[{"project":[{"name":"Quantitative analysis of DNA methylation maintenance with chromatin","grant_number":"725746","call_identifier":"H2020","_id":"62935a00-2b32-11ec-9570-eff30fa39068"}],"doi":"10.7554/elife.72676","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"citation":{"chicago":"Choi, Jaemyung, David B Lyons, and Daniel Zilberman. “Histone H1 Prevents Non-CG Methylation-Mediated Small RNA Biogenesis in Arabidopsis Heterochromatin.” <i>ELife</i>. eLife Sciences Publications, 2021. <a href=\"https://doi.org/10.7554/elife.72676\">https://doi.org/10.7554/elife.72676</a>.","short":"J. Choi, D.B. Lyons, D. Zilberman, ELife 10 (2021).","mla":"Choi, Jaemyung, et al. “Histone H1 Prevents Non-CG Methylation-Mediated Small RNA Biogenesis in Arabidopsis Heterochromatin.” <i>ELife</i>, vol. 10, e72676, eLife Sciences Publications, 2021, doi:<a href=\"https://doi.org/10.7554/elife.72676\">10.7554/elife.72676</a>.","ieee":"J. Choi, D. B. Lyons, and D. Zilberman, “Histone H1 prevents non-CG methylation-mediated small RNA biogenesis in Arabidopsis heterochromatin,” <i>eLife</i>, vol. 10. eLife Sciences Publications, 2021.","ama":"Choi J, Lyons DB, Zilberman D. Histone H1 prevents non-CG methylation-mediated small RNA biogenesis in Arabidopsis heterochromatin. <i>eLife</i>. 2021;10. doi:<a href=\"https://doi.org/10.7554/elife.72676\">10.7554/elife.72676</a>","apa":"Choi, J., Lyons, D. B., &#38; Zilberman, D. (2021). Histone H1 prevents non-CG methylation-mediated small RNA biogenesis in Arabidopsis heterochromatin. <i>ELife</i>. eLife Sciences Publications. <a href=\"https://doi.org/10.7554/elife.72676\">https://doi.org/10.7554/elife.72676</a>","ista":"Choi J, Lyons DB, Zilberman D. 2021. Histone H1 prevents non-CG methylation-mediated small RNA biogenesis in Arabidopsis heterochromatin. eLife. 10, e72676."},"department":[{"_id":"DaZi"}],"scopus_import":"1","volume":10,"_id":"10533","oa_version":"Published Version","quality_controlled":"1","license":"https://creativecommons.org/licenses/by/4.0/","external_id":{"isi":["000754832000001"],"pmid":["34850679"]},"publication_identifier":{"issn":["2050-084X"]},"acknowledgement":"We thank X Feng for helpful comments on the manuscript. This work was supported by a European Research Council grant MaintainMeth (725746) to DZ.","article_type":"original","file_date_updated":"2022-05-16T10:42:22Z","day":"01","date_updated":"2025-04-14T07:57:42Z","title":"Histone H1 prevents non-CG methylation-mediated small RNA biogenesis in Arabidopsis heterochromatin","author":[{"last_name":"Choi","first_name":"Jaemyung","full_name":"Choi, Jaemyung"},{"last_name":"Lyons","first_name":"David B","full_name":"Lyons, David B"},{"full_name":"Zilberman, Daniel","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","first_name":"Daniel","last_name":"Zilberman","orcid":"0000-0002-0123-8649"}],"language":[{"iso":"eng"}],"intvolume":"        10","pmid":1,"date_created":"2021-12-10T13:12:08Z","abstract":[{"text":"Flowering plants utilize small RNA molecules to guide DNA methyltransferases to genomic sequences. This RNA-directed DNA methylation (RdDM) pathway preferentially targets euchromatic transposable elements. However, RdDM is thought to be recruited by methylation of histone H3 at lysine 9 (H3K9me), a hallmark of heterochromatin. How RdDM is targeted to euchromatin despite an affinity for H3K9me is unclear. Here we show that loss of histone H1 enhances heterochromatic RdDM, preferentially at nucleosome linker DNA. Surprisingly, this does not require SHH1, the RdDM component that binds H3K9me. Furthermore, H3K9me is dispensable for RdDM, as is CG DNA methylation. Instead, we find that non-CG methylation is specifically associated with small RNA biogenesis, and without H1 small RNA production quantitatively expands to non-CG methylated loci. Our results demonstrate that H1 enforces the separation of euchromatic and heterochromatic DNA methylation pathways by excluding the small RNA-generating branch of RdDM from non-CG methylated heterochromatin.","lang":"eng"}],"has_accepted_license":"1","publisher":"eLife Sciences Publications","publication":"eLife","corr_author":"1","ddc":["570"],"month":"12","status":"public","ec_funded":1,"type":"journal_article","isi":1,"oa":1,"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","date_published":"2021-12-01T00:00:00Z","article_number":"e72676","year":"2021","keyword":["genetics and molecular biology"],"article_processing_charge":"No","publication_status":"published","file":[{"access_level":"open_access","content_type":"application/pdf","file_size":2715200,"file_name":"2021_eLife_Choi.pdf","creator":"dernst","checksum":"22ed4c55fb550f6da02ae55c359be651","date_created":"2022-05-16T10:42:22Z","relation":"main_file","date_updated":"2022-05-16T10:42:22Z","file_id":"11384","success":1}]},{"intvolume":"         9","language":[{"iso":"eng"}],"publisher":"Royal Society of Chemistry","date_created":"2021-12-12T23:01:27Z","abstract":[{"lang":"eng","text":"For many years, fullerene derivatives have been the main n-type material of organic electronics and optoelectronics. Recently, fullerene derivatives functionalized with ethylene glycol (EG) side chains have been showing important properties such as enhanced dielectric constants, facile doping and enhanced self-assembly capabilities. Here, we have prepared field-effect transistors using a series of these fullerene derivatives equipped with EG side chains of different lengths. Transport data show the beneficial effect of increasing the EG side chain. In order to understand the material properties, full structural determination of these fullerene derivatives has been achieved by coupling the X-ray data with molecular dynamics (MD) simulations. The increase in transport properties is paired with the formation of extended layered structures, efficient molecular packing and an increase in the crystallite alignment. The layer-like structure is composed of conducting layers, containing of closely packed C60 balls approaching the inter-distance of 1 nm, that are separated by well-defined EG layers, where the EG chains are rather splayed with the chain direction almost perpendicular to the layer normal. Such a layered structure appears highly ordered and highly aligned with the C60 planes oriented parallel to the substrate in the thin film configuration. The order inside the thin film increases with the EG chain length, allowing the systems to achieve mobilities as high as 0.053 cm2 V−1 s−1. Our work elucidates the structure of these interesting semiconducting organic molecules and shows that the synergistic use of X-ray structural analysis and MD simulations is a powerful tool to identify the structure of thin organic films for optoelectronic applications."}],"has_accepted_license":"1","publication":"Journal of Materials Chemistry C","ddc":["540"],"month":"12","status":"public","issue":"45","oa":1,"type":"journal_article","isi":1,"page":"16217-16225","date_published":"2021-12-07T00:00:00Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","file":[{"success":1,"file_id":"10538","date_updated":"2021-12-13T09:24:42Z","relation":"main_file","date_created":"2021-12-13T09:24:42Z","file_name":"2021_JMaterChemC_Dong.pdf","checksum":"6b73c214ce54a6894a5854b4364413d7","creator":"cchlebak","file_size":4979390,"content_type":"application/pdf","access_level":"open_access"}],"publication_status":"published","year":"2021","article_processing_charge":"No","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"doi":"10.1039/d1tc02753k","citation":{"ista":"Dong J, Sami S, Balazs D, Alessandri R, Jahani F, Qiu L, Marrink SJ, Havenith RWA, Hummelen JC, Loi MA, Portale G. 2021. Fullerene derivatives with oligoethylene-glycol side chains: An investigation on the origin of their outstanding transport properties. Journal of Materials Chemistry C. 9(45), 16217–16225.","ama":"Dong J, Sami S, Balazs D, et al. Fullerene derivatives with oligoethylene-glycol side chains: An investigation on the origin of their outstanding transport properties. <i>Journal of Materials Chemistry C</i>. 2021;9(45):16217-16225. doi:<a href=\"https://doi.org/10.1039/d1tc02753k\">10.1039/d1tc02753k</a>","apa":"Dong, J., Sami, S., Balazs, D., Alessandri, R., Jahani, F., Qiu, L., … Portale, G. (2021). Fullerene derivatives with oligoethylene-glycol side chains: An investigation on the origin of their outstanding transport properties. <i>Journal of Materials Chemistry C</i>. Royal Society of Chemistry. <a href=\"https://doi.org/10.1039/d1tc02753k\">https://doi.org/10.1039/d1tc02753k</a>","ieee":"J. Dong <i>et al.</i>, “Fullerene derivatives with oligoethylene-glycol side chains: An investigation on the origin of their outstanding transport properties,” <i>Journal of Materials Chemistry C</i>, vol. 9, no. 45. Royal Society of Chemistry, pp. 16217–16225, 2021.","mla":"Dong, Jingjin, et al. “Fullerene Derivatives with Oligoethylene-Glycol Side Chains: An Investigation on the Origin of Their Outstanding Transport Properties.” <i>Journal of Materials Chemistry C</i>, vol. 9, no. 45, Royal Society of Chemistry, 2021, pp. 16217–25, doi:<a href=\"https://doi.org/10.1039/d1tc02753k\">10.1039/d1tc02753k</a>.","short":"J. Dong, S. Sami, D. Balazs, R. Alessandri, F. Jahani, L. Qiu, S.J. Marrink, R.W.A. Havenith, J.C. Hummelen, M.A. Loi, G. Portale, Journal of Materials Chemistry C 9 (2021) 16217–16225.","chicago":"Dong, Jingjin, Selim Sami, Daniel Balazs, Riccardo Alessandri, Fatimeh Jahani, Li Qiu, Siewert J. Marrink, et al. “Fullerene Derivatives with Oligoethylene-Glycol Side Chains: An Investigation on the Origin of Their Outstanding Transport Properties.” <i>Journal of Materials Chemistry C</i>. Royal Society of Chemistry, 2021. <a href=\"https://doi.org/10.1039/d1tc02753k\">https://doi.org/10.1039/d1tc02753k</a>."},"volume":9,"department":[{"_id":"MaIb"}],"scopus_import":"1","oa_version":"Published Version","quality_controlled":"1","_id":"10534","external_id":{"isi":["000688135700001"]},"day":"07","article_type":"original","file_date_updated":"2021-12-13T09:24:42Z","acknowledgement":"J. D. gratefully acknowledges the China Scholarship Council (CSC No. 201606340158) for supporting his PhD studies. S. S. thanks J. Antoja-Lleonart for insightful discussions on simulating the X-ray diffraction patterns. Part of the work was sponsored by NWO Exact and Natural Sciences for the use of supercomputer facilities (Contract no. 17197 7095). Regarding S. S., R. A., R. W. A. H., J. C. H., and M. A. L., this is a publication by the FOM Focus Group “Next Generation Organic Photovoltaics”, participating in the Dutch Institute for Fundamental Energy Research (DIFFER). The ESRF is acknowledged for providing the beamtime. J. D. and G. P. are grateful to the BM26B staff for their great support during the beamtime. M. A. L., D. M. B. are grateful for the financial support of the European Research Council via a Starting Grant (HySPOD, No. 306983).","publication_identifier":{"issn":["2050-7534"],"eissn":["2050-7526"]},"title":"Fullerene derivatives with oligoethylene-glycol side chains: An investigation on the origin of their outstanding transport properties","date_updated":"2023-08-17T06:18:44Z","author":[{"full_name":"Dong, Jingjin","first_name":"Jingjin","last_name":"Dong"},{"full_name":"Sami, Selim","first_name":"Selim","last_name":"Sami"},{"last_name":"Balazs","orcid":"0000-0001-7597-043X","first_name":"Daniel","full_name":"Balazs, Daniel","id":"302BADF6-85FC-11EA-9E3B-B9493DDC885E"},{"full_name":"Alessandri, Riccardo","last_name":"Alessandri","first_name":"Riccardo"},{"full_name":"Jahani, Fatimeh","last_name":"Jahani","first_name":"Fatimeh"},{"full_name":"Qiu, Li","last_name":"Qiu","first_name":"Li"},{"full_name":"Marrink, Siewert J.","last_name":"Marrink","first_name":"Siewert J."},{"full_name":"Havenith, Remco W.A.","first_name":"Remco W.A.","last_name":"Havenith"},{"last_name":"Hummelen","first_name":"Jan C.","full_name":"Hummelen, Jan C."},{"full_name":"Loi, Maria A.","last_name":"Loi","first_name":"Maria A."},{"first_name":"Giuseppe","last_name":"Portale","full_name":"Portale, Giuseppe"}]},{"publisher":"Public Library of Science","pmid":1,"has_accepted_license":"1","date_created":"2021-12-12T23:01:27Z","abstract":[{"lang":"eng","text":"Realistic models of biological processes typically involve interacting components on multiple scales, driven by changing environment and inherent stochasticity. Such models are often analytically and numerically intractable. We revisit a dynamic maximum entropy method that combines a static maximum entropy with a quasi-stationary approximation. This allows us to reduce stochastic non-equilibrium dynamics expressed by the Fokker-Planck equation to a simpler low-dimensional deterministic dynamics, without the need to track microscopic details. Although the method has been previously applied to a few (rather complicated) applications in population genetics, our main goal here is to explain and to better understand how the method works. We demonstrate the usefulness of the method for two widely studied stochastic problems, highlighting its accuracy in capturing important macroscopic quantities even in rapidly changing non-stationary conditions. For the Ornstein-Uhlenbeck process, the method recovers the exact dynamics whilst for a stochastic island model with migration from other habitats, the approximation retains high macroscopic accuracy under a wide range of scenarios in a dynamic environment."}],"intvolume":"        17","language":[{"iso":"eng"}],"issue":"12","acknowledged_ssus":[{"_id":"ScienComp"}],"month":"12","publication":"PLoS Computational Biology","ddc":["570"],"corr_author":"1","status":"public","oa":1,"type":"journal_article","file":[{"access_level":"open_access","content_type":"application/pdf","file_size":2299486,"file_name":"2021_PLOsComBio_Bodova.pdf","creator":"dernst","checksum":"dcd185d4f7e0acee25edf1d6537f447e","date_created":"2022-05-16T08:53:11Z","relation":"main_file","date_updated":"2022-05-16T08:53:11Z","file_id":"11383","success":1}],"year":"2021","article_processing_charge":"No","publication_status":"published","date_published":"2021-12-01T00:00:00Z","article_number":"e1009661","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","volume":17,"scopus_import":"1","department":[{"_id":"NiBa"},{"_id":"GaTk"}],"citation":{"ieee":"K. Bodova, E. Szep, and N. H. Barton, “Dynamic maximum entropy provides accurate approximation of structured population dynamics,” <i>PLoS Computational Biology</i>, vol. 17, no. 12. Public Library of Science, 2021.","mla":"Bodova, Katarina, et al. “Dynamic Maximum Entropy Provides Accurate Approximation of Structured Population Dynamics.” <i>PLoS Computational Biology</i>, vol. 17, no. 12, e1009661, Public Library of Science, 2021, doi:<a href=\"https://doi.org/10.1371/journal.pcbi.1009661\">10.1371/journal.pcbi.1009661</a>.","apa":"Bodova, K., Szep, E., &#38; Barton, N. H. (2021). Dynamic maximum entropy provides accurate approximation of structured population dynamics. <i>PLoS Computational Biology</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pcbi.1009661\">https://doi.org/10.1371/journal.pcbi.1009661</a>","ista":"Bodova K, Szep E, Barton NH. 2021. Dynamic maximum entropy provides accurate approximation of structured population dynamics. PLoS Computational Biology. 17(12), e1009661.","ama":"Bodova K, Szep E, Barton NH. Dynamic maximum entropy provides accurate approximation of structured population dynamics. <i>PLoS Computational Biology</i>. 2021;17(12). doi:<a href=\"https://doi.org/10.1371/journal.pcbi.1009661\">10.1371/journal.pcbi.1009661</a>","chicago":"Bodova, Katarina, Eniko Szep, and Nicholas H Barton. “Dynamic Maximum Entropy Provides Accurate Approximation of Structured Population Dynamics.” <i>PLoS Computational Biology</i>. Public Library of Science, 2021. <a href=\"https://doi.org/10.1371/journal.pcbi.1009661\">https://doi.org/10.1371/journal.pcbi.1009661</a>.","short":"K. Bodova, E. Szep, N.H. Barton, PLoS Computational Biology 17 (2021)."},"tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"doi":"10.1371/journal.pcbi.1009661","quality_controlled":"1","oa_version":"Published Version","_id":"10535","arxiv":1,"publication_identifier":{"issn":["1553-734X"],"eissn":["1553-7358"]},"acknowledgement":"Computational resources for the study were provided by the Institute of Science and Technology, Austria.\r\nKB received funding from the Scientific Grant Agency of the Slovak Republic under the Grants Nos. 1/0755/19 and 1/0521/20.","file_date_updated":"2022-05-16T08:53:11Z","article_type":"original","day":"01","external_id":{"arxiv":["2102.03669"],"pmid":["34851948"]},"author":[{"first_name":"Katarína","last_name":"Bod'ová","orcid":"0000-0002-7214-0171","full_name":"Bod'ová, Katarína","id":"2BA24EA0-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Szep","first_name":"Eniko","full_name":"Szep, Eniko","id":"485BB5A4-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Nicholas H","orcid":"0000-0002-8548-5240","last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","full_name":"Barton, Nicholas H"}],"date_updated":"2024-10-09T21:01:16Z","title":"Dynamic maximum entropy provides accurate approximation of structured population dynamics"},{"language":[{"iso":"eng"}],"intvolume":"        11","has_accepted_license":"1","abstract":[{"text":"TGFβ overexpression is commonly detected in cancer patients and correlates with poor prognosis and metastasis. Cancer progression is often associated with an enhanced recruitment of myeloid-derived cells to the tumor microenvironment. Here we show that functional TGFβ-signaling in myeloid cells is required for metastasis to the lungs and the liver. Myeloid-specific deletion of Tgfbr2 resulted in reduced spontaneous lung metastasis, which was associated with a reduction of proinflammatory cytokines in the metastatic microenvironment. Notably, CD8+ T cell depletion in myeloid-specific Tgfbr2-deficient mice rescued lung metastasis. Myeloid-specific Tgfbr2-deficiency resulted in reduced liver metastasis with an almost complete absence of myeloid cells within metastatic foci. On contrary, an accumulation of Tgfβ-responsive myeloid cells was associated with an increased recruitment of monocytes and granulocytes and higher proinflammatory cytokine levels in control mice. Monocytic cells isolated from metastatic livers of Tgfbr2-deficient mice showed increased polarization towards the M1 phenotype, Tnfα and Il-1β expression, reduced levels of M2 markers and reduced production of chemokines responsible for myeloid-cell recruitment. No significant differences in Tgfβ levels were observed at metastatic sites of any model. These data demonstrate that Tgfβ signaling in monocytic myeloid cells suppresses CD8+ T cell activity during lung metastasis, while these cells actively contribute to tumor growth during liver metastasis. Thus, myeloid cells modulate metastasis through different mechanisms in a tissue-specific manner.","lang":"eng"}],"pmid":1,"date_created":"2021-12-12T23:01:27Z","publisher":"Frontiers","month":"11","status":"public","ddc":["610"],"publication":"Frontiers in Oncology","type":"journal_article","isi":1,"oa":1,"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","article_number":"765151","date_published":"2021-11-18T00:00:00Z","article_processing_charge":"No","year":"2021","publication_status":"published","file":[{"file_id":"10539","success":1,"date_updated":"2021-12-13T13:32:37Z","date_created":"2021-12-13T13:32:37Z","relation":"main_file","checksum":"56cbac80e6891ce750511a30161b7792","creator":"alisjak","file_name":"2021_Frontiers_Stefanescu.pdf","file_size":9245199,"access_level":"open_access","content_type":"application/pdf"}],"tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"doi":"10.3389/fonc.2021.765151","citation":{"ista":"Stefanescu C, Van Gogh M, Roblek M, Heikenwalder M, Borsig L. 2021. TGFβ signaling in myeloid cells promotes lung and liver metastasis through different mechanisms. Frontiers in Oncology. 11, 765151.","ama":"Stefanescu C, Van Gogh M, Roblek M, Heikenwalder M, Borsig L. TGFβ signaling in myeloid cells promotes lung and liver metastasis through different mechanisms. <i>Frontiers in Oncology</i>. 2021;11. doi:<a href=\"https://doi.org/10.3389/fonc.2021.765151\">10.3389/fonc.2021.765151</a>","apa":"Stefanescu, C., Van Gogh, M., Roblek, M., Heikenwalder, M., &#38; Borsig, L. (2021). TGFβ signaling in myeloid cells promotes lung and liver metastasis through different mechanisms. <i>Frontiers in Oncology</i>. Frontiers. <a href=\"https://doi.org/10.3389/fonc.2021.765151\">https://doi.org/10.3389/fonc.2021.765151</a>","mla":"Stefanescu, Cristina, et al. “TGFβ Signaling in Myeloid Cells Promotes Lung and Liver Metastasis through Different Mechanisms.” <i>Frontiers in Oncology</i>, vol. 11, 765151, Frontiers, 2021, doi:<a href=\"https://doi.org/10.3389/fonc.2021.765151\">10.3389/fonc.2021.765151</a>.","ieee":"C. Stefanescu, M. Van Gogh, M. Roblek, M. Heikenwalder, and L. Borsig, “TGFβ signaling in myeloid cells promotes lung and liver metastasis through different mechanisms,” <i>Frontiers in Oncology</i>, vol. 11. Frontiers, 2021.","short":"C. Stefanescu, M. Van Gogh, M. Roblek, M. Heikenwalder, L. Borsig, Frontiers in Oncology 11 (2021).","chicago":"Stefanescu, Cristina, Merel Van Gogh, Marko Roblek, Mathias Heikenwalder, and Lubor Borsig. “TGFβ Signaling in Myeloid Cells Promotes Lung and Liver Metastasis through Different Mechanisms.” <i>Frontiers in Oncology</i>. Frontiers, 2021. <a href=\"https://doi.org/10.3389/fonc.2021.765151\">https://doi.org/10.3389/fonc.2021.765151</a>."},"scopus_import":"1","department":[{"_id":"DaSi"}],"volume":11,"_id":"10536","quality_controlled":"1","oa_version":"Published Version","external_id":{"pmid":["34868988"],"isi":["000726603400001"]},"publication_identifier":{"eissn":["2234-943X"]},"article_type":"original","file_date_updated":"2021-12-13T13:32:37Z","acknowledgement":"The authors acknowledge the assistance of the Laboratory Animal Services Center (LASC) – UZH, Center for Microscopy and Image Analysis, and the Flow Cytometry Center of the University of Zurich.","day":"18","date_updated":"2023-08-17T06:20:32Z","title":"TGFβ signaling in myeloid cells promotes lung and liver metastasis through different mechanisms","author":[{"first_name":"Cristina","last_name":"Stefanescu","full_name":"Stefanescu, Cristina"},{"last_name":"Van Gogh","first_name":"Merel","full_name":"Van Gogh, Merel"},{"id":"3047D808-F248-11E8-B48F-1D18A9856A87","full_name":"Roblek, Marko","first_name":"Marko","orcid":"0000-0001-9588-1389","last_name":"Roblek"},{"full_name":"Heikenwalder, Mathias","first_name":"Mathias","last_name":"Heikenwalder"},{"full_name":"Borsig, Lubor","last_name":"Borsig","first_name":"Lubor"}]},{"year":"2021","article_processing_charge":"No","publication_status":"published","article_number":"062423","date_published":"2021-12-14T00:00:00Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa":1,"type":"journal_article","ec_funded":1,"isi":1,"issue":"6","publication":"Physical Review A","month":"12","status":"public","publisher":"American Physical Society","abstract":[{"lang":"eng","text":"Classical models with complex energy landscapes represent a perspective avenue for the near-term application of quantum simulators. Until now, many theoretical works studied the performance of quantum algorithms for models with a unique ground state. However, when the classical problem is in a so-called clustering phase, the ground state manifold is highly degenerate. As an example, we consider a 3-XORSAT model defined on simple hypergraphs. The degeneracy of classical ground state manifold translates into the emergence of an extensive number of Z2 symmetries, which remain intact even in the presence of a quantum transverse magnetic field. We establish a general duality approach that restricts the quantum problem to a given sector of conserved Z2 charges and use it to study how the outcome of the quantum adiabatic algorithm depends on the hypergraph geometry. We show that the tree hypergraph which corresponds to a classically solvable instance of the 3-XORSAT problem features a constant gap, whereas the closed hypergraph encounters a second-order phase transition with a gap vanishing as a power-law in the problem size. The duality developed in this work provides a practical tool for studies of quantum models with classically degenerate energy manifold and reveals potential connections between glasses and gauge theories."}],"date_created":"2021-12-14T20:46:07Z","intvolume":"       104","language":[{"iso":"eng"}],"author":[{"full_name":"Medina Ramos, Raimel A","id":"CE680B90-D85A-11E9-B684-C920E6697425","last_name":"Medina Ramos","orcid":"0000-0002-5383-2869","first_name":"Raimel A"},{"full_name":"Serbyn, Maksym","id":"47809E7E-F248-11E8-B48F-1D18A9856A87","last_name":"Serbyn","orcid":"0000-0002-2399-5827","first_name":"Maksym"}],"date_updated":"2026-04-07T12:43:22Z","title":"Duality approach to quantum annealing of the 3-variable exclusive-or satisfiability problem (3-XORSAT)","arxiv":1,"publication_identifier":{"eissn":["2469-9934"],"issn":["2469-9926"]},"article_type":"original","related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"17208"}]},"acknowledgement":"We would like to thank S. De Nicola, A. Michaidilis, T. Gulden, Y. Nez-Fernndez, P. Brighi, and S. Sack for fruitful discussions and valuable feedback on the manuscript. M.S. acknowledges useful discussions with E. Altman, L. Cugliandolo, and C. Laumann. We acknowledge support from the European Research Council (ERC) under the European Union's Horizon 2020 Research and Innovation Programme Grant Agreement No. 850899.","day":"14","external_id":{"isi":["000753659200004"],"arxiv":["2106.06344"]},"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2106.06344"}],"oa_version":"Preprint","quality_controlled":"1","_id":"10545","volume":104,"department":[{"_id":"MaSe"}],"scopus_import":"1","citation":{"short":"R.A. Medina Ramos, M. Serbyn, Physical Review A 104 (2021).","chicago":"Medina Ramos, Raimel A, and Maksym Serbyn. “Duality Approach to Quantum Annealing of the 3-Variable Exclusive-or Satisfiability Problem (3-XORSAT).” <i>Physical Review A</i>. American Physical Society, 2021. <a href=\"https://doi.org/10.1103/physreva.104.062423\">https://doi.org/10.1103/physreva.104.062423</a>.","apa":"Medina Ramos, R. A., &#38; Serbyn, M. (2021). Duality approach to quantum annealing of the 3-variable exclusive-or satisfiability problem (3-XORSAT). <i>Physical Review A</i>. American Physical Society. <a href=\"https://doi.org/10.1103/physreva.104.062423\">https://doi.org/10.1103/physreva.104.062423</a>","ista":"Medina Ramos RA, Serbyn M. 2021. Duality approach to quantum annealing of the 3-variable exclusive-or satisfiability problem (3-XORSAT). Physical Review A. 104(6), 062423.","ama":"Medina Ramos RA, Serbyn M. Duality approach to quantum annealing of the 3-variable exclusive-or satisfiability problem (3-XORSAT). <i>Physical Review A</i>. 2021;104(6). doi:<a href=\"https://doi.org/10.1103/physreva.104.062423\">10.1103/physreva.104.062423</a>","ieee":"R. A. Medina Ramos and M. Serbyn, “Duality approach to quantum annealing of the 3-variable exclusive-or satisfiability problem (3-XORSAT),” <i>Physical Review A</i>, vol. 104, no. 6. American Physical Society, 2021.","mla":"Medina Ramos, Raimel A., and Maksym Serbyn. “Duality Approach to Quantum Annealing of the 3-Variable Exclusive-or Satisfiability Problem (3-XORSAT).” <i>Physical Review A</i>, vol. 104, no. 6, 062423, American Physical Society, 2021, doi:<a href=\"https://doi.org/10.1103/physreva.104.062423\">10.1103/physreva.104.062423</a>."},"doi":"10.1103/physreva.104.062423","project":[{"call_identifier":"H2020","_id":"23841C26-32DE-11EA-91FC-C7463DDC885E","name":"Non-Ergodic Quantum Matter: Universality, Dynamics and Control","grant_number":"850899"}]},{"external_id":{"isi":["000668431200001"],"arxiv":["1908.02273"]},"acknowledgement":"Open access funding provided by Institute of Science and Technology (IST Austria). SN acknowledges partial support by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) – project number 405009441.","article_type":"original","publication_identifier":{"issn":["0003-9527"],"eissn":["1432-0673"]},"file_date_updated":"2021-12-16T14:58:08Z","day":"30","arxiv":1,"date_updated":"2023-08-17T06:23:21Z","title":"Optimal homogenization rates in stochastic homogenization of nonlinear uniformly elliptic equations and systems","author":[{"orcid":"0000-0002-0479-558X","last_name":"Fischer","first_name":"Julian L","id":"2C12A0B0-F248-11E8-B48F-1D18A9856A87","full_name":"Fischer, Julian L"},{"first_name":"Stefan","last_name":"Neukamm","full_name":"Neukamm, Stefan"}],"tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"citation":{"chicago":"Fischer, Julian L, and Stefan Neukamm. “Optimal Homogenization Rates in Stochastic Homogenization of Nonlinear Uniformly Elliptic Equations and Systems.” <i>Archive for Rational Mechanics and Analysis</i>. Springer Nature, 2021. <a href=\"https://doi.org/10.1007/s00205-021-01686-9\">https://doi.org/10.1007/s00205-021-01686-9</a>.","short":"J.L. Fischer, S. Neukamm, Archive for Rational Mechanics and Analysis 242 (2021) 343–452.","ieee":"J. L. Fischer and S. Neukamm, “Optimal homogenization rates in stochastic homogenization of nonlinear uniformly elliptic equations and systems,” <i>Archive for Rational Mechanics and Analysis</i>, vol. 242, no. 1. Springer Nature, pp. 343–452, 2021.","mla":"Fischer, Julian L., and Stefan Neukamm. “Optimal Homogenization Rates in Stochastic Homogenization of Nonlinear Uniformly Elliptic Equations and Systems.” <i>Archive for Rational Mechanics and Analysis</i>, vol. 242, no. 1, Springer Nature, 2021, pp. 343–452, doi:<a href=\"https://doi.org/10.1007/s00205-021-01686-9\">10.1007/s00205-021-01686-9</a>.","ama":"Fischer JL, Neukamm S. Optimal homogenization rates in stochastic homogenization of nonlinear uniformly elliptic equations and systems. <i>Archive for Rational Mechanics and Analysis</i>. 2021;242(1):343-452. doi:<a href=\"https://doi.org/10.1007/s00205-021-01686-9\">10.1007/s00205-021-01686-9</a>","apa":"Fischer, J. L., &#38; Neukamm, S. (2021). Optimal homogenization rates in stochastic homogenization of nonlinear uniformly elliptic equations and systems. <i>Archive for Rational Mechanics and Analysis</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s00205-021-01686-9\">https://doi.org/10.1007/s00205-021-01686-9</a>","ista":"Fischer JL, Neukamm S. 2021. Optimal homogenization rates in stochastic homogenization of nonlinear uniformly elliptic equations and systems. Archive for Rational Mechanics and Analysis. 242(1), 343–452."},"doi":"10.1007/s00205-021-01686-9","scopus_import":"1","department":[{"_id":"JuFi"}],"volume":242,"_id":"10549","oa_version":"Published Version","quality_controlled":"1","isi":1,"type":"journal_article","oa":1,"page":"343-452","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","date_published":"2021-06-30T00:00:00Z","article_processing_charge":"Yes (via OA deal)","keyword":["Mechanical Engineering","Mathematics (miscellaneous)","Analysis"],"year":"2021","publication_status":"published","file":[{"success":1,"file_id":"10558","date_updated":"2021-12-16T14:58:08Z","creator":"cchlebak","checksum":"cc830b739aed83ca2e32c4e0ce266a4c","file_name":"2021_ArchRatMechAnalysis_Fischer.pdf","date_created":"2021-12-16T14:58:08Z","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_size":1640121}],"language":[{"iso":"eng"}],"intvolume":"       242","abstract":[{"lang":"eng","text":"We derive optimal-order homogenization rates for random nonlinear elliptic PDEs with monotone nonlinearity in the uniformly elliptic case. More precisely, for a random monotone operator on \\mathbb {R}^d with stationary law (that is spatially homogeneous statistics) and fast decay of correlations on scales larger than the microscale \\varepsilon >0, we establish homogenization error estimates of the order \\varepsilon in case d\\geqq 3, and of the order \\varepsilon |\\log \\varepsilon |^{1/2} in case d=2. Previous results in nonlinear stochastic homogenization have been limited to a small algebraic rate of convergence \\varepsilon ^\\delta . We also establish error estimates for the approximation of the homogenized operator by the method of representative volumes of the order (L/\\varepsilon )^{-d/2} for a representative volume of size L. Our results also hold in the case of systems for which a (small-scale) C^{1,\\alpha } regularity theory is available."}],"date_created":"2021-12-16T12:12:33Z","has_accepted_license":"1","publisher":"Springer Nature","publication":"Archive for Rational Mechanics and Analysis","ddc":["530"],"month":"06","status":"public","issue":"1"},{"title":"One-sided Frank-Wolfe algorithms for saddle problems","date_updated":"2025-07-16T08:04:23Z","author":[{"first_name":"Vladimir","last_name":"Kolmogorov","full_name":"Kolmogorov, Vladimir","id":"3D50B0BA-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Thomas","last_name":"Pock","full_name":"Pock, Thomas"}],"external_id":{"arxiv":["2101.12617"]},"conference":{"end_date":"2021-07-24","location":"Virtual","name":"ICML: International Conference on Machine Learning","start_date":"2021-07-18"},"arxiv":1,"day":"01","acknowledgement":"Vladimir Kolmogorov was supported by the European Research Council under the European Unions Seventh Framework Programme (FP7/2007-2013)/ERC grant agreement no 616160. Thomas Pock acknowledges support by an ERC grant HOMOVIS, no 640156.","oa_version":"Preprint","quality_controlled":"1","main_file_link":[{"url":"https://arxiv.org/abs/2101.12617","open_access":"1"}],"_id":"10552","citation":{"mla":"Kolmogorov, Vladimir, and Thomas Pock. “One-Sided Frank-Wolfe Algorithms for Saddle Problems.” <i>38th International Conference on Machine Learning</i>, 2021.","ieee":"V. Kolmogorov and T. Pock, “One-sided Frank-Wolfe algorithms for saddle problems,” in <i>38th International Conference on Machine Learning</i>, Virtual, 2021.","apa":"Kolmogorov, V., &#38; Pock, T. (2021). One-sided Frank-Wolfe algorithms for saddle problems. In <i>38th International Conference on Machine Learning</i>. Virtual.","ista":"Kolmogorov V, Pock T. 2021. One-sided Frank-Wolfe algorithms for saddle problems. 38th International Conference on Machine Learning. ICML: International Conference on Machine Learning.","ama":"Kolmogorov V, Pock T. One-sided Frank-Wolfe algorithms for saddle problems. In: <i>38th International Conference on Machine Learning</i>. ; 2021.","chicago":"Kolmogorov, Vladimir, and Thomas Pock. “One-Sided Frank-Wolfe Algorithms for Saddle Problems.” In <i>38th International Conference on Machine Learning</i>, 2021.","short":"V. Kolmogorov, T. Pock, in:, 38th International Conference on Machine Learning, 2021."},"project":[{"name":"Discrete Optimization in Computer Vision: Theory and Practice","grant_number":"616160","call_identifier":"FP7","_id":"25FBA906-B435-11E9-9278-68D0E5697425"}],"scopus_import":"1","department":[{"_id":"VlKo"}],"date_published":"2021-07-01T00:00:00Z","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publication_status":"published","year":"2021","article_processing_charge":"No","oa":1,"type":"conference","ec_funded":1,"publication":"38th International Conference on Machine Learning","status":"public","month":"07","corr_author":"1","language":[{"iso":"eng"}],"date_created":"2021-12-16T12:41:20Z","abstract":[{"lang":"eng","text":"We study a class of convex-concave saddle-point problems of the form minxmaxy⟨Kx,y⟩+fP(x)−h∗(y) where K is a linear operator, fP is the sum of a convex function f with a Lipschitz-continuous gradient and the indicator function of a bounded convex polytope P, and h∗ is a convex (possibly nonsmooth) function. Such problem arises, for example, as a Lagrangian relaxation of various discrete optimization problems. Our main assumptions are the existence of an efficient linear minimization oracle (lmo) for fP and an efficient proximal map for h∗ which motivate the solution via a blend of proximal primal-dual algorithms and Frank-Wolfe algorithms. In case h∗ is the indicator function of a linear constraint and function f is quadratic, we show a O(1/n2) convergence rate on the dual objective, requiring O(nlogn) calls of lmo. If the problem comes from the constrained optimization problem minx∈Rd{fP(x)|Ax−b=0} then we additionally get bound O(1/n2) both on the primal gap and on the infeasibility gap. In the most general case, we show a O(1/n) convergence rate of the primal-dual gap again requiring O(nlogn) calls of lmo. To the best of our knowledge, this improves on the known convergence rates for the considered class of saddle-point problems. We show applications to labeling problems frequently appearing in machine learning and computer vision."}]},{"page":"187-190","oa":1,"type":"conference","isi":1,"publication_status":"published","keyword":["optimal","state machine replication","fallback","asynchrony","byzantine faults"],"year":"2021","article_processing_charge":"No","date_published":"2021-07-21T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Association for Computing Machinery","abstract":[{"text":"The popularity of permissioned blockchain systems demands BFT SMR protocols that are efficient under good network conditions (synchrony) and robust under bad network conditions (asynchrony). The state-of-the-art partially synchronous BFT SMR protocols provide optimal linear communication cost per decision under synchrony and good leaders, but lose liveness under asynchrony. On the other hand, the state-of-the-art asynchronous BFT SMR protocols are live even under asynchrony, but always pay quadratic cost even under synchrony. In this paper, we propose a BFT SMR protocol that achieves the best of both worlds -- optimal linear cost per decision under good networks and leaders, optimal quadratic cost per decision under bad networks, and remains always live.","lang":"eng"}],"date_created":"2021-12-16T13:20:19Z","language":[{"iso":"eng"}],"status":"public","month":"07","publication":"Proceedings of the 2021 ACM Symposium on Principles of Distributed Computing","arxiv":1,"day":"21","publication_identifier":{"isbn":["9-781-4503-8548-0"]},"external_id":{"arxiv":["2103.03181"],"isi":["000744439800018"]},"conference":{"start_date":"2021-07-26","location":"Virtual, Italy","name":"PODC: Principles of Distributed Computing","end_date":"2021-07-30"},"author":[{"full_name":"Gelashvili, Rati","first_name":"Rati","last_name":"Gelashvili"},{"id":"f5983044-d7ef-11ea-ac6d-fd1430a26d30","full_name":"Kokoris Kogias, Eleftherios","first_name":"Eleftherios","last_name":"Kokoris Kogias"},{"full_name":"Spiegelman, Alexander","first_name":"Alexander","last_name":"Spiegelman"},{"last_name":"Xiang","first_name":"Zhuolun","full_name":"Xiang, Zhuolun"}],"title":"Brief announcement: Be prepared when network goes bad: An asynchronous view-change protocol","date_updated":"2023-09-04T11:42:10Z","scopus_import":"1","department":[{"_id":"ElKo"}],"citation":{"chicago":"Gelashvili, Rati, Eleftherios Kokoris Kogias, Alexander Spiegelman, and Zhuolun Xiang. “Brief Announcement: Be Prepared When Network Goes Bad: An Asynchronous View-Change Protocol.” In <i>Proceedings of the 2021 ACM Symposium on Principles of Distributed Computing</i>, 187–90. Association for Computing Machinery, 2021. <a href=\"https://doi.org/10.1145/3465084.3467941\">https://doi.org/10.1145/3465084.3467941</a>.","short":"R. Gelashvili, E. Kokoris Kogias, A. Spiegelman, Z. Xiang, in:, Proceedings of the 2021 ACM Symposium on Principles of Distributed Computing, Association for Computing Machinery, 2021, pp. 187–190.","ieee":"R. Gelashvili, E. Kokoris Kogias, A. Spiegelman, and Z. Xiang, “Brief announcement: Be prepared when network goes bad: An asynchronous view-change protocol,” in <i>Proceedings of the 2021 ACM Symposium on Principles of Distributed Computing</i>, Virtual, Italy, 2021, pp. 187–190.","mla":"Gelashvili, Rati, et al. “Brief Announcement: Be Prepared When Network Goes Bad: An Asynchronous View-Change Protocol.” <i>Proceedings of the 2021 ACM Symposium on Principles of Distributed Computing</i>, Association for Computing Machinery, 2021, pp. 187–90, doi:<a href=\"https://doi.org/10.1145/3465084.3467941\">10.1145/3465084.3467941</a>.","apa":"Gelashvili, R., Kokoris Kogias, E., Spiegelman, A., &#38; Xiang, Z. (2021). Brief announcement: Be prepared when network goes bad: An asynchronous view-change protocol. In <i>Proceedings of the 2021 ACM Symposium on Principles of Distributed Computing</i> (pp. 187–190). Virtual, Italy: Association for Computing Machinery. <a href=\"https://doi.org/10.1145/3465084.3467941\">https://doi.org/10.1145/3465084.3467941</a>","ista":"Gelashvili R, Kokoris Kogias E, Spiegelman A, Xiang Z. 2021. Brief announcement: Be prepared when network goes bad: An asynchronous view-change protocol. Proceedings of the 2021 ACM Symposium on Principles of Distributed Computing. PODC: Principles of Distributed Computing, 187–190.","ama":"Gelashvili R, Kokoris Kogias E, Spiegelman A, Xiang Z. Brief announcement: Be prepared when network goes bad: An asynchronous view-change protocol. In: <i>Proceedings of the 2021 ACM Symposium on Principles of Distributed Computing</i>. Association for Computing Machinery; 2021:187-190. doi:<a href=\"https://doi.org/10.1145/3465084.3467941\">10.1145/3465084.3467941</a>"},"doi":"10.1145/3465084.3467941","quality_controlled":"1","oa_version":"Preprint","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2103.03181"}],"_id":"10553"},{"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","date_published":"2021-07-21T00:00:00Z","article_processing_charge":"No","year":"2021","publication_status":"published","isi":1,"type":"conference","oa":1,"page":"165-175","publication":"Proceedings of the 2021 ACM Symposium on Principles of Distributed Computing","status":"public","month":"07","language":[{"iso":"eng"}],"abstract":[{"text":"We present DAG-Rider, the first asynchronous Byzantine Atomic Broadcast protocol that achieves optimal resilience, optimal amortized communication complexity, and optimal time complexity. DAG-Rider is post-quantum safe and ensures that all values proposed by correct processes eventually get delivered. We construct DAG-Rider in two layers: In the first layer, processes reliably broadcast their proposals and build a structured Directed Acyclic Graph (DAG) of the communication among them. In the second layer, processes locally observe their DAGs and totally order all proposals with no extra communication.","lang":"eng"}],"date_created":"2021-12-16T13:21:13Z","publisher":"Association for Computing Machinery","date_updated":"2023-08-17T06:24:44Z","title":"All You Need is DAG","author":[{"full_name":"Keidar, Idit","first_name":"Idit","last_name":"Keidar"},{"id":"f5983044-d7ef-11ea-ac6d-fd1430a26d30","full_name":"Kokoris Kogias, Eleftherios","last_name":"Kokoris Kogias","first_name":"Eleftherios"},{"last_name":"Naor","first_name":"Oded","full_name":"Naor, Oded"},{"last_name":"Spiegelman","first_name":"Alexander","full_name":"Spiegelman, Alexander"}],"conference":{"name":"PODC: Principles of Distributed Computing","location":"Virtual, Italy","start_date":"2021-07-26","end_date":"2021-07-30"},"external_id":{"isi":["000744439800016"],"arxiv":["2102.08325"]},"publication_identifier":{"isbn":["978-1-4503-8548-0"]},"acknowledgement":"Oded Naor is grateful to the Technion Hiroshi Fujiwara Cyber-Security Research Center for providing a research grant. Part of Oded’s work was done while at Novi Research. This work was funded by the Novi team at Facebook. We also wish to thank the Novi Research team for valuable feedback, and in particular George Danezis, Alberto Sonnino, and Dahlia Malkhi.\r\n","day":"21","arxiv":1,"_id":"10554","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2102.08325"}],"oa_version":"Preprint","quality_controlled":"1","citation":{"ieee":"I. Keidar, E. Kokoris Kogias, O. Naor, and A. Spiegelman, “All You Need is DAG,” in <i>Proceedings of the 2021 ACM Symposium on Principles of Distributed Computing</i>, Virtual, Italy, 2021, pp. 165–175.","mla":"Keidar, Idit, et al. “All You Need Is DAG.” <i>Proceedings of the 2021 ACM Symposium on Principles of Distributed Computing</i>, Association for Computing Machinery, 2021, pp. 165–75, doi:<a href=\"https://doi.org/10.1145/3465084.3467905\">10.1145/3465084.3467905</a>.","ista":"Keidar I, Kokoris Kogias E, Naor O, Spiegelman A. 2021. All You Need is DAG. Proceedings of the 2021 ACM Symposium on Principles of Distributed Computing. PODC: Principles of Distributed Computing, 165–175.","ama":"Keidar I, Kokoris Kogias E, Naor O, Spiegelman A. All You Need is DAG. In: <i>Proceedings of the 2021 ACM Symposium on Principles of Distributed Computing</i>. Association for Computing Machinery; 2021:165-175. doi:<a href=\"https://doi.org/10.1145/3465084.3467905\">10.1145/3465084.3467905</a>","apa":"Keidar, I., Kokoris Kogias, E., Naor, O., &#38; Spiegelman, A. (2021). All You Need is DAG. In <i>Proceedings of the 2021 ACM Symposium on Principles of Distributed Computing</i> (pp. 165–175). Virtual, Italy: Association for Computing Machinery. <a href=\"https://doi.org/10.1145/3465084.3467905\">https://doi.org/10.1145/3465084.3467905</a>","chicago":"Keidar, Idit, Eleftherios Kokoris Kogias, Oded Naor, and Alexander Spiegelman. “All You Need Is DAG.” In <i>Proceedings of the 2021 ACM Symposium on Principles of Distributed Computing</i>, 165–75. Association for Computing Machinery, 2021. <a href=\"https://doi.org/10.1145/3465084.3467905\">https://doi.org/10.1145/3465084.3467905</a>.","short":"I. Keidar, E. Kokoris Kogias, O. Naor, A. Spiegelman, in:, Proceedings of the 2021 ACM Symposium on Principles of Distributed Computing, Association for Computing Machinery, 2021, pp. 165–175."},"doi":"10.1145/3465084.3467905","scopus_import":"1","department":[{"_id":"ElKo"}]},{"issue":"2","acknowledged_ssus":[{"_id":"NanoFab"},{"_id":"M-Shop"}],"publication":"Physical Review Research","status":"public","ddc":["620"],"month":"04","corr_author":"1","date_created":"2021-12-16T18:50:57Z","abstract":[{"text":"Hole gases in planar germanium can have high mobilities in combination with strong spin-orbit interaction and electrically tunable g factors, and are therefore emerging as a promising platform for creating hybrid superconductor-semiconductor devices. A key challenge towards hybrid Ge-based quantum technologies is the design of high-quality interfaces and superconducting contacts that are robust against magnetic fields. In this work, by combining the assets of aluminum, which provides good contact to the Ge, and niobium, which has a significant superconducting gap, we demonstrate highly transparent low-disordered JoFETs with relatively large ICRN products that are capable of withstanding high magnetic fields. We furthermore demonstrate the ability of phase-biasing individual JoFETs, opening up an avenue to explore topological superconductivity in planar Ge. The persistence of superconductivity in the reported hybrid devices beyond 1.8 T paves the way towards integrating spin qubits and proximity-induced superconductivity on the same chip.","lang":"eng"}],"has_accepted_license":"1","publisher":"American Physical Society","language":[{"iso":"eng"}],"intvolume":"         3","keyword":["general engineering"],"year":"2021","article_processing_charge":"No","publication_status":"published","file":[{"date_updated":"2021-12-17T08:12:37Z","file_id":"10561","success":1,"file_size":1917512,"access_level":"open_access","content_type":"application/pdf","date_created":"2021-12-17T08:12:37Z","relation":"main_file","file_name":"2021_PhysRevResearch_Aggarwal.pdf","checksum":"60a1bc9c9b616b1b155044bb8cfc6484","creator":"cchlebak"}],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","date_published":"2021-04-15T00:00:00Z","article_number":"L022005","type":"journal_article","ec_funded":1,"oa":1,"_id":"10559","quality_controlled":"1","oa_version":"Published Version","department":[{"_id":"GeKa"}],"scopus_import":"1","volume":3,"project":[{"name":"Majorana bound states in Ge/SiGe heterostructures","grant_number":"844511","call_identifier":"H2020","_id":"26A151DA-B435-11E9-9278-68D0E5697425"},{"call_identifier":"H2020","_id":"237E5020-32DE-11EA-91FC-C7463DDC885E","name":"TOPOLOGICALLY PROTECTED AND SCALABLE QUANTUM BITS","grant_number":"862046"}],"doi":"10.1103/physrevresearch.3.l022005","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"citation":{"ama":"Aggarwal K, Hofmann AC, Jirovec D, et al. Enhancement of proximity-induced superconductivity in a planar Ge hole gas. <i>Physical Review Research</i>. 2021;3(2). doi:<a href=\"https://doi.org/10.1103/physrevresearch.3.l022005\">10.1103/physrevresearch.3.l022005</a>","ista":"Aggarwal K, Hofmann AC, Jirovec D, Prieto Gonzalez I, Sammak A, Botifoll M, Martí-Sánchez S, Veldhorst M, Arbiol J, Scappucci G, Danon J, Katsaros G. 2021. Enhancement of proximity-induced superconductivity in a planar Ge hole gas. Physical Review Research. 3(2), L022005.","apa":"Aggarwal, K., Hofmann, A. C., Jirovec, D., Prieto Gonzalez, I., Sammak, A., Botifoll, M., … Katsaros, G. (2021). Enhancement of proximity-induced superconductivity in a planar Ge hole gas. <i>Physical Review Research</i>. American Physical Society. <a href=\"https://doi.org/10.1103/physrevresearch.3.l022005\">https://doi.org/10.1103/physrevresearch.3.l022005</a>","mla":"Aggarwal, Kushagra, et al. “Enhancement of Proximity-Induced Superconductivity in a Planar Ge Hole Gas.” <i>Physical Review Research</i>, vol. 3, no. 2, L022005, American Physical Society, 2021, doi:<a href=\"https://doi.org/10.1103/physrevresearch.3.l022005\">10.1103/physrevresearch.3.l022005</a>.","ieee":"K. Aggarwal <i>et al.</i>, “Enhancement of proximity-induced superconductivity in a planar Ge hole gas,” <i>Physical Review Research</i>, vol. 3, no. 2. American Physical Society, 2021.","short":"K. Aggarwal, A.C. Hofmann, D. Jirovec, I. Prieto Gonzalez, A. Sammak, M. Botifoll, S. Martí-Sánchez, M. Veldhorst, J. Arbiol, G. Scappucci, J. Danon, G. Katsaros, Physical Review Research 3 (2021).","chicago":"Aggarwal, Kushagra, Andrea C Hofmann, Daniel Jirovec, Ivan Prieto Gonzalez, Amir Sammak, Marc Botifoll, Sara Martí-Sánchez, et al. “Enhancement of Proximity-Induced Superconductivity in a Planar Ge Hole Gas.” <i>Physical Review Research</i>. American Physical Society, 2021. <a href=\"https://doi.org/10.1103/physrevresearch.3.l022005\">https://doi.org/10.1103/physrevresearch.3.l022005</a>."},"author":[{"id":"b22ab905-3539-11eb-84c3-fc159dcd79cb","full_name":"Aggarwal, Kushagra","first_name":"Kushagra","orcid":"0000-0001-9985-9293","last_name":"Aggarwal"},{"first_name":"Andrea C","last_name":"Hofmann","id":"340F461A-F248-11E8-B48F-1D18A9856A87","full_name":"Hofmann, Andrea C"},{"id":"4C473F58-F248-11E8-B48F-1D18A9856A87","full_name":"Jirovec, Daniel","first_name":"Daniel","orcid":"0000-0002-7197-4801","last_name":"Jirovec"},{"first_name":"Ivan","last_name":"Prieto Gonzalez","orcid":"0000-0002-7370-5357","full_name":"Prieto Gonzalez, Ivan","id":"2A307FE2-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Sammak","first_name":"Amir","full_name":"Sammak, Amir"},{"full_name":"Botifoll, Marc","first_name":"Marc","last_name":"Botifoll"},{"full_name":"Martí-Sánchez, Sara","last_name":"Martí-Sánchez","first_name":"Sara"},{"last_name":"Veldhorst","first_name":"Menno","full_name":"Veldhorst, Menno"},{"full_name":"Arbiol, Jordi","first_name":"Jordi","last_name":"Arbiol"},{"first_name":"Giordano","last_name":"Scappucci","full_name":"Scappucci, Giordano"},{"full_name":"Danon, Jeroen","first_name":"Jeroen","last_name":"Danon"},{"last_name":"Katsaros","orcid":"0000-0001-8342-202X","first_name":"Georgios","full_name":"Katsaros, Georgios","id":"38DB5788-F248-11E8-B48F-1D18A9856A87"}],"date_updated":"2025-04-15T08:38:16Z","title":"Enhancement of proximity-induced superconductivity in a planar Ge hole gas","article_type":"original","file_date_updated":"2021-12-17T08:12:37Z","acknowledgement":"This research and related results were made possible with the support of the NOMIS Foundation. This research was supported by the Scientific Service Units of IST Austria through resources provided by the MIBA Machine Shop and the nanofabrication facility, the European Union's Horizon 2020 research and innovation program under the Marie Sklodowska-Curie Grant agreement No. 844511 Grant Agreement No. 862046. ICN2 acknowledge funding from Generalitat de Catalunya 2017 SGR 327. ICN2 is supported by the Severo Ochoa program from Spanish MINECO (Grant No. SEV-2017-0706) and is funded by the CERCA Programme/Generalitat de Catalunya. Part of the present work has been performed in the framework of Universitat Autnoma de Barcelona Materials Science PhD program. The HAADF-STEM microscopy was conducted in the Laboratorio de Microscopias Avanzadas at Instituto de Nanociencia de Aragon-Universidad de Zaragoza. Authors acknowledge the LMA-INA for offering access to their instruments and expertise. We acknowledge support from CSIC Research Platform on Quantum Technologies PTI-001. This project has received funding from the European Union's Horizon 2020 research and innovation programme under Grant Agreement No. 823717 ESTEEM3. M.B. acknowledges support from SUR Generalitat de Catalunya and the EU Social Fund; project ref. 2020 FI 00103. G.S. and M.V. acknowledge support through a projectruimte grant associated with the Netherlands Organization of Scientific Research (NWO). J.D. acknowledges support through FRIPRO-project 274853, which is funded by the Research Council of Norway.","related_material":{"record":[{"id":"8834","relation":"research_data","status":"public"},{"id":"8831","relation":"earlier_version","status":"public"}]},"publication_identifier":{"issn":["2643-1564"]},"day":"15","arxiv":1,"external_id":{"arxiv":["2012.00322"]}},{"issue":"4","publication":"STAR Protocols","status":"public","month":"12","ddc":["573"],"acknowledged_ssus":[{"_id":"Bio"}],"date_created":"2021-12-19T23:01:32Z","abstract":[{"text":"Enzymatic digestion of the extracellular matrix with chondroitinase-ABC reinstates juvenile-like plasticity in the adult cortex as it also disassembles the perineuronal nets (PNNs). The disadvantage of the enzyme is that it must be applied intracerebrally and it degrades the ECM for several weeks. Here, we provide two minimally invasive and transient protocols for microglia-enabled PNN disassembly in mouse cortex: repeated treatment with ketamine-xylazine-acepromazine (KXA) anesthesia and 60-Hz light entrainment. We also discuss how to analyze PNNs within microglial endosomes-lysosomes. For complete details on the use and execution of this protocol, please refer to Venturino et al. (2021).","lang":"eng"}],"has_accepted_license":"1","publisher":"Elsevier","language":[{"iso":"eng"}],"intvolume":"         2","publication_status":"published","article_processing_charge":"Yes","year":"2021","file":[{"date_updated":"2021-12-20T08:58:40Z","success":1,"file_id":"10570","file_size":6207060,"content_type":"application/pdf","access_level":"open_access","relation":"main_file","date_created":"2021-12-20T08:58:40Z","checksum":"9ea2501056c5df99e84726b845e9b976","creator":"cchlebak","file_name":"2021_STARProt_Venturino.pdf"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2021-12-17T00:00:00Z","article_number":"101012","type":"journal_article","ec_funded":1,"oa":1,"_id":"10565","oa_version":"Published Version","quality_controlled":"1","department":[{"_id":"SaSi"}],"scopus_import":"1","volume":2,"project":[{"name":"Microglia action towards neuronal circuit formation and function in health and disease","grant_number":"715571","call_identifier":"H2020","_id":"25D4A630-B435-11E9-9278-68D0E5697425"}],"tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"citation":{"ista":"Venturino A, Siegert S. 2021. Minimally invasive protocols and quantification for microglia-mediated perineuronal net disassembly in mouse brain. STAR Protocols. 2(4), 101012.","apa":"Venturino, A., &#38; Siegert, S. (2021). Minimally invasive protocols and quantification for microglia-mediated perineuronal net disassembly in mouse brain. <i>STAR Protocols</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.xpro.2021.101012\">https://doi.org/10.1016/j.xpro.2021.101012</a>","ama":"Venturino A, Siegert S. Minimally invasive protocols and quantification for microglia-mediated perineuronal net disassembly in mouse brain. <i>STAR Protocols</i>. 2021;2(4). doi:<a href=\"https://doi.org/10.1016/j.xpro.2021.101012\">10.1016/j.xpro.2021.101012</a>","ieee":"A. Venturino and S. Siegert, “Minimally invasive protocols and quantification for microglia-mediated perineuronal net disassembly in mouse brain,” <i>STAR Protocols</i>, vol. 2, no. 4. Elsevier, 2021.","mla":"Venturino, Alessandro, and Sandra Siegert. “Minimally Invasive Protocols and Quantification for Microglia-Mediated Perineuronal Net Disassembly in Mouse Brain.” <i>STAR Protocols</i>, vol. 2, no. 4, 101012, Elsevier, 2021, doi:<a href=\"https://doi.org/10.1016/j.xpro.2021.101012\">10.1016/j.xpro.2021.101012</a>.","short":"A. Venturino, S. Siegert, STAR Protocols 2 (2021).","chicago":"Venturino, Alessandro, and Sandra Siegert. “Minimally Invasive Protocols and Quantification for Microglia-Mediated Perineuronal Net Disassembly in Mouse Brain.” <i>STAR Protocols</i>. Elsevier, 2021. <a href=\"https://doi.org/10.1016/j.xpro.2021.101012\">https://doi.org/10.1016/j.xpro.2021.101012</a>."},"doi":"10.1016/j.xpro.2021.101012","author":[{"orcid":"0000-0003-2356-9403","last_name":"Venturino","first_name":"Alessandro","id":"41CB84B2-F248-11E8-B48F-1D18A9856A87","full_name":"Venturino, Alessandro"},{"first_name":"Sandra","orcid":"0000-0001-8635-0877","last_name":"Siegert","id":"36ACD32E-F248-11E8-B48F-1D18A9856A87","full_name":"Siegert, Sandra"}],"title":"Minimally invasive protocols and quantification for microglia-mediated perineuronal net disassembly in mouse brain","date_updated":"2025-05-14T11:26:30Z","day":"17","acknowledgement":"This research was supported by the European Research Council (grant 715571 to S.S.). We thank Rouven Schulz, Michael Schunn, Claudia Gold, Gabriel Krens, Sarah Gorkiewicz, Margaret Maes, Jürgen Siegert, Marco Benevento, and Sara Oakeley for comments on the manuscript and the IST Austria Bioimaging Facility for the technical support.","file_date_updated":"2021-12-20T08:58:40Z","publication_identifier":{"eissn":["2666-1667"]},"article_type":"original"},{"language":[{"iso":"eng"}],"intvolume":"         9","date_created":"2021-12-20T07:53:19Z","abstract":[{"text":"Genetic adaptation and phenotypic plasticity facilitate the migration into new habitats and enable organisms to cope with a rapidly changing environment. In contrast to genetic adaptation that spans multiple generations as an evolutionary process, phenotypic plasticity allows acclimation within the life-time of an organism. Genetic adaptation and phenotypic plasticity are usually studied in isolation, however, only by including their interactive impact, we can understand acclimation and adaptation in nature. We aimed to explore the contribution of adaptation and plasticity in coping with an abiotic (salinity) and a biotic (Vibrio bacteria) stressor using six different populations of the broad-nosed pipefish Syngnathus typhle that originated from either high [14–17 Practical Salinity Unit (PSU)] or low (7–11 PSU) saline environments along the German coastline of the Baltic Sea. We exposed wild caught animals, to either high (15 PSU) or low (7 PSU) salinity, representing native and novel salinity conditions and allowed animals to mate. After male pregnancy, offspring was split and each half was exposed to one of the two salinities and infected with Vibrio alginolyticus bacteria that were evolved at either of the two salinities in a fully reciprocal design. We investigated life-history traits of fathers and expression of 47 target genes in mothers and offspring. Pregnant males originating from high salinity exposed to low salinity were highly susceptible to opportunistic fungi infections resulting in decreased offspring size and number. In contrast, no signs of fungal infection were identified in fathers originating from low saline conditions suggesting that genetic adaptation has the potential to overcome the challenges encountered at low salinity. Offspring from parents with low saline origin survived better at low salinity suggesting genetic adaptation to low salinity. In addition, gene expression analyses of juveniles indicated patterns of local adaptation, trans-generational plasticity and developmental plasticity. In conclusion, our study suggests that pipefish are locally adapted to the low salinity in their environment, however, they are retaining phenotypic plasticity, which allows them to also cope with ancestral salinity levels and prevailing pathogens.","lang":"eng"}],"has_accepted_license":"1","publisher":"Frontiers Media","ddc":["597"],"publication":"Frontiers in Ecology and Evolution","status":"public","month":"03","isi":1,"type":"journal_article","oa":1,"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","date_published":"2021-03-25T00:00:00Z","article_number":"626442","keyword":["ecology","evolution","behavior and systematics","trans-generational plasticity","genetic adaptation","local adaptation","phenotypic plasticity","Baltic Sea","climate change","salinity","syngnathids"],"year":"2021","article_processing_charge":"No","publication_status":"published","file":[{"relation":"main_file","date_created":"2021-12-20T10:44:20Z","file_name":"2021_Frontiers_Goehlich.pdf","creator":"alisjak","checksum":"8d6e2b767bb0240a9b5a3a3555be51fd","file_size":3175085,"content_type":"application/pdf","access_level":"open_access","success":1,"file_id":"10572","date_updated":"2021-12-20T10:44:20Z"}],"doi":"10.3389/fevo.2021.626442","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"citation":{"ista":"Goehlich H, Sartoris L, Wagner K-S, Wendling CC, Roth O. 2021. Pipefish locally adapted to low salinity in the Baltic Sea retain phenotypic plasticity to cope with ancestral salinity levels. Frontiers in Ecology and Evolution. 9, 626442.","ama":"Goehlich H, Sartoris L, Wagner K-S, Wendling CC, Roth O. Pipefish locally adapted to low salinity in the Baltic Sea retain phenotypic plasticity to cope with ancestral salinity levels. <i>Frontiers in Ecology and Evolution</i>. 2021;9. doi:<a href=\"https://doi.org/10.3389/fevo.2021.626442\">10.3389/fevo.2021.626442</a>","apa":"Goehlich, H., Sartoris, L., Wagner, K.-S., Wendling, C. C., &#38; Roth, O. (2021). Pipefish locally adapted to low salinity in the Baltic Sea retain phenotypic plasticity to cope with ancestral salinity levels. <i>Frontiers in Ecology and Evolution</i>. Frontiers Media. <a href=\"https://doi.org/10.3389/fevo.2021.626442\">https://doi.org/10.3389/fevo.2021.626442</a>","mla":"Goehlich, Henry, et al. “Pipefish Locally Adapted to Low Salinity in the Baltic Sea Retain Phenotypic Plasticity to Cope with Ancestral Salinity Levels.” <i>Frontiers in Ecology and Evolution</i>, vol. 9, 626442, Frontiers Media, 2021, doi:<a href=\"https://doi.org/10.3389/fevo.2021.626442\">10.3389/fevo.2021.626442</a>.","ieee":"H. Goehlich, L. Sartoris, K.-S. Wagner, C. C. Wendling, and O. Roth, “Pipefish locally adapted to low salinity in the Baltic Sea retain phenotypic plasticity to cope with ancestral salinity levels,” <i>Frontiers in Ecology and Evolution</i>, vol. 9. Frontiers Media, 2021.","short":"H. Goehlich, L. Sartoris, K.-S. Wagner, C.C. Wendling, O. Roth, Frontiers in Ecology and Evolution 9 (2021).","chicago":"Goehlich, Henry, Linda Sartoris, Kim-Sara Wagner, Carolin C. Wendling, and Olivia Roth. “Pipefish Locally Adapted to Low Salinity in the Baltic Sea Retain Phenotypic Plasticity to Cope with Ancestral Salinity Levels.” <i>Frontiers in Ecology and Evolution</i>. Frontiers Media, 2021. <a href=\"https://doi.org/10.3389/fevo.2021.626442\">https://doi.org/10.3389/fevo.2021.626442</a>."},"scopus_import":"1","department":[{"_id":"SyCr"}],"volume":9,"_id":"10568","quality_controlled":"1","oa_version":"Published Version","external_id":{"isi":["000637736300001"]},"file_date_updated":"2021-12-20T10:44:20Z","acknowledgement":"We are grateful for the help of Kristina Dauven, Andreas Ebner, Janina Röckner, and Paulina Urban for fish collection in the field and fish maintenance. Furthermore, we thank Fabian Wendt for setting up the aquaria system and Tatjana Liese, Paulina Urban, Jakob Gismann, and Thorsten Reusch for support with DNA extraction and analysis of pipefish population structure. The authors acknowledge support of Isabel Tanger, Agnes Piecyk, Jonas Müller, Grace Walls, Sebastian Albrecht, Julia Böge, and Julia Stefanschitz for their support in preparing cDNA and running of Fluidigm chips. A special thank goes to Diana Gill for general lab support, ordering materials and just being the good spirit of our molecular lab, to Till Bayer for bioinformatics support and to Melanie Heckwolf for fruitful discussion and feedback on the manuscript. HG is very grateful for inspirational office space with ocean view provided by Lisa Hentschel and family. This manuscript has been released as a pre-print at BIORXIV.","article_type":"original","publication_identifier":{"issn":["2296-701X"]},"day":"25","date_updated":"2023-08-17T06:27:22Z","title":"Pipefish locally adapted to low salinity in the Baltic Sea retain phenotypic plasticity to cope with ancestral salinity levels","author":[{"full_name":"Goehlich, Henry","first_name":"Henry","last_name":"Goehlich"},{"last_name":"Sartoris","first_name":"Linda","full_name":"Sartoris, Linda","id":"2B9284CA-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Wagner, Kim-Sara","first_name":"Kim-Sara","last_name":"Wagner"},{"first_name":"Carolin C.","last_name":"Wendling","full_name":"Wendling, Carolin C."},{"full_name":"Roth, Olivia","first_name":"Olivia","last_name":"Roth"}]},{"article_processing_charge":"No","year":"2021","publication_status":"published","file":[{"date_updated":"2021-12-20T10:14:14Z","success":1,"file_id":"10571","file_size":607096,"content_type":"application/pdf","access_level":"open_access","relation":"main_file","date_created":"2021-12-20T10:14:14Z","creator":"cchlebak","checksum":"75d13a5ec8e3b90e3bc02bd8a9c17eef","file_name":"2021_JExpBio_Szabo.pdf"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","date_published":"2021-12-16T00:00:00Z","article_number":"jeb243647","type":"journal_article","isi":1,"oa":1,"issue":"24","publication":"Journal of Experimental Biology","ddc":["573"],"month":"12","status":"public","pmid":1,"abstract":[{"lang":"eng","text":"For animals to survive until reproduction, it is crucial that juveniles successfully detect potential predators and respond with appropriate behavior. The recognition of cues originating from predators can be innate or learned. Cues of various modalities might be used alone or in multi-modal combinations to detect and distinguish predators but studies investigating multi-modal integration in predator avoidance are scarce. Here, we used wild, naive tadpoles of the Neotropical poison frog Allobates femoralis ( Boulenger, 1884) to test their reaction to cues with two modalities from two different sympatrically occurring potential predators: heterospecific predatory Dendrobates tinctorius tadpoles and dragonfly larvae. We presented A. femoralis tadpoles with olfactory or visual cues, or a combination of the two, and compared their reaction to a water control in a between-individual design. In our trials, A. femoralis tadpoles reacted to multi-modal stimuli (a combination of visual and chemical information) originating from dragonfly larvae with avoidance but showed no reaction to uni-modal cues or cues from heterospecific tadpoles. In addition, visual cues from conspecifics increased swimming activity while cues from predators had no effect on tadpole activity. Our results show that A. femoralis tadpoles can innately recognize some predators and probably need both visual and chemical information to effectively avoid them. This is the first study looking at anti-predator behavior in poison frog tadpoles. We discuss how parental care might influence the expression of predator avoidance responses in tadpoles."}],"date_created":"2021-12-20T07:54:22Z","has_accepted_license":"1","publisher":"The Company of Biologists","language":[{"iso":"eng"}],"intvolume":"       224","author":[{"last_name":"Szabo","first_name":"B","full_name":"Szabo, B"},{"last_name":"Mangione","first_name":"R","full_name":"Mangione, R"},{"last_name":"Rath","first_name":"M","full_name":"Rath, M"},{"last_name":"Pašukonis","first_name":"A","full_name":"Pašukonis, A"},{"full_name":"Reber, SA","first_name":"SA","last_name":"Reber"},{"orcid":"0000-0001-7425-2372","last_name":"Oh","first_name":"Jinook","id":"403169A4-080F-11EA-9993-BF3F3DDC885E","full_name":"Oh, Jinook"},{"full_name":"Ringler, M","last_name":"Ringler","first_name":"M"},{"full_name":"Ringler, E","last_name":"Ringler","first_name":"E"}],"date_updated":"2024-10-21T06:02:05Z","title":"Naïve poison frog tadpoles use bi-modal cues to avoid insect predators but not heterospecific predatory tadpoles","article_type":"original","acknowledgement":"We are grateful to Véronique Helfer, Walter Hödl, Lisa Schretzmeyer and Julia Wotke, who assisted with fieldwork in French Guiana. This work was supported by the Austrian Science Fund (FWF) [P24788, T699 and P31518 to E.R.; P33728 to M.R.; J3827 to Thomas Bugnyar, Tecumseh Fitch and Ludwig Huber]; and by the Austrian Bundesministerium für Wissenschaft, Forschung und Wirtschaft [IS761001 to J.O. (Tecumseh Fitch, Thomas Bugnyar and Ludwig Huber)]. A.P. was supported by the European Union's Horizon 2020 research and innovation programme under the Marie Sklodowska-Curie grant agreement no. 835530. S.A.R. was supported by the HT faculty, Lund University. We thank the CNRS Nouragues Ecological Research Station, which benefited from the ‘Investissement d'Avenir’ grants managed by the Agence Nationale de la Recherche (AnaEE France ANR-11-INBS-0001; Labex CEBA ANR-10-LABX-25-01). Open access funding provided by University of Vienna. Deposited in PMC for immediate release.","publication_identifier":{"issn":["0022-0949"],"eissn":["1477-9145"]},"file_date_updated":"2021-12-20T10:14:14Z","day":"16","external_id":{"pmid":["34845497"],"isi":["000738259300013"]},"_id":"10569","oa_version":"Published Version","quality_controlled":"1","department":[{"_id":"SyCr"}],"scopus_import":"1","volume":224,"tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"doi":"10.1242/jeb.243647","citation":{"chicago":"Szabo, B, R Mangione, M Rath, A Pašukonis, SA Reber, Jinook Oh, M Ringler, and E Ringler. “Naïve Poison Frog Tadpoles Use Bi-Modal Cues to Avoid Insect Predators but Not Heterospecific Predatory Tadpoles.” <i>Journal of Experimental Biology</i>. The Company of Biologists, 2021. <a href=\"https://doi.org/10.1242/jeb.243647\">https://doi.org/10.1242/jeb.243647</a>.","short":"B. Szabo, R. Mangione, M. Rath, A. Pašukonis, S. Reber, J. Oh, M. Ringler, E. Ringler, Journal of Experimental Biology 224 (2021).","mla":"Szabo, B., et al. “Naïve Poison Frog Tadpoles Use Bi-Modal Cues to Avoid Insect Predators but Not Heterospecific Predatory Tadpoles.” <i>Journal of Experimental Biology</i>, vol. 224, no. 24, jeb243647, The Company of Biologists, 2021, doi:<a href=\"https://doi.org/10.1242/jeb.243647\">10.1242/jeb.243647</a>.","ieee":"B. Szabo <i>et al.</i>, “Naïve poison frog tadpoles use bi-modal cues to avoid insect predators but not heterospecific predatory tadpoles,” <i>Journal of Experimental Biology</i>, vol. 224, no. 24. The Company of Biologists, 2021.","apa":"Szabo, B., Mangione, R., Rath, M., Pašukonis, A., Reber, S., Oh, J., … Ringler, E. (2021). Naïve poison frog tadpoles use bi-modal cues to avoid insect predators but not heterospecific predatory tadpoles. <i>Journal of Experimental Biology</i>. The Company of Biologists. <a href=\"https://doi.org/10.1242/jeb.243647\">https://doi.org/10.1242/jeb.243647</a>","ista":"Szabo B, Mangione R, Rath M, Pašukonis A, Reber S, Oh J, Ringler M, Ringler E. 2021. Naïve poison frog tadpoles use bi-modal cues to avoid insect predators but not heterospecific predatory tadpoles. Journal of Experimental Biology. 224(24), jeb243647.","ama":"Szabo B, Mangione R, Rath M, et al. Naïve poison frog tadpoles use bi-modal cues to avoid insect predators but not heterospecific predatory tadpoles. <i>Journal of Experimental Biology</i>. 2021;224(24). doi:<a href=\"https://doi.org/10.1242/jeb.243647\">10.1242/jeb.243647</a>"}},{"external_id":{"isi":["000735387500002"]},"day":"22","publication_identifier":{"issn":["0092-8674"],"eissn":["1097-4172"]},"acknowledgement":"We thank Ian Swinburne, Sandy Nandagopal, and Toru Kawanishi for support, discussions, and reagents. We thank Vanessa Barone, Joseph Nasser, and members of the Megason lab for useful comments on the manuscript and general feedback. We are grateful to the Heisenberg and Knaut labs for transgenic fish. Diagrams on the right in the graphical abstract were created using BioRender. This work was supported by NIH R01DC015478 and NIH R01GM107733 to S.G.M. A.M. was supported by Human Frontiers Science Program LTF and NIH K99HD098918.","article_type":"original","title":"Extracellular hyaluronate pressure shaped by cellular tethers drives tissue morphogenesis","date_updated":"2025-05-14T11:26:20Z","author":[{"full_name":"Munjal, Akankshi","first_name":"Akankshi","last_name":"Munjal"},{"id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","full_name":"Hannezo, Edouard B","orcid":"0000-0001-6005-1561","last_name":"Hannezo","first_name":"Edouard B"},{"last_name":"Tsai","first_name":"Tony Y.C.","full_name":"Tsai, Tony Y.C."},{"full_name":"Mitchison, Timothy J.","first_name":"Timothy J.","last_name":"Mitchison"},{"first_name":"Sean G.","last_name":"Megason","full_name":"Megason, Sean G."}],"citation":{"short":"A. Munjal, E.B. Hannezo, T.Y.C. Tsai, T.J. Mitchison, S.G. Megason, Cell 184 (2021) 6313–6325.e18.","chicago":"Munjal, Akankshi, Edouard B Hannezo, Tony Y.C. Tsai, Timothy J. Mitchison, and Sean G. Megason. “Extracellular Hyaluronate Pressure Shaped by Cellular Tethers Drives Tissue Morphogenesis.” <i>Cell</i>. Elsevier, 2021. <a href=\"https://doi.org/10.1016/j.cell.2021.11.025\">https://doi.org/10.1016/j.cell.2021.11.025</a>.","ama":"Munjal A, Hannezo EB, Tsai TYC, Mitchison TJ, Megason SG. Extracellular hyaluronate pressure shaped by cellular tethers drives tissue morphogenesis. <i>Cell</i>. 2021;184(26):6313-6325.e18. doi:<a href=\"https://doi.org/10.1016/j.cell.2021.11.025\">10.1016/j.cell.2021.11.025</a>","apa":"Munjal, A., Hannezo, E. B., Tsai, T. Y. C., Mitchison, T. J., &#38; Megason, S. G. (2021). Extracellular hyaluronate pressure shaped by cellular tethers drives tissue morphogenesis. <i>Cell</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.cell.2021.11.025\">https://doi.org/10.1016/j.cell.2021.11.025</a>","ista":"Munjal A, Hannezo EB, Tsai TYC, Mitchison TJ, Megason SG. 2021. Extracellular hyaluronate pressure shaped by cellular tethers drives tissue morphogenesis. Cell. 184(26), 6313–6325.e18.","ieee":"A. Munjal, E. B. Hannezo, T. Y. C. Tsai, T. J. Mitchison, and S. G. Megason, “Extracellular hyaluronate pressure shaped by cellular tethers drives tissue morphogenesis,” <i>Cell</i>, vol. 184, no. 26. Elsevier, p. 6313–6325.e18, 2021.","mla":"Munjal, Akankshi, et al. “Extracellular Hyaluronate Pressure Shaped by Cellular Tethers Drives Tissue Morphogenesis.” <i>Cell</i>, vol. 184, no. 26, Elsevier, 2021, p. 6313–6325.e18, doi:<a href=\"https://doi.org/10.1016/j.cell.2021.11.025\">10.1016/j.cell.2021.11.025</a>."},"doi":"10.1016/j.cell.2021.11.025","volume":184,"scopus_import":"1","department":[{"_id":"EdHa"}],"quality_controlled":"1","oa_version":"Preprint","main_file_link":[{"url":"https://www.biorxiv.org/content/10.1101/2020.09.28.316042","open_access":"1"}],"_id":"10573","oa":1,"type":"journal_article","isi":1,"page":"6313-6325.e18","date_published":"2021-12-22T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_status":"published","article_processing_charge":"No","year":"2021","intvolume":"       184","language":[{"iso":"eng"}],"publisher":"Elsevier","abstract":[{"lang":"eng","text":"How tissues acquire complex shapes is a fundamental question in biology and regenerative medicine. Zebrafish semicircular canals form from invaginations in the otic epithelium (buds) that extend and fuse to form the hubs of each canal. We find that conventional actomyosin-driven behaviors are not required. Instead, local secretion of hyaluronan, made by the enzymes uridine 5′-diphosphate dehydrogenase (ugdh) and hyaluronan synthase 3 (has3), drives canal morphogenesis. Charged hyaluronate polymers osmotically swell with water and generate isotropic extracellular pressure to deform the overlying epithelium into buds. The mechanical anisotropy needed to shape buds into tubes is conferred by a polarized distribution of actomyosin and E-cadherin-rich membrane tethers, which we term cytocinches. Most work on tissue morphogenesis ascribes actomyosin contractility as the driving force, while the extracellular matrix shapes tissues through differential stiffness. Our work inverts this expectation. Hyaluronate pressure shaped by anisotropic tissue stiffness may be a widespread mechanism for powering morphological change in organogenesis and tissue engineering."}],"date_created":"2021-12-26T23:01:26Z","publication":"Cell","status":"public","month":"12","issue":"26"},{"page":"2975-2987","oa":1,"isi":1,"type":"journal_article","file":[{"date_updated":"2021-12-27T13:51:08Z","success":1,"file_id":"10578","file_size":5741094,"access_level":"open_access","content_type":"application/pdf","date_created":"2021-12-27T13:51:08Z","relation":"main_file","creator":"cchlebak","file_name":"2021_VisComput_Chen.pdf","checksum":"244cfcac0479ca6e3444c098ab2860a1"}],"publication_status":"published","year":"2021","article_processing_charge":"Yes","date_published":"2021-12-01T00:00:00Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publisher":"Springer Nature","abstract":[{"text":"The understanding of material appearance perception is a complex problem due to interactions between material reflectance, surface geometry, and illumination. Recently, Serrano et al. collected the largest dataset to date with subjective ratings of material appearance attributes, including glossiness, metallicness, sharpness and contrast of reflections. In this work, we make use of their dataset to investigate for the first time the impact of the interactions between illumination, geometry, and eight different material categories in perceived appearance attributes. After an initial analysis, we select for further analysis the four material categories that cover the largest range for all perceptual attributes: fabric, plastic, ceramic, and metal. Using a cumulative link mixed model (CLMM) for robust regression, we discover interactions between these material categories and four representative illuminations and object geometries. We believe that our findings contribute to expanding the knowledge on material appearance perception and can be useful for many applications, such as scene design, where any particular material in a given shape can be aligned with dominant classes of illumination, so that a desired strength of appearance attributes can be achieved.","lang":"eng"}],"has_accepted_license":"1","date_created":"2021-12-26T23:01:26Z","intvolume":"        37","language":[{"iso":"eng"}],"issue":"12","ddc":["000"],"status":"public","month":"12","publication":"Visual Computer","day":"01","publication_identifier":{"eissn":["1432-2315"],"issn":["0178-2789"]},"article_type":"original","acknowledgement":"This project has received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Sklodowska-Curie, grant agreement N∘ 765911 (RealVision) and from the European Research Council (ERC), grant agreement N∘ 804226 (PERDY). Open Access funding enabled and organized by Projekt DEAL.","file_date_updated":"2021-12-27T13:51:08Z","external_id":{"isi":["000673536600003"]},"author":[{"full_name":"Chen, Bin","last_name":"Chen","first_name":"Bin"},{"full_name":"Wang, Chao","first_name":"Chao","last_name":"Wang"},{"full_name":"Piovarci, Michael","id":"62E473F4-5C99-11EA-A40E-AF823DDC885E","first_name":"Michael","last_name":"Piovarci","orcid":"0000-0002-5062-4474"},{"last_name":"Seidel","first_name":"Hans Peter","full_name":"Seidel, Hans Peter"},{"full_name":"Didyk, Piotr","first_name":"Piotr","last_name":"Didyk"},{"full_name":"Myszkowski, Karol","last_name":"Myszkowski","first_name":"Karol"},{"full_name":"Serrano, Ana","first_name":"Ana","last_name":"Serrano"}],"title":"The effect of geometry and illumination on appearance perception of different material categories","date_updated":"2023-08-17T06:29:34Z","volume":37,"scopus_import":"1","department":[{"_id":"BeBi"}],"tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"doi":"10.1007/s00371-021-02227-x","citation":{"short":"B. Chen, C. Wang, M. Piovarci, H.P. Seidel, P. Didyk, K. Myszkowski, A. Serrano, Visual Computer 37 (2021) 2975–2987.","chicago":"Chen, Bin, Chao Wang, Michael Piovarci, Hans Peter Seidel, Piotr Didyk, Karol Myszkowski, and Ana Serrano. “The Effect of Geometry and Illumination on Appearance Perception of Different Material Categories.” <i>Visual Computer</i>. Springer Nature, 2021. <a href=\"https://doi.org/10.1007/s00371-021-02227-x\">https://doi.org/10.1007/s00371-021-02227-x</a>.","ista":"Chen B, Wang C, Piovarci M, Seidel HP, Didyk P, Myszkowski K, Serrano A. 2021. The effect of geometry and illumination on appearance perception of different material categories. Visual Computer. 37(12), 2975–2987.","apa":"Chen, B., Wang, C., Piovarci, M., Seidel, H. P., Didyk, P., Myszkowski, K., &#38; Serrano, A. (2021). The effect of geometry and illumination on appearance perception of different material categories. <i>Visual Computer</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s00371-021-02227-x\">https://doi.org/10.1007/s00371-021-02227-x</a>","ama":"Chen B, Wang C, Piovarci M, et al. The effect of geometry and illumination on appearance perception of different material categories. <i>Visual Computer</i>. 2021;37(12):2975-2987. doi:<a href=\"https://doi.org/10.1007/s00371-021-02227-x\">10.1007/s00371-021-02227-x</a>","mla":"Chen, Bin, et al. “The Effect of Geometry and Illumination on Appearance Perception of Different Material Categories.” <i>Visual Computer</i>, vol. 37, no. 12, Springer Nature, 2021, pp. 2975–87, doi:<a href=\"https://doi.org/10.1007/s00371-021-02227-x\">10.1007/s00371-021-02227-x</a>.","ieee":"B. Chen <i>et al.</i>, “The effect of geometry and illumination on appearance perception of different material categories,” <i>Visual Computer</i>, vol. 37, no. 12. Springer Nature, pp. 2975–2987, 2021."},"oa_version":"Published Version","quality_controlled":"1","_id":"10574"},{"_id":"10585","quality_controlled":"1","oa_version":"Published Version","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"doi":"10.3390/atoms9040106","citation":{"chicago":"Brooks, Morris, Mikhail Lemeshko, Douglas Lundholm, and Enderalp Yakaboylu. “Emergence of Anyons on the Two-Sphere in Molecular Impurities.” <i>Atoms</i>. MDPI, 2021. <a href=\"https://doi.org/10.3390/atoms9040106\">https://doi.org/10.3390/atoms9040106</a>.","short":"M. Brooks, M. Lemeshko, D. Lundholm, E. Yakaboylu, Atoms 9 (2021).","ieee":"M. Brooks, M. Lemeshko, D. Lundholm, and E. Yakaboylu, “Emergence of anyons on the two-sphere in molecular impurities,” <i>Atoms</i>, vol. 9, no. 4. MDPI, 2021.","mla":"Brooks, Morris, et al. “Emergence of Anyons on the Two-Sphere in Molecular Impurities.” <i>Atoms</i>, vol. 9, no. 4, 106, MDPI, 2021, doi:<a href=\"https://doi.org/10.3390/atoms9040106\">10.3390/atoms9040106</a>.","apa":"Brooks, M., Lemeshko, M., Lundholm, D., &#38; Yakaboylu, E. (2021). Emergence of anyons on the two-sphere in molecular impurities. <i>Atoms</i>. MDPI. <a href=\"https://doi.org/10.3390/atoms9040106\">https://doi.org/10.3390/atoms9040106</a>","ista":"Brooks M, Lemeshko M, Lundholm D, Yakaboylu E. 2021. Emergence of anyons on the two-sphere in molecular impurities. Atoms. 9(4), 106.","ama":"Brooks M, Lemeshko M, Lundholm D, Yakaboylu E. Emergence of anyons on the two-sphere in molecular impurities. <i>Atoms</i>. 2021;9(4). doi:<a href=\"https://doi.org/10.3390/atoms9040106\">10.3390/atoms9040106</a>"},"department":[{"_id":"MiLe"},{"_id":"RoSe"}],"scopus_import":"1","volume":9,"title":"Emergence of anyons on the two-sphere in molecular impurities","date_updated":"2024-10-09T21:01:20Z","author":[{"full_name":"Brooks, Morris","id":"B7ECF9FC-AA38-11E9-AC9A-0930E6697425","last_name":"Brooks","orcid":"0000-0002-6249-0928","first_name":"Morris"},{"last_name":"Lemeshko","orcid":"0000-0002-6990-7802","first_name":"Mikhail","full_name":"Lemeshko, Mikhail","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Lundholm","first_name":"Douglas","full_name":"Lundholm, Douglas"},{"id":"38CB71F6-F248-11E8-B48F-1D18A9856A87","full_name":"Yakaboylu, Enderalp","first_name":"Enderalp","orcid":"0000-0001-5973-0874","last_name":"Yakaboylu"}],"external_id":{"arxiv":["2108.06966"]},"day":"02","acknowledgement":"D. Lundholm acknowledges financial support from the Göran Gustafsson Foundation (grant no. 1804).","file_date_updated":"2022-01-03T10:15:05Z","article_type":"original","publication_identifier":{"eissn":["2218-2004"]},"arxiv":1,"publication":"Atoms","ddc":["530"],"status":"public","corr_author":"1","month":"12","issue":"4","language":[{"iso":"eng"}],"intvolume":"         9","has_accepted_license":"1","abstract":[{"lang":"eng","text":"Recently it was shown that anyons on the two-sphere naturally arise from a system of molecular impurities exchanging angular momentum with a many-particle bath (Phys. Rev. Lett. 126, 015301 (2021)). Here we further advance this approach and rigorously demonstrate that in the experimentally realized regime the lowest spectrum of two linear molecules immersed in superfluid helium corresponds to the spectrum of two anyons on the sphere. We develop the formalism within the framework of the recently experimentally observed angulon quasiparticle"}],"date_created":"2022-01-02T23:01:33Z","publisher":"MDPI","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","date_published":"2021-12-02T00:00:00Z","article_number":"106","publication_status":"published","keyword":["anyons","quasiparticles","Quantum Hall Effect","topological states of matter"],"year":"2021","article_processing_charge":"Yes","file":[{"success":1,"file_id":"10592","date_updated":"2022-01-03T10:15:05Z","date_created":"2022-01-03T10:15:05Z","relation":"main_file","file_name":"2021_Atoms_Brooks.pdf","creator":"alisjak","checksum":"d0e44b95f36c9e06724f66832af0f8c3","file_size":303070,"access_level":"open_access","content_type":"application/pdf"}],"type":"journal_article","oa":1},{"publication_status":"published","year":"2021","article_processing_charge":"No","file":[{"date_updated":"2022-01-03T09:46:53Z","success":1,"file_id":"10591","access_level":"open_access","content_type":"application/pdf","file_size":4569639,"file_name":"2021_Crystals_Yuzheng.pdf","creator":"alisjak","checksum":"668e9d777608ce0a3bc2e305133bd06b","date_created":"2022-01-03T09:46:53Z","relation":"main_file"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","article_number":"1509","date_published":"2021-12-03T00:00:00Z","type":"journal_article","isi":1,"oa":1,"issue":"12","ddc":["620"],"publication":"Crystals","status":"public","month":"12","abstract":[{"text":"A facile approach for developing an interfacial solar evaporator by heat localization of solar-thermal energy conversion at water-air liquid composed by in-situ polymerization of Fe2O3 nanoparticles (Fe2O3@PPy) deposited over a facial sponge is proposed. The demonstrated system consists of a floating solar receiver having a vertically cross-linked microchannel for wicking up saline water. The in situ polymerized Fe2O3@PPy interfacial layer promotes diffuse reflection and its rough black surface allows Omni-directional solar absorption (94%) and facilitates efficient thermal localization at the water/air interface and offers a defect-rich surface to promote heat localization (41.9 °C) and excellent thermal management due to cellulosic content. The self-floating composite foam reveals continuous vapors generation at a rate of 1.52 kg m−2 h−1 under one 1 kW m−2 and profound evaporating efficiency (95%) without heat losses that dissipates in its surroundings. Indeed, long-term evaporation experiments reveal the negligible disparity in continuous evaporation rate (33.84 kg m−2/8.3 h) receiving two sun solar intensity, and ensures the stability of the device under intense seawater conditions synchronized with excellent salt rejection potential. More importantly, Raman spectroscopy investigation validates the orange dye rejection via Fe2O3@PPy solar evaporator. The combined advantages of high efficiency, self-floating capability, multimedia rejection, low cost, and this configuration are promising for producing large-scale solar steam generating systems appropriate for commercial clean water yield due to their scalable fabrication.","lang":"eng"}],"date_created":"2022-01-02T23:01:34Z","has_accepted_license":"1","alternative_title":["Hybrid and Composite Crystalline Materials"],"publisher":"MDPI","language":[{"iso":"eng"}],"intvolume":"        11","author":[{"full_name":"Lu, Yuzheng","last_name":"Lu","first_name":"Yuzheng"},{"full_name":"Arshad, Naila","first_name":"Naila","last_name":"Arshad"},{"full_name":"Irshad, Muhammad Sultan","first_name":"Muhammad Sultan","last_name":"Irshad"},{"full_name":"Ahmed, Iftikhar","last_name":"Ahmed","first_name":"Iftikhar"},{"full_name":"Ahmad, Shafiq","first_name":"Shafiq","last_name":"Ahmad"},{"last_name":"Alshahrani","first_name":"Lina Abdullah","full_name":"Alshahrani, Lina Abdullah"},{"last_name":"Yousaf","first_name":"Muhammad","full_name":"Yousaf, Muhammad"},{"last_name":"Sayed","first_name":"Abdelaty Edrees","full_name":"Sayed, Abdelaty Edrees"},{"last_name":"Nauman","orcid":"0000-0002-2111-4846","first_name":"Muhammad","full_name":"Nauman, Muhammad","id":"32c21954-2022-11eb-9d5f-af9f93c24e71"}],"title":"Fe2O3 nanoparticles deposited over self-floating facial sponge for facile interfacial seawater solar desalination","date_updated":"2023-08-17T06:31:20Z","day":"03","acknowledgement":"The authors extend their appreciation to King Saud University for funding this work through Researchers Supporting Project number (RSP-2021/387), King Saud University, Riyadh, Saudi Arabia.","article_type":"original","publication_identifier":{"eissn":["2073-4352"]},"file_date_updated":"2022-01-03T09:46:53Z","external_id":{"isi":["000736602200001"]},"_id":"10586","oa_version":"Published Version","quality_controlled":"1","department":[{"_id":"KiMo"}],"scopus_import":"1","volume":11,"tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"citation":{"ieee":"Y. Lu <i>et al.</i>, “Fe2O3 nanoparticles deposited over self-floating facial sponge for facile interfacial seawater solar desalination,” <i>Crystals</i>, vol. 11, no. 12. MDPI, 2021.","mla":"Lu, Yuzheng, et al. “Fe2O3 Nanoparticles Deposited over Self-Floating Facial Sponge for Facile Interfacial Seawater Solar Desalination.” <i>Crystals</i>, vol. 11, no. 12, 1509, MDPI, 2021, doi:<a href=\"https://doi.org/10.3390/cryst11121509\">10.3390/cryst11121509</a>.","ama":"Lu Y, Arshad N, Irshad MS, et al. Fe2O3 nanoparticles deposited over self-floating facial sponge for facile interfacial seawater solar desalination. <i>Crystals</i>. 2021;11(12). doi:<a href=\"https://doi.org/10.3390/cryst11121509\">10.3390/cryst11121509</a>","ista":"Lu Y, Arshad N, Irshad MS, Ahmed I, Ahmad S, Alshahrani LA, Yousaf M, Sayed AE, Nauman M. 2021. Fe2O3 nanoparticles deposited over self-floating facial sponge for facile interfacial seawater solar desalination. Crystals. 11(12), 1509.","apa":"Lu, Y., Arshad, N., Irshad, M. S., Ahmed, I., Ahmad, S., Alshahrani, L. A., … Nauman, M. (2021). Fe2O3 nanoparticles deposited over self-floating facial sponge for facile interfacial seawater solar desalination. <i>Crystals</i>. MDPI. <a href=\"https://doi.org/10.3390/cryst11121509\">https://doi.org/10.3390/cryst11121509</a>","chicago":"Lu, Yuzheng, Naila Arshad, Muhammad Sultan Irshad, Iftikhar Ahmed, Shafiq Ahmad, Lina Abdullah Alshahrani, Muhammad Yousaf, Abdelaty Edrees Sayed, and Muhammad Nauman. “Fe2O3 Nanoparticles Deposited over Self-Floating Facial Sponge for Facile Interfacial Seawater Solar Desalination.” <i>Crystals</i>. MDPI, 2021. <a href=\"https://doi.org/10.3390/cryst11121509\">https://doi.org/10.3390/cryst11121509</a>.","short":"Y. Lu, N. Arshad, M.S. Irshad, I. Ahmed, S. Ahmad, L.A. Alshahrani, M. Yousaf, A.E. Sayed, M. Nauman, Crystals 11 (2021)."},"doi":"10.3390/cryst11121509"},{"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2106.02356"}],"quality_controlled":"1","oa_version":"Preprint","_id":"10593","volume":35,"department":[{"_id":"MaMo"}],"scopus_import":"1","citation":{"short":"M. Mondelli, R. Venkataramanan, in:, 35th Conference on Neural Information Processing Systems, Neural Information Processing Systems Foundation, 2021, pp. 29616–29629.","chicago":"Mondelli, Marco, and Ramji Venkataramanan. “PCA Initialization for Approximate Message Passing in Rotationally Invariant Models.” In <i>35th Conference on Neural Information Processing Systems</i>, 35:29616–29. Neural Information Processing Systems Foundation, 2021.","apa":"Mondelli, M., &#38; Venkataramanan, R. (2021). PCA initialization for approximate message passing in rotationally invariant models. In <i>35th Conference on Neural Information Processing Systems</i> (Vol. 35, pp. 29616–29629). Virtual: Neural Information Processing Systems Foundation.","ista":"Mondelli M, Venkataramanan R. 2021. PCA initialization for approximate message passing in rotationally invariant models. 35th Conference on Neural Information Processing Systems. NeurIPS: Neural Information Processing Systems vol. 35, 29616–29629.","ama":"Mondelli M, Venkataramanan R. PCA initialization for approximate message passing in rotationally invariant models. In: <i>35th Conference on Neural Information Processing Systems</i>. Vol 35. Neural Information Processing Systems Foundation; 2021:29616-29629.","mla":"Mondelli, Marco, and Ramji Venkataramanan. “PCA Initialization for Approximate Message Passing in Rotationally Invariant Models.” <i>35th Conference on Neural Information Processing Systems</i>, vol. 35, Neural Information Processing Systems Foundation, 2021, pp. 29616–29.","ieee":"M. Mondelli and R. Venkataramanan, “PCA initialization for approximate message passing in rotationally invariant models,” in <i>35th Conference on Neural Information Processing Systems</i>, Virtual, 2021, vol. 35, pp. 29616–29629."},"project":[{"name":"Prix Lopez-Loretta 2019 - Marco Mondelli","_id":"059876FA-7A3F-11EA-A408-12923DDC885E"}],"author":[{"full_name":"Mondelli, Marco","id":"27EB676C-8706-11E9-9510-7717E6697425","first_name":"Marco","last_name":"Mondelli","orcid":"0000-0002-3242-7020"},{"full_name":"Venkataramanan, Ramji","last_name":"Venkataramanan","first_name":"Ramji"}],"date_updated":"2025-04-15T07:50:11Z","title":"PCA initialization for approximate message passing in rotationally invariant models","arxiv":1,"acknowledgement":"M. Mondelli would like to thank László Erdős for helpful discussions. M. Mondelli was partially supported by the 2019 Lopez-Loreta Prize. R. Venkataramanan was partially supported by the Alan Turing Institute under the EPSRC grant EP/N510129/1.\r\n","publication_identifier":{"issn":["1049-5258"],"isbn":["9781713845393"]},"day":"01","external_id":{"arxiv":["2106.02356"]},"conference":{"name":"NeurIPS: Neural Information Processing Systems","location":"Virtual","start_date":"2021-12-06","end_date":"2021-12-14"},"publication":"35th Conference on Neural Information Processing Systems","status":"public","corr_author":"1","month":"12","publisher":"Neural Information Processing Systems Foundation","abstract":[{"text":"We study the problem of estimating a rank-$1$ signal in the presence of rotationally invariant noise-a class of perturbations more general than Gaussian noise. Principal Component Analysis (PCA) provides a natural estimator, and sharp results on its performance have been obtained in the high-dimensional regime. Recently, an Approximate Message Passing (AMP) algorithm has been proposed as an alternative estimator with the potential to improve the accuracy of PCA. However, the existing analysis of AMP requires an initialization that is both correlated with the signal and independent of the noise, which is often unrealistic in practice. In this work, we combine the two methods, and propose to initialize AMP with PCA. Our main result is a rigorous asymptotic characterization of the performance of this estimator. Both the AMP algorithm and its analysis differ from those previously derived in the Gaussian setting: at every iteration, our AMP algorithm requires a specific term to account for PCA initialization, while in the Gaussian case, PCA initialization affects only the first iteration of AMP. The proof is based on a two-phase artificial AMP that first approximates the PCA estimator and then mimics the true AMP. Our numerical simulations show an excellent agreement between AMP results and theoretical predictions, and suggest an interesting open direction on achieving Bayes-optimal performance.","lang":"eng"}],"date_created":"2022-01-03T10:50:02Z","intvolume":"        35","language":[{"iso":"eng"}],"article_processing_charge":"No","year":"2021","publication_status":"published","date_published":"2021-12-01T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","page":"29616-29629","oa":1,"type":"conference"},{"title":"When are solutions connected in deep networks?","date_updated":"2025-04-15T07:50:11Z","author":[{"full_name":"Nguyen, Quynh","last_name":"Nguyen","first_name":"Quynh"},{"full_name":"Bréchet, Pierre","first_name":"Pierre","last_name":"Bréchet"},{"orcid":"0000-0002-3242-7020","last_name":"Mondelli","first_name":"Marco","id":"27EB676C-8706-11E9-9510-7717E6697425","full_name":"Mondelli, Marco"}],"conference":{"start_date":"2021-12-06","location":"Virtual","name":"35th Conference on Neural Information Processing Systems","end_date":"2021-12-14"},"external_id":{"arxiv":["2102.09671"]},"day":"01","acknowledgement":"MM was partially supported by the 2019 Lopez-Loreta Prize. QN and PB acknowledge support from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement no 757983).","publication_identifier":{"isbn":["9781713845393"],"issn":["1049-5258"]},"arxiv":1,"_id":"10594","oa_version":"Preprint","quality_controlled":"1","main_file_link":[{"url":"https://arxiv.org/abs/2102.09671","open_access":"1"}],"project":[{"name":"Prix Lopez-Loretta 2019 - Marco Mondelli","_id":"059876FA-7A3F-11EA-A408-12923DDC885E"}],"citation":{"short":"Q. Nguyen, P. Bréchet, M. Mondelli, in:, 35th Conference on Neural Information Processing Systems, Neural Information Processing Systems Foundation, 2021.","chicago":"Nguyen, Quynh, Pierre Bréchet, and Marco Mondelli. “When Are Solutions Connected in Deep Networks?” In <i>35th Conference on Neural Information Processing Systems</i>, Vol. 35. Neural Information Processing Systems Foundation, 2021.","ama":"Nguyen Q, Bréchet P, Mondelli M. When are solutions connected in deep networks? In: <i>35th Conference on Neural Information Processing Systems</i>. Vol 35. Neural Information Processing Systems Foundation; 2021.","ista":"Nguyen Q, Bréchet P, Mondelli M. 2021. When are solutions connected in deep networks? 35th Conference on Neural Information Processing Systems. 35th Conference on Neural Information Processing Systems vol. 35.","apa":"Nguyen, Q., Bréchet, P., &#38; Mondelli, M. (2021). When are solutions connected in deep networks? In <i>35th Conference on Neural Information Processing Systems</i> (Vol. 35). Virtual: Neural Information Processing Systems Foundation.","mla":"Nguyen, Quynh, et al. “When Are Solutions Connected in Deep Networks?” <i>35th Conference on Neural Information Processing Systems</i>, vol. 35, Neural Information Processing Systems Foundation, 2021.","ieee":"Q. Nguyen, P. Bréchet, and M. Mondelli, “When are solutions connected in deep networks?,” in <i>35th Conference on Neural Information Processing Systems</i>, Virtual, 2021, vol. 35."},"department":[{"_id":"MaMo"}],"volume":35,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2021-12-01T00:00:00Z","publication_status":"published","year":"2021","article_processing_charge":"No","type":"conference","oa":1,"publication":"35th Conference on Neural Information Processing Systems","month":"12","status":"public","corr_author":"1","language":[{"iso":"eng"}],"intvolume":"        35","date_created":"2022-01-03T10:56:20Z","abstract":[{"lang":"eng","text":"The question of how and why the phenomenon of mode connectivity occurs in training deep neural networks has gained remarkable attention in the research community. From a theoretical perspective, two possible explanations have been proposed: (i) the loss function has connected sublevel sets, and (ii) the solutions found by stochastic gradient descent are dropout stable. While these explanations provide insights into the phenomenon, their assumptions are not always satisfied in practice. In particular, the first approach requires the network to have one layer with order of N neurons (N being the number of training samples), while the second one requires the loss to be almost invariant after removing half of the neurons at each layer (up to some rescaling of the remaining ones). In this work, we improve both conditions by exploiting the quality of the features at every intermediate layer together with a milder over-parameterization condition. More specifically, we show that: (i) under generic assumptions on the features of intermediate layers, it suffices that the last two hidden layers have order of N−−√ neurons, and (ii) if subsets of features at each layer are linearly separable, then no over-parameterization is needed to show the connectivity. Our experiments confirm that the proposed condition ensures the connectivity of solutions found by stochastic gradient descent, even in settings where the previous requirements do not hold."}],"publisher":"Neural Information Processing Systems Foundation"},{"publisher":"ML Research Press","alternative_title":["Proceedings of Machine Learning Research"],"date_created":"2022-01-03T10:57:49Z","abstract":[{"text":"A recent line of work has analyzed the theoretical properties of deep neural networks via the Neural Tangent Kernel (NTK). In particular, the smallest eigenvalue of the NTK has been related to the memorization capacity, the global convergence of gradient descent algorithms and the generalization of deep nets. However, existing results either provide bounds in the two-layer setting or assume that the spectrum of the NTK matrices is bounded away from 0 for multi-layer networks. In this paper, we provide tight bounds on the smallest eigenvalue of NTK matrices for deep ReLU nets, both in the limiting case of infinite widths and for finite widths. In the finite-width setting, the network architectures we consider are fairly general: we require the existence of a wide layer with roughly order of $N$ neurons, $N$ being the number of data samples; and the scaling of the remaining layer widths is arbitrary (up to logarithmic factors). To obtain our results, we analyze various quantities of independent interest: we give lower bounds on the smallest singular value of hidden feature matrices, and upper bounds on the Lipschitz constant of input-output feature maps.","lang":"eng"}],"intvolume":"       139","language":[{"iso":"eng"}],"publication":"Proceedings of the 38th International Conference on Machine Learning","month":"01","status":"public","ddc":["000"],"page":"8119-8129","editor":[{"first_name":"Marina","last_name":"Meila","full_name":"Meila, Marina"},{"full_name":"Zhang, Tong","first_name":"Tong","last_name":"Zhang"}],"oa":1,"type":"conference","article_processing_charge":"No","year":"2021","publication_status":"published","date_published":"2021-01-01T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","volume":139,"department":[{"_id":"MaMo"}],"citation":{"ama":"Nguyen Q, Mondelli M, Montufar GF. Tight bounds on the smallest eigenvalue of the neural tangent kernel for deep ReLU networks. In: Meila M, Zhang T, eds. <i>Proceedings of the 38th International Conference on Machine Learning</i>. Vol 139. ML Research Press; 2021:8119-8129.","apa":"Nguyen, Q., Mondelli, M., &#38; Montufar, G. F. (2021). Tight bounds on the smallest eigenvalue of the neural tangent kernel for deep ReLU networks. In M. Meila &#38; T. Zhang (Eds.), <i>Proceedings of the 38th International Conference on Machine Learning</i> (Vol. 139, pp. 8119–8129). Virtual: ML Research Press.","ista":"Nguyen Q, Mondelli M, Montufar GF. 2021. Tight bounds on the smallest eigenvalue of the neural tangent kernel for deep ReLU networks. Proceedings of the 38th International Conference on Machine Learning. ICML: International Conference on Machine Learning, Proceedings of Machine Learning Research, vol. 139, 8119–8129.","mla":"Nguyen, Quynh, et al. “Tight Bounds on the Smallest Eigenvalue of the Neural Tangent Kernel for Deep ReLU Networks.” <i>Proceedings of the 38th International Conference on Machine Learning</i>, edited by Marina Meila and Tong Zhang, vol. 139, ML Research Press, 2021, pp. 8119–29.","ieee":"Q. Nguyen, M. Mondelli, and G. F. Montufar, “Tight bounds on the smallest eigenvalue of the neural tangent kernel for deep ReLU networks,” in <i>Proceedings of the 38th International Conference on Machine Learning</i>, Virtual, 2021, vol. 139, pp. 8119–8129.","short":"Q. Nguyen, M. Mondelli, G.F. Montufar, in:, M. Meila, T. Zhang (Eds.), Proceedings of the 38th International Conference on Machine Learning, ML Research Press, 2021, pp. 8119–8129.","chicago":"Nguyen, Quynh, Marco Mondelli, and Guido F Montufar. “Tight Bounds on the Smallest Eigenvalue of the Neural Tangent Kernel for Deep ReLU Networks.” In <i>Proceedings of the 38th International Conference on Machine Learning</i>, edited by Marina Meila and Tong Zhang, 139:8119–29. ML Research Press, 2021."},"project":[{"name":"Prix Lopez-Loretta 2019 - Marco Mondelli","_id":"059876FA-7A3F-11EA-A408-12923DDC885E"}],"main_file_link":[{"url":"http://proceedings.mlr.press/v139/nguyen21g.html","open_access":"1"}],"quality_controlled":"1","oa_version":"Published Version","_id":"10595","arxiv":1,"acknowledgement":"The authors would like to thank the anonymous reviewers for their helpful comments. MM was partially supported\r\nby the 2019 Lopez-Loreta Prize. QN and GM acknowledge support from the European Research Council (ERC) under\r\nthe European Union’s Horizon 2020 research and innovation programme (grant agreement no 757983).","day":"01","external_id":{"arxiv":["2012.11654"]},"conference":{"start_date":"2021-07-18","location":"Virtual","name":"ICML: International Conference on Machine Learning","end_date":"2021-07-24"},"author":[{"full_name":"Nguyen, Quynh","first_name":"Quynh","last_name":"Nguyen"},{"orcid":"0000-0002-3242-7020","last_name":"Mondelli","first_name":"Marco","id":"27EB676C-8706-11E9-9510-7717E6697425","full_name":"Mondelli, Marco"},{"full_name":"Montufar, Guido F","last_name":"Montufar","first_name":"Guido F"}],"date_updated":"2026-06-18T08:43:54Z","title":"Tight bounds on the smallest eigenvalue of the neural tangent kernel for deep ReLU networks"}]