[{"quality_controlled":"1","abstract":[{"text":"Decentralized optimization is emerging as a viable alternative for scalable distributed machine learning, but also introduces new challenges in terms of synchronization costs. To this end, several communication-reduction techniques, such as non-blocking communication, quantization, and local steps, have been explored in the decentralized setting. Due to the complexity of analyzing optimization in such a relaxed setting, this line of work often assumes \\emph{global} communication rounds, which require additional synchronization. In this paper, we consider decentralized optimization in the simpler, but harder to analyze, \\emph{asynchronous gossip} model, in which communication occurs in discrete, randomly chosen pairings among nodes. Perhaps surprisingly, we show that a variant of SGD called \\emph{SwarmSGD} still converges in this setting, even if \\emph{non-blocking communication}, \\emph{quantization}, and \\emph{local steps} are all applied \\emph{in conjunction}, and even if the node data distributions and underlying graph topology are both \\emph{heterogenous}. Our analysis is based on a new connection with multi-dimensional load-balancing processes. We implement this algorithm and deploy it in a super-computing environment, showing that it can outperform previous decentralized methods in terms of end-to-end training time, and that it can even rival carefully-tuned large-batch SGD for certain tasks.","lang":"eng"}],"publication_status":"published","language":[{"iso":"eng"}],"status":"public","type":"conference","citation":{"ieee":"G. Nadiradze, A. Sabour, P. Davies, S. Li, and D.-A. Alistarh, “Asynchronous decentralized SGD with quantized and local updates,” in <i>35th Conference on Neural Information Processing Systems</i>, Sydney, Australia, 2021.","short":"G. Nadiradze, A. Sabour, P. Davies, S. Li, D.-A. Alistarh, in:, 35th Conference on Neural Information Processing Systems, Neural Information Processing Systems Foundation, 2021.","apa":"Nadiradze, G., Sabour, A., Davies, P., Li, S., &#38; Alistarh, D.-A. (2021). Asynchronous decentralized SGD with quantized and local updates. In <i>35th Conference on Neural Information Processing Systems</i>. Sydney, Australia: Neural Information Processing Systems Foundation.","mla":"Nadiradze, Giorgi, et al. “Asynchronous Decentralized SGD with Quantized and Local Updates.” <i>35th Conference on Neural Information Processing Systems</i>, Neural Information Processing Systems Foundation, 2021.","ista":"Nadiradze G, Sabour A, Davies P, Li S, Alistarh D-A. 2021. Asynchronous decentralized SGD with quantized and local updates. 35th Conference on Neural Information Processing Systems. NeurIPS: Neural Information Processing Systems.","ama":"Nadiradze G, Sabour A, Davies P, Li S, Alistarh D-A. Asynchronous decentralized SGD with quantized and local updates. In: <i>35th Conference on Neural Information Processing Systems</i>. Neural Information Processing Systems Foundation; 2021.","chicago":"Nadiradze, Giorgi, Amirmojtaba Sabour, Peter Davies, Shigang Li, and Dan-Adrian Alistarh. “Asynchronous Decentralized SGD with Quantized and Local Updates.” In <i>35th Conference on Neural Information Processing Systems</i>. Neural Information Processing Systems Foundation, 2021."},"author":[{"last_name":"Nadiradze","full_name":"Nadiradze, Giorgi","orcid":"0000-0001-5634-0731","first_name":"Giorgi","id":"3279A00C-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Amirmojtaba","id":"bcc145fd-e77f-11ea-ae8b-80d661dbff67","last_name":"Sabour","full_name":"Sabour, Amirmojtaba"},{"id":"11396234-BB50-11E9-B24C-90FCE5697425","first_name":"Peter","last_name":"Davies","orcid":"0000-0002-5646-9524","full_name":"Davies, Peter"},{"first_name":"Shigang","full_name":"Li, Shigang","last_name":"Li"},{"first_name":"Dan-Adrian","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","last_name":"Alistarh","full_name":"Alistarh, Dan-Adrian","orcid":"0000-0003-3650-940X"}],"conference":{"end_date":"2021-12-14","location":"Sydney, Australia","start_date":"2021-12-06","name":"NeurIPS: Neural Information Processing Systems"},"year":"2021","department":[{"_id":"DaAl"}],"publisher":"Neural Information Processing Systems Foundation","day":"01","arxiv":1,"oa_version":"Published Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","acknowledgement":"We gratefully acknowledge funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement No 805223 ScaleML). PD partly conducted this work while at IST Austria and was supported by the European Union’s Horizon 2020 programme under the Marie Skłodowska-Curie grant agreement No. 754411. SL was funded in part by European Research Council (ERC) under the European Union’s Horizon 2020 programme (grant agreement DAPP, No. 678880, and EPiGRAM-HS, No. 801039).\r\n","oa":1,"related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"10429"}]},"main_file_link":[{"url":"https://papers.nips.cc/paper/2021/hash/362c99307cdc3f2d8b410652386a9dd1-Abstract.html","open_access":"1"}],"date_published":"2021-12-01T00:00:00Z","article_processing_charge":"No","ec_funded":1,"date_updated":"2023-10-17T11:48:56Z","title":"Asynchronous decentralized SGD with quantized and local updates","month":"12","project":[{"_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411","call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships"},{"name":"Elastic Coordination for Scalable Machine Learning","grant_number":"805223","_id":"268A44D6-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"_id":"10435","date_created":"2021-12-09T10:59:12Z","external_id":{"arxiv":["1910.12308"]},"publication":"35th Conference on Neural Information Processing Systems"},{"author":[{"id":"4AF46FD6-F248-11E8-B48F-1D18A9856A87","first_name":"Areg","full_name":"Ghazaryan, Areg","orcid":"0000-0001-9666-3543","last_name":"Ghazaryan"},{"first_name":"Tobias","full_name":"Holder, Tobias","last_name":"Holder"},{"last_name":"Serbyn","orcid":"0000-0002-2399-5827","full_name":"Serbyn, Maksym","first_name":"Maksym","id":"47809E7E-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Berg","full_name":"Berg, Erez","first_name":"Erez"}],"isi":1,"year":"2021","publication_identifier":{"eissn":["1079-7114"],"issn":["0031-9007"]},"department":[{"_id":"MaSe"}],"day":"09","publisher":"American Physical Society","oa_version":"Preprint","arxiv":1,"doi":"10.1103/physrevlett.127.247001","quality_controlled":"1","language":[{"iso":"eng"}],"status":"public","publication_status":"published","abstract":[{"lang":"eng","text":"We show that in a two-dimensional electron gas with an annular Fermi surface, long-range Coulomb interactions can lead to unconventional superconductivity by the Kohn-Luttinger mechanism. Superconductivity is strongly enhanced when the inner and outer Fermi surfaces are close to each other. The most prevalent state has chiral p-wave symmetry, but d-wave and extended s-wave pairing are also possible. We discuss these results in the context of rhombohedral trilayer graphene, where superconductivity was recently discovered in regimes where the normal state has an annular Fermi surface. Using realistic parameters, our mechanism can account for the order of magnitude of Tc, as well as its trends as a function of electron density and perpendicular displacement field. Moreover, it naturally explains some of the outstanding puzzles in this material, that include the weak temperature dependence of the resistivity above Tc, and the proximity of spin singlet superconductivity to the ferromagnetic phase."}],"article_type":"original","type":"journal_article","citation":{"ieee":"A. Ghazaryan, T. Holder, M. Serbyn, and E. Berg, “Unconventional superconductivity in systems with annular Fermi surfaces: Application to rhombohedral trilayer graphene,” <i>Physical Review Letters</i>, vol. 127, no. 24. American Physical Society, 2021.","apa":"Ghazaryan, A., Holder, T., Serbyn, M., &#38; Berg, E. (2021). Unconventional superconductivity in systems with annular Fermi surfaces: Application to rhombohedral trilayer graphene. <i>Physical Review Letters</i>. American Physical Society. <a href=\"https://doi.org/10.1103/physrevlett.127.247001\">https://doi.org/10.1103/physrevlett.127.247001</a>","short":"A. Ghazaryan, T. Holder, M. Serbyn, E. Berg, Physical Review Letters 127 (2021).","mla":"Ghazaryan, Areg, et al. “Unconventional Superconductivity in Systems with Annular Fermi Surfaces: Application to Rhombohedral Trilayer Graphene.” <i>Physical Review Letters</i>, vol. 127, no. 24, 247001, American Physical Society, 2021, doi:<a href=\"https://doi.org/10.1103/physrevlett.127.247001\">10.1103/physrevlett.127.247001</a>.","ista":"Ghazaryan A, Holder T, Serbyn M, Berg E. 2021. Unconventional superconductivity in systems with annular Fermi surfaces: Application to rhombohedral trilayer graphene. Physical Review Letters. 127(24), 247001.","chicago":"Ghazaryan, Areg, Tobias Holder, Maksym Serbyn, and Erez Berg. “Unconventional Superconductivity in Systems with Annular Fermi Surfaces: Application to Rhombohedral Trilayer Graphene.” <i>Physical Review Letters</i>. American Physical Society, 2021. <a href=\"https://doi.org/10.1103/physrevlett.127.247001\">https://doi.org/10.1103/physrevlett.127.247001</a>.","ama":"Ghazaryan A, Holder T, Serbyn M, Berg E. Unconventional superconductivity in systems with annular Fermi surfaces: Application to rhombohedral trilayer graphene. <i>Physical Review Letters</i>. 2021;127(24). doi:<a href=\"https://doi.org/10.1103/physrevlett.127.247001\">10.1103/physrevlett.127.247001</a>"},"ec_funded":1,"date_published":"2021-12-09T00:00:00Z","article_processing_charge":"No","keyword":["general physics and astronomy"],"month":"12","date_updated":"2023-08-14T13:19:13Z","title":"Unconventional superconductivity in systems with annular Fermi surfaces: Application to rhombohedral trilayer graphene","date_created":"2021-12-10T07:51:33Z","external_id":{"isi":["000923819400004"],"arxiv":["2109.00011"]},"_id":"10527","project":[{"name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"publication":"Physical Review Letters","issue":"24","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","acknowledgement":"We thank Yang-Zhi Chou, Andrey Chubukov, Johannes Hofmann, Steve Kivelson, Sri Raghu, and Sankar das Sarma, Jay Sau, Fengcheng Wu, and Andrea Young for many stimulating discussions and for their comments on the manuscript. E.B. thanks S. Chatterjee, T. Wang, and M. Zaletel for a collaboration on a related topic. A.G. acknowledges support by the European Unions Horizon 2020 research and innovation program under the Marie Sklodowska-Curie Grant Agreement No. 754411. E.B. and T.H. were supported by the European Research Council (ERC) under grant HQMAT (Grant Agreement No. 817799), by the Israel-USA Binational Science Foundation (BSF), and by a Research grant from Irving and Cherna Moskowitz.","intvolume":"       127","oa":1,"article_number":"247001","volume":127,"related_material":{"link":[{"url":"https://ist.ac.at/en/news/resolving-the-puzzles-of-graphene-superconductivity/","description":"News on IST Webpage","relation":"press_release"}]},"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2109.00011"}],"scopus_import":"1"},{"quality_controlled":"1","language":[{"iso":"eng"}],"pmid":1,"has_accepted_license":"1","status":"public","publication_status":"published","abstract":[{"lang":"eng","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."}],"article_type":"original","ddc":["570"],"citation":{"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.","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>","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>.","ista":"Choi J, Lyons DB, Zilberman D. 2021. Histone H1 prevents non-CG methylation-mediated small RNA biogenesis in Arabidopsis heterochromatin. eLife. 10, e72676.","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>","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>."},"type":"journal_article","file":[{"file_id":"11384","creator":"dernst","date_created":"2022-05-16T10:42:22Z","checksum":"22ed4c55fb550f6da02ae55c359be651","relation":"main_file","date_updated":"2022-05-16T10:42:22Z","content_type":"application/pdf","file_size":2715200,"file_name":"2021_eLife_Choi.pdf","success":1,"access_level":"open_access"}],"isi":1,"author":[{"first_name":"Jaemyung","full_name":"Choi, Jaemyung","last_name":"Choi"},{"first_name":"David B","last_name":"Lyons","full_name":"Lyons, David B"},{"full_name":"Zilberman, Daniel","orcid":"0000-0002-0123-8649","last_name":"Zilberman","first_name":"Daniel","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1"}],"year":"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"},"department":[{"_id":"DaZi"}],"publication_identifier":{"issn":["2050-084X"]},"day":"01","publisher":"eLife Sciences Publications","oa_version":"Published Version","doi":"10.7554/elife.72676","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","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.","intvolume":"        10","oa":1,"article_number":"e72676","volume":10,"scopus_import":"1","license":"https://creativecommons.org/licenses/by/4.0/","ec_funded":1,"date_published":"2021-12-01T00:00:00Z","article_processing_charge":"No","keyword":["genetics and molecular biology"],"month":"12","date_updated":"2023-08-17T06:21:08Z","title":"Histone H1 prevents non-CG methylation-mediated small RNA biogenesis in Arabidopsis heterochromatin","date_created":"2021-12-10T13:12:08Z","external_id":{"pmid":["34850679"],"isi":["000754832000001"]},"_id":"10533","project":[{"name":"Quantitative analysis of DNA methylation maintenance with chromatin","_id":"62935a00-2b32-11ec-9570-eff30fa39068","grant_number":"725746","call_identifier":"H2020"}],"file_date_updated":"2022-05-16T10:42:22Z","publication":"eLife"},{"scopus_import":"1","intvolume":"         9","oa":1,"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","issue":"45","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).","volume":9,"external_id":{"isi":["000688135700001"]},"date_created":"2021-12-12T23:01:27Z","_id":"10534","page":"16217-16225","publication":"Journal of Materials Chemistry C","file_date_updated":"2021-12-13T09:24:42Z","article_processing_charge":"No","date_published":"2021-12-07T00:00:00Z","month":"12","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","article_type":"original","ddc":["540"],"type":"journal_article","citation":{"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>.","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.","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>.","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>","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.","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.","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>"},"file":[{"file_id":"10538","date_created":"2021-12-13T09:24:42Z","creator":"cchlebak","relation":"main_file","checksum":"6b73c214ce54a6894a5854b4364413d7","content_type":"application/pdf","date_updated":"2021-12-13T09:24:42Z","file_size":4979390,"file_name":"2021_JMaterChemC_Dong.pdf","success":1,"access_level":"open_access"}],"quality_controlled":"1","status":"public","has_accepted_license":"1","language":[{"iso":"eng"}],"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."}],"publication_status":"published","day":"07","publisher":"Royal Society of Chemistry","oa_version":"Published Version","doi":"10.1039/d1tc02753k","year":"2021","isi":1,"author":[{"first_name":"Jingjin","full_name":"Dong, Jingjin","last_name":"Dong"},{"full_name":"Sami, Selim","last_name":"Sami","first_name":"Selim"},{"full_name":"Balazs, Daniel","orcid":"0000-0001-7597-043X","last_name":"Balazs","first_name":"Daniel","id":"302BADF6-85FC-11EA-9E3B-B9493DDC885E"},{"first_name":"Riccardo","full_name":"Alessandri, Riccardo","last_name":"Alessandri"},{"first_name":"Fatimeh","full_name":"Jahani, Fatimeh","last_name":"Jahani"},{"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.","last_name":"Havenith","first_name":"Remco W.A."},{"first_name":"Jan C.","full_name":"Hummelen, Jan C.","last_name":"Hummelen"},{"last_name":"Loi","full_name":"Loi, Maria A.","first_name":"Maria A."},{"last_name":"Portale","full_name":"Portale, Giuseppe","first_name":"Giuseppe"}],"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"},"publication_identifier":{"eissn":["2050-7526"],"issn":["2050-7534"]},"department":[{"_id":"MaIb"}]},{"volume":17,"article_number":"e1009661","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.","issue":"12","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa":1,"intvolume":"        17","scopus_import":"1","date_updated":"2022-08-01T10:48:04Z","title":"Dynamic maximum entropy provides accurate approximation of structured population dynamics","month":"12","date_published":"2021-12-01T00:00:00Z","article_processing_charge":"No","file_date_updated":"2022-05-16T08:53:11Z","publication":"PLoS Computational Biology","_id":"10535","date_created":"2021-12-12T23:01:27Z","external_id":{"pmid":["34851948"],"arxiv":["2102.03669"]},"abstract":[{"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.","lang":"eng"}],"publication_status":"published","language":[{"iso":"eng"}],"has_accepted_license":"1","status":"public","pmid":1,"quality_controlled":"1","file":[{"creator":"dernst","date_created":"2022-05-16T08:53:11Z","file_id":"11383","file_name":"2021_PLOsComBio_Bodova.pdf","access_level":"open_access","success":1,"checksum":"dcd185d4f7e0acee25edf1d6537f447e","relation":"main_file","file_size":2299486,"content_type":"application/pdf","date_updated":"2022-05-16T08:53:11Z"}],"type":"journal_article","citation":{"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>.","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>.","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.","short":"K. Bodova, E. Szep, N.H. Barton, PLoS Computational Biology 17 (2021).","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>"},"acknowledged_ssus":[{"_id":"ScienComp"}],"ddc":["570"],"article_type":"original","publication_identifier":{"issn":["1553-734X"],"eissn":["1553-7358"]},"department":[{"_id":"NiBa"},{"_id":"GaTk"}],"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"},"author":[{"first_name":"Katarína","id":"2BA24EA0-F248-11E8-B48F-1D18A9856A87","last_name":"Bod'ová","orcid":"0000-0002-7214-0171","full_name":"Bod'ová, Katarína"},{"first_name":"Eniko","id":"485BB5A4-F248-11E8-B48F-1D18A9856A87","full_name":"Szep, Eniko","last_name":"Szep"},{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H","full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240","last_name":"Barton"}],"year":"2021","doi":"10.1371/journal.pcbi.1009661","oa_version":"Published Version","arxiv":1,"publisher":"Public Library of Science","day":"01"},{"file":[{"creator":"alisjak","date_created":"2021-12-13T13:32:37Z","file_id":"10539","file_name":"2021_Frontiers_Stefanescu.pdf","access_level":"open_access","success":1,"checksum":"56cbac80e6891ce750511a30161b7792","relation":"main_file","file_size":9245199,"content_type":"application/pdf","date_updated":"2021-12-13T13:32:37Z"}],"type":"journal_article","citation":{"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>","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>.","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>.","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.","short":"C. Stefanescu, M. Van Gogh, M. Roblek, M. Heikenwalder, L. Borsig, Frontiers in Oncology 11 (2021).","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>","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."},"ddc":["610"],"article_type":"original","abstract":[{"lang":"eng","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."}],"publication_status":"published","pmid":1,"status":"public","has_accepted_license":"1","language":[{"iso":"eng"}],"quality_controlled":"1","doi":"10.3389/fonc.2021.765151","oa_version":"Published Version","publisher":"Frontiers","day":"18","publication_identifier":{"eissn":["2234-943X"]},"department":[{"_id":"DaSi"}],"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"},"year":"2021","isi":1,"author":[{"first_name":"Cristina","full_name":"Stefanescu, Cristina","last_name":"Stefanescu"},{"last_name":"Van Gogh","full_name":"Van Gogh, Merel","first_name":"Merel"},{"first_name":"Marko","id":"3047D808-F248-11E8-B48F-1D18A9856A87","last_name":"Roblek","orcid":"0000-0001-9588-1389","full_name":"Roblek, Marko"},{"full_name":"Heikenwalder, Mathias","last_name":"Heikenwalder","first_name":"Mathias"},{"last_name":"Borsig","full_name":"Borsig, Lubor","first_name":"Lubor"}],"scopus_import":"1","volume":11,"article_number":"765151","intvolume":"        11","oa":1,"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","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.","publication":"Frontiers in Oncology","file_date_updated":"2021-12-13T13:32:37Z","_id":"10536","external_id":{"pmid":["34868988"],"isi":["000726603400001"]},"date_created":"2021-12-12T23:01:27Z","title":"TGFβ signaling in myeloid cells promotes lung and liver metastasis through different mechanisms","date_updated":"2023-08-17T06:20:32Z","month":"11","article_processing_charge":"No","date_published":"2021-11-18T00:00:00Z"},{"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2103.08224"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","acknowledgement":"NB was supported by Gruppo Nazionale per la Fisica Matematica (GNFM). RS was supported by the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (Grant Agreement No. 694227). PTN was supported by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) under Germany’s Excellence Strategy (EXC-2111-390814868). MP was supported by the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (ERC StG MaMBoQ, Grant Agreement No. 802901). BS was supported by the NCCR SwissMAP, the Swiss National Science Foundation through the Grant “Dynamical and energetic properties of Bose-Einstein condensates,” and the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program through the ERC-AdG CLaQS (Grant Agreement No. 834782).","oa":1,"scopus_import":"1","month":"12","date_updated":"2023-08-17T06:19:14Z","title":"Bosonization of fermionic many-body dynamics","ec_funded":1,"date_published":"2021-12-02T00:00:00Z","article_processing_charge":"No","publication":"Annales Henri Poincaré","date_created":"2021-12-12T23:01:28Z","external_id":{"isi":["000725405700001"],"arxiv":["2103.08224"]},"project":[{"name":"Analysis of quantum many-body systems","call_identifier":"H2020","grant_number":"694227","_id":"25C6DC12-B435-11E9-9278-68D0E5697425"}],"_id":"10537","language":[{"iso":"eng"}],"status":"public","publication_status":"published","abstract":[{"text":"We consider the quantum many-body evolution of a homogeneous Fermi gas in three dimensions in the coupled semiclassical and mean-field scaling regime. We study a class of initial data describing collective particle–hole pair excitations on the Fermi ball. Using a rigorous version of approximate bosonization, we prove that the many-body evolution can be approximated in Fock space norm by a quasi-free bosonic evolution of the collective particle–hole excitations.","lang":"eng"}],"quality_controlled":"1","type":"journal_article","citation":{"mla":"Benedikter, Niels P., et al. “Bosonization of Fermionic Many-Body Dynamics.” <i>Annales Henri Poincaré</i>, Springer Nature, 2021, doi:<a href=\"https://doi.org/10.1007/s00023-021-01136-y\">10.1007/s00023-021-01136-y</a>.","ista":"Benedikter NP, Nam PT, Porta M, Schlein B, Seiringer R. 2021. Bosonization of fermionic many-body dynamics. Annales Henri Poincaré.","chicago":"Benedikter, Niels P, Phan Thành Nam, Marcello Porta, Benjamin Schlein, and Robert Seiringer. “Bosonization of Fermionic Many-Body Dynamics.” <i>Annales Henri Poincaré</i>. Springer Nature, 2021. <a href=\"https://doi.org/10.1007/s00023-021-01136-y\">https://doi.org/10.1007/s00023-021-01136-y</a>.","ama":"Benedikter NP, Nam PT, Porta M, Schlein B, Seiringer R. Bosonization of fermionic many-body dynamics. <i>Annales Henri Poincaré</i>. 2021. doi:<a href=\"https://doi.org/10.1007/s00023-021-01136-y\">10.1007/s00023-021-01136-y</a>","ieee":"N. P. Benedikter, P. T. Nam, M. Porta, B. Schlein, and R. Seiringer, “Bosonization of fermionic many-body dynamics,” <i>Annales Henri Poincaré</i>. Springer Nature, 2021.","short":"N.P. Benedikter, P.T. Nam, M. Porta, B. Schlein, R. Seiringer, Annales Henri Poincaré (2021).","apa":"Benedikter, N. P., Nam, P. T., Porta, M., Schlein, B., &#38; Seiringer, R. (2021). Bosonization of fermionic many-body dynamics. <i>Annales Henri Poincaré</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s00023-021-01136-y\">https://doi.org/10.1007/s00023-021-01136-y</a>"},"article_type":"original","publication_identifier":{"issn":["1424-0637"]},"department":[{"_id":"RoSe"}],"isi":1,"author":[{"first_name":"Niels P","id":"3DE6C32A-F248-11E8-B48F-1D18A9856A87","last_name":"Benedikter","full_name":"Benedikter, Niels P","orcid":"0000-0002-1071-6091"},{"first_name":"Phan Thành","full_name":"Nam, Phan Thành","last_name":"Nam"},{"first_name":"Marcello","last_name":"Porta","full_name":"Porta, Marcello"},{"first_name":"Benjamin","full_name":"Schlein, Benjamin","last_name":"Schlein"},{"id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","first_name":"Robert","full_name":"Seiringer, Robert","orcid":"0000-0002-6781-0521","last_name":"Seiringer"}],"year":"2021","arxiv":1,"oa_version":"Preprint","doi":"10.1007/s00023-021-01136-y","day":"02","publisher":"Springer Nature"},{"oa_version":"Preprint","arxiv":1,"doi":"10.1103/physreva.104.062423","day":"14","publisher":"American Physical Society","department":[{"_id":"MaSe"}],"publication_identifier":{"eissn":["2469-9934"],"issn":["2469-9926"]},"year":"2021","isi":1,"author":[{"last_name":"Medina Ramos","orcid":"0000-0002-5383-2869","full_name":"Medina Ramos, Raimel A","id":"CE680B90-D85A-11E9-B684-C920E6697425","first_name":"Raimel A"},{"first_name":"Maksym","id":"47809E7E-F248-11E8-B48F-1D18A9856A87","last_name":"Serbyn","orcid":"0000-0002-2399-5827","full_name":"Serbyn, Maksym"}],"citation":{"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>.","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.","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>.","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.","short":"R.A. Medina Ramos, M. Serbyn, Physical Review A 104 (2021).","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>"},"type":"journal_article","article_type":"original","status":"public","language":[{"iso":"eng"}],"abstract":[{"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.","lang":"eng"}],"publication_status":"published","quality_controlled":"1","publication":"Physical Review A","external_id":{"isi":["000753659200004"],"arxiv":["2106.06344"]},"date_created":"2021-12-14T20:46:07Z","project":[{"_id":"23841C26-32DE-11EA-91FC-C7463DDC885E","grant_number":"850899","call_identifier":"H2020","name":"Non-Ergodic Quantum Matter: Universality, Dynamics and Control"}],"_id":"10545","month":"12","title":"Duality approach to quantum annealing of the 3-variable exclusive-or satisfiability problem (3-XORSAT)","date_updated":"2023-08-17T06:22:49Z","ec_funded":1,"article_processing_charge":"No","date_published":"2021-12-14T00:00:00Z","main_file_link":[{"url":"https://arxiv.org/abs/2106.06344","open_access":"1"}],"volume":104,"oa":1,"intvolume":"       104","issue":"6","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","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.","article_number":"062423"},{"doi":"10.1007/s00205-021-01686-9","oa_version":"Published Version","arxiv":1,"publisher":"Springer Nature","day":"30","department":[{"_id":"JuFi"}],"publication_identifier":{"issn":["0003-9527"],"eissn":["1432-0673"]},"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"},"year":"2021","author":[{"id":"2C12A0B0-F248-11E8-B48F-1D18A9856A87","first_name":"Julian L","orcid":"0000-0002-0479-558X","full_name":"Fischer, Julian L","last_name":"Fischer"},{"full_name":"Neukamm, Stefan","last_name":"Neukamm","first_name":"Stefan"}],"isi":1,"file":[{"file_name":"2021_ArchRatMechAnalysis_Fischer.pdf","access_level":"open_access","success":1,"checksum":"cc830b739aed83ca2e32c4e0ce266a4c","relation":"main_file","file_size":1640121,"content_type":"application/pdf","date_updated":"2021-12-16T14:58:08Z","date_created":"2021-12-16T14:58:08Z","creator":"cchlebak","file_id":"10558"}],"type":"journal_article","citation":{"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.","short":"J.L. Fischer, S. Neukamm, Archive for Rational Mechanics and Analysis 242 (2021) 343–452.","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>","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>.","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.","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>.","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>"},"ddc":["530"],"article_type":"original","publication_status":"published","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."}],"has_accepted_license":"1","status":"public","language":[{"iso":"eng"}],"quality_controlled":"1","publication":"Archive for Rational Mechanics and Analysis","file_date_updated":"2021-12-16T14:58:08Z","page":"343-452","_id":"10549","external_id":{"arxiv":["1908.02273"],"isi":["000668431200001"]},"date_created":"2021-12-16T12:12:33Z","date_updated":"2023-08-17T06:23:21Z","title":"Optimal homogenization rates in stochastic homogenization of nonlinear uniformly elliptic equations and systems","month":"06","article_processing_charge":"Yes (via OA deal)","keyword":["Mechanical Engineering","Mathematics (miscellaneous)","Analysis"],"date_published":"2021-06-30T00:00:00Z","scopus_import":"1","volume":242,"intvolume":"       242","oa":1,"issue":"1","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.","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8"},{"citation":{"mla":"Kolmogorov, Vladimir, and Thomas Pock. “One-Sided Frank-Wolfe Algorithms for Saddle Problems.” <i>38th International Conference on Machine Learning</i>, 2021.","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.","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.","short":"V. Kolmogorov, T. Pock, in:, 38th International Conference on Machine Learning, 2021."},"type":"conference","language":[{"iso":"eng"}],"status":"public","abstract":[{"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.","lang":"eng"}],"publication_status":"published","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2101.12617"}],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","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":1,"quality_controlled":"1","oa_version":"Preprint","arxiv":1,"publication":"38th International Conference on Machine Learning","date_created":"2021-12-16T12:41:20Z","day":"01","external_id":{"arxiv":["2101.12617"]},"_id":"10552","project":[{"name":"Discrete Optimization in Computer Vision: Theory and Practice","call_identifier":"FP7","_id":"25FBA906-B435-11E9-9278-68D0E5697425","grant_number":"616160"}],"month":"07","title":"One-sided Frank-Wolfe algorithms for saddle problems","date_updated":"2021-12-17T09:06:46Z","department":[{"_id":"VlKo"}],"ec_funded":1,"date_published":"2021-07-01T00:00:00Z","author":[{"full_name":"Kolmogorov, Vladimir","last_name":"Kolmogorov","first_name":"Vladimir","id":"3D50B0BA-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Pock, Thomas","last_name":"Pock","first_name":"Thomas"}],"article_processing_charge":"No","year":"2021","conference":{"name":"ICML: International Conference on Machine Learning","start_date":"2021-07-18","location":"Virtual","end_date":"2021-07-24"}},{"oa_version":"Preprint","arxiv":1,"doi":"10.1145/3465084.3467941","day":"21","publisher":"Association for Computing Machinery","department":[{"_id":"ElKo"}],"publication_identifier":{"isbn":["9-781-4503-8548-0"]},"isi":1,"author":[{"first_name":"Rati","full_name":"Gelashvili, Rati","last_name":"Gelashvili"},{"last_name":"Kokoris Kogias","full_name":"Kokoris Kogias, Eleftherios","id":"f5983044-d7ef-11ea-ac6d-fd1430a26d30","first_name":"Eleftherios"},{"last_name":"Spiegelman","full_name":"Spiegelman, Alexander","first_name":"Alexander"},{"first_name":"Zhuolun","last_name":"Xiang","full_name":"Xiang, Zhuolun"}],"conference":{"name":"PODC: Principles of Distributed Computing","end_date":"2021-07-30","location":"Virtual, Italy","start_date":"2021-07-26"},"year":"2021","type":"conference","citation":{"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>","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>.","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>.","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.","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.","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>","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."},"language":[{"iso":"eng"}],"status":"public","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"}],"publication_status":"published","quality_controlled":"1","page":"187-190","publication":"Proceedings of the 2021 ACM Symposium on Principles of Distributed Computing","date_created":"2021-12-16T13:20:19Z","external_id":{"arxiv":["2103.03181"],"isi":["000744439800018"]},"_id":"10553","month":"07","title":"Brief announcement: Be prepared when network goes bad: An asynchronous view-change protocol","date_updated":"2023-09-04T11:42:10Z","date_published":"2021-07-21T00:00:00Z","article_processing_charge":"No","keyword":["optimal","state machine replication","fallback","asynchrony","byzantine faults"],"scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2103.03181"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa":1},{"citation":{"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>","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>.","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.","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>.","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>","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.","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."},"type":"conference","quality_controlled":"1","publication_status":"published","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"}],"status":"public","language":[{"iso":"eng"}],"publisher":"Association for Computing Machinery","day":"21","doi":"10.1145/3465084.3467905","arxiv":1,"oa_version":"Preprint","year":"2021","conference":{"name":"PODC: Principles of Distributed Computing","end_date":"2021-07-30","location":"Virtual, Italy","start_date":"2021-07-26"},"isi":1,"author":[{"first_name":"Idit","full_name":"Keidar, Idit","last_name":"Keidar"},{"id":"f5983044-d7ef-11ea-ac6d-fd1430a26d30","first_name":"Eleftherios","full_name":"Kokoris Kogias, Eleftherios","last_name":"Kokoris Kogias"},{"last_name":"Naor","full_name":"Naor, Oded","first_name":"Oded"},{"last_name":"Spiegelman","full_name":"Spiegelman, Alexander","first_name":"Alexander"}],"department":[{"_id":"ElKo"}],"publication_identifier":{"isbn":["978-1-4503-8548-0"]},"scopus_import":"1","oa":1,"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","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","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2102.08325"}],"_id":"10554","external_id":{"arxiv":["2102.08325"],"isi":["000744439800016"]},"date_created":"2021-12-16T13:21:13Z","publication":"Proceedings of the 2021 ACM Symposium on Principles of Distributed Computing","page":"165-175","article_processing_charge":"No","date_published":"2021-07-21T00:00:00Z","title":"All You Need is DAG","date_updated":"2023-08-17T06:24:44Z","month":"07"},{"scopus_import":"1","article_number":"L022005","oa":1,"intvolume":"         3","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.","issue":"2","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","related_material":{"record":[{"status":"public","relation":"earlier_version","id":"8831"},{"relation":"research_data","status":"public","id":"8834"}]},"volume":3,"_id":"10559","project":[{"call_identifier":"H2020","_id":"26A151DA-B435-11E9-9278-68D0E5697425","grant_number":"844511","name":"Majorana bound states in Ge/SiGe heterostructures"},{"_id":"237E5020-32DE-11EA-91FC-C7463DDC885E","grant_number":"862046","call_identifier":"H2020","name":"TOPOLOGICALLY PROTECTED AND SCALABLE QUANTUM BITS"}],"external_id":{"arxiv":["2012.00322"]},"date_created":"2021-12-16T18:50:57Z","publication":"Physical Review Research","file_date_updated":"2021-12-17T08:12:37Z","keyword":["general engineering"],"article_processing_charge":"No","date_published":"2021-04-15T00:00:00Z","ec_funded":1,"title":"Enhancement of proximity-induced superconductivity in a planar Ge hole gas","date_updated":"2024-02-21T12:41:26Z","month":"04","acknowledged_ssus":[{"_id":"NanoFab"},{"_id":"M-Shop"}],"ddc":["620"],"article_type":"original","file":[{"creator":"cchlebak","date_created":"2021-12-17T08:12:37Z","file_id":"10561","access_level":"open_access","success":1,"file_name":"2021_PhysRevResearch_Aggarwal.pdf","file_size":1917512,"content_type":"application/pdf","date_updated":"2021-12-17T08:12:37Z","relation":"main_file","checksum":"60a1bc9c9b616b1b155044bb8cfc6484"}],"type":"journal_article","citation":{"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.","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>","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).","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.","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>.","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>","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>."},"quality_controlled":"1","publication_status":"published","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"}],"status":"public","has_accepted_license":"1","language":[{"iso":"eng"}],"publisher":"American Physical Society","day":"15","doi":"10.1103/physrevresearch.3.l022005","oa_version":"Published Version","arxiv":1,"year":"2021","author":[{"last_name":"Aggarwal","full_name":"Aggarwal, Kushagra","orcid":"0000-0001-9985-9293","id":"b22ab905-3539-11eb-84c3-fc159dcd79cb","first_name":"Kushagra"},{"full_name":"Hofmann, Andrea C","last_name":"Hofmann","id":"340F461A-F248-11E8-B48F-1D18A9856A87","first_name":"Andrea C"},{"id":"4C473F58-F248-11E8-B48F-1D18A9856A87","first_name":"Daniel","last_name":"Jirovec","orcid":"0000-0002-7197-4801","full_name":"Jirovec, Daniel"},{"last_name":"Prieto Gonzalez","full_name":"Prieto Gonzalez, Ivan","orcid":"0000-0002-7370-5357","first_name":"Ivan","id":"2A307FE2-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Sammak, Amir","last_name":"Sammak","first_name":"Amir"},{"first_name":"Marc","last_name":"Botifoll","full_name":"Botifoll, Marc"},{"first_name":"Sara","last_name":"Martí-Sánchez","full_name":"Martí-Sánchez, Sara"},{"last_name":"Veldhorst","full_name":"Veldhorst, Menno","first_name":"Menno"},{"last_name":"Arbiol","full_name":"Arbiol, Jordi","first_name":"Jordi"},{"full_name":"Scappucci, Giordano","last_name":"Scappucci","first_name":"Giordano"},{"first_name":"Jeroen","last_name":"Danon","full_name":"Danon, Jeroen"},{"orcid":"0000-0001-8342-202X","full_name":"Katsaros, Georgios","last_name":"Katsaros","id":"38DB5788-F248-11E8-B48F-1D18A9856A87","first_name":"Georgios"}],"department":[{"_id":"GeKa"}],"publication_identifier":{"issn":["2643-1564"]},"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"}},{"oa_version":"Published Version","doi":"10.1016/j.xpro.2021.101012","day":"17","publisher":"Elsevier ; Cell Press","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"},"department":[{"_id":"SaSi"}],"publication_identifier":{"eissn":["2666-1667"]},"author":[{"full_name":"Venturino, Alessandro","orcid":"0000-0003-2356-9403","last_name":"Venturino","first_name":"Alessandro","id":"41CB84B2-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Sandra","id":"36ACD32E-F248-11E8-B48F-1D18A9856A87","last_name":"Siegert","orcid":"0000-0001-8635-0877","full_name":"Siegert, Sandra"}],"year":"2021","type":"journal_article","citation":{"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 ; Cell Press, 2021. <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>","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 ; Cell Press, 2021, doi:<a href=\"https://doi.org/10.1016/j.xpro.2021.101012\">10.1016/j.xpro.2021.101012</a>.","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 ; Cell Press. <a href=\"https://doi.org/10.1016/j.xpro.2021.101012\">https://doi.org/10.1016/j.xpro.2021.101012</a>","short":"A. Venturino, S. Siegert, STAR Protocols 2 (2021).","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 ; Cell Press, 2021."},"file":[{"file_name":"2021_STARProt_Venturino.pdf","access_level":"open_access","success":1,"checksum":"9ea2501056c5df99e84726b845e9b976","relation":"main_file","file_size":6207060,"content_type":"application/pdf","date_updated":"2021-12-20T08:58:40Z","date_created":"2021-12-20T08:58:40Z","creator":"cchlebak","file_id":"10570"}],"article_type":"original","acknowledged_ssus":[{"_id":"Bio"}],"ddc":["573"],"language":[{"iso":"eng"}],"status":"public","has_accepted_license":"1","abstract":[{"lang":"eng","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)."}],"publication_status":"published","quality_controlled":"1","file_date_updated":"2021-12-20T08:58:40Z","publication":"STAR Protocols","date_created":"2021-12-19T23:01:32Z","project":[{"_id":"25D4A630-B435-11E9-9278-68D0E5697425","grant_number":"715571","call_identifier":"H2020","name":"Microglia action towards neuronal circuit formation and function in health and disease"}],"_id":"10565","month":"12","date_updated":"2023-11-16T13:11:04Z","title":"Minimally invasive protocols and quantification for microglia-mediated perineuronal net disassembly in mouse brain","ec_funded":1,"date_published":"2021-12-17T00:00:00Z","article_processing_charge":"Yes","scopus_import":"1","volume":2,"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","issue":"4","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.","oa":1,"intvolume":"         2","article_number":"101012"},{"year":"2021","isi":1,"author":[{"first_name":"Henry","full_name":"Goehlich, Henry","last_name":"Goehlich"},{"last_name":"Sartoris","full_name":"Sartoris, Linda","first_name":"Linda","id":"2B9284CA-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Wagner, Kim-Sara","last_name":"Wagner","first_name":"Kim-Sara"},{"full_name":"Wendling, Carolin C.","last_name":"Wendling","first_name":"Carolin C."},{"first_name":"Olivia","full_name":"Roth, Olivia","last_name":"Roth"}],"publication_identifier":{"issn":["2296-701X"]},"department":[{"_id":"SyCr"}],"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"},"publisher":"Frontiers Media","day":"25","doi":"10.3389/fevo.2021.626442","oa_version":"Published Version","quality_controlled":"1","publication_status":"published","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","status":"public","language":[{"iso":"eng"}],"ddc":["597"],"article_type":"original","file":[{"date_updated":"2021-12-20T10:44:20Z","content_type":"application/pdf","file_size":3175085,"checksum":"8d6e2b767bb0240a9b5a3a3555be51fd","relation":"main_file","success":1,"access_level":"open_access","file_name":"2021_Frontiers_Goehlich.pdf","file_id":"10572","date_created":"2021-12-20T10:44:20Z","creator":"alisjak"}],"type":"journal_article","citation":{"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>","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>.","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.","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>.","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>","short":"H. Goehlich, L. Sartoris, K.-S. Wagner, C.C. Wendling, O. Roth, Frontiers in Ecology and Evolution 9 (2021).","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."},"article_processing_charge":"No","keyword":["ecology","evolution","behavior and systematics","trans-generational plasticity","genetic adaptation","local adaptation","phenotypic plasticity","Baltic Sea","climate change","salinity","syngnathids"],"date_published":"2021-03-25T00:00:00Z","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","month":"03","_id":"10568","external_id":{"isi":["000637736300001"]},"date_created":"2021-12-20T07:53:19Z","publication":"Frontiers in Ecology and Evolution","file_date_updated":"2021-12-20T10:44:20Z","article_number":"626442","oa":1,"intvolume":"         9","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.","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","volume":9,"scopus_import":"1"},{"day":"16","publisher":"The Company of Biologists","oa_version":"Published Version","doi":"10.1242/jeb.243647","year":"2021","isi":1,"author":[{"last_name":"Szabo","full_name":"Szabo, B","first_name":"B"},{"full_name":"Mangione, R","last_name":"Mangione","first_name":"R"},{"full_name":"Rath, M","last_name":"Rath","first_name":"M"},{"first_name":"A","last_name":"Pašukonis","full_name":"Pašukonis, A"},{"full_name":"Reber, SA","last_name":"Reber","first_name":"SA"},{"orcid":"0000-0001-7425-2372","full_name":"Oh, Jinook","last_name":"Oh","first_name":"Jinook","id":"403169A4-080F-11EA-9993-BF3F3DDC885E"},{"first_name":"M","last_name":"Ringler","full_name":"Ringler, M"},{"first_name":"E","full_name":"Ringler, E","last_name":"Ringler"}],"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"},"publication_identifier":{"eissn":["1477-9145"],"issn":["0022-0949"]},"department":[{"_id":"SyCr"}],"article_type":"original","ddc":["573"],"type":"journal_article","citation":{"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>","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>.","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.","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>.","short":"B. Szabo, R. Mangione, M. Rath, A. Pašukonis, S. Reber, J. Oh, M. Ringler, E. Ringler, Journal of Experimental Biology 224 (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>","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."},"file":[{"checksum":"75d13a5ec8e3b90e3bc02bd8a9c17eef","relation":"main_file","content_type":"application/pdf","date_updated":"2021-12-20T10:14:14Z","file_size":607096,"file_name":"2021_JExpBio_Szabo.pdf","success":1,"access_level":"open_access","file_id":"10571","date_created":"2021-12-20T10:14:14Z","creator":"cchlebak"}],"quality_controlled":"1","has_accepted_license":"1","status":"public","pmid":1,"language":[{"iso":"eng"}],"publication_status":"published","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."}],"external_id":{"pmid":["34845497"],"isi":["000738259300013"]},"date_created":"2021-12-20T07:54:22Z","_id":"10569","publication":"Journal of Experimental Biology","file_date_updated":"2021-12-20T10:14:14Z","article_processing_charge":"No","date_published":"2021-12-16T00:00:00Z","month":"12","date_updated":"2023-08-17T06:26:15Z","title":"Naïve poison frog tadpoles use bi-modal cues to avoid insect predators but not heterospecific predatory tadpoles","intvolume":"       224","oa":1,"issue":"24","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","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.","article_number":"jeb243647","volume":224},{"publisher":"Elsevier ; Cell Press","day":"22","doi":"10.1016/j.cell.2021.11.025","oa_version":"Preprint","year":"2021","isi":1,"author":[{"first_name":"Akankshi","last_name":"Munjal","full_name":"Munjal, Akankshi"},{"first_name":"Edouard B","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6005-1561","full_name":"Hannezo, Edouard B","last_name":"Hannezo"},{"first_name":"Tony Y.C.","full_name":"Tsai, Tony Y.C.","last_name":"Tsai"},{"last_name":"Mitchison","full_name":"Mitchison, Timothy J.","first_name":"Timothy J."},{"first_name":"Sean G.","full_name":"Megason, Sean G.","last_name":"Megason"}],"publication_identifier":{"eissn":["1097-4172"],"issn":["0092-8674"]},"department":[{"_id":"EdHa"}],"article_type":"original","type":"journal_article","citation":{"mla":"Munjal, Akankshi, et al. “Extracellular Hyaluronate Pressure Shaped by Cellular Tethers Drives Tissue Morphogenesis.” <i>Cell</i>, vol. 184, no. 26, Elsevier ; Cell Press, 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>.","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.","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 ; Cell Press, 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>","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 ; Cell Press, p. 6313–6325.e18, 2021.","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 ; Cell Press. <a href=\"https://doi.org/10.1016/j.cell.2021.11.025\">https://doi.org/10.1016/j.cell.2021.11.025</a>","short":"A. Munjal, E.B. Hannezo, T.Y.C. Tsai, T.J. Mitchison, S.G. Megason, Cell 184 (2021) 6313–6325.e18."},"quality_controlled":"1","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."}],"publication_status":"published","status":"public","language":[{"iso":"eng"}],"_id":"10573","external_id":{"isi":["000735387500002"]},"date_created":"2021-12-26T23:01:26Z","publication":"Cell","page":"6313-6325.e18","article_processing_charge":"No","date_published":"2021-12-22T00:00:00Z","title":"Extracellular hyaluronate pressure shaped by cellular tethers drives tissue morphogenesis","date_updated":"2023-08-17T06:28:25Z","month":"12","scopus_import":"1","intvolume":"       184","oa":1,"issue":"26","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.","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","main_file_link":[{"open_access":"1","url":"https://www.biorxiv.org/content/10.1101/2020.09.28.316042"}],"volume":184},{"volume":37,"issue":"12","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","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.","intvolume":"        37","oa":1,"scopus_import":"1","title":"The effect of geometry and illumination on appearance perception of different material categories","date_updated":"2023-08-17T06:29:34Z","month":"12","date_published":"2021-12-01T00:00:00Z","article_processing_charge":"Yes","file_date_updated":"2021-12-27T13:51:08Z","publication":"Visual Computer","page":"2975-2987","_id":"10574","date_created":"2021-12-26T23:01:26Z","external_id":{"isi":["000673536600003"]},"publication_status":"published","abstract":[{"lang":"eng","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."}],"language":[{"iso":"eng"}],"status":"public","has_accepted_license":"1","quality_controlled":"1","file":[{"file_id":"10578","creator":"cchlebak","date_created":"2021-12-27T13:51:08Z","checksum":"244cfcac0479ca6e3444c098ab2860a1","relation":"main_file","file_size":5741094,"content_type":"application/pdf","date_updated":"2021-12-27T13:51:08Z","file_name":"2021_VisComput_Chen.pdf","access_level":"open_access","success":1}],"citation":{"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>","short":"B. Chen, C. Wang, M. Piovarci, H.P. Seidel, P. Didyk, K. Myszkowski, A. Serrano, Visual Computer 37 (2021) 2975–2987.","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.","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>.","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>.","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."},"type":"journal_article","ddc":["000"],"article_type":"original","department":[{"_id":"BeBi"}],"publication_identifier":{"eissn":["1432-2315"],"issn":["0178-2789"]},"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"},"isi":1,"author":[{"first_name":"Bin","full_name":"Chen, Bin","last_name":"Chen"},{"first_name":"Chao","full_name":"Wang, Chao","last_name":"Wang"},{"last_name":"Piovarci","full_name":"Piovarci, Michael","orcid":"0000-0002-5062-4474","id":"62E473F4-5C99-11EA-A40E-AF823DDC885E","first_name":"Michael"},{"last_name":"Seidel","full_name":"Seidel, Hans Peter","first_name":"Hans Peter"},{"last_name":"Didyk","full_name":"Didyk, Piotr","first_name":"Piotr"},{"first_name":"Karol","full_name":"Myszkowski, Karol","last_name":"Myszkowski"},{"first_name":"Ana","last_name":"Serrano","full_name":"Serrano, Ana"}],"year":"2021","doi":"10.1007/s00371-021-02227-x","oa_version":"Published Version","publisher":"Springer Nature","day":"01"},{"quality_controlled":"1","status":"public","has_accepted_license":"1","language":[{"iso":"eng"}],"publication_status":"published","abstract":[{"lang":"eng","text":"The choice of the boundary conditions in mechanical problems has to reflect the interaction of the considered material with the surface. Still the assumption of the no-slip condition is preferred in order to avoid boundary terms in the analysis and slipping effects are usually overlooked. Besides the “static slip models”, there are phenomena that are not accurately described by them, e.g. at the moment when the slip changes rapidly, the wall shear stress and the slip can exhibit a sudden overshoot and subsequent relaxation. When these effects become significant, the so-called dynamic slip phenomenon occurs. We develop a mathematical analysis of Navier–Stokes-like problems with a dynamic slip boundary condition, which requires a proper generalization of the Gelfand triplet and the corresponding function space setting."}],"article_type":"original","ddc":["510"],"type":"journal_article","citation":{"apa":"Abbatiello, A., Bulíček, M., &#38; Maringová, E. (2021). On the dynamic slip boundary condition for Navier-Stokes-like problems. <i>Mathematical Models and Methods in Applied Sciences</i>. World Scientific Publishing. <a href=\"https://doi.org/10.1142/S0218202521500470\">https://doi.org/10.1142/S0218202521500470</a>","short":"A. Abbatiello, M. Bulíček, E. Maringová, Mathematical Models and Methods in Applied Sciences 31 (2021) 2165–2212.","ieee":"A. Abbatiello, M. Bulíček, and E. Maringová, “On the dynamic slip boundary condition for Navier-Stokes-like problems,” <i>Mathematical Models and Methods in Applied Sciences</i>, vol. 31, no. 11. World Scientific Publishing, pp. 2165–2212, 2021.","chicago":"Abbatiello, Anna, Miroslav Bulíček, and Erika Maringová. “On the Dynamic Slip Boundary Condition for Navier-Stokes-like Problems.” <i>Mathematical Models and Methods in Applied Sciences</i>. World Scientific Publishing, 2021. <a href=\"https://doi.org/10.1142/S0218202521500470\">https://doi.org/10.1142/S0218202521500470</a>.","ama":"Abbatiello A, Bulíček M, Maringová E. On the dynamic slip boundary condition for Navier-Stokes-like problems. <i>Mathematical Models and Methods in Applied Sciences</i>. 2021;31(11):2165-2212. doi:<a href=\"https://doi.org/10.1142/S0218202521500470\">10.1142/S0218202521500470</a>","mla":"Abbatiello, Anna, et al. “On the Dynamic Slip Boundary Condition for Navier-Stokes-like Problems.” <i>Mathematical Models and Methods in Applied Sciences</i>, vol. 31, no. 11, World Scientific Publishing, 2021, pp. 2165–212, doi:<a href=\"https://doi.org/10.1142/S0218202521500470\">10.1142/S0218202521500470</a>.","ista":"Abbatiello A, Bulíček M, Maringová E. 2021. On the dynamic slip boundary condition for Navier-Stokes-like problems. Mathematical Models and Methods in Applied Sciences. 31(11), 2165–2212."},"file":[{"relation":"main_file","checksum":"8c0a9396335f0b70e1f5cbfe450a987a","content_type":"application/pdf","date_updated":"2022-05-16T10:55:45Z","file_size":795483,"file_name":"2021_MathModelsMethods_Abbatiello.pdf","success":1,"access_level":"open_access","file_id":"11385","date_created":"2022-05-16T10:55:45Z","creator":"dernst"}],"year":"2021","isi":1,"author":[{"first_name":"Anna","last_name":"Abbatiello","full_name":"Abbatiello, Anna"},{"last_name":"Bulíček","full_name":"Bulíček, Miroslav","first_name":"Miroslav"},{"first_name":"Erika","id":"dbabca31-66eb-11eb-963a-fb9c22c880b4","full_name":"Maringová, Erika","last_name":"Maringová"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png"},"department":[{"_id":"JuFi"}],"publication_identifier":{"eissn":["1793-6314"],"issn":["0218-2025"]},"day":"13","publisher":"World Scientific Publishing","oa_version":"Published Version","arxiv":1,"doi":"10.1142/S0218202521500470","intvolume":"        31","oa":1,"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","issue":"11","acknowledgement":"The research of A. Abbatiello is supported by Einstein Foundation, Berlin. A. Abbatiello is also member of the Italian National Group for the Mathematical Physics (GNFM) of INdAM. M. Bulíček acknowledges the support of the project No. 20-11027X financed by Czech Science Foundation (GACR). M. Bulíček is member of the Jindřich Nečas Center for Mathematical Modelling. E. Maringová acknowledges support from Charles University Research program UNCE/SCI/023, the grant SVV-2020-260583 by the Ministry of Education, Youth and Sports, Czech Republic and from the Austrian Science Fund (FWF), grants P30000, W1245, and F65.","volume":31,"license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","scopus_import":"1","article_processing_charge":"No","date_published":"2021-10-13T00:00:00Z","month":"10","date_updated":"2023-08-17T06:29:01Z","title":"On the dynamic slip boundary condition for Navier-Stokes-like problems","external_id":{"isi":["000722309400001"],"arxiv":["2009.09057"]},"date_created":"2021-12-26T23:01:27Z","project":[{"name":"Taming Complexity in Partial Differential Systems","grant_number":"F6504","_id":"fc31cba2-9c52-11eb-aca3-ff467d239cd2"},{"name":"Dissipation and Dispersion in Nonlinear Partial Differential Equations","call_identifier":"FWF","_id":"260788DE-B435-11E9-9278-68D0E5697425"}],"_id":"10575","page":"2165-2212","publication":"Mathematical Models and Methods in Applied Sciences","file_date_updated":"2022-05-16T10:55:45Z"},{"main_file_link":[{"url":"https://arxiv.org/abs/2112.13558","open_access":"1"}],"abstract":[{"text":"We consider a totally asymmetric simple exclusion process (TASEP) consisting of particles on a lattice that require binding by a \"token\" to move. Using a combination of theory and simulations, we address the following questions: (i) How token binding kinetics affects the current-density relation; (ii) How the current-density relation depends on the scarcity of tokens; (iii) How tokens propagate the effects of the locally-imposed disorder (such a slow site) over the entire lattice; (iv) How a shared pool of tokens couples concurrent TASEPs running on multiple lattices; (v) How our results translate to TASEPs with open boundaries that exchange particles with the reservoir. Since real particle motion (including in systems that inspired the standard TASEP model, e.g., protein synthesis or movement of molecular motors) is often catalyzed, regulated, actuated, or otherwise mediated, the token-driven TASEP dynamics analyzed in this paper should allow for a better understanding of real systems and enable a closer match between TASEP theory and experimental observations.","lang":"eng"}],"publication_status":"submitted","status":"public","has_accepted_license":"1","language":[{"iso":"eng"}],"article_number":"2112.13558","oa":1,"acknowledgement":"B.K. thanks Stefano Elefante, Simon Rella, and Michal Hledík for their help with the usage of the cluster. B.K. additionally thanks Călin Guet and his group for help and advice. We thank M. Hennessey-Wesen for constructive comments on the manuscript. We thank Ankita Gupta (Indian Institute of Technology) for spotting a typographical error in Eq. (49) in the preprint version of this paper.","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"preprint","citation":{"short":"B. Kavcic, G. Tkačik, ArXiv (n.d.).","apa":"Kavcic, B., &#38; Tkačik, G. (n.d.). Token-driven totally asymmetric simple exclusion process. <i>arXiv</i>. <a href=\"https://doi.org/10.48550/arXiv.2112.13558\">https://doi.org/10.48550/arXiv.2112.13558</a>","ieee":"B. Kavcic and G. Tkačik, “Token-driven totally asymmetric simple exclusion process,” <i>arXiv</i>. .","ama":"Kavcic B, Tkačik G. Token-driven totally asymmetric simple exclusion process. <i>arXiv</i>. doi:<a href=\"https://doi.org/10.48550/arXiv.2112.13558\">10.48550/arXiv.2112.13558</a>","chicago":"Kavcic, Bor, and Gašper Tkačik. “Token-Driven Totally Asymmetric Simple Exclusion Process.” <i>ArXiv</i>, n.d. <a href=\"https://doi.org/10.48550/arXiv.2112.13558\">https://doi.org/10.48550/arXiv.2112.13558</a>.","mla":"Kavcic, Bor, and Gašper Tkačik. “Token-Driven Totally Asymmetric Simple Exclusion Process.” <i>ArXiv</i>, 2112.13558, doi:<a href=\"https://doi.org/10.48550/arXiv.2112.13558\">10.48550/arXiv.2112.13558</a>.","ista":"Kavcic B, Tkačik G. Token-driven totally asymmetric simple exclusion process. arXiv, 2112.13558."},"ddc":["530"],"department":[{"_id":"GaTk"}],"title":"Token-driven totally asymmetric simple exclusion process","date_updated":"2023-05-03T10:54:05Z","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png"},"month":"12","year":"2021","article_processing_charge":"No","date_published":"2021-12-27T00:00:00Z","author":[{"last_name":"Kavcic","orcid":"0000-0001-6041-254X","full_name":"Kavcic, Bor","first_name":"Bor","id":"350F91D2-F248-11E8-B48F-1D18A9856A87"},{"id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","first_name":"Gašper","last_name":"Tkačik","full_name":"Tkačik, Gašper","orcid":"0000-0002-6699-1455"}],"doi":"10.48550/arXiv.2112.13558","publication":"arXiv","arxiv":1,"oa_version":"Preprint","_id":"10579","day":"27","external_id":{"arxiv":["2112.13558"]},"date_created":"2021-12-28T06:52:09Z"}]