[{"year":"2021","_id":"10167","type":"journal_article","date_created":"2021-10-21T07:49:12Z","author":[{"id":"0B46FACA-A8E1-11E9-9BD3-79D1E5697425","orcid":"0000-0002-5328-7231","full_name":"Elkrewi, Marwan N","last_name":"Elkrewi","first_name":"Marwan N"},{"orcid":"0000-0002-8876-6494","id":"c8bb7f32-3315-11ec-b58b-e5950e6c14a0","full_name":"Moldovan, Mikhail A.","last_name":"Moldovan","first_name":"Mikhail A."},{"first_name":"Marion A L","last_name":"Picard","full_name":"Picard, Marion A L","orcid":"0000-0002-8101-2518","id":"2C921A7A-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0002-4579-8306","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","last_name":"Vicoso","first_name":"Beatriz","full_name":"Vicoso, Beatriz"}],"project":[{"name":"Sex chromosome evolution under male- and female- heterogamety","_id":"250ED89C-B435-11E9-9278-68D0E5697425","grant_number":"P28842-B22","call_identifier":"FWF"}],"publication_status":"published","acknowledged_ssus":[{"_id":"ScienComp"}],"month":"06","isi":1,"has_accepted_license":"1","quality_controlled":"1","date_updated":"2023-08-14T08:03:06Z","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"abstract":[{"text":"Schistosomes, the human parasites responsible for snail fever, are female-heterogametic. Different parts of their ZW sex chromosomes have stopped recombining in distinct lineages, creating “evolutionary strata” of various ages. Although the Z-chromosome is well characterized at the genomic and molecular level, the W-chromosome has remained largely unstudied from an evolutionary perspective, as only a few W-linked genes have been detected outside of the model species Schistosoma mansoni. Here, we characterize the gene content and evolution of the W-chromosomes of S. mansoni and of the divergent species S. japonicum. We use a combined RNA/DNA k-mer based pipeline to assemble around 100 candidate W-specific transcripts in each of the species. About half of them map to known protein coding genes, the majority homologous to S. mansoni Z-linked genes. We perform an extended analysis of the evolutionary strata present in the two species (including characterizing a previously undetected young stratum in S. japonicum) to infer patterns of sequence and expression evolution of W-linked genes at different time points after recombination was lost. W-linked genes show evidence of degeneration, including high rates of protein evolution and reduced expression. Most are found in young lineage-specific strata, with only a few high expression ancestral W-genes remaining, consistent with the progressive erosion of nonrecombining regions. Among these, the splicing factor u2af2 stands out as a promising candidate for primary sex determination, opening new avenues for understanding the molecular basis of the reproductive biology of this group.","lang":"eng"}],"citation":{"ista":"Elkrewi MN, Moldovan MA, Picard MAL, Vicoso B. 2021. Schistosome W-Linked genes inform temporal dynamics of sex chromosome evolution and suggest candidate for sex determination. Molecular Biology and Evolution.","apa":"Elkrewi, M. N., Moldovan, M. A., Picard, M. A. L., &#38; Vicoso, B. (2021). Schistosome W-Linked genes inform temporal dynamics of sex chromosome evolution and suggest candidate for sex determination. <i>Molecular Biology and Evolution</i>. Oxford University Press . <a href=\"https://doi.org/10.1093/molbev/msab178\">https://doi.org/10.1093/molbev/msab178</a>","mla":"Elkrewi, Marwan N., et al. “Schistosome W-Linked Genes Inform Temporal Dynamics of Sex Chromosome Evolution and Suggest Candidate for Sex Determination.” <i>Molecular Biology and Evolution</i>, Oxford University Press , 2021, doi:<a href=\"https://doi.org/10.1093/molbev/msab178\">10.1093/molbev/msab178</a>.","ieee":"M. N. Elkrewi, M. A. Moldovan, M. A. L. Picard, and B. Vicoso, “Schistosome W-Linked genes inform temporal dynamics of sex chromosome evolution and suggest candidate for sex determination,” <i>Molecular Biology and Evolution</i>. Oxford University Press , 2021.","ama":"Elkrewi MN, Moldovan MA, Picard MAL, Vicoso B. Schistosome W-Linked genes inform temporal dynamics of sex chromosome evolution and suggest candidate for sex determination. <i>Molecular Biology and Evolution</i>. 2021. doi:<a href=\"https://doi.org/10.1093/molbev/msab178\">10.1093/molbev/msab178</a>","chicago":"Elkrewi, Marwan N, Mikhail A. Moldovan, Marion A L Picard, and Beatriz Vicoso. “Schistosome W-Linked Genes Inform Temporal Dynamics of Sex Chromosome Evolution and Suggest Candidate for Sex Determination.” <i>Molecular Biology and Evolution</i>. Oxford University Press , 2021. <a href=\"https://doi.org/10.1093/molbev/msab178\">https://doi.org/10.1093/molbev/msab178</a>.","short":"M.N. Elkrewi, M.A. Moldovan, M.A.L. Picard, B. Vicoso, Molecular Biology and Evolution (2021)."},"publisher":"Oxford University Press ","pmid":1,"department":[{"_id":"BeVi"}],"keyword":["sex chromosomes","evolutionary strata","W-linked gene","sex determining gene","schistosome parasites"],"title":"Schistosome W-Linked genes inform temporal dynamics of sex chromosome evolution and suggest candidate for sex determination","article_processing_charge":"No","publication":"Molecular Biology and Evolution","language":[{"iso":"eng"}],"file_date_updated":"2022-05-06T09:47:18Z","ddc":["610"],"status":"public","article_type":"original","date_published":"2021-06-19T00:00:00Z","acknowledgement":"The authors thank IT support at IST Austria for providing an optimal environment for bioinformatic analyses. This work was supported by an Austrian Science Foundation FWF grant (Project P28842) to B.V.","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa":1,"day":"19","oa_version":"Published Version","doi":"10.1093/molbev/msab178","external_id":{"pmid":["34146097"],"isi":["000741368600009"]},"scopus_import":"1","publication_identifier":{"issn":["0737-4038"],"eissn":["1537-1719"]},"file":[{"content_type":"application/pdf","relation":"main_file","checksum":"1b096702fb356d9c0eb88e1b3fcff5f8","file_id":"11352","date_updated":"2022-05-06T09:47:18Z","access_level":"open_access","file_name":"2021_MolecularBiolEvolution_Elkrewi.pdf","date_created":"2022-05-06T09:47:18Z","file_size":1008594,"success":1,"creator":"dernst"}]},{"date_created":"2021-10-23T10:50:55Z","status":"public","author":[{"id":"fea1b376-906f-11eb-847d-b2c0cf46455b","full_name":"Clozeau, Nicolas","first_name":"Nicolas","last_name":"Clozeau"},{"last_name":"Gloria","first_name":"Antoine","full_name":"Gloria, Antoine"}],"month":"04","user_id":"D865714E-FA4E-11E9-B85B-F5C5E5697425","publication_status":"submitted","date_published":"2021-04-09T00:00:00Z","acknowledgement":"The authors warmly thank Mitia Duerinckx for discussions on annealed estimates, and Mathias Schäffner for pointing out that the conditions of [14] apply to  ̄a in the setting of Theorem 2.2 and for discussions on regularity theory for operators with non-standard growth conditions. The authors received financial support from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (Grant Agreement n◦ 864066).","arxiv":1,"article_processing_charge":"No","title":"Quantitative nonlinear homogenization: control of oscillations","language":[{"iso":"eng"}],"publication":"arXiv","_id":"10174","year":"2021","article_number":"2104.04263","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2104.04263"}],"type":"preprint","oa_version":"Preprint","department":[{"_id":"JuFi"}],"external_id":{"arxiv":["2104.04263"]},"abstract":[{"lang":"eng","text":"Quantitative stochastic homogenization of linear elliptic operators is by now well-understood. In this contribution we move forward to the nonlinear setting of monotone operators with p-growth. This first work is dedicated to a quantitative two-scale expansion result. Fluctuations will be addressed in companion articles. By treating the range of exponents 2≤p<∞ in dimensions d≤3, we are able to consider genuinely nonlinear elliptic equations and systems such as −∇⋅A(x)(1+|∇u|p−2)∇u=f (with A random, non-necessarily symmetric) for the first time. When going from p=2 to p>2, the main difficulty is to analyze the associated linearized operator, whose coefficients are degenerate, unbounded, and depend on the random input A via the solution of a nonlinear equation. One of our main achievements is the control of this intricate nonlinear dependence, leading to annealed Meyers' estimates for the linearized operator, which are key to the quantitative two-scale expansion result."}],"date_updated":"2021-10-28T15:44:05Z","day":"09","citation":{"ista":"Clozeau N, Gloria A. Quantitative nonlinear homogenization: control of oscillations. arXiv, 2104.04263.","chicago":"Clozeau, Nicolas, and Antoine Gloria. “Quantitative Nonlinear Homogenization: Control of Oscillations.” <i>ArXiv</i>, n.d.","short":"N. Clozeau, A. Gloria, ArXiv (n.d.).","ama":"Clozeau N, Gloria A. Quantitative nonlinear homogenization: control of oscillations. <i>arXiv</i>.","ieee":"N. Clozeau and A. Gloria, “Quantitative nonlinear homogenization: control of oscillations,” <i>arXiv</i>. .","mla":"Clozeau, Nicolas, and Antoine Gloria. “Quantitative Nonlinear Homogenization: Control of Oscillations.” <i>ArXiv</i>, 2104.04263.","apa":"Clozeau, N., &#38; Gloria, A. (n.d.). Quantitative nonlinear homogenization: control of oscillations. <i>arXiv</i>."},"oa":1},{"main_file_link":[{"url":"https://arxiv.org/abs/1802.09978","open_access":"1"}],"language":[{"iso":"eng"}],"publication":"Journal of Mathematical Physics","arxiv":1,"title":"Topological field theory on r-spin surfaces and the Arf-invariant","article_processing_charge":"No","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","acknowledgement":"We would like to thank Nils Carqueville, Tobias Dyckerhoff, Jan Hesse, Ehud Meir, Sebastian Novak, Louis-Hadrien Robert, Nick Salter, Walker Stern, and Lukas Woike for helpful discussions and comments. L.S. was supported by the DFG Research Training Group 1670 “Mathematics Inspired by String Theory and Quantum Field Theory.”","date_published":"2021-10-01T00:00:00Z","article_type":"original","status":"public","day":"01","oa":1,"publication_identifier":{"issn":["00222488"]},"issue":"10","scopus_import":"1","external_id":{"isi":["000755638500010"],"arxiv":["1802.09978"]},"doi":"10.1063/5.0037826","oa_version":"Preprint","article_number":"102302","type":"journal_article","_id":"10176","year":"2021","month":"10","isi":1,"publication_status":"published","author":[{"full_name":"Runkel, Ingo","last_name":"Runkel","first_name":"Ingo"},{"orcid":"0000-0003-2834-5054","id":"7943226E-220E-11EA-94C7-D59F3DDC885E","first_name":"Lorant","last_name":"Szegedy","full_name":"Szegedy, Lorant"}],"intvolume":"        62","date_created":"2021-10-24T22:01:32Z","volume":62,"citation":{"apa":"Runkel, I., &#38; Szegedy, L. (2021). Topological field theory on r-spin surfaces and the Arf-invariant. <i>Journal of Mathematical Physics</i>. AIP Publishing. <a href=\"https://doi.org/10.1063/5.0037826\">https://doi.org/10.1063/5.0037826</a>","mla":"Runkel, Ingo, and Lorant Szegedy. “Topological Field Theory on R-Spin Surfaces and the Arf-Invariant.” <i>Journal of Mathematical Physics</i>, vol. 62, no. 10, 102302, AIP Publishing, 2021, doi:<a href=\"https://doi.org/10.1063/5.0037826\">10.1063/5.0037826</a>.","ieee":"I. Runkel and L. Szegedy, “Topological field theory on r-spin surfaces and the Arf-invariant,” <i>Journal of Mathematical Physics</i>, vol. 62, no. 10. AIP Publishing, 2021.","short":"I. Runkel, L. Szegedy, Journal of Mathematical Physics 62 (2021).","chicago":"Runkel, Ingo, and Lorant Szegedy. “Topological Field Theory on R-Spin Surfaces and the Arf-Invariant.” <i>Journal of Mathematical Physics</i>. AIP Publishing, 2021. <a href=\"https://doi.org/10.1063/5.0037826\">https://doi.org/10.1063/5.0037826</a>.","ama":"Runkel I, Szegedy L. Topological field theory on r-spin surfaces and the Arf-invariant. <i>Journal of Mathematical Physics</i>. 2021;62(10). doi:<a href=\"https://doi.org/10.1063/5.0037826\">10.1063/5.0037826</a>","ista":"Runkel I, Szegedy L. 2021. Topological field theory on r-spin surfaces and the Arf-invariant. Journal of Mathematical Physics. 62(10), 102302."},"abstract":[{"text":"We give a combinatorial model for r-spin surfaces with parameterized boundary based on Novak (“Lattice topological field theories in two dimensions,” Ph.D. thesis, Universität Hamburg, 2015). The r-spin structure is encoded in terms of ℤ𝑟-valued indices assigned to the edges of a polygonal decomposition. This combinatorial model is designed for our state-sum construction of two-dimensional topological field theories on r-spin surfaces. We show that an example of such a topological field theory computes the Arf-invariant of an r-spin surface as introduced by Randal-Williams [J. Topol. 7, 155 (2014)] and Geiges et al. [Osaka J. Math. 49, 449 (2012)]. This implies, in particular, that the r-spin Arf-invariant is constant on orbits of the mapping class group, providing an alternative proof of that fact.","lang":"eng"}],"date_updated":"2023-08-14T08:04:12Z","quality_controlled":"1","department":[{"_id":"MiLe"}],"publisher":"AIP Publishing"},{"publisher":"American Association for the Advancement of Science","department":[{"_id":"NanoFab"}],"quality_controlled":"1","has_accepted_license":"1","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","short":"CC BY-NC (4.0)"},"date_updated":"2023-08-14T08:04:42Z","abstract":[{"text":"Phonon polaritons (PhPs)—light coupled to lattice vibrations—with in-plane hyperbolic dispersion exhibit ray-like propagation with large wave vectors and enhanced density of optical states along certain directions on a surface. As such, they have raised a surge of interest, promising unprecedented manipulation of infrared light at the nanoscale in a planar circuitry. Here, we demonstrate focusing of in-plane hyperbolic PhPs propagating along thin slabs of α-MoO3. To that end, we developed metallic nanoantennas of convex geometries for both efficient launching and focusing of the polaritons. The foci obtained exhibit enhanced near-field confinement and absorption compared to foci produced by in-plane isotropic PhPs. Foci sizes as small as λp/4.5 = λ0/50 were achieved (λp is the polariton wavelength and λ0 is the photon wavelength). Focusing of in-plane hyperbolic polaritons introduces a first and most basic building block developing planar polariton optics using in-plane anisotropic van der Waals materials.","lang":"eng"}],"volume":7,"citation":{"ista":"Martín-Sánchez J, Duan J, Taboada-Gutiérrez J, Álvarez-Pérez G, Voronin KV, Prieto Gonzalez I, Ma W, Bao Q, Volkov VS, Hillenbrand R, Nikitin AY, Alonso-González P. 2021. Focusing of in-plane hyperbolic polaritons in van der Waals crystals with tailored infrared nanoantennas. Science Advances. 7(41), abj0127.","mla":"Martín-Sánchez, Javier, et al. “Focusing of In-Plane Hyperbolic Polaritons in van Der Waals Crystals with Tailored Infrared Nanoantennas.” <i>Science Advances</i>, vol. 7, no. 41, abj0127, American Association for the Advancement of Science, 2021, doi:<a href=\"https://doi.org/10.1126/sciadv.abj0127\">10.1126/sciadv.abj0127</a>.","apa":"Martín-Sánchez, J., Duan, J., Taboada-Gutiérrez, J., Álvarez-Pérez, G., Voronin, K. V., Prieto Gonzalez, I., … Alonso-González, P. (2021). Focusing of in-plane hyperbolic polaritons in van der Waals crystals with tailored infrared nanoantennas. <i>Science Advances</i>. American Association for the Advancement of Science. <a href=\"https://doi.org/10.1126/sciadv.abj0127\">https://doi.org/10.1126/sciadv.abj0127</a>","ama":"Martín-Sánchez J, Duan J, Taboada-Gutiérrez J, et al. Focusing of in-plane hyperbolic polaritons in van der Waals crystals with tailored infrared nanoantennas. <i>Science Advances</i>. 2021;7(41). doi:<a href=\"https://doi.org/10.1126/sciadv.abj0127\">10.1126/sciadv.abj0127</a>","short":"J. Martín-Sánchez, J. Duan, J. Taboada-Gutiérrez, G. Álvarez-Pérez, K.V. Voronin, I. Prieto Gonzalez, W. Ma, Q. Bao, V.S. Volkov, R. Hillenbrand, A.Y. Nikitin, P. Alonso-González, Science Advances 7 (2021).","chicago":"Martín-Sánchez, Javier, Jiahua Duan, Javier Taboada-Gutiérrez, Gonzalo Álvarez-Pérez, Kirill V. Voronin, Ivan Prieto Gonzalez, Weiliang Ma, et al. “Focusing of In-Plane Hyperbolic Polaritons in van Der Waals Crystals with Tailored Infrared Nanoantennas.” <i>Science Advances</i>. American Association for the Advancement of Science, 2021. <a href=\"https://doi.org/10.1126/sciadv.abj0127\">https://doi.org/10.1126/sciadv.abj0127</a>.","ieee":"J. Martín-Sánchez <i>et al.</i>, “Focusing of in-plane hyperbolic polaritons in van der Waals crystals with tailored infrared nanoantennas,” <i>Science Advances</i>, vol. 7, no. 41. American Association for the Advancement of Science, 2021."},"date_created":"2021-10-24T22:01:33Z","intvolume":"         7","author":[{"first_name":"Javier","last_name":"Martín-Sánchez","full_name":"Martín-Sánchez, Javier"},{"last_name":"Duan","first_name":"Jiahua","full_name":"Duan, Jiahua"},{"last_name":"Taboada-Gutiérrez","first_name":"Javier","full_name":"Taboada-Gutiérrez, Javier"},{"first_name":"Gonzalo","last_name":"Álvarez-Pérez","full_name":"Álvarez-Pérez, Gonzalo"},{"last_name":"Voronin","first_name":"Kirill V.","full_name":"Voronin, Kirill V."},{"full_name":"Prieto Gonzalez, Ivan","last_name":"Prieto Gonzalez","first_name":"Ivan","id":"2A307FE2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7370-5357"},{"full_name":"Ma, Weiliang","first_name":"Weiliang","last_name":"Ma"},{"first_name":"Qiaoliang","last_name":"Bao","full_name":"Bao, Qiaoliang"},{"full_name":"Volkov, Valentyn S.","first_name":"Valentyn S.","last_name":"Volkov"},{"full_name":"Hillenbrand, Rainer","last_name":"Hillenbrand","first_name":"Rainer"},{"first_name":"Alexey Y.","last_name":"Nikitin","full_name":"Nikitin, Alexey Y."},{"full_name":"Alonso-González, Pablo","first_name":"Pablo","last_name":"Alonso-González"}],"publication_status":"published","isi":1,"month":"10","_id":"10177","year":"2021","type":"journal_article","article_number":"abj0127","oa_version":"Published Version","doi":"10.1126/sciadv.abj0127","external_id":{"isi":["000704912700024"],"arxiv":["2103.10852"]},"issue":"41","scopus_import":"1","file":[{"file_name":"2021_ScienceAdv_Martin-Sanchez.pdf","access_level":"open_access","date_updated":"2021-10-27T14:16:06Z","checksum":"0a470ef6a47d2b8a96ede4c4d28cfacd","file_id":"10189","relation":"main_file","content_type":"application/pdf","creator":"cziletti","success":1,"file_size":2441163,"date_created":"2021-10-27T14:16:06Z"}],"publication_identifier":{"eissn":["23752548"]},"oa":1,"day":"08","ddc":["530"],"status":"public","article_type":"original","acknowledgement":"J.M.-S. acknowledges financial support from the Ramón y Cajal Program of the Government of Spain and FSE (RYC2018-026196-I) and the Spanish Ministry of Science and Innovation (State Plan for Scientific and Technical Research and Innovation grant number PID2019-110308GA-I00). P.A.-G. acknowledges support from the European Research Council under starting grant no. 715496, 2DNANOPTICA, and the Spanish Ministry of Science and Innovation (State Plan for Scientific and Technical Research and Innovation grant number PID2019-111156GB-I00). J.T.-G. acknowledges support through the Severo Ochoa Program from the Government of the Principality of Asturias (PA-18-PF-BP17-126). G.A.-P. acknowledges support through the Severo Ochoa Program from the Government of the Principality of Asturias (PA-20-PF-BP19-053). K.V.V. and V.S.V. acknowledge the financial support from the Ministry of Science and Higher Education of the Russian Federation (agreement no. 075-15-2021-606). A.Y.N. acknowledges the Spanish Ministry of Science, Innovation, and Universities (national projects MAT2017-88358-C3-3-R and PID2020-115221GB-C42) and the Basque Department of Education (PIBA-2020-1-0014). R.H. acknowledges financial support from the Spanish Ministry of Science, Innovation, and Universities (national project number RTI2018-094830-B-100 and project number MDM-2016-0618 of the Marie de Maeztu Units of Excellence Program) and the Basque Government (grant number IT1164-19).","date_published":"2021-10-08T00:00:00Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","article_processing_charge":"Yes","title":"Focusing of in-plane hyperbolic polaritons in van der Waals crystals with tailored infrared nanoantennas","arxiv":1,"publication":"Science Advances","language":[{"iso":"eng"}],"file_date_updated":"2021-10-27T14:16:06Z"},{"external_id":{"isi":["000702042400001"],"arxiv":["2102.05397"]},"scopus_import":"1","issue":"9","file":[{"creator":"cziletti","success":1,"file_size":2215016,"date_created":"2021-10-28T12:06:01Z","file_name":"2021_NewJPhys_Sahu.pdf","file_id":"10193","checksum":"ace603e8f0962b3ba55f23fa34f57764","access_level":"open_access","date_updated":"2021-10-28T12:06:01Z","content_type":"application/pdf","relation":"main_file"}],"publication_identifier":{"eissn":["13672630"]},"oa_version":"Published Version","doi":"10.1088/1367-2630/ac23f1","oa":1,"day":"29","article_type":"original","date_published":"2021-09-29T00:00:00Z","acknowledgement":"We thank Paula Sanematsu, Matthias Merkel, Daniel Sussman, Cristina Marchetti and Edouard Hannezo for helpful discussions, and M Merkel for developing and sharing the original version of the 3D Voronoi code. This work was primarily funded by NSF-PHY-1607416, NSF-PHY-2014192 , and are in the division of physics at the National Science Foundation. PS and MLM acknowledge additional support from Simons Grant No. 454947.\r\n","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","ddc":["570"],"status":"public","file_date_updated":"2021-10-28T12:06:01Z","article_processing_charge":"Yes","title":"Geometric signatures of tissue surface tension in a three-dimensional model of confluent tissue","arxiv":1,"publication":"New Journal of Physics","language":[{"iso":"eng"}],"department":[{"_id":"EdHa"}],"publisher":"IOP Publishing","citation":{"apa":"Sahu, P., Schwarz, J. M., &#38; Manning, M. L. (2021). Geometric signatures of tissue surface tension in a three-dimensional model of confluent tissue. <i>New Journal of Physics</i>. IOP Publishing. <a href=\"https://doi.org/10.1088/1367-2630/ac23f1\">https://doi.org/10.1088/1367-2630/ac23f1</a>","mla":"Sahu, Preeti, et al. “Geometric Signatures of Tissue Surface Tension in a Three-Dimensional Model of Confluent Tissue.” <i>New Journal of Physics</i>, vol. 23, no. 9, 093043, IOP Publishing, 2021, doi:<a href=\"https://doi.org/10.1088/1367-2630/ac23f1\">10.1088/1367-2630/ac23f1</a>.","ieee":"P. Sahu, J. M. Schwarz, and M. L. Manning, “Geometric signatures of tissue surface tension in a three-dimensional model of confluent tissue,” <i>New Journal of Physics</i>, vol. 23, no. 9. IOP Publishing, 2021.","ama":"Sahu P, Schwarz JM, Manning ML. Geometric signatures of tissue surface tension in a three-dimensional model of confluent tissue. <i>New Journal of Physics</i>. 2021;23(9). doi:<a href=\"https://doi.org/10.1088/1367-2630/ac23f1\">10.1088/1367-2630/ac23f1</a>","short":"P. Sahu, J.M. Schwarz, M.L. Manning, New Journal of Physics 23 (2021).","chicago":"Sahu, Preeti, J. M. Schwarz, and M. Lisa Manning. “Geometric Signatures of Tissue Surface Tension in a Three-Dimensional Model of Confluent Tissue.” <i>New Journal of Physics</i>. IOP Publishing, 2021. <a href=\"https://doi.org/10.1088/1367-2630/ac23f1\">https://doi.org/10.1088/1367-2630/ac23f1</a>.","ista":"Sahu P, Schwarz JM, Manning ML. 2021. Geometric signatures of tissue surface tension in a three-dimensional model of confluent tissue. New Journal of Physics. 23(9), 093043."},"volume":23,"quality_controlled":"1","has_accepted_license":"1","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"date_updated":"2023-08-14T08:10:31Z","abstract":[{"lang":"eng","text":"In dense biological tissues, cell types performing different roles remain segregated by maintaining sharp interfaces. To better understand the mechanisms for such sharp compartmentalization, we study the effect of an imposed heterotypic tension at the interface between two distinct cell types in a fully 3D Voronoi model for confluent tissues. We find that cells rapidly sort and self-organize to generate a tissue-scale interface between cell types, and cells adjacent to this interface exhibit signature geometric features including nematic-like ordering, bimodal facet areas, and registration, or alignment, of cell centers on either side of the two-tissue interface. The magnitude of these features scales directly with the magnitude of the imposed tension, suggesting that biologists can estimate the magnitude of tissue surface tension between two tissue types simply by segmenting a 3D tissue. To uncover the underlying physical mechanisms driving these geometric features, we develop two minimal, ordered models using two different underlying lattices that identify an energetic competition between bulk cell shapes and tissue interface area. When the interface area dominates, changes to neighbor topology are costly and occur less frequently, which generates the observed geometric features."}],"author":[{"full_name":"Sahu, Preeti","last_name":"Sahu","first_name":"Preeti","id":"55BA52EE-A185-11EA-88FD-18AD3DDC885E"},{"full_name":"Schwarz, J. M.","first_name":"J. M.","last_name":"Schwarz"},{"first_name":"M. Lisa","last_name":"Manning","full_name":"Manning, M. Lisa"}],"publication_status":"published","month":"09","isi":1,"date_created":"2021-10-24T22:01:34Z","intvolume":"        23","year":"2021","_id":"10178","type":"journal_article","article_number":"093043"},{"volume":40,"citation":{"ista":"Bajaj S, Bagley JA, Sommer CM, Vertesy A, Nagumo Wong S, Krenn V, Lévi-Strauss J, Knoblich JA. 2021. Neurotransmitter signaling regulates distinct phases of multimodal human interneuron migration. EMBO Journal. 40(23), e108714.","apa":"Bajaj, S., Bagley, J. A., Sommer, C. M., Vertesy, A., Nagumo Wong, S., Krenn, V., … Knoblich, J. A. (2021). Neurotransmitter signaling regulates distinct phases of multimodal human interneuron migration. <i>EMBO Journal</i>. Embo Press. <a href=\"https://doi.org/10.15252/embj.2021108714\">https://doi.org/10.15252/embj.2021108714</a>","mla":"Bajaj, Sunanjay, et al. “Neurotransmitter Signaling Regulates Distinct Phases of Multimodal Human Interneuron Migration.” <i>EMBO Journal</i>, vol. 40, no. 23, e108714, Embo Press, 2021, doi:<a href=\"https://doi.org/10.15252/embj.2021108714\">10.15252/embj.2021108714</a>.","ama":"Bajaj S, Bagley JA, Sommer CM, et al. Neurotransmitter signaling regulates distinct phases of multimodal human interneuron migration. <i>EMBO Journal</i>. 2021;40(23). doi:<a href=\"https://doi.org/10.15252/embj.2021108714\">10.15252/embj.2021108714</a>","short":"S. Bajaj, J.A. Bagley, C.M. Sommer, A. Vertesy, S. Nagumo Wong, V. Krenn, J. Lévi-Strauss, J.A. Knoblich, EMBO Journal 40 (2021).","ieee":"S. Bajaj <i>et al.</i>, “Neurotransmitter signaling regulates distinct phases of multimodal human interneuron migration,” <i>EMBO Journal</i>, vol. 40, no. 23. Embo Press, 2021.","chicago":"Bajaj, Sunanjay, Joshua A. Bagley, Christoph M Sommer, Abel Vertesy, Sakurako Nagumo Wong, Veronica Krenn, Julie Lévi-Strauss, and Juergen A. Knoblich. “Neurotransmitter Signaling Regulates Distinct Phases of Multimodal Human Interneuron Migration.” <i>EMBO Journal</i>. Embo Press, 2021. <a href=\"https://doi.org/10.15252/embj.2021108714\">https://doi.org/10.15252/embj.2021108714</a>."},"tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"date_updated":"2023-08-14T08:05:23Z","abstract":[{"lang":"eng","text":"Inhibitory GABAergic interneurons migrate over long distances from their extracortical origin into the developing cortex. In humans, this process is uniquely slow and prolonged, and it is unclear whether guidance cues unique to humans govern the various phases of this complex developmental process. Here, we use fused cerebral organoids to identify key roles of neurotransmitter signaling pathways in guiding the migratory behavior of human cortical interneurons. We use scRNAseq to reveal expression of GABA, glutamate, glycine, and serotonin receptors along distinct maturation trajectories across interneuron migration. We develop an image analysis software package, TrackPal, to simultaneously assess 48 parameters for entire migration tracks of individual cells. By chemical screening, we show that different modes of interneuron migration depend on distinct neurotransmitter signaling pathways, linking transcriptional maturation of interneurons with their migratory behavior. Altogether, our study provides a comprehensive quantitative analysis of human interneuron migration and its functional modulation by neurotransmitter signaling."}],"has_accepted_license":"1","quality_controlled":"1","department":[{"_id":"Bio"}],"pmid":1,"publisher":"Embo Press","type":"journal_article","article_number":"e108714","year":"2021","_id":"10179","publication_status":"published","month":"10","isi":1,"author":[{"last_name":"Bajaj","first_name":"Sunanjay","full_name":"Bajaj, Sunanjay"},{"first_name":"Joshua A.","last_name":"Bagley","full_name":"Bagley, Joshua A."},{"first_name":"Christoph M","last_name":"Sommer","full_name":"Sommer, Christoph M","orcid":"0000-0003-1216-9105","id":"4DF26D8C-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Abel","last_name":"Vertesy","full_name":"Vertesy, Abel"},{"first_name":"Sakurako","last_name":"Nagumo Wong","full_name":"Nagumo Wong, Sakurako"},{"full_name":"Krenn, Veronica","last_name":"Krenn","first_name":"Veronica"},{"full_name":"Lévi-Strauss, Julie","first_name":"Julie","last_name":"Lévi-Strauss"},{"first_name":"Juergen A.","last_name":"Knoblich","full_name":"Knoblich, Juergen A."}],"intvolume":"        40","date_created":"2021-10-24T22:01:34Z","oa":1,"day":"18","file":[{"file_id":"10541","checksum":"78d2d02e775322297e774f72810a41a4","date_updated":"2021-12-13T14:54:14Z","access_level":"open_access","content_type":"application/pdf","relation":"main_file","file_name":"2021_EMBO_Bajaj.pdf","file_size":7819881,"date_created":"2021-12-13T14:54:14Z","creator":"alisjak","success":1}],"publication_identifier":{"issn":["0261-4189"],"eissn":["1460-2075"]},"external_id":{"isi":["000708012800001"],"pmid":["34661293"]},"issue":"23","scopus_import":"1","oa_version":"Published Version","doi":"10.15252/embj.2021108714","file_date_updated":"2021-12-13T14:54:14Z","publication":"EMBO Journal","language":[{"iso":"eng"}],"article_processing_charge":"Yes (in subscription journal)","title":"Neurotransmitter signaling regulates distinct phases of multimodal human interneuron migration","acknowledgement":"We thank all Knoblich laboratory members for continued support and discussions. We thank the IMP/IMBA BioOptics facility, particularly Pawel Pasierbek, Alberto Moreno Cencerrado and Gerald Schmauss, the IMP/IMBA Molecular Biology Service, in particular Robert Heinen, the IMP Bioinformatics facility, in particular Thomas Burkard, the Vienna Biocenter Core Facilities (VBCF) Histopathology facility, in particular Tamara Engelmaier, and the VBCF Next Generation Sequencing Facility, notably Volodymyr Shubchynskyy and Carmen Czepe. We would also like to thank Simon Haendeler for advice on statistical analyses, Jose Guzman for discussions and assistance with slice culture setups, Oliver L. Eichmueller for discussions and assistance with microscopy, and E.H. Gustafson, S. Wolfinger, and D. Reumann for technical assistance regarding generation of cerebral organoids. This project received funding from the European Union’s Horizon 2020 research and innovation program under the Marie Skłodowska-Curie fellowship agreement Nr.707109 awarded to J.A.B. Work in J.A.K.'s laboratory is supported by the Austrian Federal Ministry of Education, Science and Research, the Austrian Academy of Sciences, the City of Vienna, a Research Program of the Austrian Science Fund FWF (SFBF78 Stem Cell, F 7803-B) and a European Research Council (ERC) Advanced Grant under the European 20 Union’s Horizon 2020 program (grant agreement no. 695642).","date_published":"2021-10-18T00:00:00Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","article_type":"original","status":"public","ddc":["610"]},{"oa":1,"day":"01","oa_version":"Published Version","file":[{"checksum":"3389d9d01fc58f8fb4c1a53e14a8abbf","file_id":"10192","date_updated":"2021-10-27T15:34:18Z","access_level":"open_access","relation":"main_file","content_type":"application/pdf","file_name":"2021_JMachLearnRes_Hoefler.pdf","file_size":3527521,"date_created":"2021-10-27T15:34:18Z","creator":"cziletti","success":1}],"publication_identifier":{"issn":["1532-4435"],"eissn":["1533-7928"]},"external_id":{"arxiv":["2102.00554"]},"scopus_import":"1","issue":"241","publication":"Journal of Machine Learning Research","language":[{"iso":"eng"}],"title":"Sparsity in deep learning: Pruning and growth for efficient inference and training in neural networks","article_processing_charge":"No","arxiv":1,"main_file_link":[{"url":"https://www.jmlr.org/papers/v22/21-0366.html","open_access":"1"}],"file_date_updated":"2021-10-27T15:34:18Z","status":"public","ddc":["000"],"acknowledgement":"We thank Doug Burger, Steve Scott, Marco Heddes, and the respective teams at Microsoft for inspiring discussions on the topic. We thank Angelika Steger for uplifting debates about the connections to biological brains, Sidak Pal Singh for his support regarding experimental results, and Utku Evci as well as Xin Wang for comments on previous versions of this\r\nwork. Special thanks go to Bernhard Schölkopf, our JMLR editor Samy Bengio, and the three anonymous reviewers who provided excellent comprehensive, pointed, and deep review comments that improved the quality of our manuscript significantly.","date_published":"2021-09-01T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_type":"original","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"date_updated":"2022-05-13T09:36:08Z","abstract":[{"text":"The growing energy and performance costs of deep learning have driven the community to reduce the size of neural networks by selectively pruning components. Similarly to their biological counterparts, sparse networks generalize just as well, sometimes even better than, the original dense networks. Sparsity promises to reduce the memory footprint of regular networks to fit mobile devices, as well as shorten training time for ever growing networks. In this paper, we survey prior work on sparsity in deep learning and provide an extensive tutorial of sparsification for both inference and training. We describe approaches to remove and add elements of neural networks, different training strategies to achieve model sparsity, and mechanisms to exploit sparsity in practice. Our work distills ideas from more than 300 research papers and provides guidance to practitioners who wish to utilize sparsity today, as well as to researchers whose goal is to push the frontier forward. We include the necessary background on mathematical methods in sparsification, describe phenomena such as early structure adaptation, the intricate relations between sparsity and the training process, and show techniques for achieving acceleration on real hardware. We also define a metric of pruned parameter efficiency that could serve as a baseline for comparison of different sparse networks. We close by speculating on how sparsity can improve future workloads and outline major open problems in the field.","lang":"eng"}],"has_accepted_license":"1","quality_controlled":"1","page":"1-124","volume":22,"citation":{"ista":"Hoefler T, Alistarh D-A, Ben-Nun T, Dryden N, Peste E-A. 2021. Sparsity in deep learning: Pruning and growth for efficient inference and training in neural networks. Journal of Machine Learning Research. 22(241), 1–124.","ama":"Hoefler T, Alistarh D-A, Ben-Nun T, Dryden N, Peste E-A. Sparsity in deep learning: Pruning and growth for efficient inference and training in neural networks. <i>Journal of Machine Learning Research</i>. 2021;22(241):1-124.","short":"T. Hoefler, D.-A. Alistarh, T. Ben-Nun, N. Dryden, E.-A. Peste, Journal of Machine Learning Research 22 (2021) 1–124.","chicago":"Hoefler, Torsten, Dan-Adrian Alistarh, Tal Ben-Nun, Nikoli Dryden, and Elena-Alexandra Peste. “Sparsity in Deep Learning: Pruning and Growth for Efficient Inference and Training in Neural Networks.” <i>Journal of Machine Learning Research</i>. Journal of Machine Learning Research, 2021.","ieee":"T. Hoefler, D.-A. Alistarh, T. Ben-Nun, N. Dryden, and E.-A. Peste, “Sparsity in deep learning: Pruning and growth for efficient inference and training in neural networks,” <i>Journal of Machine Learning Research</i>, vol. 22, no. 241. Journal of Machine Learning Research, pp. 1–124, 2021.","apa":"Hoefler, T., Alistarh, D.-A., Ben-Nun, T., Dryden, N., &#38; Peste, E.-A. (2021). Sparsity in deep learning: Pruning and growth for efficient inference and training in neural networks. <i>Journal of Machine Learning Research</i>. Journal of Machine Learning Research.","mla":"Hoefler, Torsten, et al. “Sparsity in Deep Learning: Pruning and Growth for Efficient Inference and Training in Neural Networks.” <i>Journal of Machine Learning Research</i>, vol. 22, no. 241, Journal of Machine Learning Research, 2021, pp. 1–124."},"publisher":"Journal of Machine Learning Research","department":[{"_id":"DaAl"}],"type":"journal_article","_id":"10180","year":"2021","intvolume":"        22","date_created":"2021-10-24T22:01:34Z","publication_status":"published","month":"09","author":[{"last_name":"Hoefler","first_name":"Torsten","full_name":"Hoefler, Torsten"},{"full_name":"Alistarh, Dan-Adrian","first_name":"Dan-Adrian","last_name":"Alistarh","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-3650-940X"},{"full_name":"Ben-Nun, Tal","last_name":"Ben-Nun","first_name":"Tal"},{"first_name":"Nikoli","last_name":"Dryden","full_name":"Dryden, Nikoli"},{"id":"32D78294-F248-11E8-B48F-1D18A9856A87","full_name":"Peste, Elena-Alexandra","first_name":"Elena-Alexandra","last_name":"Peste"}]},{"publisher":"Springer Nature","department":[{"_id":"UlWa"}],"date_updated":"2023-08-14T08:11:38Z","abstract":[{"lang":"eng","text":"In this article we study some geometric properties of proximally smooth sets. First, we introduce a modification of the metric projection and prove its existence. Then we provide an algorithm for constructing a rectifiable curve between two sufficiently close points of a proximally smooth set in a uniformly convex and uniformly smooth Banach space, with the moduli of smoothness and convexity of power type. Our algorithm returns a reasonably short curve between two sufficiently close points of a proximally smooth set, is iterative and uses our modification of the metric projection. We estimate the length of the constructed curve and its deviation from the segment with the same endpoints. These estimates coincide up to a constant factor with those for the geodesics in a proximally smooth set in a Hilbert space."}],"quality_controlled":"1","citation":{"ista":"Ivanov G, Lopushanski MS. 2021. Rectifiable curves in proximally smooth sets. Set-Valued and Variational Analysis.","apa":"Ivanov, G., &#38; Lopushanski, M. S. (2021). Rectifiable curves in proximally smooth sets. <i>Set-Valued and Variational Analysis</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s11228-021-00612-1\">https://doi.org/10.1007/s11228-021-00612-1</a>","mla":"Ivanov, Grigory, and Mariana S. Lopushanski. “Rectifiable Curves in Proximally Smooth Sets.” <i>Set-Valued and Variational Analysis</i>, Springer Nature, 2021, doi:<a href=\"https://doi.org/10.1007/s11228-021-00612-1\">10.1007/s11228-021-00612-1</a>.","ama":"Ivanov G, Lopushanski MS. Rectifiable curves in proximally smooth sets. <i>Set-Valued and Variational Analysis</i>. 2021. doi:<a href=\"https://doi.org/10.1007/s11228-021-00612-1\">10.1007/s11228-021-00612-1</a>","chicago":"Ivanov, Grigory, and Mariana S. Lopushanski. “Rectifiable Curves in Proximally Smooth Sets.” <i>Set-Valued and Variational Analysis</i>. Springer Nature, 2021. <a href=\"https://doi.org/10.1007/s11228-021-00612-1\">https://doi.org/10.1007/s11228-021-00612-1</a>.","short":"G. Ivanov, M.S. Lopushanski, Set-Valued and Variational Analysis (2021).","ieee":"G. Ivanov and M. S. Lopushanski, “Rectifiable curves in proximally smooth sets,” <i>Set-Valued and Variational Analysis</i>. Springer Nature, 2021."},"date_created":"2021-10-24T22:01:35Z","publication_status":"published","isi":1,"month":"10","author":[{"full_name":"Ivanov, Grigory","first_name":"Grigory","last_name":"Ivanov","id":"87744F66-5C6F-11EA-AFE0-D16B3DDC885E"},{"first_name":"Mariana S.","last_name":"Lopushanski","full_name":"Lopushanski, Mariana S."}],"type":"journal_article","_id":"10181","year":"2021","oa_version":"Published Version","doi":"10.1007/s11228-021-00612-1","publication_identifier":{"eissn":["1877-0541"],"issn":["0927-6947"]},"external_id":{"isi":["000705774800001"],"arxiv":["2012.10691"]},"scopus_import":"1","oa":1,"day":"09","status":"public","date_published":"2021-10-09T00:00:00Z","acknowledgement":"Theorem 2 was obtained at Steklov Mathematical Institute RAS and supported by Russian Science Foundation, grant N 19-11-00087.","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","article_type":"original","publication":"Set-Valued and Variational Analysis","language":[{"iso":"eng"}],"title":"Rectifiable curves in proximally smooth sets","article_processing_charge":"No","arxiv":1,"main_file_link":[{"url":"https://arxiv.org/abs/2012.10691","open_access":"1"}]},{"date_updated":"2024-02-28T12:52:48Z","abstract":[{"text":"We introduce a novel technique to automatically decompose an input object’s volume into a set of parts that can be represented by two opposite height fields. Such decomposition enables the manufacturing of individual parts using two-piece reusable rigid molds. Our decomposition strategy relies on a new energy formulation that utilizes a pre-computed signal on the mesh volume representing the accessibility for a predefined set of extraction directions. Thanks to this novel formulation, our method allows for efficient optimization of a fabrication-aware partitioning of volumes in a completely\r\nautomatic way. We demonstrate the efficacy of our approach by generating valid volume partitionings for a wide range of complex objects and physically reproducing several of them.","lang":"eng"}],"has_accepted_license":"1","quality_controlled":"1","citation":{"mla":"Alderighi, Thomas, et al. “Volume Decomposition for Two-Piece Rigid Casting.” <i>ACM Transactions on Graphics</i>, vol. 40, no. 6, 272, Association for Computing Machinery, 2021, doi:<a href=\"https://doi.org/10.1145/3478513.3480555\">10.1145/3478513.3480555</a>.","apa":"Alderighi, T., Malomo, L., Bickel, B., Cignoni, P., &#38; Pietroni, N. (2021). Volume decomposition for two-piece rigid casting. <i>ACM Transactions on Graphics</i>. Association for Computing Machinery. <a href=\"https://doi.org/10.1145/3478513.3480555\">https://doi.org/10.1145/3478513.3480555</a>","short":"T. Alderighi, L. Malomo, B. Bickel, P. Cignoni, N. Pietroni, ACM Transactions on Graphics 40 (2021).","ama":"Alderighi T, Malomo L, Bickel B, Cignoni P, Pietroni N. Volume decomposition for two-piece rigid casting. <i>ACM Transactions on Graphics</i>. 2021;40(6). doi:<a href=\"https://doi.org/10.1145/3478513.3480555\">10.1145/3478513.3480555</a>","chicago":"Alderighi, Thomas, Luigi Malomo, Bernd Bickel, Paolo Cignoni, and Nico Pietroni. “Volume Decomposition for Two-Piece Rigid Casting.” <i>ACM Transactions on Graphics</i>. Association for Computing Machinery, 2021. <a href=\"https://doi.org/10.1145/3478513.3480555\">https://doi.org/10.1145/3478513.3480555</a>.","ieee":"T. Alderighi, L. Malomo, B. Bickel, P. Cignoni, and N. Pietroni, “Volume decomposition for two-piece rigid casting,” <i>ACM Transactions on Graphics</i>, vol. 40, no. 6. Association for Computing Machinery, 2021.","ista":"Alderighi T, Malomo L, Bickel B, Cignoni P, Pietroni N. 2021. Volume decomposition for two-piece rigid casting. ACM Transactions on Graphics. 40(6), 272."},"volume":40,"publisher":"Association for Computing Machinery","department":[{"_id":"BeBi"}],"type":"journal_article","article_number":"272","_id":"10184","year":"2021","intvolume":"        40","date_created":"2021-10-27T07:08:19Z","project":[{"_id":"24F9549A-B435-11E9-9278-68D0E5697425","name":"MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and Modeling","grant_number":"715767","call_identifier":"H2020"}],"publication_status":"published","ec_funded":1,"isi":1,"month":"12","author":[{"full_name":"Alderighi, Thomas","first_name":"Thomas","last_name":"Alderighi"},{"first_name":"Luigi","last_name":"Malomo","full_name":"Malomo, Luigi"},{"id":"49876194-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6511-9385","full_name":"Bickel, Bernd","last_name":"Bickel","first_name":"Bernd"},{"full_name":"Cignoni, Paolo","last_name":"Cignoni","first_name":"Paolo"},{"full_name":"Pietroni, Nico","first_name":"Nico","last_name":"Pietroni"}],"oa":1,"day":"01","oa_version":"Submitted Version","doi":"10.1145/3478513.3480555","file":[{"file_name":"rigidmolds-authorversion.pdf","file_id":"10185","checksum":"384ece7a9ad1026787ba9560b04336d5","date_updated":"2021-10-27T07:08:07Z","access_level":"open_access","relation":"main_file","content_type":"application/pdf","creator":"bbickel","file_size":107708317,"date_created":"2021-10-27T07:08:07Z"}],"publication_identifier":{"issn":["0730-0301"],"eissn":["1557-7368 "]},"external_id":{"isi":["000729846700077"]},"issue":"6","publication":"ACM Transactions on Graphics","language":[{"iso":"eng"}],"article_processing_charge":"No","title":"Volume decomposition for two-piece rigid casting","main_file_link":[{"url":"http://vcg.isti.cnr.it/Publications/2021/AMBCP21","open_access":"1"}],"file_date_updated":"2021-10-27T07:08:07Z","status":"public","ddc":["000"],"acknowledgement":"The authors thank Marco Callieri for all his precious help with the resin casts. The models used in the paper are courtesy of the Stanford 3D Scanning Repository, the AIM@SHAPE Shape Repository, and Thingi10K Repository. The research was partially funded by the European Research Council (ERC) MATERIALIZABLE: Intelligent fabrication-oriented computational design and modeling (grant no. 715767).","date_published":"2021-12-01T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_type":"original"},{"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","acknowledgement":"The research was partially funded by the ERC CoG 863818 (ForM-SMArt) and the Vienna Science\r\nand Technology Fund (WWTF) through project ICT15-003.","date_published":"2021-10-15T00:00:00Z","article_type":"original","status":"public","ddc":["000"],"file_date_updated":"2021-11-04T07:24:48Z","language":[{"iso":"eng"}],"publication":"Proceedings of the ACM on Programming Languages","arxiv":1,"article_processing_charge":"No","title":"The reads-from equivalence for the TSO and PSO memory models","file":[{"file_size":2903485,"date_created":"2021-11-04T07:24:48Z","creator":"cchlebak","success":1,"checksum":"9d6dce7b611853c529bb7b1915ac579e","file_id":"10215","access_level":"open_access","date_updated":"2021-11-04T07:24:48Z","relation":"main_file","content_type":"application/pdf","file_name":"2021_ProcACMPL_Bui.pdf"}],"publication_identifier":{"eissn":["2475-1421"]},"scopus_import":"1","issue":"OOPSLA","external_id":{"arxiv":["2011.11763"]},"doi":"10.1145/3485541","oa_version":"Published Version","day":"15","oa":1,"month":"10","ec_funded":1,"publication_status":"published","project":[{"name":"Formal Methods for Stochastic Models: Algorithms and Applications","_id":"0599E47C-7A3F-11EA-A408-12923DDC885E","grant_number":"863818","call_identifier":"H2020"},{"_id":"25892FC0-B435-11E9-9278-68D0E5697425","name":"Efficient Algorithms for Computer Aided Verification","grant_number":"ICT15-003"}],"author":[{"full_name":"Bui, Truc Lam","last_name":"Bui","first_name":"Truc Lam"},{"full_name":"Chatterjee, Krishnendu","first_name":"Krishnendu","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X"},{"full_name":"Gautam, Tushar","first_name":"Tushar","last_name":"Gautam"},{"full_name":"Pavlogiannis, Andreas","first_name":"Andreas","last_name":"Pavlogiannis","orcid":"0000-0002-8943-0722","id":"49704004-F248-11E8-B48F-1D18A9856A87"},{"id":"3AF3DA7C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9036-063X","full_name":"Toman, Viktor","first_name":"Viktor","last_name":"Toman"}],"intvolume":"         5","date_created":"2021-10-27T15:05:34Z","article_number":"164","related_material":{"record":[{"relation":"dissertation_contains","id":"10199","status":"public"}]},"type":"journal_article","_id":"10191","year":"2021","department":[{"_id":"GradSch"},{"_id":"KrCh"}],"keyword":["safety","risk","reliability and quality","software"],"publisher":"Association for Computing Machinery","citation":{"mla":"Bui, Truc Lam, et al. “The Reads-from Equivalence for the TSO and PSO Memory Models.” <i>Proceedings of the ACM on Programming Languages</i>, vol. 5, no. OOPSLA, 164, Association for Computing Machinery, 2021, doi:<a href=\"https://doi.org/10.1145/3485541\">10.1145/3485541</a>.","apa":"Bui, T. L., Chatterjee, K., Gautam, T., Pavlogiannis, A., &#38; Toman, V. (2021). The reads-from equivalence for the TSO and PSO memory models. <i>Proceedings of the ACM on Programming Languages</i>. Association for Computing Machinery. <a href=\"https://doi.org/10.1145/3485541\">https://doi.org/10.1145/3485541</a>","ama":"Bui TL, Chatterjee K, Gautam T, Pavlogiannis A, Toman V. The reads-from equivalence for the TSO and PSO memory models. <i>Proceedings of the ACM on Programming Languages</i>. 2021;5(OOPSLA). doi:<a href=\"https://doi.org/10.1145/3485541\">10.1145/3485541</a>","ieee":"T. L. Bui, K. Chatterjee, T. Gautam, A. Pavlogiannis, and V. Toman, “The reads-from equivalence for the TSO and PSO memory models,” <i>Proceedings of the ACM on Programming Languages</i>, vol. 5, no. OOPSLA. Association for Computing Machinery, 2021.","short":"T.L. Bui, K. Chatterjee, T. Gautam, A. Pavlogiannis, V. Toman, Proceedings of the ACM on Programming Languages 5 (2021).","chicago":"Bui, Truc Lam, Krishnendu Chatterjee, Tushar Gautam, Andreas Pavlogiannis, and Viktor Toman. “The Reads-from Equivalence for the TSO and PSO Memory Models.” <i>Proceedings of the ACM on Programming Languages</i>. Association for Computing Machinery, 2021. <a href=\"https://doi.org/10.1145/3485541\">https://doi.org/10.1145/3485541</a>.","ista":"Bui TL, Chatterjee K, Gautam T, Pavlogiannis A, Toman V. 2021. The reads-from equivalence for the TSO and PSO memory models. Proceedings of the ACM on Programming Languages. 5(OOPSLA), 164."},"volume":5,"abstract":[{"text":"In this work we solve the algorithmic problem of consistency verification for the TSO and PSO memory models given a reads-from map, denoted VTSO-rf and VPSO-rf, respectively. For an execution of n events over k threads and d variables, we establish novel bounds that scale as nk+1 for TSO and as nk+1· min(nk2, 2k· d) for PSO. Moreover, based on our solution to these problems, we develop an SMC algorithm under TSO and PSO that uses the RF equivalence. The algorithm is exploration-optimal, in the sense that it is guaranteed to explore each class of the RF partitioning exactly once, and spends polynomial time per class when k is bounded. Finally, we implement all our algorithms in the SMC tool Nidhugg, and perform a large number of experiments over benchmarks from existing literature. Our experimental results show that our algorithms for VTSO-rf and VPSO-rf provide significant scalability improvements over standard alternatives. Moreover, when used for SMC, the RF partitioning is often much coarser than the standard Shasha-Snir partitioning for TSO/PSO, which yields a significant speedup in the model checking task.\r\n\r\n","lang":"eng"}],"tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"date_updated":"2025-07-14T09:10:16Z","has_accepted_license":"1","quality_controlled":"1"},{"ddc":["000"],"status":"public","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","alternative_title":["ISTA Thesis"],"date_published":"2021-10-31T00:00:00Z","title":"Improved verification techniques for concurrent systems","article_processing_charge":"No","language":[{"iso":"eng"}],"file_date_updated":"2021-11-09T09:00:50Z","doi":"10.15479/at:ista:10199","oa_version":"Published Version","file":[{"access_level":"open_access","date_updated":"2021-11-08T14:12:22Z","checksum":"4f412a1ee60952221b499a4b1268df35","file_id":"10225","content_type":"application/pdf","relation":"main_file","file_name":"toman_th_final.pdf","file_size":2915234,"date_created":"2021-11-08T14:12:22Z","creator":"vtoman"},{"relation":"source_file","content_type":"application/zip","date_updated":"2021-11-09T09:00:50Z","access_level":"closed","file_id":"10226","checksum":"9584943f99127be2dd2963f6784c37d4","file_name":"toman_thesis.zip","date_created":"2021-11-08T14:12:46Z","file_size":8616056,"creator":"vtoman"}],"publication_identifier":{"issn":["2663-337X"]},"degree_awarded":"PhD","day":"31","oa":1,"date_created":"2021-10-29T20:09:01Z","author":[{"id":"3AF3DA7C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9036-063X","full_name":"Toman, Viktor","first_name":"Viktor","last_name":"Toman"}],"month":"10","ec_funded":1,"project":[{"grant_number":"665385","call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","name":"International IST Doctoral Program"},{"call_identifier":"FWF","grant_number":"S11402-N23","_id":"25F2ACDE-B435-11E9-9278-68D0E5697425","name":"Rigorous Systems Engineering"},{"_id":"25892FC0-B435-11E9-9278-68D0E5697425","name":"Efficient Algorithms for Computer Aided Verification","grant_number":"ICT15-003"},{"grant_number":"863818","call_identifier":"H2020","name":"Formal Methods for Stochastic Models: Algorithms and Applications","_id":"0599E47C-7A3F-11EA-A408-12923DDC885E"}],"publication_status":"published","acknowledged_ssus":[{"_id":"SSU"}],"year":"2021","_id":"10199","related_material":{"record":[{"relation":"part_of_dissertation","id":"10190","status":"public"},{"relation":"part_of_dissertation","id":"9987","status":"public"},{"relation":"part_of_dissertation","status":"public","id":"141"},{"relation":"part_of_dissertation","status":"public","id":"10191"}]},"type":"dissertation","publisher":"Institute of Science and Technology Austria","department":[{"_id":"GradSch"},{"_id":"KrCh"}],"keyword":["concurrency","verification","model checking"],"has_accepted_license":"1","abstract":[{"lang":"eng","text":"The design and verification of concurrent systems remains an open challenge due to the non-determinism that arises from the inter-process communication. In particular, concurrent programs are notoriously difficult both to be written correctly and to be analyzed formally, as complex thread interaction has to be accounted for. The difficulties are further exacerbated when concurrent programs get executed on modern-day hardware, which contains various buffering and caching mechanisms for efficiency reasons. This causes further subtle non-determinism, which can often produce very unintuitive behavior of the concurrent programs. Model checking is at the forefront of tackling the verification problem, where the task is to decide, given as input a concurrent system and a desired property, whether the system satisfies the property. The inherent state-space explosion problem in model checking of concurrent systems causes naïve explicit methods not to scale, thus more inventive methods are required. One such method is stateless model checking (SMC), which explores in memory-efficient manner the program executions rather than the states of the program. State-of-the-art SMC is typically coupled with partial order reduction (POR) techniques, which argue that certain executions provably produce identical system behavior, thus limiting the amount of executions one needs to explore in order to cover all possible behaviors. Another method to tackle the state-space explosion is symbolic model checking, where the considered techniques operate on a succinct implicit representation of the input system rather than explicitly accessing the system. In this thesis we present new techniques for verification of concurrent systems. We present several novel POR methods for SMC of concurrent programs under various models of semantics, some of which account for write-buffering mechanisms. Additionally, we present novel algorithms for symbolic model checking of finite-state concurrent systems, where the desired property of the systems is to ensure a formally defined notion of fairness."}],"supervisor":[{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu","first_name":"Krishnendu","last_name":"Chatterjee"}],"date_updated":"2025-07-14T09:10:16Z","page":"166","citation":{"ista":"Toman V. 2021. Improved verification techniques for concurrent systems. Institute of Science and Technology Austria.","apa":"Toman, V. (2021). <i>Improved verification techniques for concurrent systems</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:10199\">https://doi.org/10.15479/at:ista:10199</a>","mla":"Toman, Viktor. <i>Improved Verification Techniques for Concurrent Systems</i>. Institute of Science and Technology Austria, 2021, doi:<a href=\"https://doi.org/10.15479/at:ista:10199\">10.15479/at:ista:10199</a>.","short":"V. Toman, Improved Verification Techniques for Concurrent Systems, Institute of Science and Technology Austria, 2021.","ama":"Toman V. Improved verification techniques for concurrent systems. 2021. doi:<a href=\"https://doi.org/10.15479/at:ista:10199\">10.15479/at:ista:10199</a>","chicago":"Toman, Viktor. “Improved Verification Techniques for Concurrent Systems.” Institute of Science and Technology Austria, 2021. <a href=\"https://doi.org/10.15479/at:ista:10199\">https://doi.org/10.15479/at:ista:10199</a>.","ieee":"V. Toman, “Improved verification techniques for concurrent systems,” Institute of Science and Technology Austria, 2021."}},{"oa":1,"day":"19","oa_version":"Published Version","doi":"10.1038/s41467-021-26234-7","file":[{"date_created":"2021-11-09T13:59:26Z","file_size":7144437,"creator":"cziletti","success":1,"content_type":"application/pdf","relation":"main_file","checksum":"c40a69ae94435ecd3a30c9874a11ef2b","file_id":"10262","access_level":"open_access","date_updated":"2021-11-09T13:59:26Z","file_name":"2021_NatureComm_Pradhan.pdf"}],"publication_identifier":{"eissn":["20411723"]},"external_id":{"pmid":["34667153"],"isi":["000709050300016"]},"scopus_import":"1","issue":"1","publication":"Nature Communications","language":[{"iso":"eng"}],"title":"Satb2 acts as a gatekeeper for major developmental transitions during early vertebrate embryogenesis","article_processing_charge":"Yes","file_date_updated":"2021-11-09T13:59:26Z","status":"public","ddc":["570"],"acknowledgement":"We are grateful to the members of C.-P.H. and SG lab for discussions. Authors thank Shubha Tole for providing embryonic mouse tissues. Authors are grateful to Alessandro Mongera and Chetana Sachidanandan for generous help with Tg: Sox10: GFP line. Authors would like to thank Satyajeet Khare, Vanessa Barone, Jyothish S., Shalini Mishra, Yoshita Bhide, and Keshav Jha for assistance in experiments. We would also like to thank Chaitanya Dingare for valuable suggestions. We thank Diana Pinhiero and Alexandra Schauer for critical reading of early versions of the manuscript. This work was supported by the Centre of Excellence in Epigenetics program of the Department of Biotechnology, Government of India Phase I (BT/01/COE/09/07) to S.G. and R.K.M., and Phase II (BT/COE/34/SP17426/2016) to S.G. and JC Bose Fellowship (JCB/2019/000013) from Science and Engineering Research Board, Government of India to S.G., DST-BMWF Indo-Austrian bilateral program grant to S.G. and C.-P.H. The work using animal models was partly supported by the infrastructure support grants from the Department of Biotechnology (National Facility for Laboratory Model Organisms: BT/INF/22/SP17358/2016 and Establishment of a Pune Biotech Cluster, Model Organism to Human Disease: B-2 Whole Animal Imaging & Tissue Processing FacilityBT/Pune-Biocluster/01/2015). S.J.P. was supported by Fellowship from the Council of Scientific and Industrial Research, India and travel fellowship from the Company of Biologists, UK. P.C.R. was supported by the Early Career Fellowship of the Wellcome Trust-DBT India Alliance (IA/E/16/1/503057). A.S. was supported by UGC and R.S. was supported by CSIR India. M.S. was supported by core funding from the Tata Institute of Fundamental Research (TIFR 12P-121).","date_published":"2021-10-19T00:00:00Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","article_type":"original","date_updated":"2023-08-14T10:32:48Z","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"abstract":[{"lang":"eng","text":"Zygotic genome activation (ZGA) initiates regionalized transcription underlying distinct cellular identities. ZGA is dependent upon dynamic chromatin architecture sculpted by conserved DNA-binding proteins. However, the direct mechanistic link between the onset of ZGA and the tissue-specific transcription remains unclear. Here, we have addressed the involvement of chromatin organizer Satb2 in orchestrating both processes during zebrafish embryogenesis. Integrative analysis of transcriptome, genome-wide occupancy and chromatin accessibility reveals contrasting molecular activities of maternally deposited and zygotically synthesized Satb2. Maternal Satb2 prevents premature transcription of zygotic genes by influencing the interplay between the pluripotency factors. By contrast, zygotic Satb2 activates transcription of the same group of genes during neural crest development and organogenesis. Thus, our comparative analysis of maternal versus zygotic function of Satb2 underscores how these antithetical activities are temporally coordinated and functionally implemented highlighting the evolutionary implications of the biphasic and bimodal regulation of landmark developmental transitions by a single determinant."}],"has_accepted_license":"1","quality_controlled":"1","volume":12,"citation":{"ista":"Pradhan SJ, Reddy PC, Smutny M, Sharma A, Sako K, Oak MS, Shah R, Pal M, Deshpande O, Dsilva G, Tang Y, Mishra R, Deshpande G, Giraldez AJ, Sonawane M, Heisenberg C-PJ, Galande S. 2021. Satb2 acts as a gatekeeper for major developmental transitions during early vertebrate embryogenesis. Nature Communications. 12(1), 6094.","apa":"Pradhan, S. J., Reddy, P. C., Smutny, M., Sharma, A., Sako, K., Oak, M. S., … Galande, S. (2021). Satb2 acts as a gatekeeper for major developmental transitions during early vertebrate embryogenesis. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-021-26234-7\">https://doi.org/10.1038/s41467-021-26234-7</a>","mla":"Pradhan, Saurabh J., et al. “Satb2 Acts as a Gatekeeper for Major Developmental Transitions during Early Vertebrate Embryogenesis.” <i>Nature Communications</i>, vol. 12, no. 1, 6094, Springer Nature, 2021, doi:<a href=\"https://doi.org/10.1038/s41467-021-26234-7\">10.1038/s41467-021-26234-7</a>.","ama":"Pradhan SJ, Reddy PC, Smutny M, et al. Satb2 acts as a gatekeeper for major developmental transitions during early vertebrate embryogenesis. <i>Nature Communications</i>. 2021;12(1). doi:<a href=\"https://doi.org/10.1038/s41467-021-26234-7\">10.1038/s41467-021-26234-7</a>","short":"S.J. Pradhan, P.C. Reddy, M. Smutny, A. Sharma, K. Sako, M.S. Oak, R. Shah, M. Pal, O. Deshpande, G. Dsilva, Y. Tang, R. Mishra, G. Deshpande, A.J. Giraldez, M. Sonawane, C.-P.J. Heisenberg, S. Galande, Nature Communications 12 (2021).","chicago":"Pradhan, Saurabh J., Puli Chandramouli Reddy, Michael Smutny, Ankita Sharma, Keisuke Sako, Meghana S. Oak, Rini Shah, et al. “Satb2 Acts as a Gatekeeper for Major Developmental Transitions during Early Vertebrate Embryogenesis.” <i>Nature Communications</i>. Springer Nature, 2021. <a href=\"https://doi.org/10.1038/s41467-021-26234-7\">https://doi.org/10.1038/s41467-021-26234-7</a>.","ieee":"S. J. Pradhan <i>et al.</i>, “Satb2 acts as a gatekeeper for major developmental transitions during early vertebrate embryogenesis,” <i>Nature Communications</i>, vol. 12, no. 1. Springer Nature, 2021."},"pmid":1,"publisher":"Springer Nature","department":[{"_id":"CaHe"}],"type":"journal_article","related_material":{"link":[{"relation":"earlier_version","description":"Preprint","url":"https://doi.org/10.1101/2020.11.23.394171 "}]},"article_number":"6094","_id":"10202","year":"2021","intvolume":"        12","date_created":"2021-10-31T23:01:29Z","publication_status":"published","month":"10","isi":1,"author":[{"last_name":"Pradhan","first_name":"Saurabh J.","full_name":"Pradhan, Saurabh J."},{"first_name":"Puli Chandramouli","last_name":"Reddy","full_name":"Reddy, Puli Chandramouli"},{"id":"3FE6E4E8-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-5920-9090","full_name":"Smutny, Michael","last_name":"Smutny","first_name":"Michael"},{"full_name":"Sharma, Ankita","first_name":"Ankita","last_name":"Sharma"},{"orcid":"0000-0002-6453-8075","id":"3BED66BE-F248-11E8-B48F-1D18A9856A87","full_name":"Sako, Keisuke","last_name":"Sako","first_name":"Keisuke"},{"last_name":"Oak","first_name":"Meghana S.","full_name":"Oak, Meghana S."},{"last_name":"Shah","first_name":"Rini","full_name":"Shah, Rini"},{"full_name":"Pal, Mrinmoy","last_name":"Pal","first_name":"Mrinmoy"},{"full_name":"Deshpande, Ojas","last_name":"Deshpande","first_name":"Ojas"},{"full_name":"Dsilva, Greg","first_name":"Greg","last_name":"Dsilva"},{"full_name":"Tang, Yin","first_name":"Yin","last_name":"Tang"},{"full_name":"Mishra, Rakesh","last_name":"Mishra","first_name":"Rakesh"},{"first_name":"Girish","last_name":"Deshpande","full_name":"Deshpande, Girish"},{"first_name":"Antonio J.","last_name":"Giraldez","full_name":"Giraldez, Antonio J."},{"full_name":"Sonawane, Mahendra","last_name":"Sonawane","first_name":"Mahendra"},{"full_name":"Heisenberg, Carl-Philipp J","last_name":"Heisenberg","first_name":"Carl-Philipp J","orcid":"0000-0002-0912-4566","id":"39427864-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Galande, Sanjeev","last_name":"Galande","first_name":"Sanjeev"}]},{"department":[{"_id":"BjHo"}],"publisher":"Springer Nature","volume":12,"citation":{"apa":"Sortino, L., Zotev, P. G., Phillips, C. L., Brash, A. J., Cambiasso, J., Marensi, E., … Tartakovskii, A. I. (2021). Bright single photon emitters with enhanced quantum efficiency in a two-dimensional semiconductor coupled with dielectric nano-antennas. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-021-26262-3\">https://doi.org/10.1038/s41467-021-26262-3</a>","mla":"Sortino, Luca, et al. “Bright Single Photon Emitters with Enhanced Quantum Efficiency in a Two-Dimensional Semiconductor Coupled with Dielectric Nano-Antennas.” <i>Nature Communications</i>, vol. 12, 6063, Springer Nature, 2021, doi:<a href=\"https://doi.org/10.1038/s41467-021-26262-3\">10.1038/s41467-021-26262-3</a>.","ama":"Sortino L, Zotev PG, Phillips CL, et al. Bright single photon emitters with enhanced quantum efficiency in a two-dimensional semiconductor coupled with dielectric nano-antennas. <i>Nature Communications</i>. 2021;12. doi:<a href=\"https://doi.org/10.1038/s41467-021-26262-3\">10.1038/s41467-021-26262-3</a>","ieee":"L. Sortino <i>et al.</i>, “Bright single photon emitters with enhanced quantum efficiency in a two-dimensional semiconductor coupled with dielectric nano-antennas,” <i>Nature Communications</i>, vol. 12. Springer Nature, 2021.","short":"L. Sortino, P.G. Zotev, C.L. Phillips, A.J. Brash, J. Cambiasso, E. Marensi, A.M. Fox, S.A. Maier, R. Sapienza, A.I. Tartakovskii, Nature Communications 12 (2021).","chicago":"Sortino, Luca, Panaiot G. Zotev, Catherine L. Phillips, Alistair J. Brash, Javier Cambiasso, Elena Marensi, A. Mark Fox, Stefan A. Maier, Riccardo Sapienza, and Alexander I. Tartakovskii. “Bright Single Photon Emitters with Enhanced Quantum Efficiency in a Two-Dimensional Semiconductor Coupled with Dielectric Nano-Antennas.” <i>Nature Communications</i>. Springer Nature, 2021. <a href=\"https://doi.org/10.1038/s41467-021-26262-3\">https://doi.org/10.1038/s41467-021-26262-3</a>.","ista":"Sortino L, Zotev PG, Phillips CL, Brash AJ, Cambiasso J, Marensi E, Fox AM, Maier SA, Sapienza R, Tartakovskii AI. 2021. Bright single photon emitters with enhanced quantum efficiency in a two-dimensional semiconductor coupled with dielectric nano-antennas. Nature Communications. 12, 6063."},"abstract":[{"lang":"eng","text":"Single photon emitters in atomically-thin semiconductors can be deterministically positioned using strain induced by underlying nano-structures. Here, we couple monolayer WSe2 to high-refractive-index gallium phosphide dielectric nano-antennas providing both optical enhancement and monolayer deformation. For single photon emitters formed on such nano-antennas, we find very low (femto-Joule) saturation pulse energies and up to 104 times brighter photoluminescence than in WSe2 placed on low-refractive-index SiO2 pillars. We show that the key to these observations is the increase on average by a factor of 5 of the quantum efficiency of the emitters coupled to the nano-antennas. This further allows us to gain new insights into their photoluminescence dynamics, revealing the roles of the dark exciton reservoir and Auger processes. We also find that the coherence time of such emitters is limited by intrinsic dephasing processes. Our work establishes dielectric nano-antennas as a platform for high-efficiency quantum light generation in monolayer semiconductors."}],"tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"date_updated":"2023-08-14T08:12:12Z","quality_controlled":"1","has_accepted_license":"1","isi":1,"month":"10","publication_status":"published","author":[{"full_name":"Sortino, Luca","last_name":"Sortino","first_name":"Luca"},{"full_name":"Zotev, Panaiot G.","last_name":"Zotev","first_name":"Panaiot G."},{"last_name":"Phillips","first_name":"Catherine L.","full_name":"Phillips, Catherine L."},{"full_name":"Brash, Alistair J.","first_name":"Alistair J.","last_name":"Brash"},{"first_name":"Javier","last_name":"Cambiasso","full_name":"Cambiasso, Javier"},{"orcid":"0000-0001-7173-4923","id":"0BE7553A-1004-11EA-B805-18983DDC885E","full_name":"Marensi, Elena","first_name":"Elena","last_name":"Marensi"},{"full_name":"Fox, A. Mark","first_name":"A. Mark","last_name":"Fox"},{"first_name":"Stefan A.","last_name":"Maier","full_name":"Maier, Stefan A."},{"first_name":"Riccardo","last_name":"Sapienza","full_name":"Sapienza, Riccardo"},{"full_name":"Tartakovskii, Alexander I.","last_name":"Tartakovskii","first_name":"Alexander I."}],"intvolume":"        12","date_created":"2021-10-31T23:01:30Z","article_number":"6063","type":"journal_article","_id":"10203","year":"2021","publication_identifier":{"eissn":["2041-1723"]},"file":[{"content_type":"application/pdf","relation":"main_file","access_level":"open_access","date_updated":"2021-11-03T11:31:24Z","checksum":"8580d128389860f732028c521cd5949e","file_id":"10212","file_name":"2021_NatComm_Sortino.pdf","date_created":"2021-11-03T11:31:24Z","file_size":1434201,"creator":"cchlebak","success":1}],"scopus_import":"1","external_id":{"isi":["000708601800015"],"arxiv":["2103.16986"]},"doi":"10.1038/s41467-021-26262-3","oa_version":"Published Version","day":"18","oa":1,"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","acknowledgement":"L.S., P.G.Z., and A.I.T. thank the financial support of the European Graphene Flagship Project under grant agreements 881603 and EPSRC grant EP/S030751/1. L.S. and A.I.T. thank the European Union’s Horizon 2020 research and innovation programme under ITN Spin-NANO Marie Sklodowska-Curie grant agreement no. 676108. P.G.Z. and A.I.T. thank the European Union’s Horizon 2020 research and innovation programme under ITN 4PHOTON Marie Sklodowska-Curie grant agreement no. 721394. J.C., S.A.M., and R.S. acknowledge funding by EPSRC (EP/P033369 and EP/M013812). C.L.P., A.J.B., A.I.T., and A.M.F. acknowledge funding by EPSRC Programme Grant EP/N031776/1. S.A.M. acknowledges the Lee-Lucas Chair in Physics, the Solar Energies go Hybrid (SolTech) programme, and the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) under Germany’s Excellence Strategy - EXC 2089/1 - 390776260.","date_published":"2021-10-18T00:00:00Z","article_type":"original","status":"public","ddc":["530"],"file_date_updated":"2021-11-03T11:31:24Z","language":[{"iso":"eng"}],"publication":"Nature Communications","arxiv":1,"title":"Bright single photon emitters with enhanced quantum efficiency in a two-dimensional semiconductor coupled with dielectric nano-antennas","article_processing_charge":"No"},{"citation":{"ista":"Osang GF, Edelsbrunner H, Saadatfar M. 2021. Topological signatures and stability of hexagonal close packing and Barlow stackings. Soft Matter. 17(40), 9107–9115.","short":"G.F. Osang, H. Edelsbrunner, M. Saadatfar, Soft Matter 17 (2021) 9107–9115.","ieee":"G. F. Osang, H. Edelsbrunner, and M. Saadatfar, “Topological signatures and stability of hexagonal close packing and Barlow stackings,” <i>Soft Matter</i>, vol. 17, no. 40. Royal Society of Chemistry , pp. 9107–9115, 2021.","chicago":"Osang, Georg F, Herbert Edelsbrunner, and Mohammad Saadatfar. “Topological Signatures and Stability of Hexagonal Close Packing and Barlow Stackings.” <i>Soft Matter</i>. Royal Society of Chemistry , 2021. <a href=\"https://doi.org/10.1039/d1sm00774b\">https://doi.org/10.1039/d1sm00774b</a>.","ama":"Osang GF, Edelsbrunner H, Saadatfar M. Topological signatures and stability of hexagonal close packing and Barlow stackings. <i>Soft Matter</i>. 2021;17(40):9107-9115. doi:<a href=\"https://doi.org/10.1039/d1sm00774b\">10.1039/d1sm00774b</a>","apa":"Osang, G. F., Edelsbrunner, H., &#38; Saadatfar, M. (2021). Topological signatures and stability of hexagonal close packing and Barlow stackings. <i>Soft Matter</i>. Royal Society of Chemistry . <a href=\"https://doi.org/10.1039/d1sm00774b\">https://doi.org/10.1039/d1sm00774b</a>","mla":"Osang, Georg F., et al. “Topological Signatures and Stability of Hexagonal Close Packing and Barlow Stackings.” <i>Soft Matter</i>, vol. 17, no. 40, Royal Society of Chemistry , 2021, pp. 9107–15, doi:<a href=\"https://doi.org/10.1039/d1sm00774b\">10.1039/d1sm00774b</a>."},"volume":17,"page":"9107-9115","quality_controlled":"1","has_accepted_license":"1","date_updated":"2023-10-03T09:24:27Z","abstract":[{"lang":"eng","text":"Two common representations of close packings of identical spheres consisting of hexagonal layers, called Barlow stackings, appear abundantly in minerals and metals. These motifs, however, occupy an identical portion of space and bear identical first-order topological signatures as measured by persistent homology. Here we present a novel method based on k-fold covers that unambiguously distinguishes between these patterns. Moreover, our approach provides topological evidence that the FCC motif is the more stable of the two in the context of evolving experimental sphere packings during the transition from disordered to an ordered state. We conclude that our approach can be generalised to distinguish between various Barlow stackings manifested in minerals and metals."}],"department":[{"_id":"HeEd"}],"publisher":"Royal Society of Chemistry ","pmid":1,"_id":"10204","year":"2021","type":"journal_article","author":[{"full_name":"Osang, Georg F","first_name":"Georg F","last_name":"Osang","orcid":"0000-0002-8882-5116","id":"464B40D6-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Edelsbrunner, Herbert","last_name":"Edelsbrunner","first_name":"Herbert","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9823-6833"},{"first_name":"Mohammad","last_name":"Saadatfar","full_name":"Saadatfar, Mohammad"}],"publication_status":"published","project":[{"grant_number":"788183","call_identifier":"H2020","name":"Alpha Shape Theory Extended","_id":"266A2E9E-B435-11E9-9278-68D0E5697425"},{"grant_number":"Z00342","call_identifier":"FWF","name":"The Wittgenstein Prize","_id":"268116B8-B435-11E9-9278-68D0E5697425"}],"ec_funded":1,"isi":1,"month":"10","date_created":"2021-10-31T23:01:30Z","intvolume":"        17","oa":1,"day":"20","external_id":{"isi":["000700090000001"],"pmid":["34569592"]},"issue":"40","scopus_import":"1","publication_identifier":{"eissn":["1744-6848"],"issn":["1744-683X"]},"file":[{"file_id":"14385","checksum":"b4da0c420530295e61b153960f6cb350","access_level":"open_access","date_updated":"2023-10-03T09:21:42Z","content_type":"application/pdf","relation":"main_file","file_name":"2021_SoftMatter_acceptedversion_Osang.pdf","file_size":4678788,"date_created":"2023-10-03T09:21:42Z","success":1,"creator":"dernst"}],"oa_version":"Submitted Version","doi":"10.1039/d1sm00774b","file_date_updated":"2023-10-03T09:21:42Z","title":"Topological signatures and stability of hexagonal close packing and Barlow stackings","article_processing_charge":"No","publication":"Soft Matter","language":[{"iso":"eng"}],"article_type":"original","acknowledgement":"MS acknowledges the support by Australian Research Council funding through the ARC Training Centre for M3D Innovation (IC180100008). MS thanks M. Hanifpour and N. Francois for their input and valuable discussions. This project has received funding from the European Research Council (ERC) under the European Union's Horizon 2020 research and innovation programme, grant no. 788183 and from the Wittgenstein Prize, Austrian Science Fund (FWF), grant no. Z 342-N31.","date_published":"2021-10-20T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["540"],"status":"public"},{"acknowledgement":"We thank Christoph Lampert and Alex Greengold for fruitful discussions. This research was supported in part by the Simons Institute for the Theory of Computing, the Austrian Science Fund (FWF) under grant Z211-N23 (Wittgenstein Award), and the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement No. 754411.","date_published":"2021-10-06T00:00:00Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","alternative_title":["LNCS"],"status":"public","main_file_link":[{"url":"https://arxiv.org/abs/2009.06429","open_access":"1"}],"title":"Into the unknown: active monitoring of neural networks","article_processing_charge":"No","arxiv":1,"publication":"21st International Conference on Runtime Verification","language":[{"iso":"eng"}],"external_id":{"isi":["000719383800003"],"arxiv":["2009.06429"]},"scopus_import":"1","publication_identifier":{"eissn":["1611-3349"],"eisbn":["978-3-030-88494-9"],"issn":["0302-9743"],"isbn":["9-783-0308-8493-2"]},"oa_version":"Preprint","doi":"10.1007/978-3-030-88494-9_3","oa":1,"day":"06","author":[{"first_name":"Anna","last_name":"Lukina","full_name":"Lukina, Anna","id":"CBA4D1A8-0FE8-11E9-BDE6-07BFE5697425"},{"full_name":"Schilling, Christian","first_name":"Christian","last_name":"Schilling","orcid":"0000-0003-3658-1065","id":"3A2F4DCE-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Henzinger, Thomas A","first_name":"Thomas A","last_name":"Henzinger","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2985-7724"}],"publication_status":"published","project":[{"_id":"260C2330-B435-11E9-9278-68D0E5697425","name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020","grant_number":"754411"},{"name":"The Wittgenstein Prize","_id":"25F42A32-B435-11E9-9278-68D0E5697425","grant_number":"Z211","call_identifier":"FWF"}],"ec_funded":1,"isi":1,"month":"10","date_created":"2021-10-31T23:01:31Z","year":"2021","_id":"10206","type":"conference","related_material":{"record":[{"status":"public","id":"13234","relation":"extended_version"}]},"keyword":["monitoring","neural networks","novelty detection"],"department":[{"_id":"ToHe"}],"publisher":"Springer Nature","conference":{"end_date":"2021-10-14","start_date":"2021-10-11","location":"Virtual","name":"RV: Runtime Verification"},"citation":{"ista":"Lukina A, Schilling C, Henzinger TA. 2021. Into the unknown: active monitoring of neural networks. 21st International Conference on Runtime Verification. RV: Runtime Verification, LNCS, vol. 12974, 42–61.","ieee":"A. Lukina, C. Schilling, and T. A. Henzinger, “Into the unknown: active monitoring of neural networks,” in <i>21st International Conference on Runtime Verification</i>, Virtual, 2021, vol. 12974, pp. 42–61.","short":"A. Lukina, C. Schilling, T.A. Henzinger, in:, 21st International Conference on Runtime Verification, Springer Nature, Cham, 2021, pp. 42–61.","chicago":"Lukina, Anna, Christian Schilling, and Thomas A Henzinger. “Into the Unknown: Active Monitoring of Neural Networks.” In <i>21st International Conference on Runtime Verification</i>, 12974:42–61. Cham: Springer Nature, 2021. <a href=\"https://doi.org/10.1007/978-3-030-88494-9_3\">https://doi.org/10.1007/978-3-030-88494-9_3</a>.","ama":"Lukina A, Schilling C, Henzinger TA. Into the unknown: active monitoring of neural networks. In: <i>21st International Conference on Runtime Verification</i>. Vol 12974. Cham: Springer Nature; 2021:42-61. doi:<a href=\"https://doi.org/10.1007/978-3-030-88494-9_3\">10.1007/978-3-030-88494-9_3</a>","apa":"Lukina, A., Schilling, C., &#38; Henzinger, T. A. (2021). Into the unknown: active monitoring of neural networks. In <i>21st International Conference on Runtime Verification</i> (Vol. 12974, pp. 42–61). Cham: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-030-88494-9_3\">https://doi.org/10.1007/978-3-030-88494-9_3</a>","mla":"Lukina, Anna, et al. “Into the Unknown: Active Monitoring of Neural Networks.” <i>21st International Conference on Runtime Verification</i>, vol. 12974, Springer Nature, 2021, pp. 42–61, doi:<a href=\"https://doi.org/10.1007/978-3-030-88494-9_3\">10.1007/978-3-030-88494-9_3</a>."},"volume":"12974 ","page":"42-61","place":"Cham","quality_controlled":"1","date_updated":"2024-01-30T12:06:56Z","abstract":[{"lang":"eng","text":"Neural-network classifiers achieve high accuracy when predicting the class of an input that they were trained to identify. Maintaining this accuracy in dynamic environments, where inputs frequently fall outside the fixed set of initially known classes, remains a challenge. The typical approach is to detect inputs from novel classes and retrain the classifier on an augmented dataset. However, not only the classifier but also the detection mechanism needs to adapt in order to distinguish between newly learned and yet unknown input classes. To address this challenge, we introduce an algorithmic framework for active monitoring of a neural network. A monitor wrapped in our framework operates in parallel with the neural network and interacts with a human user via a series of interpretable labeling queries for incremental adaptation. In addition, we propose an adaptive quantitative monitor to improve precision. An experimental evaluation on a diverse set of benchmarks with varying numbers of classes confirms the benefits of our active monitoring framework in dynamic scenarios."}]},{"_id":"10211","year":"2021","type":"journal_article","date_created":"2021-11-03T10:59:08Z","author":[{"id":"27EB676C-8706-11E9-9510-7717E6697425","orcid":"0000-0002-3242-7020","full_name":"Mondelli, Marco","first_name":"Marco","last_name":"Mondelli"},{"full_name":"Thrampoulidis, Christos","first_name":"Christos","last_name":"Thrampoulidis"},{"full_name":"Venkataramanan, Ramji","last_name":"Venkataramanan","first_name":"Ramji"}],"isi":1,"month":"08","project":[{"_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854","name":"IST Austria Open Access Fund"}],"publication_status":"published","has_accepted_license":"1","quality_controlled":"1","abstract":[{"lang":"eng","text":"We study the problem of recovering an unknown signal 𝑥𝑥 given measurements obtained from a generalized linear model with a Gaussian sensing matrix. Two popular solutions are based on a linear estimator 𝑥𝑥^L and a spectral estimator 𝑥𝑥^s. The former is a data-dependent linear combination of the columns of the measurement matrix, and its analysis is quite simple. The latter is the principal eigenvector of a data-dependent matrix, and a recent line of work has studied its performance. In this paper, we show how to optimally combine 𝑥𝑥^L and 𝑥𝑥^s. At the heart of our analysis is the exact characterization of the empirical joint distribution of (𝑥𝑥,𝑥𝑥^L,𝑥𝑥^s) in the high-dimensional limit. This allows us to compute the Bayes-optimal combination of 𝑥𝑥^L and 𝑥𝑥^s, given the limiting distribution of the signal 𝑥𝑥. When the distribution of the signal is Gaussian, then the Bayes-optimal combination has the form 𝜃𝑥𝑥^L+𝑥𝑥^s and we derive the optimal combination coefficient. In order to establish the limiting distribution of (𝑥𝑥,𝑥𝑥^L,𝑥𝑥^s), we design and analyze an approximate message passing algorithm whose iterates give 𝑥𝑥^L and approach 𝑥𝑥^s. Numerical simulations demonstrate the improvement of the proposed combination with respect to the two methods considered separately."}],"date_updated":"2023-09-05T14:13:57Z","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"citation":{"ista":"Mondelli M, Thrampoulidis C, Venkataramanan R. 2021. Optimal combination of linear and spectral estimators for generalized linear models. Foundations of Computational Mathematics.","mla":"Mondelli, Marco, et al. “Optimal Combination of Linear and Spectral Estimators for Generalized Linear Models.” <i>Foundations of Computational Mathematics</i>, Springer, 2021, doi:<a href=\"https://doi.org/10.1007/s10208-021-09531-x\">10.1007/s10208-021-09531-x</a>.","apa":"Mondelli, M., Thrampoulidis, C., &#38; Venkataramanan, R. (2021). Optimal combination of linear and spectral estimators for generalized linear models. <i>Foundations of Computational Mathematics</i>. Springer. <a href=\"https://doi.org/10.1007/s10208-021-09531-x\">https://doi.org/10.1007/s10208-021-09531-x</a>","ama":"Mondelli M, Thrampoulidis C, Venkataramanan R. Optimal combination of linear and spectral estimators for generalized linear models. <i>Foundations of Computational Mathematics</i>. 2021. doi:<a href=\"https://doi.org/10.1007/s10208-021-09531-x\">10.1007/s10208-021-09531-x</a>","chicago":"Mondelli, Marco, Christos Thrampoulidis, and Ramji Venkataramanan. “Optimal Combination of Linear and Spectral Estimators for Generalized Linear Models.” <i>Foundations of Computational Mathematics</i>. Springer, 2021. <a href=\"https://doi.org/10.1007/s10208-021-09531-x\">https://doi.org/10.1007/s10208-021-09531-x</a>.","ieee":"M. Mondelli, C. Thrampoulidis, and R. Venkataramanan, “Optimal combination of linear and spectral estimators for generalized linear models,” <i>Foundations of Computational Mathematics</i>. Springer, 2021.","short":"M. Mondelli, C. Thrampoulidis, R. Venkataramanan, Foundations of Computational Mathematics (2021)."},"publisher":"Springer","keyword":["Applied Mathematics","Computational Theory and Mathematics","Computational Mathematics","Analysis"],"department":[{"_id":"MaMo"}],"arxiv":1,"article_processing_charge":"Yes (via OA deal)","title":"Optimal combination of linear and spectral estimators for generalized linear models","language":[{"iso":"eng"}],"publication":"Foundations of Computational Mathematics","file_date_updated":"2021-12-13T15:47:54Z","ddc":["510"],"status":"public","article_type":"original","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","acknowledgement":"M. Mondelli would like to thank Andrea Montanari for helpful discussions. All the authors would like to thank the anonymous reviewers for their helpful comments.","date_published":"2021-08-17T00:00:00Z","day":"17","oa":1,"doi":"10.1007/s10208-021-09531-x","oa_version":"Published Version","scopus_import":"1","external_id":{"arxiv":["2008.03326"],"isi":["000685721000001"]},"file":[{"creator":"alisjak","success":1,"file_size":2305731,"date_created":"2021-12-13T15:47:54Z","file_name":"2021_Springer_Mondelli.pdf","file_id":"10542","checksum":"9ea12dd8045a0678000a3a59295221cb","access_level":"open_access","date_updated":"2021-12-13T15:47:54Z","relation":"main_file","content_type":"application/pdf"}],"publication_identifier":{"eissn":["1615-3383"],"issn":["1615-3375"]}},{"oa_version":"Published Version","doi":"10.4230/LIPIcs.DISC.2021.52","publication_identifier":{"issn":["1868-8969"],"isbn":["9-783-9597-7210-5"]},"file":[{"file_name":"2021_LIPIcsDISC_BChatterjee.pdf","content_type":"application/pdf","relation":"main_file","date_updated":"2021-11-12T09:23:22Z","access_level":"open_access","file_id":"10276","checksum":"76546df112a0ba1166c864d33d7834e2","success":1,"creator":"cchlebak","date_created":"2021-11-12T09:23:22Z","file_size":795860}],"external_id":{"arxiv":["2003.01697"]},"scopus_import":"1","oa":1,"day":"04","status":"public","ddc":["000"],"date_published":"2021-10-04T00:00:00Z","acknowledgement":"This work was partially funded by National Supercomputing Mission, Govt. of India under the project “Concurrent and Distributed Programming primitives and algorithms for Temporal Graphs”(DST/NSM/R&D_Exascale/2021/16).\r\n","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","alternative_title":["LIPIcs"],"publication":"35th International Symposium on Distributed Computing","language":[{"iso":"eng"}],"article_processing_charge":"No","title":"Brief announcement: Non-blocking dynamic unbounded graphs with worst-case amortized bounds","arxiv":1,"file_date_updated":"2021-11-12T09:23:22Z","conference":{"end_date":"2021-10-08","location":"Freiburg, Germany","start_date":"2021-10-04","name":"DISC: Distributed Computing"},"publisher":"Schloss Dagstuhl - Leibniz Zentrum für Informatik","department":[{"_id":"DaAl"}],"date_updated":"2021-11-12T09:42:55Z","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"abstract":[{"text":"This paper reports a new concurrent graph data structure that supports updates of both edges and vertices and queries: Breadth-first search, Single-source shortest-path, and Betweenness centrality. The operations are provably linearizable and non-blocking.","lang":"eng"}],"has_accepted_license":"1","quality_controlled":"1","citation":{"ieee":"B. Chatterjee, S. Peri, and M. Sa, “Brief announcement: Non-blocking dynamic unbounded graphs with worst-case amortized bounds,” in <i>35th International Symposium on Distributed Computing</i>, Freiburg, Germany, 2021, vol. 209.","ama":"Chatterjee B, Peri S, Sa M. Brief announcement: Non-blocking dynamic unbounded graphs with worst-case amortized bounds. In: <i>35th International Symposium on Distributed Computing</i>. Vol 209. Schloss Dagstuhl - Leibniz Zentrum für Informatik; 2021. doi:<a href=\"https://doi.org/10.4230/LIPIcs.DISC.2021.52\">10.4230/LIPIcs.DISC.2021.52</a>","chicago":"Chatterjee, Bapi, Sathya Peri, and Muktikanta Sa. “Brief Announcement: Non-Blocking Dynamic Unbounded Graphs with Worst-Case Amortized Bounds.” In <i>35th International Symposium on Distributed Computing</i>, Vol. 209. Schloss Dagstuhl - Leibniz Zentrum für Informatik, 2021. <a href=\"https://doi.org/10.4230/LIPIcs.DISC.2021.52\">https://doi.org/10.4230/LIPIcs.DISC.2021.52</a>.","short":"B. Chatterjee, S. Peri, M. Sa, in:, 35th International Symposium on Distributed Computing, Schloss Dagstuhl - Leibniz Zentrum für Informatik, 2021.","apa":"Chatterjee, B., Peri, S., &#38; Sa, M. (2021). Brief announcement: Non-blocking dynamic unbounded graphs with worst-case amortized bounds. In <i>35th International Symposium on Distributed Computing</i> (Vol. 209). Freiburg, Germany: Schloss Dagstuhl - Leibniz Zentrum für Informatik. <a href=\"https://doi.org/10.4230/LIPIcs.DISC.2021.52\">https://doi.org/10.4230/LIPIcs.DISC.2021.52</a>","mla":"Chatterjee, Bapi, et al. “Brief Announcement: Non-Blocking Dynamic Unbounded Graphs with Worst-Case Amortized Bounds.” <i>35th International Symposium on Distributed Computing</i>, vol. 209, 52, Schloss Dagstuhl - Leibniz Zentrum für Informatik, 2021, doi:<a href=\"https://doi.org/10.4230/LIPIcs.DISC.2021.52\">10.4230/LIPIcs.DISC.2021.52</a>.","ista":"Chatterjee B, Peri S, Sa M. 2021. Brief announcement: Non-blocking dynamic unbounded graphs with worst-case amortized bounds. 35th International Symposium on Distributed Computing. DISC: Distributed Computing, LIPIcs, vol. 209, 52."},"volume":209,"intvolume":"       209","date_created":"2021-11-07T23:01:23Z","publication_status":"published","month":"10","author":[{"id":"3C41A08A-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","first_name":"Bapi","full_name":"Chatterjee, Bapi"},{"full_name":"Peri, Sathya","first_name":"Sathya","last_name":"Peri"},{"full_name":"Sa, Muktikanta","first_name":"Muktikanta","last_name":"Sa"}],"type":"conference","article_number":"52","_id":"10216","year":"2021"},{"file_date_updated":"2021-11-12T09:33:26Z","language":[{"iso":"eng"}],"publication":"35th International Symposium on Distributed Computing","article_processing_charge":"No","title":"Lower bounds for shared-memory leader election under bounded write contention","alternative_title":["LIPIcs"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2021-10-04T00:00:00Z","acknowledgement":"Dan Alistarh: Supported in part by the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement No 805223 ScaleML). Giorgi Nadiradze: Supported in part by the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement No 805223 ScaleML). The authors would like to thank the DISC anonymous reviewers for their useful\r\nfeedback and comments.","status":"public","ddc":["000"],"day":"04","oa":1,"publication_identifier":{"isbn":["9-783-9597-7210-5"],"issn":["1868-8969"]},"file":[{"success":1,"creator":"cchlebak","file_size":706791,"date_created":"2021-11-12T09:33:26Z","file_name":"2021_LIPIcsDISC_Alistarh.pdf","file_id":"10277","checksum":"b4cdc6668c899a601c5e6a96b8ca54d9","access_level":"open_access","date_updated":"2021-11-12T09:33:26Z","content_type":"application/pdf","relation":"main_file"}],"scopus_import":"1","doi":"10.4230/LIPIcs.DISC.2021.4","oa_version":"Published Version","article_number":"4","type":"conference","_id":"10217","year":"2021","ec_funded":1,"month":"10","publication_status":"published","project":[{"_id":"268A44D6-B435-11E9-9278-68D0E5697425","name":"Elastic Coordination for Scalable Machine Learning","call_identifier":"H2020","grant_number":"805223"}],"author":[{"id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-3650-940X","first_name":"Dan-Adrian","last_name":"Alistarh","full_name":"Alistarh, Dan-Adrian"},{"last_name":"Gelashvili","first_name":"Rati","full_name":"Gelashvili, Rati"},{"full_name":"Nadiradze, Giorgi","last_name":"Nadiradze","first_name":"Giorgi","id":"3279A00C-F248-11E8-B48F-1D18A9856A87"}],"intvolume":"       209","date_created":"2021-11-07T23:01:23Z","citation":{"ista":"Alistarh D-A, Gelashvili R, Nadiradze G. 2021. Lower bounds for shared-memory leader election under bounded write contention. 35th International Symposium on Distributed Computing. DISC: Distributed Computing, LIPIcs, vol. 209, 4.","mla":"Alistarh, Dan-Adrian, et al. “Lower Bounds for Shared-Memory Leader Election under Bounded Write Contention.” <i>35th International Symposium on Distributed Computing</i>, vol. 209, 4, Schloss Dagstuhl - Leibniz Zentrum für Informatik, 2021, doi:<a href=\"https://doi.org/10.4230/LIPIcs.DISC.2021.4\">10.4230/LIPIcs.DISC.2021.4</a>.","apa":"Alistarh, D.-A., Gelashvili, R., &#38; Nadiradze, G. (2021). Lower bounds for shared-memory leader election under bounded write contention. In <i>35th International Symposium on Distributed Computing</i> (Vol. 209). Freiburg, Germany: Schloss Dagstuhl - Leibniz Zentrum für Informatik. <a href=\"https://doi.org/10.4230/LIPIcs.DISC.2021.4\">https://doi.org/10.4230/LIPIcs.DISC.2021.4</a>","ieee":"D.-A. Alistarh, R. Gelashvili, and G. Nadiradze, “Lower bounds for shared-memory leader election under bounded write contention,” in <i>35th International Symposium on Distributed Computing</i>, Freiburg, Germany, 2021, vol. 209.","short":"D.-A. Alistarh, R. Gelashvili, G. Nadiradze, in:, 35th International Symposium on Distributed Computing, Schloss Dagstuhl - Leibniz Zentrum für Informatik, 2021.","chicago":"Alistarh, Dan-Adrian, Rati Gelashvili, and Giorgi Nadiradze. “Lower Bounds for Shared-Memory Leader Election under Bounded Write Contention.” In <i>35th International Symposium on Distributed Computing</i>, Vol. 209. Schloss Dagstuhl - Leibniz Zentrum für Informatik, 2021. <a href=\"https://doi.org/10.4230/LIPIcs.DISC.2021.4\">https://doi.org/10.4230/LIPIcs.DISC.2021.4</a>.","ama":"Alistarh D-A, Gelashvili R, Nadiradze G. Lower bounds for shared-memory leader election under bounded write contention. In: <i>35th International Symposium on Distributed Computing</i>. Vol 209. Schloss Dagstuhl - Leibniz Zentrum für Informatik; 2021. doi:<a href=\"https://doi.org/10.4230/LIPIcs.DISC.2021.4\">10.4230/LIPIcs.DISC.2021.4</a>"},"volume":209,"abstract":[{"text":"This paper gives tight logarithmic lower bounds on the solo step complexity of leader election in an asynchronous shared-memory model with single-writer multi-reader (SWMR) registers, for both deterministic and randomized obstruction-free algorithms. The approach extends to lower bounds for deterministic and randomized obstruction-free algorithms using multi-writer registers under bounded write concurrency, showing a trade-off between the solo step complexity of a leader election algorithm, and the worst-case number of stalls incurred by a processor in an execution.","lang":"eng"}],"tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"date_updated":"2022-08-19T07:23:28Z","has_accepted_license":"1","quality_controlled":"1","department":[{"_id":"DaAl"}],"conference":{"name":"DISC: Distributed Computing","location":"Freiburg, Germany","start_date":"2021-10-04","end_date":"2021-10-08"},"publisher":"Schloss Dagstuhl - Leibniz Zentrum für Informatik"},{"doi":"10.4230/LIPIcs.DISC.2021.43","oa_version":"Published Version","file":[{"content_type":"application/pdf","relation":"main_file","file_id":"10274","checksum":"fd2a690f6856d21247e9aa952b0e2885","date_updated":"2021-11-12T08:16:44Z","access_level":"open_access","file_name":"2021_LIPIcsDISC_Alistarh.pdf","date_created":"2021-11-12T08:16:44Z","file_size":534219,"success":1,"creator":"cchlebak"}],"publication_identifier":{"isbn":["9-783-9597-7210-5"],"issn":["1868-8969"]},"scopus_import":"1","external_id":{"arxiv":["2102.08808"]},"day":"04","oa":1,"status":"public","ddc":["000"],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","alternative_title":["LIPIcs"],"date_published":"2021-10-04T00:00:00Z","acknowledgement":"This project has received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement No 840605.","language":[{"iso":"eng"}],"publication":"35th International Symposium on Distributed Computing","arxiv":1,"article_processing_charge":"No","title":"Brief announcement: Fast graphical population protocols","file_date_updated":"2021-11-12T08:16:44Z","conference":{"start_date":"2021-10-04","location":"Freiburg, Germany","end_date":"2021-10-08","name":"DISC: Distributed Computing "},"publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","department":[{"_id":"DaAl"}],"abstract":[{"text":"Let G be a graph on n nodes. In the stochastic population protocol model, a collection of n indistinguishable, resource-limited nodes collectively solve tasks via pairwise interactions. In each interaction, two randomly chosen neighbors first read each other’s states, and then update their local states. A rich line of research has established tight upper and lower bounds on the complexity of fundamental tasks, such as majority and leader election, in this model, when G is a clique. Specifically, in the clique, these tasks can be solved fast, i.e., in n polylog n pairwise interactions, with high probability, using at most polylog n states per node. In this work, we consider the more general setting where G is an arbitrary graph, and present a technique for simulating protocols designed for fully-connected networks in any connected regular graph. Our main result is a simulation that is efficient on many interesting graph families: roughly, the simulation overhead is polylogarithmic in the number of nodes, and quadratic in the conductance of the graph. As an example, this implies that, in any regular graph with conductance φ, both leader election and exact majority can be solved in φ^{-2} ⋅ n polylog n pairwise interactions, with high probability, using at most φ^{-2} ⋅ polylog n states per node. This shows that there are fast and space-efficient population protocols for leader election and exact majority on graphs with good expansion properties.","lang":"eng"}],"date_updated":"2023-02-21T09:24:08Z","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"has_accepted_license":"1","quality_controlled":"1","volume":209,"citation":{"ista":"Alistarh D-A, Gelashvili R, Rybicki J. 2021. Brief announcement: Fast graphical population protocols. 35th International Symposium on Distributed Computing. DISC: Distributed Computing , LIPIcs, vol. 209, 43.","short":"D.-A. Alistarh, R. Gelashvili, J. Rybicki, in:, 35th International Symposium on Distributed Computing, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2021.","ama":"Alistarh D-A, Gelashvili R, Rybicki J. Brief announcement: Fast graphical population protocols. In: <i>35th International Symposium on Distributed Computing</i>. Vol 209. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2021. doi:<a href=\"https://doi.org/10.4230/LIPIcs.DISC.2021.43\">10.4230/LIPIcs.DISC.2021.43</a>","chicago":"Alistarh, Dan-Adrian, Rati Gelashvili, and Joel Rybicki. “Brief Announcement: Fast Graphical Population Protocols.” In <i>35th International Symposium on Distributed Computing</i>, Vol. 209. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2021. <a href=\"https://doi.org/10.4230/LIPIcs.DISC.2021.43\">https://doi.org/10.4230/LIPIcs.DISC.2021.43</a>.","ieee":"D.-A. Alistarh, R. Gelashvili, and J. Rybicki, “Brief announcement: Fast graphical population protocols,” in <i>35th International Symposium on Distributed Computing</i>, Freiburg, Germany, 2021, vol. 209.","apa":"Alistarh, D.-A., Gelashvili, R., &#38; Rybicki, J. (2021). Brief announcement: Fast graphical population protocols. In <i>35th International Symposium on Distributed Computing</i> (Vol. 209). Freiburg, Germany: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. <a href=\"https://doi.org/10.4230/LIPIcs.DISC.2021.43\">https://doi.org/10.4230/LIPIcs.DISC.2021.43</a>","mla":"Alistarh, Dan-Adrian, et al. “Brief Announcement: Fast Graphical Population Protocols.” <i>35th International Symposium on Distributed Computing</i>, vol. 209, 43, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2021, doi:<a href=\"https://doi.org/10.4230/LIPIcs.DISC.2021.43\">10.4230/LIPIcs.DISC.2021.43</a>."},"intvolume":"       209","date_created":"2021-11-07T23:01:24Z","month":"10","ec_funded":1,"project":[{"grant_number":"840605","call_identifier":"H2020","_id":"26A5D39A-B435-11E9-9278-68D0E5697425","name":"Coordination in constrained and natural distributed systems"}],"publication_status":"published","author":[{"last_name":"Alistarh","first_name":"Dan-Adrian","full_name":"Alistarh, Dan-Adrian","orcid":"0000-0003-3650-940X","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Rati","last_name":"Gelashvili","full_name":"Gelashvili, Rati"},{"orcid":"0000-0002-6432-6646","id":"334EFD2E-F248-11E8-B48F-1D18A9856A87","last_name":"Rybicki","first_name":"Joel","full_name":"Rybicki, Joel"}],"article_number":"43","type":"conference","year":"2021","_id":"10218"},{"status":"public","ddc":["000"],"date_published":"2021-10-04T00:00:00Z","acknowledgement":"Janne H. Korhonen: Project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement No 805223 ScaleML). Ami Paz: We acknowledge the Austrian Science Fund (FWF) and netIDEE SCIENCE project P 33775-N. Stefan Schmid: Research supported by the Austrian Science Fund (FWF) project ADVISE, I 4800-N, 2020-2023.\r\n","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","alternative_title":["LIPIcs"],"publication":"35th International Symposium on Distributed Computing","language":[{"iso":"eng"}],"title":"Brief announcement: Sinkless orientation is hard also in the supported LOCAL model","article_processing_charge":"No","arxiv":1,"file_date_updated":"2021-11-12T08:27:42Z","oa_version":"Published Version","doi":"10.4230/LIPIcs.DISC.2021.58","publication_identifier":{"issn":["1868-8969"],"isbn":["9-783-9597-7210-5"]},"file":[{"file_id":"10275","checksum":"c43188dc2070bbd2bf5fd6fdaf9ce36d","access_level":"open_access","date_updated":"2021-11-12T08:27:42Z","content_type":"application/pdf","relation":"main_file","file_name":"2021_LIPIcsDISC_Korhonen.pdf","file_size":474242,"date_created":"2021-11-12T08:27:42Z","creator":"cchlebak","success":1}],"external_id":{"arxiv":["2108.02655"]},"scopus_import":"1","oa":1,"day":"04","intvolume":"       209","date_created":"2021-11-07T23:01:24Z","publication_status":"published","project":[{"call_identifier":"H2020","grant_number":"805223","_id":"268A44D6-B435-11E9-9278-68D0E5697425","name":"Elastic Coordination for Scalable Machine Learning"}],"month":"10","ec_funded":1,"author":[{"id":"C5402D42-15BC-11E9-A202-CA2BE6697425","last_name":"Korhonen","first_name":"Janne","full_name":"Korhonen, Janne"},{"full_name":"Paz, Ami","last_name":"Paz","first_name":"Ami"},{"id":"334EFD2E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6432-6646","full_name":"Rybicki, Joel","first_name":"Joel","last_name":"Rybicki"},{"last_name":"Schmid","first_name":"Stefan","full_name":"Schmid, Stefan"},{"first_name":"Jukka","last_name":"Suomela","full_name":"Suomela, Jukka"}],"type":"conference","article_number":"58","year":"2021","_id":"10219","conference":{"end_date":"2021-10-08","location":"Freiburg, Germany","start_date":"2021-10-04","name":"DISC: Distributed Computing "},"publisher":"Schloss Dagstuhl - Leibniz Zentrum für Informatik","department":[{"_id":"DaAl"}],"tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"date_updated":"2021-11-12T09:37:18Z","abstract":[{"lang":"eng","text":"We show that any algorithm that solves the sinkless orientation problem in the supported LOCAL model requires Ω(log n) rounds, and this is tight. The supported LOCAL is at least as strong as the usual LOCAL model, and as a corollary this also gives a new, short and elementary proof that shows that the round complexity of the sinkless orientation problem in the deterministic LOCAL model is Ω(log n)."}],"has_accepted_license":"1","quality_controlled":"1","citation":{"ista":"Korhonen J, Paz A, Rybicki J, Schmid S, Suomela J. 2021. Brief announcement: Sinkless orientation is hard also in the supported LOCAL model. 35th International Symposium on Distributed Computing. DISC: Distributed Computing , LIPIcs, vol. 209, 58.","mla":"Korhonen, Janne, et al. “Brief Announcement: Sinkless Orientation Is Hard Also in the Supported LOCAL Model.” <i>35th International Symposium on Distributed Computing</i>, vol. 209, 58, Schloss Dagstuhl - Leibniz Zentrum für Informatik, 2021, doi:<a href=\"https://doi.org/10.4230/LIPIcs.DISC.2021.58\">10.4230/LIPIcs.DISC.2021.58</a>.","apa":"Korhonen, J., Paz, A., Rybicki, J., Schmid, S., &#38; Suomela, J. (2021). Brief announcement: Sinkless orientation is hard also in the supported LOCAL model. In <i>35th International Symposium on Distributed Computing</i> (Vol. 209). Freiburg, Germany: Schloss Dagstuhl - Leibniz Zentrum für Informatik. <a href=\"https://doi.org/10.4230/LIPIcs.DISC.2021.58\">https://doi.org/10.4230/LIPIcs.DISC.2021.58</a>","chicago":"Korhonen, Janne, Ami Paz, Joel Rybicki, Stefan Schmid, and Jukka Suomela. “Brief Announcement: Sinkless Orientation Is Hard Also in the Supported LOCAL Model.” In <i>35th International Symposium on Distributed Computing</i>, Vol. 209. Schloss Dagstuhl - Leibniz Zentrum für Informatik, 2021. <a href=\"https://doi.org/10.4230/LIPIcs.DISC.2021.58\">https://doi.org/10.4230/LIPIcs.DISC.2021.58</a>.","ama":"Korhonen J, Paz A, Rybicki J, Schmid S, Suomela J. Brief announcement: Sinkless orientation is hard also in the supported LOCAL model. In: <i>35th International Symposium on Distributed Computing</i>. Vol 209. Schloss Dagstuhl - Leibniz Zentrum für Informatik; 2021. doi:<a href=\"https://doi.org/10.4230/LIPIcs.DISC.2021.58\">10.4230/LIPIcs.DISC.2021.58</a>","ieee":"J. Korhonen, A. Paz, J. Rybicki, S. Schmid, and J. Suomela, “Brief announcement: Sinkless orientation is hard also in the supported LOCAL model,” in <i>35th International Symposium on Distributed Computing</i>, Freiburg, Germany, 2021, vol. 209.","short":"J. Korhonen, A. Paz, J. Rybicki, S. Schmid, J. Suomela, in:, 35th International Symposium on Distributed Computing, Schloss Dagstuhl - Leibniz Zentrum für Informatik, 2021."},"volume":209}]