controlled by Dnd1. <i>Developmental Cell</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.devcel.2023.06.009\">https://doi.org/10.1016/j.devcel.2023.06.009</a>","mla":"Westerich, Kim Joana, et al. “Spatial Organization and Function of RNA Molecules within Phase-Separated Condensates in Zebrafish Are Controlled by Dnd1.” <i>Developmental Cell</i>, vol. 58, no. 17, Elsevier, 2023, p. 1578–1592.e5, doi:<a href=\"https://doi.org/10.1016/j.devcel.2023.06.009\">10.1016/j.devcel.2023.06.009</a>."},"author":[{"full_name":"Westerich, Kim Joana","last_name":"Westerich","first_name":"Kim Joana"},{"last_name":"Tarbashevich","first_name":"Katsiaryna","full_name":"Tarbashevich, Katsiaryna"},{"last_name":"Schick","first_name":"Jan","full_name":"Schick, Jan"},{"last_name":"Gupta","first_name":"Antra","full_name":"Gupta, Antra"},{"full_name":"Zhu, Mingzhao","first_name":"Mingzhao","last_name":"Zhu"},{"full_name":"Hull, Kenneth","last_name":"Hull","first_name":"Kenneth"},{"last_name":"Romo","first_name":"Daniel","full_name":"Romo, Daniel"},{"full_name":"Zeuschner, Dagmar","first_name":"Dagmar","last_name":"Zeuschner"},{"full_name":"Goudarzi, Mohammad","id":"3384113A-F248-11E8-B48F-1D18A9856A87","last_name":"Goudarzi","first_name":"Mohammad"},{"first_name":"Theresa","last_name":"Gross-Thebing","full_name":"Gross-Thebing, Theresa"},{"first_name":"Erez","last_name":"Raz","full_name":"Raz, Erez"}],"date_updated":"2024-01-16T08:56:36Z","issue":"17","title":"Spatial organization and function of RNA molecules within phase-separated condensates in zebrafish are controlled by Dnd1","external_id":{"pmid":["37463577"]},"pmid":1,"date_created":"2024-01-10T09:41:21Z","_id":"14781","year":"2023","quality_controlled":"1","article_processing_charge":"No","keyword":["Developmental Biology","Cell Biology","General Biochemistry","Genetics and Molecular Biology","Molecular Biology"],"oa_version":"Preprint","article_type":"original","publication_status":"published","abstract":[{"lang":"eng","text":"Germ granules, condensates of phase-separated RNA and protein, are organelles that are essential for germline development in different organisms. The patterning of the granules and their relevance for germ cell fate are not fully understood. Combining three-dimensional in vivo structural and functional analyses, we study the dynamic spatial organization of molecules within zebrafish germ granules. We find that the localization of RNA molecules to the periphery of the granules, where ribosomes are localized, depends on translational activity at this location. In addition, we find that the vertebrate-specific Dead end (Dnd1) protein is essential for nanos3 RNA localization at the condensates’ periphery. Accordingly, in the absence of Dnd1, or when translation is inhibited, nanos3 RNA translocates into the granule interior, away from the ribosomes, a process that is correlated with the loss of germ cell fate. These findings highlight the relevance of sub-granule compartmentalization for post-transcriptional control and its importance for preserving germ cell totipotency."}]},{"author":[{"last_name":"Baldauf","first_name":"Lucia","full_name":"Baldauf, Lucia"},{"full_name":"Frey, Felix F","id":"a0270b37-8f1a-11ec-95c7-8e710c59a4f3","last_name":"Frey","first_name":"Felix F"},{"last_name":"Arribas Perez","first_name":"Marcos","full_name":"Arribas Perez, Marcos"},{"full_name":"Idema, Timon","last_name":"Idema","first_name":"Timon"},{"first_name":"Gijsje H.","last_name":"Koenderink","full_name":"Koenderink, Gijsje H."}],"date_updated":"2024-01-16T09:20:03Z","citation":{"short":"L. Baldauf, F.F. Frey, M. Arribas Perez, T. Idema, G.H. Koenderink, Biophysical Journal 122 (2023) 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>","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>","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.","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."},"oa":1,"publication_identifier":{"issn":["0006-3495"]},"publication":"Biophysical Journal","day":"06","title":"Branched actin cortices reconstituted in vesicles sense membrane curvature","external_id":{"pmid":["36806830"],"isi":["001016792600001"]},"issue":"11","has_accepted_license":"1","_id":"14782","year":"2023","date_created":"2024-01-10T09:45:48Z","pmid":1,"abstract":[{"lang":"eng","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."}],"file":[{"date_created":"2024-01-16T09:09:29Z","success":1,"relation":"main_file","file_id":"14807","file_name":"2023_BiophysicalJournal_Baldauf.pdf","date_updated":"2024-01-16T09:09:29Z","content_type":"application/pdf","file_size":3285810,"checksum":"70566e54cd95ea6df340909ad44c5cd5","creator":"dernst","access_level":"open_access"}],"related_material":{"link":[{"url":"https://github.com/BioSoftMatterGroup/actin-curvature-sensing","relation":"software"}]},"article_type":"original","publication_status":"published","article_processing_charge":"Yes (in subscription journal)","keyword":["Biophysics"],"oa_version":"Published Version","quality_controlled":"1","volume":122,"type":"journal_article","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file_date_updated":"2024-01-16T09:09:29Z","status":"public","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"},"language":[{"iso":"eng"}],"date_published":"2023-06-06T00:00:00Z","doi":"10.1016/j.bpj.2023.02.018","intvolume":"       122","ddc":["570"],"page":"2311-2324","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.","month":"06","department":[{"_id":"AnSa"}],"publisher":"Elsevier","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.","isi":1,"month":"04","department":[{"_id":"SiHi"}],"publisher":"MDPI","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file_date_updated":"2024-01-16T09:26:52Z","volume":12,"type":"journal_article","intvolume":"        12","ddc":["570"],"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":"2023-04-11T00:00:00Z","doi":"10.3390/cells12081133","_id":"14783","year":"2023","date_created":"2024-01-10T09:46:35Z","pmid":1,"keyword":["General Medicine"],"article_processing_charge":"Yes","oa_version":"Published Version","quality_controlled":"1","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":[{"date_updated":"2024-01-16T09:26:52Z","file_name":"2023_Cells_Cheung.pdf","success":1,"relation":"main_file","date_created":"2024-01-16T09:26:52Z","file_id":"14808","creator":"dernst","access_level":"open_access","checksum":"6798cd75d8857976fbc58a43fd173d68","content_type":"application/pdf","file_size":7931643}],"article_type":"original","publication_status":"published","oa":1,"publication_identifier":{"issn":["2073-4409"]},"publication":"Cells","day":"11","date_updated":"2024-01-16T09:29:35Z","citation":{"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>.","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.","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>.","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>","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.","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>","short":"G.T. Cheung, O. Chever, A. Rollenhagen, N. Quenech’du, P. Ezan, J.H.R. Lübke, N. Rouach, Cells 12 (2023)."},"author":[{"last_name":"Cheung","first_name":"Giselle T","id":"471195F6-F248-11E8-B48F-1D18A9856A87","full_name":"Cheung, Giselle T","orcid":"0000-0001-8457-2572"},{"full_name":"Chever, Oana","first_name":"Oana","last_name":"Chever"},{"full_name":"Rollenhagen, Astrid","last_name":"Rollenhagen","first_name":"Astrid"},{"full_name":"Quenech’du, Nicole","last_name":"Quenech’du","first_name":"Nicole"},{"last_name":"Ezan","first_name":"Pascal","full_name":"Ezan, Pascal"},{"last_name":"Lübke","first_name":"Joachim H. R.","full_name":"Lübke, Joachim H. R."},{"last_name":"Rouach","first_name":"Nathalie","full_name":"Rouach, Nathalie"}],"article_number":"1133","issue":"8","has_accepted_license":"1","title":"Astroglial connexin 43 regulates synaptic vesicle release at hippocampal synapses","external_id":{"isi":["000977445700001"],"pmid":["37190042"]}},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file_date_updated":"2024-01-16T09:35:28Z","volume":9,"type":"journal_article","ddc":["570"],"intvolume":"         9","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":"2023-08-25T00:00:00Z","doi":"10.1126/sciadv.adg1610","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.","isi":1,"month":"08","department":[{"_id":"FlSc"}],"publisher":"American Association for the Advancement of Science","oa":1,"publication":"Science Advances","publication_identifier":{"issn":["2375-2548"]},"day":"25","date_updated":"2024-01-16T09:38:58Z","author":[{"full_name":"Gallardo-Dodd, Carlos J.","last_name":"Gallardo-Dodd","first_name":"Carlos J."},{"first_name":"Christian","last_name":"Oertlin","full_name":"Oertlin, Christian"},{"full_name":"Record, Julien","last_name":"Record","first_name":"Julien"},{"full_name":"Galvani, Rômulo G.","last_name":"Galvani","first_name":"Rômulo G."},{"full_name":"Sommerauer, Christian","first_name":"Christian","last_name":"Sommerauer"},{"last_name":"Kuznetsov","first_name":"Nikolai V.","full_name":"Kuznetsov, Nikolai V."},{"full_name":"Doukoumopoulos, Evangelos","last_name":"Doukoumopoulos","first_name":"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"},{"id":"45adb726-eb97-11eb-a6c2-c7c3d3caabe9","full_name":"Percipalle, Mathias","first_name":"Mathias","last_name":"Percipalle"},{"full_name":"Nikić, Tijana","last_name":"Nikić","first_name":"Tijana"},{"full_name":"Sadova, Anastasia A.","first_name":"Anastasia A.","last_name":"Sadova"},{"first_name":"Sofia M.","last_name":"Shulgina","full_name":"Shulgina, Sofia M."},{"full_name":"Shmarov, Vjacheslav A.","last_name":"Shmarov","first_name":"Vjacheslav A."},{"full_name":"Kutko, Olga V.","first_name":"Olga V.","last_name":"Kutko"},{"full_name":"Vlasova, Daria D.","last_name":"Vlasova","first_name":"Daria D."},{"full_name":"Orlova, Kseniya D.","last_name":"Orlova","first_name":"Kseniya D."},{"full_name":"Rykova, Marina P.","first_name":"Marina P.","last_name":"Rykova"},{"full_name":"Andersson, John","last_name":"Andersson","first_name":"John"},{"first_name":"Piergiorgio","last_name":"Percipalle","full_name":"Percipalle, Piergiorgio"},{"first_name":"Claudia","last_name":"Kutter","full_name":"Kutter, Claudia"},{"last_name":"Ponomarev","first_name":"Sergey A.","full_name":"Ponomarev, Sergey A."},{"first_name":"Lisa S.","last_name":"Westerberg","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>.","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>","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.","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>."},"issue":"34","article_number":"adg1610","has_accepted_license":"1","title":"Exposure of volunteers to microgravity by dry immersion bed over 21 days results in gene expression changes and adaptation of T cells","external_id":{"isi":["001054596800007"],"pmid":["37624890"]},"_id":"14784","year":"2023","date_created":"2024-01-10T09:48:01Z","pmid":1,"keyword":["Multidisciplinary"],"article_processing_charge":"Yes","oa_version":"Published Version","quality_controlled":"1","abstract":[{"lang":"eng","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."}],"file":[{"file_name":"2023_ScienceAdvances_GallardoDodd.pdf","date_created":"2024-01-16T09:35:28Z","relation":"main_file","success":1,"file_id":"14809","date_updated":"2024-01-16T09:35:28Z","checksum":"b9072e20e2d5d9d34d2c53319bafee41","file_size":1596639,"content_type":"application/pdf","creator":"dernst","access_level":"open_access"}],"publication_status":"published","article_type":"original"},{"article_type":"original","publication_status":"published","file":[{"creator":"dernst","access_level":"open_access","content_type":"application/pdf","file_size":1518350,"checksum":"d09ebb68fee61f4e2e09ec286c9cf1d3","date_updated":"2024-01-16T09:42:10Z","relation":"main_file","success":1,"date_created":"2024-01-16T09:42:10Z","file_id":"14810","file_name":"2023_EnvirMicroBiolReports_Nies.pdf"}],"abstract":[{"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.","lang":"eng"}],"quality_controlled":"1","oa_version":"Published Version","article_processing_charge":"Yes (in subscription journal)","keyword":["Agricultural and Biological Sciences (miscellaneous)","Ecology","Evolution","Behavior and Systematics"],"date_created":"2024-01-10T10:41:07Z","pmid":1,"year":"2023","_id":"14785","title":"Role of natural transformation in the evolution of small cryptic plasmids in Synechocystis sp. PCC 6803","external_id":{"isi":["001080203100001"],"pmid":["37794696"]},"has_accepted_license":"1","issue":"6","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.","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>.","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>","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.","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>","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>.","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."},"date_updated":"2024-01-16T09:46:12Z","author":[{"last_name":"Nies","first_name":"Fabian","full_name":"Nies, Fabian"},{"last_name":"Wein","first_name":"Tanita","full_name":"Wein, Tanita"},{"last_name":"Hanke","first_name":"Dustin M.","full_name":"Hanke, Dustin M."},{"id":"b4eb62ef-ac72-11ed-9503-ed3b4d66c083","full_name":"Springstein, Benjamin L","orcid":"0000-0002-3461-5391","first_name":"Benjamin L","last_name":"Springstein"},{"first_name":"Jaime","last_name":"Alcorta","full_name":"Alcorta, Jaime"},{"last_name":"Taubenheim","first_name":"Claudia","full_name":"Taubenheim, Claudia"},{"first_name":"Tal","last_name":"Dagan","full_name":"Dagan, Tal"}],"day":"01","publication_identifier":{"eissn":["1758-2229"]},"publication":"Environmental Microbiology Reports","oa":1,"publisher":"Wiley","department":[{"_id":"MaLo"}],"month":"12","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","doi":"10.1111/1758-2229.13203","date_published":"2023-12-01T00:00:00Z","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)"},"intvolume":"        15","ddc":["570"],"type":"journal_article","volume":15,"file_date_updated":"2024-01-16T09:42:10Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"acknowledgement":"The authors thank the Czech Science Foundation (project No. 19-28399X) and the Czech Academy of Sciences (RVO: 60077344) and are sincerely grateful to the Bordeaux Imaging Centre (member of the France BioImaging national infrastructure, ANR-10-INBS-04) for help with TEM and to members of the Laboratory of Biological Effects of Metals and Laboratory of Aquaculture and Pathology of Aquatic Organisms (Ruđer Bošković Institute, Croatia) for the assistance with fieldwork.","month":"08","department":[{"_id":"LifeSc"}],"publisher":"Elsevier","isi":1,"volume":887,"type":"journal_article","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","language":[{"iso":"eng"}],"date_published":"2023-08-20T00:00:00Z","doi":"10.1016/j.scitotenv.2023.164010","intvolume":"       887","_id":"14786","year":"2023","pmid":1,"date_created":"2024-01-10T10:43:08Z","abstract":[{"lang":"eng","text":"Acanthocephalans, intestinal parasites of vertebrates, are characterised by orders of magnitude higher metal accumulation than free-living organisms, but the mechanism of such effective metal accumulation is still unknown. The aim of our study was to gain new insights into the high-resolution localization of elements in the bodies of acanthocephalans, thus taking an initial step towards elucidating metal uptake and accumulation in organisms under real environmental conditions. For the first time, nanoscale secondary ion mass spectrometry (NanoSIMS) was used for high-resolution mapping of 12 elements (C, Ca, Cu, Fe, N, Na, O, P, Pb, S, Se, and Tl) in three selected body parts (trunk spines, inner part of the proboscis receptacle and inner surface of the tegument) of Dentitruncus truttae, a parasite of brown trout (Salmo trutta) from the Krka River in Croatia. In addition, the same body parts were examined using transmission electron microscopy (TEM) and correlated with NanoSIMS images. Metal concentrations determined using HR ICP-MS confirmed higher accumulation in D. truttae than in the fish intestine. The chemical composition of the acanthocephalan body showed the highest density of C, Ca, N, Na, O, S, as important and constitutive elements in living cells in all studied structures, while Fe was predominant among trace elements. In general, higher element density was found in trunk spines and tegument, as body structures responsible for substance absorption in parasites. The results obtained with NanoSIMS and TEM-NanoSIMS correlative imaging represent pilot data for mapping of elements at nanoscale resolution in the ultrastructure of various body parts of acanthocephalans and generally provide a contribution for further application of this technique in all parasite species."}],"publication_status":"published","article_type":"original","article_processing_charge":"No","keyword":["Pollution","Waste Management and Disposal","Environmental Chemistry","Environmental Engineering"],"oa_version":"None","quality_controlled":"1","author":[{"last_name":"Filipović Marijić","first_name":"Vlatka","full_name":"Filipović Marijić, Vlatka"},{"full_name":"Subirana, Maria Angels","last_name":"Subirana","first_name":"Maria Angels"},{"full_name":"Schaumlöffel, Dirk","last_name":"Schaumlöffel","first_name":"Dirk"},{"first_name":"Josip","last_name":"Barišić","full_name":"Barišić, Josip"},{"last_name":"Gontier","first_name":"Etienne","full_name":"Gontier, Etienne"},{"full_name":"Krasnici, Nesrete","id":"cb5852d4-287f-11ed-baf0-bc1dd2d5c745","last_name":"Krasnici","first_name":"Nesrete"},{"first_name":"Tatjana","last_name":"Mijošek","full_name":"Mijošek, Tatjana"},{"full_name":"Hernández-Orts, Jesús S.","first_name":"Jesús S.","last_name":"Hernández-Orts"},{"full_name":"Scholz, Tomáš","last_name":"Scholz","first_name":"Tomáš"},{"full_name":"Erk, Marijana","first_name":"Marijana","last_name":"Erk"}],"date_updated":"2024-01-16T10:04:57Z","citation":{"chicago":"Filipović Marijić, Vlatka, Maria Angels Subirana, Dirk Schaumlöffel, Josip Barišić, Etienne Gontier, Nesrete Krasnici, Tatjana Mijošek, Jesús S. Hernández-Orts, Tomáš Scholz, and Marijana Erk. “First Insight in Element Localisation in Different Body Parts of the Acanthocephalan Dentitruncus Truttae Using TEM and NanoSIMS.” <i>Science of The Total Environment</i>. Elsevier, 2023. <a href=\"https://doi.org/10.1016/j.scitotenv.2023.164010\">https://doi.org/10.1016/j.scitotenv.2023.164010</a>.","ista":"Filipović Marijić V, Subirana MA, Schaumlöffel D, Barišić J, Gontier E, Krasnici N, Mijošek T, Hernández-Orts JS, Scholz T, Erk M. 2023. First insight in element localisation in different body parts of the acanthocephalan Dentitruncus truttae using TEM and NanoSIMS. Science of The Total Environment. 887, 164010.","mla":"Filipović Marijić, Vlatka, et al. “First Insight in Element Localisation in Different Body Parts of the Acanthocephalan Dentitruncus Truttae Using TEM and NanoSIMS.” <i>Science of The Total Environment</i>, vol. 887, 164010, Elsevier, 2023, doi:<a href=\"https://doi.org/10.1016/j.scitotenv.2023.164010\">10.1016/j.scitotenv.2023.164010</a>.","ieee":"V. Filipović Marijić <i>et al.</i>, “First insight in element localisation in different body parts of the acanthocephalan Dentitruncus truttae using TEM and NanoSIMS,” <i>Science of The Total Environment</i>, vol. 887. Elsevier, 2023.","apa":"Filipović Marijić, V., Subirana, M. A., Schaumlöffel, D., Barišić, J., Gontier, E., Krasnici, N., … Erk, M. (2023). First insight in element localisation in different body parts of the acanthocephalan Dentitruncus truttae using TEM and NanoSIMS. <i>Science of The Total Environment</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.scitotenv.2023.164010\">https://doi.org/10.1016/j.scitotenv.2023.164010</a>","ama":"Filipović Marijić V, Subirana MA, Schaumlöffel D, et al. First insight in element localisation in different body parts of the acanthocephalan Dentitruncus truttae using TEM and NanoSIMS. <i>Science of The Total Environment</i>. 2023;887. doi:<a href=\"https://doi.org/10.1016/j.scitotenv.2023.164010\">10.1016/j.scitotenv.2023.164010</a>","short":"V. Filipović Marijić, M.A. Subirana, D. Schaumlöffel, J. Barišić, E. Gontier, N. Krasnici, T. Mijošek, J.S. Hernández-Orts, T. Scholz, M. Erk, Science of The Total Environment 887 (2023)."},"publication_identifier":{"issn":["0048-9697"]},"publication":"Science of The Total Environment","day":"20","title":"First insight in element localisation in different body parts of the acanthocephalan Dentitruncus truttae using TEM and NanoSIMS","external_id":{"isi":["001002645100001"],"pmid":["37169189"]},"article_number":"164010"},{"intvolume":"        32","doi":"10.1111/mec.16849","date_published":"2023-04-01T00:00:00Z","language":[{"iso":"eng"}],"status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"journal_article","volume":32,"isi":1,"main_file_link":[{"url":"https://doi.org/10.1101/2022.01.28.478139","open_access":"1"}],"department":[{"_id":"NiBa"}],"publisher":"Wiley","month":"04","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","issue":"8","external_id":{"isi":["000919244600001"],"pmid":["36651268"]},"title":"Integrating top‐down and bottom‐up approaches to understand the genetic architecture of speciation across a monkeyflower hybrid zone","day":"01","publication":"Molecular Ecology","publication_identifier":{"eissn":["1365-294X"],"issn":["0962-1083"]},"oa":1,"date_updated":"2024-01-16T10:10:00Z","author":[{"first_name":"Sean","last_name":"Stankowski","full_name":"Stankowski, Sean","id":"43161670-5719-11EA-8025-FABC3DDC885E"},{"last_name":"Chase","first_name":"Madeline A.","full_name":"Chase, 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":{"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>","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>","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>.","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>.","short":"S. Stankowski, M.A. Chase, H. McIntosh, M.A. Streisfeld, Molecular Ecology 32 (2023) 2041–2054."},"quality_controlled":"1","oa_version":"Preprint","article_processing_charge":"No","keyword":["Genetics","Ecology","Evolution","Behavior and Systematics"],"article_type":"original","publication_status":"published","abstract":[{"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.","lang":"eng"}],"pmid":1,"date_created":"2024-01-10T10:44:45Z","year":"2023","_id":"14787"},{"day":"03","publication_identifier":{"issn":["0021-9525"],"eissn":["1540-8140"]},"publication":"Journal of Cell Biology","oa":1,"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).","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.","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>.","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>","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.","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>","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>."},"author":[{"last_name":"Mund","first_name":"Markus","full_name":"Mund, Markus"},{"full_name":"Tschanz, Aline","first_name":"Aline","last_name":"Tschanz"},{"last_name":"Wu","first_name":"Yu-Le","full_name":"Wu, 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"},{"full_name":"Mehl, Johanna L.","last_name":"Mehl","first_name":"Johanna L."},{"last_name":"Kaksonen","first_name":"Marko","full_name":"Kaksonen, Marko"},{"first_name":"Ori","last_name":"Avinoam","full_name":"Avinoam, Ori"},{"first_name":"Ulrich S.","last_name":"Schwarz","full_name":"Schwarz, Ulrich S."},{"full_name":"Ries, Jonas","first_name":"Jonas","last_name":"Ries"}],"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","date_created":"2024-01-10T10:45:55Z","pmid":1,"year":"2023","_id":"14788","quality_controlled":"1","oa_version":"Published Version","article_processing_charge":"No","keyword":["Cell Biology"],"article_type":"original","publication_status":"published","file":[{"content_type":"application/pdf","file_size":5678069,"checksum":"505d5cac36c14b073b68c7fed1a92bd3","creator":"dernst","access_level":"open_access","date_created":"2024-01-16T10:15:09Z","success":1,"relation":"main_file","file_id":"14811","file_name":"2023_JCB_Mund.pdf","date_updated":"2024-01-16T10:15:09Z"}],"abstract":[{"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.","lang":"eng"}],"file_date_updated":"2024-01-16T10:15:09Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"journal_article","volume":222,"ddc":["570"],"intvolume":"       222","doi":"10.1083/jcb.202206038","date_published":"2023-02-03T00:00:00Z","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)"},"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.","isi":1,"publisher":"Rockefeller University Press","department":[{"_id":"AnSa"}],"month":"02"},{"conference":{"location":"Sydney, Australia","start_date":"2023-12-12","name":"SIGGRAPH: Computer Graphics and Interactive Techniques Conference","end_date":"2023-12-15"},"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","department":[{"_id":"BeBi"}],"publisher":"Association for Computing Machinery","month":"12","type":"conference","file_date_updated":"2024-01-17T08:33:06Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","doi":"10.1145/3610548.3618226","date_published":"2023-12-10T00:00:00Z","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","ddc":["000"],"date_created":"2024-01-14T23:00:57Z","year":"2023","_id":"14798","publication_status":"published","file":[{"date_updated":"2024-01-17T08:33:06Z","file_id":"14823","success":1,"relation":"main_file","date_created":"2024-01-17T08:33:06Z","file_name":"2023_SA_Chen.pdf","access_level":"open_access","creator":"dernst","content_type":"application/pdf","file_size":95967451,"checksum":"8abe27432ed222b50d1af9b3388db1b0"}],"abstract":[{"lang":"eng","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."}],"quality_controlled":"1","oa_version":"Published Version","article_processing_charge":"Yes (in subscription journal)","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.","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>.","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>","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>.","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."},"date_updated":"2024-01-17T08:38:35Z","author":[{"last_name":"Chen","first_name":"Bin","full_name":"Chen, Bin"},{"full_name":"Jindal, Akshay","last_name":"Jindal","first_name":"Akshay"},{"last_name":"Piovarci","first_name":"Michael","orcid":"0000-0002-5062-4474","full_name":"Piovarci, Michael","id":"62E473F4-5C99-11EA-A40E-AF823DDC885E"},{"first_name":"Chao","last_name":"Wang","full_name":"Wang, Chao"},{"last_name":"Seidel","first_name":"Hans Peter","full_name":"Seidel, Hans Peter"},{"last_name":"Didyk","first_name":"Piotr","full_name":"Didyk, Piotr"},{"full_name":"Myszkowski, Karol","last_name":"Myszkowski","first_name":"Karol"},{"first_name":"Ana","last_name":"Serrano","full_name":"Serrano, Ana"},{"last_name":"Mantiuk","first_name":"Rafał K.","full_name":"Mantiuk, Rafał K."}],"day":"10","publication":"Proceedings of the SIGGRAPH Asia 2023 Conference","publication_identifier":{"isbn":["9798400703157"]},"oa":1,"project":[{"_id":"eb901961-77a9-11ec-83b8-f5c883a62027","grant_number":"M03319","name":"Perception-Aware Appearance Fabrication"}],"title":"The effect of display capabilities on the gloss consistency between real and virtual objects","has_accepted_license":"1","article_number":"90"},{"date_published":"2023-12-01T00:00:00Z","doi":"10.1107/S1600576723008324","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"}],"intvolume":"        56","ddc":["540"],"type":"journal_article","volume":56,"file_date_updated":"2024-01-17T07:47:35Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"12","department":[{"_id":"LifeSc"}],"arxiv":1,"page":"1618-1629","acknowledgement":"KT acknowledges the NIST–NRC postdoctoral fellowship program for support. This work was partially funded through the European Metrology Programme for Innovation and Research (EMPIR) project No. 17NRM04.\r\nCertain commercial equipment, instruments, materials or software are identified in this article in order to specify the experimental procedure adequately. Such identification is not intended to imply recommendation or endorsement by NIST, nor is it intended to imply that the materials or equipment identified are necessarily the best available for the purpose. Open access funding enabled and organized by Projekt DEAL.","scopus_import":"1","title":"The human factor: Results of a small-angle scattering data analysis round robin","external_id":{"arxiv":["2303.03772"]},"has_accepted_license":"1","issue":"6","date_updated":"2024-01-17T07:49:52Z","author":[{"last_name":"Pauw","first_name":"Brian R.","full_name":"Pauw, Brian R."},{"full_name":"Smales, Glen J.","last_name":"Smales","first_name":"Glen J."},{"full_name":"Anker, Andy S.","first_name":"Andy S.","last_name":"Anker"},{"last_name":"Annadurai","first_name":"Venkatasamy","full_name":"Annadurai, Venkatasamy"},{"full_name":"Balazs, Daniel","id":"302BADF6-85FC-11EA-9E3B-B9493DDC885E","orcid":"0000-0001-7597-043X","last_name":"Balazs","first_name":"Daniel"},{"last_name":"Bienert","first_name":"Ralf","full_name":"Bienert, Ralf"},{"full_name":"Bouwman, Wim G.","last_name":"Bouwman","first_name":"Wim G."},{"first_name":"Ingo","last_name":"Breßler","full_name":"Breßler, Ingo"},{"full_name":"Breternitz, Joachim","first_name":"Joachim","last_name":"Breternitz"},{"last_name":"Brok","first_name":"Erik S.","full_name":"Brok, Erik S."},{"full_name":"Bryant, Gary","last_name":"Bryant","first_name":"Gary"},{"first_name":"Andrew J.","last_name":"Clulow","full_name":"Clulow, Andrew J."},{"full_name":"Crater, Erin R.","first_name":"Erin R.","last_name":"Crater"},{"last_name":"De Geuser","first_name":"Frédéric","full_name":"De Geuser, Frédéric"},{"full_name":"Giudice, Alessandra Del","first_name":"Alessandra Del","last_name":"Giudice"},{"first_name":"Jérôme","last_name":"Deumer","full_name":"Deumer, Jérôme"},{"last_name":"Disch","first_name":"Sabrina","full_name":"Disch, Sabrina"},{"full_name":"Dutt, Shankar","first_name":"Shankar","last_name":"Dutt"},{"full_name":"Frank, Kilian","last_name":"Frank","first_name":"Kilian"},{"full_name":"Fratini, Emiliano","last_name":"Fratini","first_name":"Emiliano"},{"last_name":"Garcia","first_name":"Paulo R.A.F.","full_name":"Garcia, Paulo R.A.F."},{"full_name":"Gilbert, Elliot P.","first_name":"Elliot P.","last_name":"Gilbert"},{"first_name":"Marc B.","last_name":"Hahn","full_name":"Hahn, Marc B."},{"first_name":"James","last_name":"Hallett","full_name":"Hallett, James"},{"full_name":"Hohenschutz, Max","last_name":"Hohenschutz","first_name":"Max"},{"full_name":"Hollamby, Martin","first_name":"Martin","last_name":"Hollamby"},{"full_name":"Huband, Steven","last_name":"Huband","first_name":"Steven"},{"last_name":"Ilavsky","first_name":"Jan","full_name":"Ilavsky, Jan"},{"full_name":"Jochum, Johanna K.","first_name":"Johanna K.","last_name":"Jochum"},{"last_name":"Juelsholt","first_name":"Mikkel","full_name":"Juelsholt, Mikkel"},{"full_name":"Mansel, Bradley W.","first_name":"Bradley W.","last_name":"Mansel"},{"first_name":"Paavo","last_name":"Penttilä","full_name":"Penttilä, Paavo"},{"full_name":"Pittkowski, Rebecca K.","last_name":"Pittkowski","first_name":"Rebecca K."},{"first_name":"Giuseppe","last_name":"Portale","full_name":"Portale, Giuseppe"},{"full_name":"Pozzo, Lilo D.","last_name":"Pozzo","first_name":"Lilo D."},{"full_name":"Rochels, Leonhard","last_name":"Rochels","first_name":"Leonhard"},{"last_name":"Rosalie","first_name":"Julian M.","full_name":"Rosalie, Julian M."},{"last_name":"Saloga","first_name":"Patrick E.J.","full_name":"Saloga, Patrick E.J."},{"last_name":"Seibt","first_name":"Susanne","full_name":"Seibt, Susanne"},{"full_name":"Smith, Andrew J.","last_name":"Smith","first_name":"Andrew J."},{"full_name":"Smith, Gregory N.","last_name":"Smith","first_name":"Gregory N."},{"full_name":"Spiering, Glenn A.","last_name":"Spiering","first_name":"Glenn A."},{"full_name":"Stawski, Tomasz M.","first_name":"Tomasz M.","last_name":"Stawski"},{"last_name":"Taché","first_name":"Olivier","full_name":"Taché, Olivier"},{"last_name":"Thünemann","first_name":"Andreas F.","full_name":"Thünemann, Andreas F."},{"full_name":"Toth, Kristof","first_name":"Kristof","last_name":"Toth"},{"last_name":"Whitten","first_name":"Andrew E.","full_name":"Whitten, Andrew E."},{"full_name":"Wuttke, Joachim","last_name":"Wuttke","first_name":"Joachim"}],"citation":{"short":"B.R. Pauw, G.J. Smales, A.S. Anker, V. Annadurai, D. Balazs, R. Bienert, W.G. Bouwman, I. Breßler, J. Breternitz, E.S. Brok, G. Bryant, A.J. Clulow, E.R. Crater, F. De Geuser, A.D. Giudice, J. Deumer, S. Disch, S. Dutt, K. Frank, E. Fratini, P.R.A.F. Garcia, E.P. Gilbert, M.B. Hahn, J. Hallett, M. Hohenschutz, M. Hollamby, S. Huband, J. Ilavsky, J.K. Jochum, M. Juelsholt, B.W. Mansel, P. Penttilä, R.K. Pittkowski, G. Portale, L.D. Pozzo, L. Rochels, J.M. Rosalie, P.E.J. Saloga, S. Seibt, A.J. Smith, G.N. Smith, G.A. Spiering, T.M. Stawski, O. Taché, A.F. Thünemann, K. Toth, A.E. Whitten, J. Wuttke, Journal of Applied Crystallography 56 (2023) 1618–1629.","mla":"Pauw, Brian R., et al. “The Human Factor: Results of a Small-Angle Scattering Data Analysis Round Robin.” <i>Journal of Applied Crystallography</i>, vol. 56, no. 6, 2023, pp. 1618–29, doi:<a href=\"https://doi.org/10.1107/S1600576723008324\">10.1107/S1600576723008324</a>.","ama":"Pauw BR, Smales GJ, Anker AS, et al. The human factor: Results of a small-angle scattering data analysis round robin. <i>Journal of Applied Crystallography</i>. 2023;56(6):1618-1629. doi:<a href=\"https://doi.org/10.1107/S1600576723008324\">10.1107/S1600576723008324</a>","apa":"Pauw, B. R., Smales, G. J., Anker, A. S., Annadurai, V., Balazs, D., Bienert, R., … Wuttke, J. (2023). The human factor: Results of a small-angle scattering data analysis round robin. <i>Journal of Applied Crystallography</i>. <a href=\"https://doi.org/10.1107/S1600576723008324\">https://doi.org/10.1107/S1600576723008324</a>","ieee":"B. R. Pauw <i>et al.</i>, “The human factor: Results of a small-angle scattering data analysis round robin,” <i>Journal of Applied Crystallography</i>, vol. 56, no. 6. pp. 1618–1629, 2023.","chicago":"Pauw, Brian R., Glen J. Smales, Andy S. Anker, Venkatasamy Annadurai, Daniel Balazs, Ralf Bienert, Wim G. Bouwman, et al. “The Human Factor: Results of a Small-Angle Scattering Data Analysis Round Robin.” <i>Journal of Applied Crystallography</i>, 2023. <a href=\"https://doi.org/10.1107/S1600576723008324\">https://doi.org/10.1107/S1600576723008324</a>.","ista":"Pauw BR, Smales GJ, Anker AS, Annadurai V, Balazs D, Bienert R, Bouwman WG, Breßler I, Breternitz J, Brok ES, Bryant G, Clulow AJ, Crater ER, De Geuser F, Giudice AD, Deumer J, Disch S, Dutt S, Frank K, Fratini E, Garcia PRAF, Gilbert EP, Hahn MB, Hallett J, Hohenschutz M, Hollamby M, Huband S, Ilavsky J, Jochum JK, Juelsholt M, Mansel BW, Penttilä P, Pittkowski RK, Portale G, Pozzo LD, Rochels L, Rosalie JM, Saloga PEJ, Seibt S, Smith AJ, Smith GN, Spiering GA, Stawski TM, Taché O, Thünemann AF, Toth K, Whitten AE, Wuttke J. 2023. The human factor: Results of a small-angle scattering data analysis round robin. Journal of Applied Crystallography. 56(6), 1618–1629."},"day":"01","oa":1,"publication":"Journal of Applied Crystallography","publication_identifier":{"issn":["0021-8898"],"eissn":["1600-5767"]},"publication_status":"published","article_type":"original","abstract":[{"text":"A round-robin study has been carried out to estimate the impact of the human element in small-angle scattering data analysis. Four corrected datasets were provided to participants ready for analysis. All datasets were measured on samples containing spherical scatterers, with two datasets in dilute dispersions and two from powders. Most of the 46 participants correctly identified the number of populations in the dilute dispersions, with half of the population\r\nmean entries within 1.5% and half of the population width entries within 40%. Due to the added complexity of the structure factor, far fewer people submitted answers on the powder datasets. For those that did, half of the entries for the means and widths were within 44 and 86%, respectively. This round-robin experiment highlights several causes for the discrepancies, for which solutions are proposed.","lang":"eng"}],"file":[{"content_type":"application/pdf","file_size":2165864,"checksum":"dab30d4556360f2cecf99f4b7efb0ee9","creator":"dernst","access_level":"open_access","relation":"main_file","date_created":"2024-01-17T07:47:35Z","success":1,"file_id":"14822","file_name":"2023_JourApplCrystallography_Pauw.pdf","date_updated":"2024-01-17T07:47:35Z"}],"quality_controlled":"1","article_processing_charge":"Yes (via OA deal)","oa_version":"Published Version","date_created":"2024-01-14T23:00:57Z","_id":"14799","year":"2023"},{"abstract":[{"lang":"eng","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"}],"month":"09","department":[{"_id":"NiBa"}],"related_material":{"record":[{"id":"14796","status":"for_moderation","relation":"used_in_publication"}]},"publisher":"Zenodo","article_processing_charge":"No","oa_version":"Published Version","main_file_link":[{"open_access":"1","url":"https://doi.org/10.5281/zenodo.8318995"}],"_id":"14812","year":"2023","date_created":"2024-01-16T10:23:01Z","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","title":"Data and code for: The genetic architecture of a recent transition to live-bearing in marine snails","date_published":"2023-09-05T00:00:00Z","doi":"10.5281/ZENODO.8318995","ddc":["570"],"has_accepted_license":"1","author":[{"last_name":"Stankowski","first_name":"Sean","id":"43161670-5719-11EA-8025-FABC3DDC885E","full_name":"Stankowski, Sean"}],"date_updated":"2025-08-12T09:04:30Z","citation":{"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>.","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>.","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>","ieee":"S. Stankowski, “Data and code for: The genetic architecture of a recent transition to live-bearing in marine snails.” Zenodo, 2023.","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>.","short":"S. Stankowski, (2023)."},"type":"research_data_reference","oa":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","day":"05","contributor":[{"last_name":"Zagrodzka","first_name":"Zusanna"},{"last_name":"Garlovsky","first_name":"Martin"},{"id":"6AAB2240-CA9A-11E9-9C1A-D9D1E5697425","orcid":"0000-0002-4530-8469","first_name":"Arka","last_name":"Pal"},{"first_name":"Daria","last_name":"Shipilina","id":"428A94B0-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-1145-9226"},{"first_name":"Diego Fernando","last_name":"Garcia Castillo","id":"ae681a14-dc74-11ea-a0a7-c6ef18161701"},{"last_name":"Lifchitz","first_name":"Hila","id":"d6ab5470-2fb3-11ed-8633-986a9b84edac"},{"first_name":"Alan","last_name":"Le Moan"},{"first_name":"Erica","last_name":"Leder"},{"last_name":"Reeve","first_name":"James"},{"first_name":"Kerstin","last_name":"Johannesson"},{"last_name":"Westram","first_name":"Anja M","orcid":"0000-0003-1050-4969","id":"3C147470-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Butlin","first_name":"Roger"}]},{"article_processing_charge":"Yes (in subscription journal)","oa_version":"Published Version","quality_controlled":"1","abstract":[{"lang":"eng","text":"In the last few years, various communication compression techniques have emerged as an indispensable tool helping to alleviate the communication bottleneck in distributed learning. However, despite the fact biased compressors often show superior performance in practice when compared to the much more studied and understood unbiased compressors, very little is known about them. In this work we study three classes of biased compression operators, two of which are new, and their performance when applied to (stochastic) gradient descent and distributed (stochastic) gradient descent. We show for the first time that biased compressors can lead to linear convergence rates both in the single node and distributed settings. We prove that distributed compressed SGD method, employed with error feedback mechanism, enjoys the ergodic rate O(δLexp[−μKδL]+(C+δD)Kμ), where δ≥1 is a compression parameter which grows when more compression is applied, L and μ are the smoothness and strong convexity constants, C captures stochastic gradient noise (C=0 if full gradients are computed on each node) and D captures the variance of the gradients at the optimum (D=0 for over-parameterized models). Further, via a theoretical study of several synthetic and empirical distributions of communicated gradients, we shed light on why and by how much biased compressors outperform their unbiased variants. Finally, we propose several new biased compressors with promising theoretical guarantees and practical performance."}],"file":[{"date_updated":"2024-01-16T12:13:27Z","file_name":"2023_JMLR_Beznosikov.pdf","success":1,"date_created":"2024-01-16T12:13:27Z","relation":"main_file","file_id":"14816","creator":"dernst","access_level":"open_access","checksum":"c50f2b9db53938b755e30a085f464059","file_size":1510993,"content_type":"application/pdf"}],"publication_status":"published","article_type":"original","_id":"14815","year":"2023","date_created":"2024-01-16T12:13:36Z","has_accepted_license":"1","title":"On biased compression for distributed learning","external_id":{"arxiv":["2002.12410"],"isi":["001111578500001"]},"oa":1,"publication":"Journal of Machine Learning Research","publication_identifier":{"eissn":["1533-7928"]},"day":"01","author":[{"full_name":"Beznosikov, Aleksandr","first_name":"Aleksandr","last_name":"Beznosikov"},{"full_name":"Horvath, Samuel","last_name":"Horvath","first_name":"Samuel"},{"last_name":"Richtarik","first_name":"Peter","full_name":"Richtarik, Peter"},{"last_name":"Safaryan","first_name":"Mher","full_name":"Safaryan, Mher","id":"dd546b39-0804-11ed-9c55-ef075c39778d"}],"date_updated":"2024-01-17T09:14:13Z","citation":{"short":"A. Beznosikov, S. Horvath, P. Richtarik, M. Safaryan, Journal of Machine Learning Research 24 (2023) 1–50.","chicago":"Beznosikov, Aleksandr, Samuel Horvath, Peter Richtarik, and Mher Safaryan. “On Biased Compression for Distributed Learning.” <i>Journal of Machine Learning Research</i>. Journal of Machine Learning Research, 2023.","ista":"Beznosikov A, Horvath S, Richtarik P, Safaryan M. 2023. On biased compression for distributed learning. Journal of Machine Learning Research. 24, 1–50.","mla":"Beznosikov, Aleksandr, et al. “On Biased Compression for Distributed Learning.” <i>Journal of Machine Learning Research</i>, vol. 24, Journal of Machine Learning Research, 2023, pp. 1–50.","ieee":"A. Beznosikov, S. Horvath, P. Richtarik, and M. Safaryan, “On biased compression for distributed learning,” <i>Journal of Machine Learning Research</i>, vol. 24. Journal of Machine Learning Research, pp. 1–50, 2023.","apa":"Beznosikov, A., Horvath, S., Richtarik, P., &#38; Safaryan, M. (2023). On biased compression for distributed learning. <i>Journal of Machine Learning Research</i>. Journal of Machine Learning Research.","ama":"Beznosikov A, Horvath S, Richtarik P, Safaryan M. On biased compression for distributed learning. <i>Journal of Machine Learning Research</i>. 2023;24:1-50."},"isi":1,"month":"10","publisher":"Journal of Machine Learning Research","department":[{"_id":"DaAl"}],"acknowledgement":"The work in Sections 1-5 was conducted while A. Beznosikov was a research intern in the Optimizationand Machine Learning Lab of Peter Richtárik at KAUST; this visit was funded by the KAUST Baseline Research Funding Scheme. The work of A. Beznosikov in Section 6 was conducted in Skoltech and was supported by Ministry of Science and Higher Education grant No. 075-10-2021-068. ","page":"1-50","arxiv":1,"intvolume":"        24","ddc":["000"],"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":"2023-10-01T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file_date_updated":"2024-01-16T12:13:27Z","volume":24,"type":"journal_article"},{"abstract":[{"text":"Understanding complex living systems, which are fundamentally constrained by physical phenomena, requires combining experimental data with theoretical physical and mathematical models. To develop such models, collaborations between experimental cell biologists and theoreticians are increasingly important but these two groups often face challenges achieving mutual understanding. To help navigate these challenges, this Perspective discusses different modelling approaches, including bottom-up hypothesis-driven and top-down data-driven models, and highlights their strengths and applications. Using cell mechanics as an example, we explore the integration of specific physical models with experimental data from the molecular, cellular and tissue level up to multiscale input. We also emphasize the importance of constraining model complexity and outline strategies for crosstalk between experimental design and model development. Furthermore, we highlight how physical models can provide conceptual insights and produce unifying and generalizable frameworks for biological phenomena. Overall, this Perspective aims to promote fruitful collaborations that advance our understanding of complex biological systems.","lang":"eng"}],"publication_status":"published","article_type":"original","keyword":["Cell Biology"],"article_processing_charge":"No","oa_version":"None","quality_controlled":"1","_id":"14827","year":"2023","pmid":1,"date_created":"2024-01-17T12:46:55Z","title":"Connecting theory and experiment in cell and tissue mechanics","external_id":{"pmid":["38149871"]},"project":[{"_id":"34e2a5b5-11ca-11ed-8bc3-b2265616ef0b","grant_number":"343-2022","name":"A mechano-chemical theory for stem cell fate decisions in organoid development"}],"article_number":"jcs.261515","issue":"24","date_updated":"2024-01-22T13:35:48Z","author":[{"full_name":"Schwayer, Cornelia","id":"3436488C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5130-2226","last_name":"Schwayer","first_name":"Cornelia"},{"first_name":"David","last_name":"Brückner","orcid":"0000-0001-7205-2975","id":"e1e86031-6537-11eb-953a-f7ab92be508d","full_name":"Brückner, David"}],"citation":{"apa":"Schwayer, C., &#38; Brückner, D. (2023). Connecting theory and experiment in cell and tissue mechanics. <i>Journal of Cell Science</i>. The Company of Biologists. <a href=\"https://doi.org/10.1242/jcs.261515\">https://doi.org/10.1242/jcs.261515</a>","ama":"Schwayer C, Brückner D. Connecting theory and experiment in cell and tissue mechanics. <i>Journal of Cell Science</i>. 2023;136(24). doi:<a href=\"https://doi.org/10.1242/jcs.261515\">10.1242/jcs.261515</a>","ieee":"C. Schwayer and D. Brückner, “Connecting theory and experiment in cell and tissue mechanics,” <i>Journal of Cell Science</i>, vol. 136, no. 24. The Company of Biologists, 2023.","mla":"Schwayer, Cornelia, and David Brückner. “Connecting Theory and Experiment in Cell and Tissue Mechanics.” <i>Journal of Cell Science</i>, vol. 136, no. 24, jcs. 261515, The Company of Biologists, 2023, doi:<a href=\"https://doi.org/10.1242/jcs.261515\">10.1242/jcs.261515</a>.","ista":"Schwayer C, Brückner D. 2023. Connecting theory and experiment in cell and tissue mechanics. Journal of Cell Science. 136(24), jcs. 261515.","chicago":"Schwayer, Cornelia, and David Brückner. “Connecting Theory and Experiment in Cell and Tissue Mechanics.” <i>Journal of Cell Science</i>. The Company of Biologists, 2023. <a href=\"https://doi.org/10.1242/jcs.261515\">https://doi.org/10.1242/jcs.261515</a>.","short":"C. Schwayer, D. Brückner, Journal of Cell Science 136 (2023)."},"publication_identifier":{"eissn":["1477-9137"],"issn":["0021-9533"]},"publication":"Journal of Cell Science","day":"27","month":"12","department":[{"_id":"EdHa"},{"_id":"CaHe"}],"publisher":"The Company of Biologists","scopus_import":"1","acknowledgement":"We thank Prisca Liberali and Edouard Hannezo for many inspiring discussions; Mehmet Can Uçar, Nicoletta I Petridou and Qiutan Yang for a critical reading of the manuscript, and Claudia Flandoli for the artwork in Figs 2 and 3. We would also like to thank The Company of Biologists for the opportunity to attend the 2023 workshop on Collective Cell Migration, and all workshop participants for discussions.\r\nC.S. was supported by a European Molecular Biology Organization (EMBO) Postdoctoral Fellowship (ALTF 660-2020) and Human Frontier Science Program (HFSP) Postdoctoral fellowship (LT000746/2021-L). D.B.B. was supported by the NOMIS Foundation as a NOMIS Fellow and by an EMBO Postdoctoral Fellowship (ALTF 343-2022).","status":"public","language":[{"iso":"eng"}],"date_published":"2023-12-27T00:00:00Z","doi":"10.1242/jcs.261515","intvolume":"       136","volume":136,"type":"journal_article","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"alternative_title":["LNCS"],"intvolume":"     13951","date_published":"2023-12-01T00:00:00Z","doi":"10.1007/978-3-031-47751-5_3","status":"public","language":[{"iso":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"conference","volume":13951,"main_file_link":[{"open_access":"1","url":"https://fc23.ifca.ai/preproceedings/150.pdf"}],"month":"12","department":[{"_id":"ElKo"}],"publisher":"Springer Nature","acknowledgement":"This work is partially supported by Meta. Eleftherios Kokoris-Kogias is partially supported by Austrian Science Fund (FWF) grant No: F8512-N. Shir Cohen is supported by the Adams Fellowship Program of the Israel Academy of Sciences and Humanities.","scopus_import":"1","page":"36-53","conference":{"location":"Bol, Brac, Croatia","start_date":"2023-05-01","name":"FC: Financial Cryptography and Data Security","end_date":"2023-05-05"},"title":"Proof of availability and retrieval in a modular blockchain architecture","project":[{"name":"Secure Network and Hardware for Efficient Blockchains","_id":"34a4ce89-11ca-11ed-8bc3-8cc37fb6e11f","grant_number":"F8512"}],"day":"01","oa":1,"publication":"27th International Conference on Financial Cryptography and Data Security","publication_identifier":{"eissn":["1611-3349"],"isbn":["9783031477508"],"eisbn":["9783031477515"],"issn":["0302-9743"]},"author":[{"full_name":"Cohen, Shir","last_name":"Cohen","first_name":"Shir"},{"full_name":"Goren, Guy","last_name":"Goren","first_name":"Guy"},{"full_name":"Kokoris Kogias, Eleftherios","id":"f5983044-d7ef-11ea-ac6d-fd1430a26d30","last_name":"Kokoris Kogias","first_name":"Eleftherios"},{"last_name":"Sonnino","first_name":"Alberto","full_name":"Sonnino, Alberto"},{"last_name":"Spiegelman","first_name":"Alexander","full_name":"Spiegelman, Alexander"}],"citation":{"short":"S. Cohen, G. Goren, E. Kokoris Kogias, A. Sonnino, A. Spiegelman, in:, 27th International Conference on Financial Cryptography and Data Security, Springer Nature, 2023, pp. 36–53.","ama":"Cohen S, Goren G, Kokoris Kogias E, Sonnino A, Spiegelman A. Proof of availability and retrieval in a modular blockchain architecture. In: <i>27th International Conference on Financial Cryptography and Data Security</i>. Vol 13951. Springer Nature; 2023:36-53. doi:<a href=\"https://doi.org/10.1007/978-3-031-47751-5_3\">10.1007/978-3-031-47751-5_3</a>","ieee":"S. Cohen, G. Goren, E. Kokoris Kogias, A. Sonnino, and A. Spiegelman, “Proof of availability and retrieval in a modular blockchain architecture,” in <i>27th International Conference on Financial Cryptography and Data Security</i>, Bol, Brac, Croatia, 2023, vol. 13951, pp. 36–53.","apa":"Cohen, S., Goren, G., Kokoris Kogias, E., Sonnino, A., &#38; Spiegelman, A. (2023). Proof of availability and retrieval in a modular blockchain architecture. In <i>27th International Conference on Financial Cryptography and Data Security</i> (Vol. 13951, pp. 36–53). Bol, Brac, Croatia: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-031-47751-5_3\">https://doi.org/10.1007/978-3-031-47751-5_3</a>","mla":"Cohen, Shir, et al. “Proof of Availability and Retrieval in a Modular Blockchain Architecture.” <i>27th International Conference on Financial Cryptography and Data Security</i>, vol. 13951, Springer Nature, 2023, pp. 36–53, doi:<a href=\"https://doi.org/10.1007/978-3-031-47751-5_3\">10.1007/978-3-031-47751-5_3</a>.","ista":"Cohen S, Goren G, Kokoris Kogias E, Sonnino A, Spiegelman A. 2023. Proof of availability and retrieval in a modular blockchain architecture. 27th International Conference on Financial Cryptography and Data Security. FC: Financial Cryptography and Data Security, LNCS, vol. 13951, 36–53.","chicago":"Cohen, Shir, Guy Goren, Eleftherios Kokoris Kogias, Alberto Sonnino, and Alexander Spiegelman. “Proof of Availability and Retrieval in a Modular Blockchain Architecture.” In <i>27th International Conference on Financial Cryptography and Data Security</i>, 13951:36–53. Springer Nature, 2023. <a href=\"https://doi.org/10.1007/978-3-031-47751-5_3\">https://doi.org/10.1007/978-3-031-47751-5_3</a>."},"date_updated":"2024-01-22T13:58:07Z","quality_controlled":"1","article_processing_charge":"No","oa_version":"Submitted Version","publication_status":"published","abstract":[{"lang":"eng","text":"This paper explores a modular design architecture aimed at helping blockchains (and other SMR implementation) to scale to a very large number of processes. This comes in contrast to existing monolithic architectures that interleave transaction dissemination, ordering, and execution in a single functionality. To achieve this we first split the monolith to multiple layers which can use existing distributed computing primitives. The exact specifications of the data dissemination part are formally defined by the Proof of Availability & Retrieval (PoA &R) abstraction. Solutions to the PoA &R problem contain two related sub-protocols: one that “pushes” information into the network and another that “pulls” this information. Regarding the latter, there is a dearth of research literature which is rectified in this paper. We present a family of pulling sub-protocols and rigorously analyze them. Extensive simulations support the theoretical claims of efficiency and robustness in case of a very large number of players. Finally, actual implementation and deployment on a small number of machines (roughly the size of several industrial systems) demonstrates the viability of the architecture’s paradigm."}],"date_created":"2024-01-18T07:41:12Z","_id":"14829","year":"2023"}]