[{"date_published":"2021-07-08T00:00:00Z","date_updated":"2024-03-06T12:30:45Z","publication_status":"submitted","year":"2021","author":[{"full_name":"Feliciangeli, Dario","orcid":"0000-0003-0754-8530","first_name":"Dario","id":"41A639AA-F248-11E8-B48F-1D18A9856A87","last_name":"Feliciangeli"},{"first_name":"Simone Anna Elvira","id":"856966FE-A408-11E9-977E-802DE6697425","last_name":"Rademacher","full_name":"Rademacher, Simone Anna Elvira","orcid":"0000-0001-5059-4466"},{"last_name":"Seiringer","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","first_name":"Robert","orcid":"0000-0002-6781-0521","full_name":"Seiringer, Robert"}],"ec_funded":1,"_id":"9791","article_number":"2107.03720 ","language":[{"iso":"eng"}],"date_created":"2021-08-06T08:49:45Z","related_material":{"record":[{"status":"public","id":"10755","relation":"later_version"},{"relation":"dissertation_contains","status":"public","id":"9733"}]},"article_processing_charge":"No","oa":1,"acknowledgement":"We thank Herbert Spohn for helpful comments. Funding from the European Union’s Horizon 2020 research and innovation programme under the ERC grant agreement No. 694227 (D.F. and R.S.) and under the Marie Skłodowska-Curie Grant Agreement No. 754411 (S.R.) is gratefully acknowledged..","status":"public","oa_version":"Preprint","project":[{"name":"ISTplus - Postdoctoral Fellowships","_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"754411"},{"_id":"25C6DC12-B435-11E9-9278-68D0E5697425","name":"Analysis of quantum many-body systems","call_identifier":"H2020","grant_number":"694227"}],"citation":{"ieee":"D. Feliciangeli, S. A. E. Rademacher, and R. Seiringer, “The effective mass problem for the Landau-Pekar equations,” <i>arXiv</i>. .","ista":"Feliciangeli D, Rademacher SAE, Seiringer R. The effective mass problem for the Landau-Pekar equations. arXiv, 2107.03720.","ama":"Feliciangeli D, Rademacher SAE, Seiringer R. The effective mass problem for the Landau-Pekar equations. <i>arXiv</i>.","chicago":"Feliciangeli, Dario, Simone Anna Elvira Rademacher, and Robert Seiringer. “The Effective Mass Problem for the Landau-Pekar Equations.” <i>ArXiv</i>, n.d.","short":"D. Feliciangeli, S.A.E. Rademacher, R. Seiringer, ArXiv (n.d.).","mla":"Feliciangeli, Dario, et al. “The Effective Mass Problem for the Landau-Pekar Equations.” <i>ArXiv</i>, 2107.03720.","apa":"Feliciangeli, D., Rademacher, S. A. E., &#38; Seiringer, R. (n.d.). The effective mass problem for the Landau-Pekar equations. <i>arXiv</i>."},"publication":"arXiv","abstract":[{"text":"We provide a definition of the effective mass for the classical polaron described by the Landau-Pekar equations. It is based on a novel variational principle, minimizing the energy functional over states with given (initial) velocity. The resulting formula for the polaron's effective mass agrees with the prediction by Landau and Pekar.","lang":"eng"}],"external_id":{"arxiv":["2107.03720"]},"ddc":["510"],"month":"07","department":[{"_id":"RoSe"}],"arxiv":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2107.03720"}],"type":"preprint","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","day":"08","title":"The effective mass problem for the Landau-Pekar equations"},{"doi":"10.48550/arXiv.2106.11217","publication":"arXiv","abstract":[{"text":"This paper establishes new connections between many-body quantum systems, One-body Reduced Density Matrices Functional Theory (1RDMFT) and Optimal Transport (OT), by interpreting the problem of computing the ground-state energy of a finite dimensional composite quantum system at positive temperature as a non-commutative entropy regularized Optimal Transport problem. We develop a new approach to fully characterize the dual-primal solutions in such non-commutative setting. The mathematical formalism is particularly relevant in quantum chemistry: numerical realizations of the many-electron ground state energy can be computed via a non-commutative version of Sinkhorn algorithm. Our approach allows to prove convergence and robustness of this algorithm, which, to our best knowledge, were unknown even in the two marginal case. Our methods are based on careful a priori estimates in the dual problem, which we believe to be of independent interest. Finally, the above results are extended in 1RDMFT setting, where bosonic or fermionic symmetry conditions are enforced on the problem.","lang":"eng"}],"ddc":["510"],"main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2106.11217","open_access":"1"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"preprint","title":"A non-commutative entropic optimal transport approach to quantum composite systems at positive temperature","date_published":"2021-07-21T00:00:00Z","year":"2021","publication_status":"submitted","ec_funded":1,"article_number":"2106.11217","related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"9733"},{"status":"public","id":"10030","relation":"dissertation_contains"},{"relation":"later_version","status":"public","id":"12911"}]},"language":[{"iso":"eng"}],"article_processing_charge":"No","oa":1,"has_accepted_license":"1","status":"public","oa_version":"Preprint","project":[{"call_identifier":"H2020","grant_number":"694227","name":"Analysis of quantum many-body systems","_id":"25C6DC12-B435-11E9-9278-68D0E5697425"},{"_id":"256E75B8-B435-11E9-9278-68D0E5697425","name":"Optimal Transport and Stochastic Dynamics","grant_number":"716117","call_identifier":"H2020"},{"grant_number":"F6504","_id":"fc31cba2-9c52-11eb-aca3-ff467d239cd2","name":"Taming Complexity in Partial Differential Systems"}],"citation":{"mla":"Feliciangeli, Dario, et al. “A Non-Commutative Entropic Optimal Transport Approach to Quantum Composite Systems at Positive Temperature.” <i>ArXiv</i>, 2106.11217, doi:<a href=\"https://doi.org/10.48550/arXiv.2106.11217\">10.48550/arXiv.2106.11217</a>.","apa":"Feliciangeli, D., Gerolin, A., &#38; Portinale, L. (n.d.). A non-commutative entropic optimal transport approach to quantum composite systems at positive temperature. <i>arXiv</i>. <a href=\"https://doi.org/10.48550/arXiv.2106.11217\">https://doi.org/10.48550/arXiv.2106.11217</a>","short":"D. Feliciangeli, A. Gerolin, L. Portinale, ArXiv (n.d.).","ama":"Feliciangeli D, Gerolin A, Portinale L. A non-commutative entropic optimal transport approach to quantum composite systems at positive temperature. <i>arXiv</i>. doi:<a href=\"https://doi.org/10.48550/arXiv.2106.11217\">10.48550/arXiv.2106.11217</a>","ista":"Feliciangeli D, Gerolin A, Portinale L. A non-commutative entropic optimal transport approach to quantum composite systems at positive temperature. arXiv, 2106.11217.","chicago":"Feliciangeli, Dario, Augusto Gerolin, and Lorenzo Portinale. “A Non-Commutative Entropic Optimal Transport Approach to Quantum Composite Systems at Positive Temperature.” <i>ArXiv</i>, n.d. <a href=\"https://doi.org/10.48550/arXiv.2106.11217\">https://doi.org/10.48550/arXiv.2106.11217</a>.","ieee":"D. Feliciangeli, A. Gerolin, and L. Portinale, “A non-commutative entropic optimal transport approach to quantum composite systems at positive temperature,” <i>arXiv</i>. ."},"external_id":{"arxiv":["2106.11217"]},"month":"07","department":[{"_id":"RoSe"},{"_id":"JaMa"}],"arxiv":1,"day":"21","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":"2023-11-14T13:21:01Z","author":[{"orcid":"0000-0003-0754-8530","full_name":"Feliciangeli, Dario","last_name":"Feliciangeli","id":"41A639AA-F248-11E8-B48F-1D18A9856A87","first_name":"Dario"},{"full_name":"Gerolin, Augusto","last_name":"Gerolin","first_name":"Augusto"},{"full_name":"Portinale, Lorenzo","id":"30AD2CBC-F248-11E8-B48F-1D18A9856A87","last_name":"Portinale","first_name":"Lorenzo"}],"license":"https://creativecommons.org/licenses/by/4.0/","_id":"9792","date_created":"2021-08-06T09:07:12Z","acknowledgement":"This work started when A.G. was visiting the Erwin Schrödinger Institute and then continued when D.F. and L.P visited the Theoretical Chemistry Department of the Vrije Universiteit Amsterdam. The authors thanks the hospitality of both places and, especially, P. Gori-Giorgi and K. Giesbertz for fruitful discussions and literature suggestions in the early state of the project. Finally, the authors also thanks J. Maas and R. Seiringer for their feedback and useful comments to a first draft of the article.  L.P. acknowledges support by the Austrian Science Fund (FWF), grants No W1245 and NoF65. D.F acknowledges support by the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreements No 716117 and No 694227). A.G. acknowledges funding by the European Research Council under H2020/MSCA-IF “OTmeetsDFT” [grant ID: 795942]."},{"pmid":1,"isi":1,"month":"08","department":[{"_id":"SiHi"}],"intvolume":"       109","day":"04","project":[{"name":"Principles of Neural Stem Cell Lineage Progression in Cerebral Cortex Development","_id":"260018B0-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"725780"}],"scopus_import":"1","citation":{"mla":"Baldwin, Katherine T., et al. “HepaCAM Controls Astrocyte Self-Organization and Coupling.” <i>Neuron</i>, vol. 109, no. 15, Elsevier, 2021, p. 2427–2442.e10, doi:<a href=\"https://doi.org/10.1016/j.neuron.2021.05.025\">10.1016/j.neuron.2021.05.025</a>.","short":"K.T. Baldwin, C.X. Tan, S.T. Strader, C. Jiang, J.T. Savage, X. Elorza-Vidal, X. Contreras, T. Rülicke, S. Hippenmeyer, R. Estévez, R.-R. Ji, C. Eroglu, Neuron 109 (2021) 2427–2442.e10.","apa":"Baldwin, K. T., Tan, C. X., Strader, S. T., Jiang, C., Savage, J. T., Elorza-Vidal, X., … Eroglu, C. (2021). HepaCAM controls astrocyte self-organization and coupling. <i>Neuron</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.neuron.2021.05.025\">https://doi.org/10.1016/j.neuron.2021.05.025</a>","ama":"Baldwin KT, Tan CX, Strader ST, et al. HepaCAM controls astrocyte self-organization and coupling. <i>Neuron</i>. 2021;109(15):2427-2442.e10. doi:<a href=\"https://doi.org/10.1016/j.neuron.2021.05.025\">10.1016/j.neuron.2021.05.025</a>","ista":"Baldwin KT, Tan CX, Strader ST, Jiang C, Savage JT, Elorza-Vidal X, Contreras X, Rülicke T, Hippenmeyer S, Estévez R, Ji R-R, Eroglu C. 2021. HepaCAM controls astrocyte self-organization and coupling. Neuron. 109(15), 2427–2442.e10.","chicago":"Baldwin, Katherine T., Christabel X. Tan, Samuel T. Strader, Changyu Jiang, Justin T. Savage, Xabier Elorza-Vidal, Ximena Contreras, et al. “HepaCAM Controls Astrocyte Self-Organization and Coupling.” <i>Neuron</i>. Elsevier, 2021. <a href=\"https://doi.org/10.1016/j.neuron.2021.05.025\">https://doi.org/10.1016/j.neuron.2021.05.025</a>.","ieee":"K. T. Baldwin <i>et al.</i>, “HepaCAM controls astrocyte self-organization and coupling,” <i>Neuron</i>, vol. 109, no. 15. Elsevier, p. 2427–2442.e10, 2021."},"external_id":{"isi":["000692851900010"],"pmid":["34171291"]},"date_created":"2021-08-06T09:08:25Z","_id":"9793","volume":109,"acknowledgement":"This work was supported by the National Institutes of Health (R01 DA047258 and R01 NS102237 to C.E., F32 NS100392 to K.T.B.) and the Holland-Trice Brain Research Award (to C.E.). K.T.B. was supported by postdoctoral fellowships from the Foerster-Bernstein Family and The Hartwell Foundation. The Hippenmeyer lab was supported by the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovations program (725780 LinPro) to S.H. R.E. was supported by Ministerio de Ciencia y Tecnología (RTI2018-093493-B-I00). We thank the Duke Light Microscopy Core Facility, the Duke Transgenic Mouse Facility, Dr. U. Schulte for assistance with proteomic experiments, and Dr. D. Silver for critical review of the manuscript. Cartoon elements of figure panels were created using BioRender.com.","issue":"15","date_updated":"2023-09-27T07:46:09Z","article_type":"original","author":[{"last_name":"Baldwin","first_name":"Katherine T.","full_name":"Baldwin, Katherine T."},{"first_name":"Christabel X.","last_name":"Tan","full_name":"Tan, Christabel X."},{"full_name":"Strader, Samuel T.","first_name":"Samuel T.","last_name":"Strader"},{"full_name":"Jiang, Changyu","first_name":"Changyu","last_name":"Jiang"},{"last_name":"Savage","first_name":"Justin T.","full_name":"Savage, Justin T."},{"last_name":"Elorza-Vidal","first_name":"Xabier","full_name":"Elorza-Vidal, Xabier"},{"full_name":"Contreras, Ximena","last_name":"Contreras","id":"475990FE-F248-11E8-B48F-1D18A9856A87","first_name":"Ximena"},{"last_name":"Rülicke","first_name":"Thomas","full_name":"Rülicke, Thomas"},{"first_name":"Simon","id":"37B36620-F248-11E8-B48F-1D18A9856A87","last_name":"Hippenmeyer","full_name":"Hippenmeyer, Simon","orcid":"0000-0003-2279-1061"},{"last_name":"Estévez","first_name":"Raúl","full_name":"Estévez, Raúl"},{"last_name":"Ji","first_name":"Ru-Rong","full_name":"Ji, Ru-Rong"},{"first_name":"Cagla","last_name":"Eroglu","full_name":"Eroglu, Cagla"}],"main_file_link":[{"url":"https://doi.org/10.1016/j.neuron.2021.05.025","open_access":"1"}],"title":"HepaCAM controls astrocyte self-organization and coupling","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"journal_article","doi":"10.1016/j.neuron.2021.05.025","publication":"Neuron","abstract":[{"lang":"eng","text":"Astrocytes extensively infiltrate the neuropil to regulate critical aspects of synaptic development and function. This process is regulated by transcellular interactions between astrocytes and neurons via cell adhesion molecules. How astrocytes coordinate developmental processes among one another to parse out the synaptic neuropil and form non-overlapping territories is unknown. Here we identify a molecular mechanism regulating astrocyte-astrocyte interactions during development to coordinate astrocyte morphogenesis and gap junction coupling. We show that hepaCAM, a disease-linked, astrocyte-enriched cell adhesion molecule, regulates astrocyte competition for territory and morphological complexity in the developing mouse cortex. Furthermore, conditional deletion of Hepacam from developing astrocytes significantly impairs gap junction coupling between astrocytes and disrupts the balance between synaptic excitation and inhibition. Mutations in HEPACAM cause megalencephalic leukoencephalopathy with subcortical cysts in humans. Therefore, our findings suggest that disruption of astrocyte self-organization mechanisms could be an underlying cause of neural pathology."}],"language":[{"iso":"eng"}],"ec_funded":1,"article_processing_charge":"No","oa":1,"oa_version":"Published Version","status":"public","date_published":"2021-08-04T00:00:00Z","publication_identifier":{"issn":["0896-6273"],"eissn":["1097-4199"]},"publication_status":"published","year":"2021","page":"2427-2442.e10","quality_controlled":"1","publisher":"Elsevier"},{"isi":1,"department":[{"_id":"JoFi"}],"month":"07","arxiv":1,"intvolume":"         6","day":"15","scopus_import":"1","citation":{"ieee":"S. Mobassem, N. J. Lambert, A. R. Rueda Sanchez, J. M. Fink, G. Leuchs, and H. G. L. Schwefel, “Thermal noise in electro-optic devices at cryogenic temperatures,” <i>Quantum Science and Technology</i>, vol. 6, no. 4. IOP Publishing, 2021.","ista":"Mobassem S, Lambert NJ, Rueda Sanchez AR, Fink JM, Leuchs G, Schwefel HGL. 2021. Thermal noise in electro-optic devices at cryogenic temperatures. Quantum Science and Technology. 6(4), 045005.","ama":"Mobassem S, Lambert NJ, Rueda Sanchez AR, Fink JM, Leuchs G, Schwefel HGL. Thermal noise in electro-optic devices at cryogenic temperatures. <i>Quantum Science and Technology</i>. 2021;6(4). doi:<a href=\"https://doi.org/10.1088/2058-9565/ac0f36\">10.1088/2058-9565/ac0f36</a>","chicago":"Mobassem, Sonia, Nicholas J. Lambert, Alfredo R Rueda Sanchez, Johannes M Fink, Gerd Leuchs, and Harald G.L. Schwefel. “Thermal Noise in Electro-Optic Devices at Cryogenic Temperatures.” <i>Quantum Science and Technology</i>. IOP Publishing, 2021. <a href=\"https://doi.org/10.1088/2058-9565/ac0f36\">https://doi.org/10.1088/2058-9565/ac0f36</a>.","mla":"Mobassem, Sonia, et al. “Thermal Noise in Electro-Optic Devices at Cryogenic Temperatures.” <i>Quantum Science and Technology</i>, vol. 6, no. 4, 045005, IOP Publishing, 2021, doi:<a href=\"https://doi.org/10.1088/2058-9565/ac0f36\">10.1088/2058-9565/ac0f36</a>.","apa":"Mobassem, S., Lambert, N. J., Rueda Sanchez, A. R., Fink, J. M., Leuchs, G., &#38; Schwefel, H. G. L. (2021). Thermal noise in electro-optic devices at cryogenic temperatures. <i>Quantum Science and Technology</i>. IOP Publishing. <a href=\"https://doi.org/10.1088/2058-9565/ac0f36\">https://doi.org/10.1088/2058-9565/ac0f36</a>","short":"S. Mobassem, N.J. Lambert, A.R. Rueda Sanchez, J.M. Fink, G. Leuchs, H.G.L. Schwefel, Quantum Science and Technology 6 (2021)."},"external_id":{"arxiv":["2008.08764"],"isi":["000673081500001"]},"date_created":"2021-08-08T22:01:25Z","_id":"9815","volume":6,"acknowledgement":"NJL is supported by the MBIE Endeavour Fund (UOOX1805) and GL is by the Julius von Haast Fellowship of New Zealand. SM acknowledges stimulating discussions with T M Jensen.","file_date_updated":"2021-08-09T12:23:13Z","issue":"4","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":"2023-10-17T12:54:54Z","author":[{"last_name":"Mobassem","first_name":"Sonia","full_name":"Mobassem, Sonia"},{"first_name":"Nicholas J.","last_name":"Lambert","full_name":"Lambert, Nicholas J."},{"id":"3B82B0F8-F248-11E8-B48F-1D18A9856A87","last_name":"Rueda Sanchez","first_name":"Alfredo R","full_name":"Rueda Sanchez, Alfredo R","orcid":"0000-0001-6249-5860"},{"first_name":"Johannes M","id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","last_name":"Fink","full_name":"Fink, Johannes M","orcid":"0000-0001-8112-028X"},{"full_name":"Leuchs, Gerd","last_name":"Leuchs","first_name":"Gerd"},{"last_name":"Schwefel","first_name":"Harald G.L.","full_name":"Schwefel, Harald G.L."}],"article_type":"original","file":[{"date_created":"2021-08-09T12:23:13Z","relation":"main_file","checksum":"b15c2c228487a75002c3b52d56f23d5c","access_level":"open_access","content_type":"application/pdf","creator":"cchlebak","file_name":"2021_QuantumScienceTechnology_Mobassem.pdf","date_updated":"2021-08-09T12:23:13Z","file_id":"9836","file_size":2366118}],"ddc":["530"],"title":"Thermal noise in electro-optic devices at cryogenic temperatures","type":"journal_article","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","doi":"10.1088/2058-9565/ac0f36","publication":"Quantum Science and Technology","abstract":[{"text":"The quantum bits (qubits) on which superconducting quantum computers are based have energy scales corresponding to photons with GHz frequencies. The energy of photons in the gigahertz domain is too low to allow transmission through the noisy room-temperature environment, where the signal would be lost in thermal noise. Optical photons, on the other hand, have much higher energies, and signals can be detected using highly efficient single-photon detectors. Transduction from microwave to optical frequencies is therefore a potential enabling technology for quantum devices. However, in such a device the optical pump can be a source of thermal noise and thus degrade the fidelity; the similarity of input microwave state to the output optical state. In order to investigate the magnitude of this effect we model the sub-Kelvin thermal behavior of an electro-optic transducer based on a lithium niobate whispering gallery mode resonator. We find that there is an optimum power level for a continuous pump, whilst pulsed operation of the pump increases the fidelity of the conversion.","lang":"eng"}],"language":[{"iso":"eng"}],"article_number":"045005","article_processing_charge":"Yes","has_accepted_license":"1","oa":1,"oa_version":"Published Version","status":"public","date_published":"2021-07-15T00:00:00Z","publication_identifier":{"eissn":["2058-9565"]},"publication_status":"published","year":"2021","quality_controlled":"1","publisher":"IOP Publishing"},{"oa_version":"Published Version","status":"public","has_accepted_license":"1","oa":1,"article_processing_charge":"Yes","language":[{"iso":"eng"}],"article_number":"e0255267","quality_controlled":"1","publisher":"Public Library of Science","publication_identifier":{"eissn":["1932-6203"]},"publication_status":"published","year":"2021","date_published":"2021-07-29T00:00:00Z","title":"Analysis of the specificity of a COVID-19 antigen test in the Slovak mass testing program","type":"journal_article","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","ddc":["610"],"file":[{"date_created":"2021-08-09T11:52:14Z","relation":"main_file","content_type":"application/pdf","access_level":"open_access","creator":"asandaue","checksum":"ae4df60eb62f4491278588548d0c1f93","file_id":"9835","date_updated":"2021-08-09T11:52:14Z","file_name":"2021_PLoSONE_Hledík.pdf","success":1,"file_size":773921}],"abstract":[{"lang":"eng","text":"Aims: Mass antigen testing programs have been challenged because of an alleged insufficient specificity, leading to a large number of false positives. The objective of this study is to derive a lower bound of the specificity of the SD Biosensor Standard Q Ag-Test in large scale practical use.\r\nMethods: Based on county data from the nationwide tests for SARS-CoV-2 in Slovakia between 31.10.–1.11. 2020 we calculate a lower confidence bound for the specificity. As positive test results were not systematically verified by PCR tests, we base the lower bound on a worst case assumption, assuming all positives to be false positives.\r\nResults: 3,625,332 persons from 79 counties were tested. The lowest positivity rate was observed in the county of Rožňava where 100 out of 34307 (0.29%) tests were positive. This implies a test specificity of at least 99.6% (97.5% one-sided lower confidence bound, adjusted for multiplicity).\r\nConclusion: The obtained lower bound suggests a higher specificity compared to earlier studies in spite of the underlying worst case assumption and the application in a mass testing setting. The actual specificity is expected to exceed 99.6% if the prevalence in the respective regions was non-negligible at the time of testing. To our knowledge, this estimate constitutes the first bound obtained from large scale practical use of an antigen test."}],"publication":"PLoS ONE","doi":"10.1371/journal.pone.0255267","volume":16,"acknowledgement":"We would like to thank Alfred Uhl, Richard Kollár and Katarína Bod’ová for very helpful comments. We also thank Matej Mišík for discussion and information regarding the Slovak testing data and Ag-Test used.","file_date_updated":"2021-08-09T11:52:14Z","issue":"7","date_created":"2021-08-08T22:01:26Z","_id":"9816","article_type":"original","author":[{"full_name":"Hledik, Michal","id":"4171253A-F248-11E8-B48F-1D18A9856A87","last_name":"Hledik","first_name":"Michal"},{"orcid":"0000-0003-0951-3112","full_name":"Polechova, Jitka","first_name":"Jitka","last_name":"Polechova","id":"3BBFB084-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Beiglböck","first_name":"Mathias","full_name":"Beiglböck, Mathias"},{"last_name":"Herdina","first_name":"Anna Nele","full_name":"Herdina, Anna Nele"},{"full_name":"Strassl, Robert","first_name":"Robert","last_name":"Strassl"},{"full_name":"Posch, Martin","first_name":"Martin","last_name":"Posch"}],"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":"2023-08-10T14:26:32Z","intvolume":"        16","day":"29","isi":1,"pmid":1,"department":[{"_id":"NiBa"}],"month":"07","external_id":{"pmid":["34324553"],"isi":["000685248200095"]},"citation":{"ista":"Hledik M, Polechova J, Beiglböck M, Herdina AN, Strassl R, Posch M. 2021. Analysis of the specificity of a COVID-19 antigen test in the Slovak mass testing program. PLoS ONE. 16(7), e0255267.","ama":"Hledik M, Polechova J, Beiglböck M, Herdina AN, Strassl R, Posch M. Analysis of the specificity of a COVID-19 antigen test in the Slovak mass testing program. <i>PLoS ONE</i>. 2021;16(7). doi:<a href=\"https://doi.org/10.1371/journal.pone.0255267\">10.1371/journal.pone.0255267</a>","chicago":"Hledik, Michal, Jitka Polechova, Mathias Beiglböck, Anna Nele Herdina, Robert Strassl, and Martin Posch. “Analysis of the Specificity of a COVID-19 Antigen Test in the Slovak Mass Testing Program.” <i>PLoS ONE</i>. Public Library of Science, 2021. <a href=\"https://doi.org/10.1371/journal.pone.0255267\">https://doi.org/10.1371/journal.pone.0255267</a>.","apa":"Hledik, M., Polechova, J., Beiglböck, M., Herdina, A. N., Strassl, R., &#38; Posch, M. (2021). Analysis of the specificity of a COVID-19 antigen test in the Slovak mass testing program. <i>PLoS ONE</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pone.0255267\">https://doi.org/10.1371/journal.pone.0255267</a>","mla":"Hledik, Michal, et al. “Analysis of the Specificity of a COVID-19 Antigen Test in the Slovak Mass Testing Program.” <i>PLoS ONE</i>, vol. 16, no. 7, e0255267, Public Library of Science, 2021, doi:<a href=\"https://doi.org/10.1371/journal.pone.0255267\">10.1371/journal.pone.0255267</a>.","short":"M. Hledik, J. Polechova, M. Beiglböck, A.N. Herdina, R. Strassl, M. Posch, PLoS ONE 16 (2021).","ieee":"M. Hledik, J. Polechova, M. Beiglböck, A. N. Herdina, R. Strassl, and M. Posch, “Analysis of the specificity of a COVID-19 antigen test in the Slovak mass testing program,” <i>PLoS ONE</i>, vol. 16, no. 7. Public Library of Science, 2021."},"scopus_import":"1"},{"oa":1,"has_accepted_license":"1","status":"public","oa_version":"Published Version","ec_funded":1,"article_number":"126","related_material":{"record":[{"id":"12897","status":"public","relation":"dissertation_contains"}],"link":[{"url":"https://ist.ac.at/en/news/designing-with-elastic-structures/","description":"News on IST Website","relation":"press_release"}]},"language":[{"iso":"eng"}],"article_processing_charge":"No","publisher":"Association for Computing Machinery","quality_controlled":"1","date_published":"2021-07-19T00:00:00Z","publication_identifier":{"issn":["0730-0301"],"eissn":["1557-7368"]},"publication_status":"published","year":"2021","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","type":"journal_article","title":"The design space of plane elastic curves","ddc":["516"],"file":[{"file_size":17064290,"date_updated":"2021-10-18T10:42:15Z","file_name":"elastic-curves-paper.pdf","success":1,"file_id":"10150","checksum":"7e5d08ce46b0451b3102eacd3d00f85f","creator":"chafner","content_type":"application/pdf","access_level":"open_access","relation":"main_file","date_created":"2021-10-18T10:42:15Z"},{"file_name":"elastic-curves-supp.pdf","date_updated":"2021-10-18T10:42:22Z","file_id":"10151","file_size":547156,"date_created":"2021-10-18T10:42:22Z","relation":"supplementary_material","checksum":"0088643478be7c01a703b5b10767348f","content_type":"application/pdf","creator":"chafner","access_level":"open_access"}],"publication":"ACM Transactions on Graphics","abstract":[{"lang":"eng","text":"Elastic bending of initially flat slender elements allows the realization and economic fabrication of intriguing curved shapes. In this work, we derive an intuitive but rigorous geometric characterization of the design space of plane elastic rods with variable stiffness. It enables designers to determine which shapes are physically viable with active bending by visual inspection alone. Building on these insights, we propose a method for efficiently designing the geometry of a flat elastic rod that realizes a target equilibrium curve, which only requires solving a linear program. We implement this method in an interactive computational design tool that gives feedback about the feasibility of a design, and computes the geometry of the structural elements necessary to realize it within an instant. The tool also offers an iterative optimization routine that improves the fabricability of a model while modifying it as little as possible. In addition, we use our geometric characterization to derive an algorithm for analyzing and recovering the stability of elastic curves that would otherwise snap out of their unstable equilibrium shapes by buckling. We show the efficacy of our approach by designing and manufacturing several physical models that are assembled from flat elements."}],"doi":"10.1145/3450626.3459800","issue":"4","file_date_updated":"2021-10-18T10:42:22Z","volume":40,"acknowledgement":"We thank the anonymous reviewers for their generous feedback, and Michal Piovarči for his help in producing the supplemental video. This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement No 715767).\r\n","_id":"9817","date_created":"2021-08-08T22:01:26Z","keyword":["Computing methodologies","shape modeling","modeling and simulation","theory of computation","computational geometry","mathematics of computing","mathematical optimization"],"article_type":"original","author":[{"full_name":"Hafner, Christian","first_name":"Christian","id":"400429CC-F248-11E8-B48F-1D18A9856A87","last_name":"Hafner"},{"id":"49876194-F248-11E8-B48F-1D18A9856A87","last_name":"Bickel","first_name":"Bernd","full_name":"Bickel, Bernd","orcid":"0000-0001-6511-9385"}],"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":"2024-03-25T23:30:26Z","day":"19","intvolume":"        40","department":[{"_id":"BeBi"}],"month":"07","isi":1,"external_id":{"isi":["000674930900091"]},"conference":{"name":"SIGGRAF: Special Interest Group on Computer Graphics and Interactive Techniques","start_date":"2021-08-09","location":"Virtual","end_date":"2021-08-13"},"scopus_import":"1","project":[{"call_identifier":"H2020","grant_number":"715767","_id":"24F9549A-B435-11E9-9278-68D0E5697425","name":"MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and Modeling"}],"citation":{"ieee":"C. Hafner and B. Bickel, “The design space of plane elastic curves,” <i>ACM Transactions on Graphics</i>, vol. 40, no. 4. Association for Computing Machinery, 2021.","short":"C. Hafner, B. Bickel, ACM Transactions on Graphics 40 (2021).","apa":"Hafner, C., &#38; Bickel, B. (2021). The design space of plane elastic curves. <i>ACM Transactions on Graphics</i>. Virtual: Association for Computing Machinery. <a href=\"https://doi.org/10.1145/3450626.3459800\">https://doi.org/10.1145/3450626.3459800</a>","mla":"Hafner, Christian, and Bernd Bickel. “The Design Space of Plane Elastic Curves.” <i>ACM Transactions on Graphics</i>, vol. 40, no. 4, 126, Association for Computing Machinery, 2021, doi:<a href=\"https://doi.org/10.1145/3450626.3459800\">10.1145/3450626.3459800</a>.","chicago":"Hafner, Christian, and Bernd Bickel. “The Design Space of Plane Elastic Curves.” <i>ACM Transactions on Graphics</i>. Association for Computing Machinery, 2021. <a href=\"https://doi.org/10.1145/3450626.3459800\">https://doi.org/10.1145/3450626.3459800</a>.","ama":"Hafner C, Bickel B. The design space of plane elastic curves. <i>ACM Transactions on Graphics</i>. 2021;40(4). doi:<a href=\"https://doi.org/10.1145/3450626.3459800\">10.1145/3450626.3459800</a>","ista":"Hafner C, Bickel B. 2021. The design space of plane elastic curves. ACM Transactions on Graphics. 40(4), 126."}},{"department":[{"_id":"GradSch"},{"_id":"ChWo"}],"month":"08","isi":1,"day":"01","intvolume":"        40","scopus_import":"1","project":[{"call_identifier":"H2020","grant_number":"638176","name":"Efficient Simulation of Natural Phenomena at Extremely Large Scales","_id":"2533E772-B435-11E9-9278-68D0E5697425"}],"citation":{"short":"G. Sperl, R. Narain, C. Wojtan, ACM Transactions on Graphics 40 (2021).","apa":"Sperl, G., Narain, R., &#38; Wojtan, C. (2021). Mechanics-aware deformation of yarn pattern geometry. <i>ACM Transactions on Graphics</i>. Association for Computing Machinery. <a href=\"https://doi.org/10.1145/3450626.3459816\">https://doi.org/10.1145/3450626.3459816</a>","mla":"Sperl, Georg, et al. “Mechanics-Aware Deformation of Yarn Pattern Geometry.” <i>ACM Transactions on Graphics</i>, vol. 40, no. 4, 168, Association for Computing Machinery, 2021, doi:<a href=\"https://doi.org/10.1145/3450626.3459816\">10.1145/3450626.3459816</a>.","ama":"Sperl G, Narain R, Wojtan C. Mechanics-aware deformation of yarn pattern geometry. <i>ACM Transactions on Graphics</i>. 2021;40(4). doi:<a href=\"https://doi.org/10.1145/3450626.3459816\">10.1145/3450626.3459816</a>","ista":"Sperl G, Narain R, Wojtan C. 2021. Mechanics-aware deformation of yarn pattern geometry. ACM Transactions on Graphics. 40(4), 168.","chicago":"Sperl, Georg, Rahul Narain, and Chris Wojtan. “Mechanics-Aware Deformation of Yarn Pattern Geometry.” <i>ACM Transactions on Graphics</i>. Association for Computing Machinery, 2021. <a href=\"https://doi.org/10.1145/3450626.3459816\">https://doi.org/10.1145/3450626.3459816</a>.","ieee":"G. Sperl, R. Narain, and C. Wojtan, “Mechanics-aware deformation of yarn pattern geometry,” <i>ACM Transactions on Graphics</i>, vol. 40, no. 4. Association for Computing Machinery, 2021."},"external_id":{"isi":["000674930900132"]},"_id":"9818","date_created":"2021-08-08T22:01:27Z","issue":"4","acknowledgement":"We wish to thank the anonymous reviewers and the members of the Visual Computing Group at IST Austria for their valuable feedback. We also thank Seddi Labs for providing the garment model with fold-over seams.\r\nThis research was supported by the Scientific Service Units (SSU) of IST Austria through resources provided by Scientific\r\nComputing. This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme under grant agreement No. 638176. Rahul Narain is supported by a Pankaj Gupta Young Faculty Fellowship and a gift from Adobe Inc.","volume":40,"date_updated":"2023-08-10T14:24:36Z","article_type":"original","author":[{"first_name":"Georg","last_name":"Sperl","id":"4DD40360-F248-11E8-B48F-1D18A9856A87","full_name":"Sperl, Georg"},{"first_name":"Rahul","last_name":"Narain","full_name":"Narain, Rahul"},{"last_name":"Wojtan","id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87","first_name":"Christopher J","orcid":"0000-0001-6646-5546","full_name":"Wojtan, Christopher J"}],"acknowledged_ssus":[{"_id":"ScienComp"}],"main_file_link":[{"url":"https://doi.org/10.1145/3450626.3459816","open_access":"1"}],"type":"journal_article","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","title":"Mechanics-aware deformation of yarn pattern geometry","doi":"10.1145/3450626.3459816","publication":"ACM Transactions on Graphics","abstract":[{"text":"Triangle mesh-based simulations are able to produce satisfying animations of knitted and woven cloth; however, they lack the rich geometric detail of yarn-level simulations. Naive texturing approaches do not consider yarn-level physics, while full yarn-level simulations may become prohibitively expensive for large garments. We propose a method to animate yarn-level cloth geometry on top of an underlying deforming mesh in a mechanics-aware fashion. Using triangle strains to interpolate precomputed yarn geometry, we are able to reproduce effects such as knit loops tightening under stretching. In combination with precomputed mesh animation or real-time mesh simulation, our method is able to animate yarn-level cloth in real-time at large scales.","lang":"eng"}],"ec_funded":1,"article_number":"168","language":[{"iso":"eng"}],"related_material":{"link":[{"url":"https://ist.ac.at/en/news/knitting-virtual-yarn/","description":"News on IST Webpage","relation":"press_release"}],"record":[{"status":"public","id":"12358","relation":"dissertation_contains"},{"status":"public","id":"9327","relation":"software"}]},"article_processing_charge":"Yes (in subscription journal)","oa":1,"status":"public","oa_version":"Published Version","date_published":"2021-08-01T00:00:00Z","publication_status":"published","year":"2021","publication_identifier":{"issn":["07300301"],"eissn":["15577368"]},"publisher":"Association for Computing Machinery","quality_controlled":"1"},{"external_id":{"arxiv":["2103.07658"],"isi":["000674930900011"]},"citation":{"ieee":"B. R. Mallikarjun <i>et al.</i>, “PhotoApp: Photorealistic appearance editing of head portraits,” <i>ACM Transactions on Graphics</i>, vol. 40, no. 4. Association for Computing Machinery, 2021.","ista":"Mallikarjun BR, Tewari A, Dib A, Weyrich T, Bickel B, Seidel HP, Pfister H, Matusik W, Chevallier L, Elgharib MA, Theobalt C. 2021. PhotoApp: Photorealistic appearance editing of head portraits. ACM Transactions on Graphics. 40(4), 44.","ama":"Mallikarjun BR, Tewari A, Dib A, et al. PhotoApp: Photorealistic appearance editing of head portraits. <i>ACM Transactions on Graphics</i>. 2021;40(4). doi:<a href=\"https://doi.org/10.1145/3450626.3459765\">10.1145/3450626.3459765</a>","chicago":"Mallikarjun, B. R., Ayush Tewari, Abdallah Dib, Tim Weyrich, Bernd Bickel, Hans Peter Seidel, Hanspeter Pfister, et al. “PhotoApp: Photorealistic Appearance Editing of Head Portraits.” <i>ACM Transactions on Graphics</i>. Association for Computing Machinery, 2021. <a href=\"https://doi.org/10.1145/3450626.3459765\">https://doi.org/10.1145/3450626.3459765</a>.","mla":"Mallikarjun, B. R., et al. “PhotoApp: Photorealistic Appearance Editing of Head Portraits.” <i>ACM Transactions on Graphics</i>, vol. 40, no. 4, 44, Association for Computing Machinery, 2021, doi:<a href=\"https://doi.org/10.1145/3450626.3459765\">10.1145/3450626.3459765</a>.","short":"B.R. Mallikarjun, A. Tewari, A. Dib, T. Weyrich, B. Bickel, H.P. Seidel, H. Pfister, W. Matusik, L. Chevallier, M.A. Elgharib, C. Theobalt, ACM Transactions on Graphics 40 (2021).","apa":"Mallikarjun, B. R., Tewari, A., Dib, A., Weyrich, T., Bickel, B., Seidel, H. P., … Theobalt, C. (2021). PhotoApp: Photorealistic appearance editing of head portraits. <i>ACM Transactions on Graphics</i>. Association for Computing Machinery. <a href=\"https://doi.org/10.1145/3450626.3459765\">https://doi.org/10.1145/3450626.3459765</a>"},"scopus_import":"1","day":"01","intvolume":"        40","arxiv":1,"month":"08","department":[{"_id":"BeBi"}],"isi":1,"author":[{"full_name":"Mallikarjun, B. R.","last_name":"Mallikarjun","first_name":"B. R."},{"full_name":"Tewari, Ayush","first_name":"Ayush","last_name":"Tewari"},{"full_name":"Dib, Abdallah","first_name":"Abdallah","last_name":"Dib"},{"full_name":"Weyrich, Tim","last_name":"Weyrich","first_name":"Tim"},{"full_name":"Bickel, Bernd","orcid":"0000-0001-6511-9385","first_name":"Bernd","id":"49876194-F248-11E8-B48F-1D18A9856A87","last_name":"Bickel"},{"full_name":"Seidel, Hans Peter","last_name":"Seidel","first_name":"Hans Peter"},{"full_name":"Pfister, Hanspeter","first_name":"Hanspeter","last_name":"Pfister"},{"full_name":"Matusik, Wojciech","last_name":"Matusik","first_name":"Wojciech"},{"full_name":"Chevallier, Louis","last_name":"Chevallier","first_name":"Louis"},{"first_name":"Mohamed A.","last_name":"Elgharib","full_name":"Elgharib, Mohamed A."},{"full_name":"Theobalt, Christian","first_name":"Christian","last_name":"Theobalt"}],"article_type":"original","date_updated":"2023-08-10T14:25:08Z","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"},"issue":"4","file_date_updated":"2021-08-09T11:41:50Z","acknowledgement":"This work was supported by the ERC Consolidator Grant 4DReply (770784). We also acknowledge support from Technicolor and InterDigital. We thank Tiancheng Sun for kindly helping us with the comparisons with Sun et al. [2019].","volume":40,"_id":"9819","date_created":"2021-08-08T22:01:27Z","abstract":[{"text":"Photorealistic editing of head portraits is a challenging task as humans are very sensitive to inconsistencies in faces. We present an approach for high-quality intuitive editing of the camera viewpoint and scene illumination (parameterised with an environment map) in a portrait image. This requires our method to capture and control the full reflectance field of the person in the image. Most editing approaches rely on supervised learning using training data captured with setups such as light and camera stages. Such datasets are expensive to acquire, not readily available and do not capture all the rich variations of in-the-wild portrait images. In addition, most supervised approaches only focus on relighting, and do not allow camera viewpoint editing. Thus, they only capture and control a subset of the reflectance field. Recently, portrait editing has been demonstrated by operating in the generative model space of StyleGAN. While such approaches do not require direct supervision, there is a significant loss of quality when compared to the supervised approaches. In this paper, we present a method which learns from limited supervised training data. The training images only include people in a fixed neutral expression with eyes closed, without much hair or background variations. Each person is captured under 150 one-light-at-a-time conditions and under 8 camera poses. Instead of training directly in the image space, we design a supervised problem which learns transformations in the latent space of StyleGAN. This combines the best of supervised learning and generative adversarial modeling. We show that the StyleGAN prior allows for generalisation to different expressions, hairstyles and backgrounds. This produces high-quality photorealistic results for in-the-wild images and significantly outperforms existing methods. Our approach can edit the illumination and pose simultaneously, and runs at interactive rates.","lang":"eng"}],"publication":"ACM Transactions on Graphics","doi":"10.1145/3450626.3459765","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","type":"journal_article","title":"PhotoApp: Photorealistic appearance editing of head portraits","ddc":["000"],"file":[{"relation":"main_file","date_created":"2021-08-09T11:41:50Z","creator":"asandaue","content_type":"application/pdf","access_level":"open_access","checksum":"51b61b7e5c175e2d7ed8fa3b35f7525a","file_id":"9834","date_updated":"2021-08-09T11:41:50Z","success":1,"file_name":"2021_ACMTransactionsOnGraphics_Mallikarjun.pdf","file_size":49840741}],"publisher":"Association for Computing Machinery","quality_controlled":"1","year":"2021","publication_status":"published","publication_identifier":{"eissn":["15577368"],"issn":["07300301"]},"date_published":"2021-08-01T00:00:00Z","status":"public","oa_version":"Published Version","oa":1,"has_accepted_license":"1","article_processing_charge":"Yes (in subscription journal)","article_number":"44","language":[{"iso":"eng"}]},{"abstract":[{"lang":"eng","text":"Material appearance hinges on material reflectance properties but also surface geometry and illumination. The unlimited number of potential combinations between these factors makes understanding and predicting material appearance a very challenging task. In this work, we collect a large-scale dataset of perceptual ratings of appearance attributes with more than 215,680 responses for 42,120 distinct combinations of material, shape, and illumination. The goal of this dataset is twofold. First, we analyze for the first time the effects of illumination and geometry in material perception across such a large collection of varied appearances. We connect our findings to those of the literature, discussing how previous knowledge generalizes across very diverse materials, shapes, and illuminations. Second, we use the collected dataset to train a deep learning architecture for predicting perceptual attributes that correlate with human judgments. We demonstrate the consistent and robust behavior of our predictor in various challenging scenarios, which, for the first time, enables estimating perceived material attributes from general 2D images. Since our predictor relies on the final appearance in an image, it can compare appearance properties across different geometries and illumination conditions. Finally, we demonstrate several applications that use our predictor, including appearance reproduction using 3D printing, BRDF editing by integrating our predictor in a differentiable renderer, illumination design, or material recommendations for scene design."}],"publication":"ACM Transactions on Graphics","doi":"10.1145/3450626.3459813","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","type":"journal_article","title":"The effect of shape and illumination on material perception: Model and applications","main_file_link":[{"url":"https://zaguan.unizar.es/record/110704/files/texto_completo.pdf","open_access":"1"}],"publisher":"Association for Computing Machinery","quality_controlled":"1","publication_status":"published","year":"2021","publication_identifier":{"issn":["07300301"],"eissn":["15577368"]},"date_published":"2021-08-01T00:00:00Z","status":"public","oa_version":"Submitted Version","oa":1,"article_processing_charge":"No","article_number":"125","language":[{"iso":"eng"}],"external_id":{"isi":["000674930900090"]},"citation":{"ieee":"A. Serrano <i>et al.</i>, “The effect of shape and illumination on material perception: Model and applications,” <i>ACM Transactions on Graphics</i>, vol. 40, no. 4. Association for Computing Machinery, 2021.","ama":"Serrano A, Chen B, Wang C, et al. The effect of shape and illumination on material perception: Model and applications. <i>ACM Transactions on Graphics</i>. 2021;40(4). doi:<a href=\"https://doi.org/10.1145/3450626.3459813\">10.1145/3450626.3459813</a>","ista":"Serrano A, Chen B, Wang C, Piovarci M, Seidel HP, Didyk P, Myszkowski K. 2021. The effect of shape and illumination on material perception: Model and applications. ACM Transactions on Graphics. 40(4), 125.","chicago":"Serrano, Ana, Bin Chen, Chao Wang, Michael Piovarci, Hans Peter Seidel, Piotr Didyk, and Karol Myszkowski. “The Effect of Shape and Illumination on Material Perception: Model and Applications.” <i>ACM Transactions on Graphics</i>. Association for Computing Machinery, 2021. <a href=\"https://doi.org/10.1145/3450626.3459813\">https://doi.org/10.1145/3450626.3459813</a>.","short":"A. Serrano, B. Chen, C. Wang, M. Piovarci, H.P. Seidel, P. Didyk, K. Myszkowski, ACM Transactions on Graphics 40 (2021).","apa":"Serrano, A., Chen, B., Wang, C., Piovarci, M., Seidel, H. P., Didyk, P., &#38; Myszkowski, K. (2021). The effect of shape and illumination on material perception: Model and applications. <i>ACM Transactions on Graphics</i>. Association for Computing Machinery. <a href=\"https://doi.org/10.1145/3450626.3459813\">https://doi.org/10.1145/3450626.3459813</a>","mla":"Serrano, Ana, et al. “The Effect of Shape and Illumination on Material Perception: Model and Applications.” <i>ACM Transactions on Graphics</i>, vol. 40, no. 4, 125, Association for Computing Machinery, 2021, doi:<a href=\"https://doi.org/10.1145/3450626.3459813\">10.1145/3450626.3459813</a>."},"scopus_import":"1","day":"01","intvolume":"        40","month":"08","department":[{"_id":"BeBi"}],"isi":1,"author":[{"first_name":"Ana","last_name":"Serrano","full_name":"Serrano, Ana"},{"first_name":"Bin","last_name":"Chen","full_name":"Chen, Bin"},{"last_name":"Wang","first_name":"Chao","full_name":"Wang, Chao"},{"full_name":"Piovarci, Michael","orcid":"0000-0002-5062-4474","first_name":"Michael","id":"62E473F4-5C99-11EA-A40E-AF823DDC885E","last_name":"Piovarci"},{"full_name":"Seidel, Hans Peter","last_name":"Seidel","first_name":"Hans Peter"},{"full_name":"Didyk, Piotr","first_name":"Piotr","last_name":"Didyk"},{"full_name":"Myszkowski, Karol","last_name":"Myszkowski","first_name":"Karol"}],"article_type":"original","date_updated":"2023-08-10T14:20:10Z","issue":"4","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 765911 (RealVision) and from the European Research Council (ERC), grant agreement Nº 804226 (PERDY).","volume":40,"_id":"9820","date_created":"2021-08-08T22:01:28Z"},{"article_type":"original","author":[{"full_name":"Graff, Grzegorz","first_name":"Grzegorz","last_name":"Graff"},{"full_name":"Graff, Beata","first_name":"Beata","last_name":"Graff"},{"full_name":"Pilarczyk, Pawel","first_name":"Pawel","last_name":"Pilarczyk","id":"3768D56A-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Grzegorz","last_name":"Jablonski","id":"4483EF78-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-3536-9866","full_name":"Jablonski, Grzegorz"},{"full_name":"Gąsecki, Dariusz","last_name":"Gąsecki","first_name":"Dariusz"},{"first_name":"Krzysztof","last_name":"Narkiewicz","full_name":"Narkiewicz, Krzysztof"}],"date_updated":"2023-08-10T14:21:42Z","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"},"issue":"7","file_date_updated":"2021-08-09T09:25:41Z","volume":16,"acknowledgement":"We express our gratitude to the anonymous referees who provided constructive comments that helped us improve the quality of the paper.","_id":"9821","date_created":"2021-08-08T22:01:28Z","external_id":{"pmid":["34292957"],"isi":["000678124900050"]},"citation":{"ieee":"G. Graff, B. Graff, P. Pilarczyk, G. Jablonski, D. Gąsecki, and K. Narkiewicz, “Persistent homology as a new method of the assessment of heart rate variability,” <i>PLoS ONE</i>, vol. 16, no. 7. Public Library of Science, 2021.","chicago":"Graff, Grzegorz, Beata Graff, Pawel Pilarczyk, Grzegorz Jablonski, Dariusz Gąsecki, and Krzysztof Narkiewicz. “Persistent Homology as a New Method of the Assessment of Heart Rate Variability.” <i>PLoS ONE</i>. Public Library of Science, 2021. <a href=\"https://doi.org/10.1371/journal.pone.0253851\">https://doi.org/10.1371/journal.pone.0253851</a>.","ama":"Graff G, Graff B, Pilarczyk P, Jablonski G, Gąsecki D, Narkiewicz K. Persistent homology as a new method of the assessment of heart rate variability. <i>PLoS ONE</i>. 2021;16(7). doi:<a href=\"https://doi.org/10.1371/journal.pone.0253851\">10.1371/journal.pone.0253851</a>","ista":"Graff G, Graff B, Pilarczyk P, Jablonski G, Gąsecki D, Narkiewicz K. 2021. Persistent homology as a new method of the assessment of heart rate variability. PLoS ONE. 16(7), e0253851.","apa":"Graff, G., Graff, B., Pilarczyk, P., Jablonski, G., Gąsecki, D., &#38; Narkiewicz, K. (2021). Persistent homology as a new method of the assessment of heart rate variability. <i>PLoS ONE</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pone.0253851\">https://doi.org/10.1371/journal.pone.0253851</a>","mla":"Graff, Grzegorz, et al. “Persistent Homology as a New Method of the Assessment of Heart Rate Variability.” <i>PLoS ONE</i>, vol. 16, no. 7, e0253851, Public Library of Science, 2021, doi:<a href=\"https://doi.org/10.1371/journal.pone.0253851\">10.1371/journal.pone.0253851</a>.","short":"G. Graff, B. Graff, P. Pilarczyk, G. Jablonski, D. Gąsecki, K. Narkiewicz, PLoS ONE 16 (2021)."},"scopus_import":"1","day":"01","intvolume":"        16","month":"07","department":[{"_id":"HeEd"}],"isi":1,"pmid":1,"publisher":"Public Library of Science","quality_controlled":"1","year":"2021","publication_status":"published","publication_identifier":{"eissn":["19326203"]},"date_published":"2021-07-01T00:00:00Z","status":"public","oa_version":"Published Version","oa":1,"has_accepted_license":"1","article_processing_charge":"Yes","article_number":"e0253851","language":[{"iso":"eng"}],"abstract":[{"text":"Heart rate variability (hrv) is a physiological phenomenon of the variation in the length of the time interval between consecutive heartbeats. In many cases it could be an indicator of the development of pathological states. The classical approach to the analysis of hrv includes time domain methods and frequency domain methods. However, attempts are still being made to define new and more effective hrv assessment tools. Persistent homology is a novel data analysis tool developed in the recent decades that is rooted at algebraic topology. The Topological Data Analysis (TDA) approach focuses on examining the shape of the data in terms of connectedness and holes, and has recently proved to be very effective in various fields of research. In this paper we propose the use of persistent homology to the hrv analysis. We recall selected topological descriptors used in the literature and we introduce some new topological descriptors that reflect the specificity of hrv, and we discuss their relation to the standard hrv measures. In particular, we show that this novel approach provides a collection of indices that might be at least as useful as the classical parameters in differentiating between series of beat-to-beat intervals (RR-intervals) in healthy subjects and patients suffering from a stroke episode.","lang":"eng"}],"publication":"PLoS ONE","doi":"10.1371/journal.pone.0253851","type":"journal_article","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","title":"Persistent homology as a new method of the assessment of heart rate variability","ddc":["006"],"file":[{"date_created":"2021-08-09T09:25:41Z","relation":"main_file","checksum":"0277aa155d5db1febd2cb384768bba5f","content_type":"application/pdf","access_level":"open_access","creator":"asandaue","date_updated":"2021-08-09T09:25:41Z","file_name":"2021_PLoSONE_Graff.pdf","success":1,"file_id":"9832","file_size":2706919}]},{"external_id":{"pmid":["34283577"],"isi":["000683741400026"]},"project":[{"_id":"25FE9508-B435-11E9-9278-68D0E5697425","name":"Cellular navigation along spatial gradients","call_identifier":"H2020","grant_number":"724373"}],"scopus_import":"1","citation":{"ieee":"T. Zisis <i>et al.</i>, “Sequential and switchable patterning for studying cellular processes under spatiotemporal control,” <i>ACS Applied Materials and Interfaces</i>, vol. 13, no. 30. American Chemical Society, pp. 35545–35560, 2021.","apa":"Zisis, T., Schwarz, J., Balles, M., Kretschmer, M., Nemethova, M., Chait, R. P., … Zahler, S. (2021). Sequential and switchable patterning for studying cellular processes under spatiotemporal control. <i>ACS Applied Materials and Interfaces</i>. American Chemical Society. <a href=\"https://doi.org/10.1021/acsami.1c09850\">https://doi.org/10.1021/acsami.1c09850</a>","mla":"Zisis, Themistoklis, et al. “Sequential and Switchable Patterning for Studying Cellular Processes under Spatiotemporal Control.” <i>ACS Applied Materials and Interfaces</i>, vol. 13, no. 30, American Chemical Society, 2021, pp. 35545–35560, doi:<a href=\"https://doi.org/10.1021/acsami.1c09850\">10.1021/acsami.1c09850</a>.","short":"T. Zisis, J. Schwarz, M. Balles, M. Kretschmer, M. Nemethova, R.P. Chait, R. Hauschild, J. Lange, C.C. Guet, M.K. Sixt, S. Zahler, ACS Applied Materials and Interfaces 13 (2021) 35545–35560.","ama":"Zisis T, Schwarz J, Balles M, et al. Sequential and switchable patterning for studying cellular processes under spatiotemporal control. <i>ACS Applied Materials and Interfaces</i>. 2021;13(30):35545–35560. doi:<a href=\"https://doi.org/10.1021/acsami.1c09850\">10.1021/acsami.1c09850</a>","chicago":"Zisis, Themistoklis, Jan Schwarz, Miriam Balles, Maibritt Kretschmer, Maria Nemethova, Remy P Chait, Robert Hauschild, et al. “Sequential and Switchable Patterning for Studying Cellular Processes under Spatiotemporal Control.” <i>ACS Applied Materials and Interfaces</i>. American Chemical Society, 2021. <a href=\"https://doi.org/10.1021/acsami.1c09850\">https://doi.org/10.1021/acsami.1c09850</a>.","ista":"Zisis T, Schwarz J, Balles M, Kretschmer M, Nemethova M, Chait RP, Hauschild R, Lange J, Guet CC, Sixt MK, Zahler S. 2021. Sequential and switchable patterning for studying cellular processes under spatiotemporal control. ACS Applied Materials and Interfaces. 13(30), 35545–35560."},"intvolume":"        13","day":"04","pmid":1,"isi":1,"department":[{"_id":"MiSi"},{"_id":"GaTk"},{"_id":"Bio"},{"_id":"CaGu"}],"month":"08","license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","article_type":"original","author":[{"first_name":"Themistoklis","last_name":"Zisis","full_name":"Zisis, Themistoklis"},{"full_name":"Schwarz, Jan","first_name":"Jan","id":"346C1EC6-F248-11E8-B48F-1D18A9856A87","last_name":"Schwarz"},{"full_name":"Balles, Miriam","first_name":"Miriam","last_name":"Balles"},{"first_name":"Maibritt","last_name":"Kretschmer","full_name":"Kretschmer, Maibritt"},{"full_name":"Nemethova, Maria","id":"34E27F1C-F248-11E8-B48F-1D18A9856A87","last_name":"Nemethova","first_name":"Maria"},{"orcid":"0000-0003-0876-3187","full_name":"Chait, Remy P","last_name":"Chait","id":"3464AE84-F248-11E8-B48F-1D18A9856A87","first_name":"Remy P"},{"full_name":"Hauschild, Robert","orcid":"0000-0001-9843-3522","id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87","last_name":"Hauschild","first_name":"Robert"},{"full_name":"Lange, Janina","last_name":"Lange","first_name":"Janina"},{"orcid":"0000-0001-6220-2052","full_name":"Guet, Calin C","last_name":"Guet","id":"47F8433E-F248-11E8-B48F-1D18A9856A87","first_name":"Calin C"},{"last_name":"Sixt","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","first_name":"Michael K","orcid":"0000-0002-4561-241X","full_name":"Sixt, Michael K"},{"full_name":"Zahler, Stefan","last_name":"Zahler","first_name":"Stefan"}],"date_updated":"2023-08-10T14:22:48Z","tmp":{"short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)"},"acknowledgement":"We would like to thank Charlott Leu for the production of our chromium wafers, Louise Ritter for her contribution of the IF stainings in Figure 4, Shokoufeh Teymouri for her help with the Bioinert coated slides, and finally Prof. Dr. Joachim Rädler for his valuable scientific guidance.","volume":13,"file_date_updated":"2021-08-09T09:44:03Z","issue":"30","date_created":"2021-08-08T22:01:28Z","_id":"9822","publication":"ACS Applied Materials and Interfaces","abstract":[{"text":"Attachment of adhesive molecules on cell culture surfaces to restrict cell adhesion to defined areas and shapes has been vital for the progress of in vitro research. In currently existing patterning methods, a combination of pattern properties such as stability, precision, specificity, high-throughput outcome, and spatiotemporal control is highly desirable but challenging to achieve. Here, we introduce a versatile and high-throughput covalent photoimmobilization technique, comprising a light-dose-dependent patterning step and a subsequent functionalization of the pattern via click chemistry. This two-step process is feasible on arbitrary surfaces and allows for generation of sustainable patterns and gradients. The method is validated in different biological systems by patterning adhesive ligands on cell-repellent surfaces, thereby constraining the growth and migration of cells to the designated areas. We then implement a sequential photopatterning approach by adding a second switchable patterning step, allowing for spatiotemporal control over two distinct surface patterns. As a proof of concept, we reconstruct the dynamics of the tip/stalk cell switch during angiogenesis. Our results show that the spatiotemporal control provided by our “sequential photopatterning” system is essential for mimicking dynamic biological processes and that our innovative approach has great potential for further applications in cell science.","lang":"eng"}],"doi":"10.1021/acsami.1c09850","title":"Sequential and switchable patterning for studying cellular processes under spatiotemporal control","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","type":"journal_article","ddc":["620","570"],"file":[{"file_size":7123293,"file_id":"9833","date_updated":"2021-08-09T09:44:03Z","file_name":"2021_ACSAppliedMaterialsAndInterfaces_Zisis.pdf","success":1,"content_type":"application/pdf","access_level":"open_access","creator":"asandaue","checksum":"b043a91d9f9200e467b970b692687ed3","relation":"main_file","date_created":"2021-08-09T09:44:03Z"}],"page":"35545–35560","quality_controlled":"1","publisher":"American Chemical Society","date_published":"2021-08-04T00:00:00Z","publication_identifier":{"eissn":["19448252"],"issn":["19448244"]},"year":"2021","publication_status":"published","has_accepted_license":"1","oa":1,"oa_version":"Published Version","status":"public","language":[{"iso":"eng"}],"ec_funded":1,"article_processing_charge":"Yes (in subscription journal)"},{"year":"2021","publication_identifier":{"isbn":["9783030795269"],"eissn":["16113349"],"issn":["03029743"]},"publication_status":"published","date_published":"2021-06-20T00:00:00Z","quality_controlled":"1","publisher":"Springer Nature","page":"87-105","article_processing_charge":"No","alternative_title":["LNCS"],"language":[{"iso":"eng"}],"oa_version":"Preprint","status":"public","oa":1,"doi":"10.1007/978-3-030-79527-6_6","abstract":[{"text":"Approximate agreement is one of the few variants of consensus that can be solved in a wait-free manner in asynchronous systems where processes communicate by reading and writing to shared memory. In this work, we consider a natural generalisation of approximate agreement on arbitrary undirected connected graphs. Each process is given a vertex of the graph as input and, if non-faulty, must output a vertex such that\r\nall the outputs are within distance 1 of one another, and\r\n\r\neach output value lies on a shortest path between two input values.\r\n\r\nFrom prior work, it is known that there is no wait-free algorithm among   𝑛≥3  processes for this problem on any cycle of length   𝑐≥4 , by reduction from 2-set agreement (Castañeda et al. 2018).\r\n\r\nIn this work, we investigate the solvability and complexity of this task on general graphs. We give a new, direct proof of the impossibility of approximate agreement on cycles of length   𝑐≥4 , via a generalisation of Sperner’s Lemma to convex polygons. We also extend the reduction from 2-set agreement to a larger class of graphs, showing that approximate agreement on these graphs is unsolvable. On the positive side, we present a wait-free algorithm for a class of graphs that properly contains the class of chordal graphs.","lang":"eng"}],"publication":"Structural Information and Communication Complexity","title":"Wait-free approximate agreement on graphs","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","type":"conference","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2103.08949"}],"date_updated":"2023-02-23T14:09:49Z","author":[{"first_name":"Dan-Adrian","last_name":"Alistarh","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-3650-940X","full_name":"Alistarh, Dan-Adrian"},{"full_name":"Ellen, Faith","last_name":"Ellen","first_name":"Faith"},{"full_name":"Rybicki, Joel","orcid":"0000-0002-6432-6646","first_name":"Joel","id":"334EFD2E-F248-11E8-B48F-1D18A9856A87","last_name":"Rybicki"}],"date_created":"2021-08-08T22:01:29Z","_id":"9823","volume":12810,"citation":{"ieee":"D.-A. Alistarh, F. Ellen, and J. Rybicki, “Wait-free approximate agreement on graphs,” in <i>Structural Information and Communication Complexity</i>, Wrocław, Poland, 2021, vol. 12810, pp. 87–105.","ista":"Alistarh D-A, Ellen F, Rybicki J. 2021. Wait-free approximate agreement on graphs. Structural Information and Communication Complexity. SIROCCO: Structural Information and Communication Complexity, LNCS, vol. 12810, 87–105.","chicago":"Alistarh, Dan-Adrian, Faith Ellen, and Joel Rybicki. “Wait-Free Approximate Agreement on Graphs.” In <i>Structural Information and Communication Complexity</i>, 12810:87–105. Springer Nature, 2021. <a href=\"https://doi.org/10.1007/978-3-030-79527-6_6\">https://doi.org/10.1007/978-3-030-79527-6_6</a>.","ama":"Alistarh D-A, Ellen F, Rybicki J. Wait-free approximate agreement on graphs. In: <i>Structural Information and Communication Complexity</i>. Vol 12810. Springer Nature; 2021:87-105. doi:<a href=\"https://doi.org/10.1007/978-3-030-79527-6_6\">10.1007/978-3-030-79527-6_6</a>","mla":"Alistarh, Dan-Adrian, et al. “Wait-Free Approximate Agreement on Graphs.” <i>Structural Information and Communication Complexity</i>, vol. 12810, Springer Nature, 2021, pp. 87–105, doi:<a href=\"https://doi.org/10.1007/978-3-030-79527-6_6\">10.1007/978-3-030-79527-6_6</a>.","apa":"Alistarh, D.-A., Ellen, F., &#38; Rybicki, J. (2021). Wait-free approximate agreement on graphs. In <i>Structural Information and Communication Complexity</i> (Vol. 12810, pp. 87–105). Wrocław, Poland: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-030-79527-6_6\">https://doi.org/10.1007/978-3-030-79527-6_6</a>","short":"D.-A. Alistarh, F. Ellen, J. Rybicki, in:, Structural Information and Communication Complexity, Springer Nature, 2021, pp. 87–105."},"scopus_import":"1","conference":{"end_date":"2021-07-01","location":"Wrocław, Poland","name":"SIROCCO: Structural Information and Communication Complexity","start_date":"2021-06-28"},"external_id":{"arxiv":["2103.08949"]},"department":[{"_id":"DaAl"}],"month":"06","intvolume":"     12810","day":"20","arxiv":1},{"author":[{"last_name":"Čomić","first_name":"Lidija","full_name":"Čomić, Lidija"},{"last_name":"Zrour","first_name":"Rita","full_name":"Zrour, Rita"},{"last_name":"Largeteau-Skapin","first_name":"Gaëlle","full_name":"Largeteau-Skapin, Gaëlle"},{"orcid":"0000-0002-5372-7890","full_name":"Biswas, Ranita","first_name":"Ranita","last_name":"Biswas","id":"3C2B033E-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Eric","last_name":"Andres","full_name":"Andres, Eric"}],"date_updated":"2022-05-31T06:58:21Z","acknowledgement":"This work has been partially supported by the Ministry of Education, Science and Technological Development of the Republic of Serbia through the project no. 451-03-68/2020-14/200156: “Innovative scientific and artistic research from the FTS (activity) domain” (LČ), the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme, grant no. 788183 (RB), and the DFG Collaborative Research Center TRR 109, ‘Discretization in Geometry and Dynamics’, Austrian Science Fund (FWF), grant no. I 02979-N35 (RB).","volume":12708,"date_created":"2021-08-08T22:01:29Z","_id":"9824","project":[{"_id":"266A2E9E-B435-11E9-9278-68D0E5697425","name":"Alpha Shape Theory Extended","grant_number":"788183","call_identifier":"H2020"},{"call_identifier":"FWF","grant_number":"I02979-N35","_id":"2561EBF4-B435-11E9-9278-68D0E5697425","name":"Persistence and stability of geometric complexes"}],"scopus_import":"1","conference":{"end_date":"2021-05-27","name":"DGMM: International Conference on Discrete Geometry and Mathematical Morphology","start_date":"2021-05-24","location":"Uppsala, Sweden"},"citation":{"mla":"Čomić, Lidija, et al. “Body Centered Cubic Grid - Coordinate System and Discrete Analytical Plane Definition.” <i>Discrete Geometry and Mathematical Morphology</i>, vol. 12708, Springer Nature, 2021, pp. 152–63, doi:<a href=\"https://doi.org/10.1007/978-3-030-76657-3_10\">10.1007/978-3-030-76657-3_10</a>.","short":"L. Čomić, R. Zrour, G. Largeteau-Skapin, R. Biswas, E. Andres, in:, Discrete Geometry and Mathematical Morphology, Springer Nature, 2021, pp. 152–163.","apa":"Čomić, L., Zrour, R., Largeteau-Skapin, G., Biswas, R., &#38; Andres, E. (2021). Body centered cubic grid - coordinate system and discrete analytical plane definition. In <i>Discrete Geometry and Mathematical Morphology</i> (Vol. 12708, pp. 152–163). Uppsala, Sweden: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-030-76657-3_10\">https://doi.org/10.1007/978-3-030-76657-3_10</a>","ista":"Čomić L, Zrour R, Largeteau-Skapin G, Biswas R, Andres E. 2021. Body centered cubic grid - coordinate system and discrete analytical plane definition. Discrete Geometry and Mathematical Morphology. DGMM: International Conference on Discrete Geometry and Mathematical Morphology, LNCS, vol. 12708, 152–163.","ama":"Čomić L, Zrour R, Largeteau-Skapin G, Biswas R, Andres E. Body centered cubic grid - coordinate system and discrete analytical plane definition. In: <i>Discrete Geometry and Mathematical Morphology</i>. Vol 12708. Springer Nature; 2021:152-163. doi:<a href=\"https://doi.org/10.1007/978-3-030-76657-3_10\">10.1007/978-3-030-76657-3_10</a>","chicago":"Čomić, Lidija, Rita Zrour, Gaëlle Largeteau-Skapin, Ranita Biswas, and Eric Andres. “Body Centered Cubic Grid - Coordinate System and Discrete Analytical Plane Definition.” In <i>Discrete Geometry and Mathematical Morphology</i>, 12708:152–63. Springer Nature, 2021. <a href=\"https://doi.org/10.1007/978-3-030-76657-3_10\">https://doi.org/10.1007/978-3-030-76657-3_10</a>.","ieee":"L. Čomić, R. Zrour, G. Largeteau-Skapin, R. Biswas, and E. Andres, “Body centered cubic grid - coordinate system and discrete analytical plane definition,” in <i>Discrete Geometry and Mathematical Morphology</i>, Uppsala, Sweden, 2021, vol. 12708, pp. 152–163."},"intvolume":"     12708","day":"16","department":[{"_id":"HeEd"}],"month":"05","page":"152-163","quality_controlled":"1","publisher":"Springer Nature","date_published":"2021-05-16T00:00:00Z","publication_identifier":{"issn":["03029743"],"eissn":["16113349"],"isbn":["9783030766566"]},"year":"2021","publication_status":"published","oa_version":"None","status":"public","alternative_title":["LNCS"],"language":[{"iso":"eng"}],"ec_funded":1,"article_processing_charge":"No","publication":"Discrete Geometry and Mathematical Morphology","abstract":[{"text":"We define a new compact coordinate system in which each integer triplet addresses a voxel in the BCC grid, and we investigate some of its properties. We propose a characterization of 3D discrete analytical planes with their topological features (in the Cartesian and in the new coordinate system) such as the interrelation between the thickness of the plane and the separability constraint we aim to obtain.","lang":"eng"}],"doi":"10.1007/978-3-030-76657-3_10","title":"Body centered cubic grid - coordinate system and discrete analytical plane definition","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"conference"},{"conference":{"location":"Virtual Event","name":"CT-RSA: Cryptographers’ Track at the RSA Conference","start_date":"2021-05-17","end_date":"2021-05-20"},"scopus_import":"1","citation":{"chicago":"Laarhoven, Thijs, and Michael Walter. “Dual Lattice Attacks for Closest Vector Problems (with Preprocessing).” In <i>Topics in Cryptology – CT-RSA 2021</i>, 12704:478–502. Springer Nature, 2021. <a href=\"https://doi.org/10.1007/978-3-030-75539-3_20\">https://doi.org/10.1007/978-3-030-75539-3_20</a>.","ista":"Laarhoven T, Walter M. 2021. Dual lattice attacks for closest vector problems (with preprocessing). Topics in Cryptology – CT-RSA 2021. CT-RSA: Cryptographers’ Track at the RSA Conference, LNCS, vol. 12704, 478–502.","ama":"Laarhoven T, Walter M. Dual lattice attacks for closest vector problems (with preprocessing). In: <i>Topics in Cryptology – CT-RSA 2021</i>. Vol 12704. Springer Nature; 2021:478-502. doi:<a href=\"https://doi.org/10.1007/978-3-030-75539-3_20\">10.1007/978-3-030-75539-3_20</a>","short":"T. Laarhoven, M. Walter, in:, Topics in Cryptology – CT-RSA 2021, Springer Nature, 2021, pp. 478–502.","apa":"Laarhoven, T., &#38; Walter, M. (2021). Dual lattice attacks for closest vector problems (with preprocessing). In <i>Topics in Cryptology – CT-RSA 2021</i> (Vol. 12704, pp. 478–502). Virtual Event: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-030-75539-3_20\">https://doi.org/10.1007/978-3-030-75539-3_20</a>","mla":"Laarhoven, Thijs, and Michael Walter. “Dual Lattice Attacks for Closest Vector Problems (with Preprocessing).” <i>Topics in Cryptology – CT-RSA 2021</i>, vol. 12704, Springer Nature, 2021, pp. 478–502, doi:<a href=\"https://doi.org/10.1007/978-3-030-75539-3_20\">10.1007/978-3-030-75539-3_20</a>.","ieee":"T. Laarhoven and M. Walter, “Dual lattice attacks for closest vector problems (with preprocessing),” in <i>Topics in Cryptology – CT-RSA 2021</i>, Virtual Event, 2021, vol. 12704, pp. 478–502."},"day":"11","intvolume":"     12704","month":"05","department":[{"_id":"KrPi"}],"author":[{"full_name":"Laarhoven, Thijs","first_name":"Thijs","last_name":"Laarhoven"},{"full_name":"Walter, Michael","orcid":"0000-0003-3186-2482","id":"488F98B0-F248-11E8-B48F-1D18A9856A87","last_name":"Walter","first_name":"Michael"}],"date_updated":"2023-02-23T14:09:54Z","acknowledgement":"The authors thank Sauvik Bhattacharya, L´eo Ducas, Rachel Player, and Christine van Vredendaal for early discussions on this topic and on preliminary results. The authors further thank the reviewers of CT-RSA 2021 for their valuable feedback.","volume":12704,"_id":"9825","date_created":"2021-08-08T22:01:30Z","publication":"Topics in Cryptology – CT-RSA 2021","abstract":[{"text":"The dual attack has long been considered a relevant attack on lattice-based cryptographic schemes relying on the hardness of learning with errors (LWE) and its structured variants. As solving LWE corresponds to finding a nearest point on a lattice, one may naturally wonder how efficient this dual approach is for solving more general closest vector problems, such as the classical closest vector problem (CVP), the variants bounded distance decoding (BDD) and approximate CVP, and preprocessing versions of these problems. While primal, sieving-based solutions to these problems (with preprocessing) were recently studied in a series of works on approximate Voronoi cells [Laa16b, DLdW19, Laa20, DLvW20], for the dual attack no such overview exists, especially for problems with preprocessing. With one of the take-away messages of the approximate Voronoi cell line of work being that primal attacks work well for approximate CVP(P) but scale poorly for BDD(P), one may further wonder if the dual attack suffers the same drawbacks, or if it is perhaps a better solution when trying to solve BDD(P).\r\n\r\nIn this work we provide an overview of cost estimates for dual algorithms for solving these “classical” closest lattice vector problems. Heuristically we expect to solve the search version of average-case CVPP in time and space   20.293𝑑+𝑜(𝑑)  in the single-target model. The distinguishing version of average-case CVPP, where we wish to distinguish between random targets and targets planted at distance (say)   0.99⋅𝑔𝑑  from the lattice, has the same complexity in the single-target model, but can be solved in time and space   20.195𝑑+𝑜(𝑑)  in the multi-target setting, when given a large number of targets from either target distribution. This suggests an inequivalence between distinguishing and searching, as we do not expect a similar improvement in the multi-target setting to hold for search-CVPP. We analyze three slightly different decoders, both for distinguishing and searching, and experimentally obtain concrete cost estimates for the dual attack in dimensions 50 to 80, which confirm our heuristic assumptions, and show that the hidden order terms in the asymptotic estimates are quite small.\r\n\r\nOur main take-away message is that the dual attack appears to mirror the approximate Voronoi cell line of work – whereas using approximate Voronoi cells works well for approximate CVP(P) but scales poorly for BDD(P), the dual approach scales well for BDD(P) instances but performs poorly on approximate CVP(P).","lang":"eng"}],"doi":"10.1007/978-3-030-75539-3_20","main_file_link":[{"url":"https://eprint.iacr.org/2021/557","open_access":"1"}],"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","type":"conference","title":"Dual lattice attacks for closest vector problems (with preprocessing)","page":"478-502","publisher":"Springer Nature","quality_controlled":"1","date_published":"2021-05-11T00:00:00Z","publication_identifier":{"isbn":["9783030755386"],"eissn":["16113349"],"issn":["03029743"]},"publication_status":"published","year":"2021","oa":1,"status":"public","oa_version":"Preprint","language":[{"iso":"eng"}],"alternative_title":["LNCS"],"article_processing_charge":"No"},{"title":"Inverse-Sybil attacks in automated contact tracing","type":"conference","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","main_file_link":[{"url":"https://eprint.iacr.org/2020/670","open_access":"1"}],"abstract":[{"lang":"eng","text":"Automated contract tracing aims at supporting manual contact tracing during pandemics by alerting users of encounters with infected people. There are currently many proposals for protocols (like the “decentralized” DP-3T and PACT or the “centralized” ROBERT and DESIRE) to be run on mobile phones, where the basic idea is to regularly broadcast (using low energy Bluetooth) some values, and at the same time store (a function of) incoming messages broadcasted by users in their proximity. In the existing proposals one can trigger false positives on a massive scale by an “inverse-Sybil” attack, where a large number of devices (malicious users or hacked phones) pretend to be the same user, such that later, just a single person needs to be diagnosed (and allowed to upload) to trigger an alert for all users who were in proximity to any of this large group of devices.\r\n\r\nWe propose the first protocols that do not succumb to such attacks assuming the devices involved in the attack do not constantly communicate, which we observe is a necessary assumption. The high level idea of the protocols is to derive the values to be broadcasted by a hash chain, so that two (or more) devices who want to launch an inverse-Sybil attack will not be able to connect their respective chains and thus only one of them will be able to upload. Our protocols also achieve security against replay, belated replay, and one of them even against relay attacks."}],"publication":"Topics in Cryptology – CT-RSA 2021","doi":"10.1007/978-3-030-75539-3_17","oa_version":"Submitted Version","status":"public","oa":1,"article_processing_charge":"No","language":[{"iso":"eng"}],"alternative_title":["LNCS"],"ec_funded":1,"quality_controlled":"1","publisher":"Springer Nature","page":"399-421","publication_identifier":{"eissn":["16113349"],"issn":["03029743"],"isbn":["9783030755386"]},"publication_status":"published","year":"2021","date_published":"2021-05-11T00:00:00Z","intvolume":"     12704","day":"11","department":[{"_id":"KrPi"},{"_id":"GradSch"}],"month":"05","citation":{"chicago":"Auerbach, Benedikt, Suvradip Chakraborty, Karen Klein, Guillermo Pascual Perez, Krzysztof Z Pietrzak, Michael Walter, and Michelle X Yeo. “Inverse-Sybil Attacks in Automated Contact Tracing.” In <i>Topics in Cryptology – CT-RSA 2021</i>, 12704:399–421. Springer Nature, 2021. <a href=\"https://doi.org/10.1007/978-3-030-75539-3_17\">https://doi.org/10.1007/978-3-030-75539-3_17</a>.","ama":"Auerbach B, Chakraborty S, Klein K, et al. Inverse-Sybil attacks in automated contact tracing. In: <i>Topics in Cryptology – CT-RSA 2021</i>. Vol 12704. Springer Nature; 2021:399-421. doi:<a href=\"https://doi.org/10.1007/978-3-030-75539-3_17\">10.1007/978-3-030-75539-3_17</a>","ista":"Auerbach B, Chakraborty S, Klein K, Pascual Perez G, Pietrzak KZ, Walter M, Yeo MX. 2021. Inverse-Sybil attacks in automated contact tracing. Topics in Cryptology – CT-RSA 2021. CT-RSA: Cryptographers’ Track at the RSA Conference, LNCS, vol. 12704, 399–421.","mla":"Auerbach, Benedikt, et al. “Inverse-Sybil Attacks in Automated Contact Tracing.” <i>Topics in Cryptology – CT-RSA 2021</i>, vol. 12704, Springer Nature, 2021, pp. 399–421, doi:<a href=\"https://doi.org/10.1007/978-3-030-75539-3_17\">10.1007/978-3-030-75539-3_17</a>.","apa":"Auerbach, B., Chakraborty, S., Klein, K., Pascual Perez, G., Pietrzak, K. Z., Walter, M., &#38; Yeo, M. X. (2021). Inverse-Sybil attacks in automated contact tracing. In <i>Topics in Cryptology – CT-RSA 2021</i> (Vol. 12704, pp. 399–421). Virtual Event: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-030-75539-3_17\">https://doi.org/10.1007/978-3-030-75539-3_17</a>","short":"B. Auerbach, S. Chakraborty, K. Klein, G. Pascual Perez, K.Z. Pietrzak, M. Walter, M.X. Yeo, in:, Topics in Cryptology – CT-RSA 2021, Springer Nature, 2021, pp. 399–421.","ieee":"B. Auerbach <i>et al.</i>, “Inverse-Sybil attacks in automated contact tracing,” in <i>Topics in Cryptology – CT-RSA 2021</i>, Virtual Event, 2021, vol. 12704, pp. 399–421."},"scopus_import":"1","project":[{"name":"International IST Doctoral Program","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"665385"},{"_id":"258AA5B2-B435-11E9-9278-68D0E5697425","name":"Teaching Old Crypto New Tricks","grant_number":"682815","call_identifier":"H2020"}],"conference":{"end_date":"2021-05-20","location":"Virtual Event","start_date":"2021-05-17","name":"CT-RSA: Cryptographers’ Track at the RSA Conference"},"volume":12704,"acknowledgement":"Guillermo Pascual-Perez and Michelle Yeo were funded by the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska–Curie Grant Agreement No. 665385; the remaining contributors to this project have received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (682815 - TOCNeT).","date_created":"2021-08-08T22:01:30Z","_id":"9826","author":[{"first_name":"Benedikt","last_name":"Auerbach","id":"D33D2B18-E445-11E9-ABB7-15F4E5697425","orcid":"0000-0002-7553-6606","full_name":"Auerbach, Benedikt"},{"full_name":"Chakraborty, Suvradip","first_name":"Suvradip","last_name":"Chakraborty","id":"B9CD0494-D033-11E9-B219-A439E6697425"},{"last_name":"Klein","id":"3E83A2F8-F248-11E8-B48F-1D18A9856A87","first_name":"Karen","full_name":"Klein, Karen"},{"full_name":"Pascual Perez, Guillermo","first_name":"Guillermo","id":"2D7ABD02-F248-11E8-B48F-1D18A9856A87","last_name":"Pascual Perez"},{"full_name":"Pietrzak, Krzysztof Z","orcid":"0000-0002-9139-1654","first_name":"Krzysztof Z","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","last_name":"Pietrzak"},{"orcid":"0000-0003-3186-2482","full_name":"Walter, Michael","first_name":"Michael","last_name":"Walter","id":"488F98B0-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Yeo, Michelle X","first_name":"Michelle X","last_name":"Yeo","id":"2D82B818-F248-11E8-B48F-1D18A9856A87"}],"date_updated":"2023-02-23T14:09:56Z"},{"date_created":"2021-08-08T22:01:31Z","_id":"9827","volume":886,"date_updated":"2023-08-10T14:27:43Z","keyword":["Concurrent data structure","kD-tree","Nearest neighbor search","Similarity search","Lock-free","Linearizability"],"article_type":"original","author":[{"full_name":"Chatterjee, Bapi","orcid":"0000-0002-2742-4028","first_name":"Bapi","id":"3C41A08A-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee"},{"last_name":"Walulya","first_name":"Ivan","full_name":"Walulya, Ivan"},{"last_name":"Tsigas","first_name":"Philippas","full_name":"Tsigas, Philippas"}],"isi":1,"month":"09","department":[{"_id":"DaAl"}],"intvolume":"       886","day":"13","scopus_import":"1","citation":{"ieee":"B. Chatterjee, I. Walulya, and P. Tsigas, “Concurrent linearizable nearest neighbour search in LockFree-kD-tree,” <i>Theoretical Computer Science</i>, vol. 886. Elsevier, pp. 27–48, 2021.","ista":"Chatterjee B, Walulya I, Tsigas P. 2021. Concurrent linearizable nearest neighbour search in LockFree-kD-tree. Theoretical Computer Science. 886, 27–48.","ama":"Chatterjee B, Walulya I, Tsigas P. Concurrent linearizable nearest neighbour search in LockFree-kD-tree. <i>Theoretical Computer Science</i>. 2021;886:27-48. doi:<a href=\"https://doi.org/10.1016/j.tcs.2021.06.041\">10.1016/j.tcs.2021.06.041</a>","chicago":"Chatterjee, Bapi, Ivan Walulya, and Philippas Tsigas. “Concurrent Linearizable Nearest Neighbour Search in LockFree-KD-Tree.” <i>Theoretical Computer Science</i>. Elsevier, 2021. <a href=\"https://doi.org/10.1016/j.tcs.2021.06.041\">https://doi.org/10.1016/j.tcs.2021.06.041</a>.","apa":"Chatterjee, B., Walulya, I., &#38; Tsigas, P. (2021). Concurrent linearizable nearest neighbour search in LockFree-kD-tree. <i>Theoretical Computer Science</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.tcs.2021.06.041\">https://doi.org/10.1016/j.tcs.2021.06.041</a>","mla":"Chatterjee, Bapi, et al. “Concurrent Linearizable Nearest Neighbour Search in LockFree-KD-Tree.” <i>Theoretical Computer Science</i>, vol. 886, Elsevier, 2021, pp. 27–48, doi:<a href=\"https://doi.org/10.1016/j.tcs.2021.06.041\">10.1016/j.tcs.2021.06.041</a>.","short":"B. Chatterjee, I. Walulya, P. Tsigas, Theoretical Computer Science 886 (2021) 27–48."},"external_id":{"isi":["000694718900004"]},"language":[{"iso":"eng"}],"article_processing_charge":"No","oa":1,"oa_version":"Submitted Version","status":"public","date_published":"2021-09-13T00:00:00Z","publication_identifier":{"issn":["0304-3975"]},"publication_status":"published","year":"2021","page":"27-48","quality_controlled":"1","publisher":"Elsevier","main_file_link":[{"url":"https://publications.lib.chalmers.se/records/fulltext/232185/232185.pdf","open_access":"1"}],"title":"Concurrent linearizable nearest neighbour search in LockFree-kD-tree","type":"journal_article","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","doi":"10.1016/j.tcs.2021.06.041","publication":"Theoretical Computer Science","abstract":[{"text":"The Nearest neighbour search (NNS) is a fundamental problem in many application domains dealing with multidimensional data. In a concurrent setting, where dynamic modifications are allowed, a linearizable implementation of the NNS is highly desirable.This paper introduces the LockFree-kD-tree (LFkD-tree ): a lock-free concurrent kD-tree, which implements an abstract data type (ADT) that provides the operations Add, Remove, Contains, and NNS. Our implementation is linearizable. The operations in the LFkD-tree use single-word read and compare-and-swap (Image 1 ) atomic primitives, which are readily supported on available multi-core processors. We experimentally evaluate the LFkD-tree using several benchmarks comprising real-world and synthetic datasets. The experiments show that the presented design is scalable and achieves significant speed-up compared to the implementations of an existing sequential kD-tree and a recently proposed multidimensional indexing structure, PH-tree.","lang":"eng"}]},{"status":"public","oa_version":"Preprint","oa":1,"article_processing_charge":"No","language":[{"iso":"eng"}],"publisher":"Institute of Electrical and Electronics Engineers","quality_controlled":"1","page":"4039 - 4054","publication_status":"published","year":"2021","publication_identifier":{"eissn":["1941-0476"],"issn":["1053-587X"]},"date_published":"2021-06-09T00:00:00Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","type":"journal_article","title":"Fast and accurate amplitude demodulation of wideband signals","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2102.04832"}],"abstract":[{"lang":"eng","text":"Amplitude demodulation is a classical operation used in signal processing. For a long time, its effective applications in practice have been limited to narrowband signals. In this work, we generalize amplitude demodulation to wideband signals. We pose demodulation as a recovery problem of an oversampled corrupted signal and introduce special iterative schemes belonging to the family of alternating projection algorithms to solve it. Sensibly chosen structural assumptions on the demodulation outputs allow us to reveal the high inferential accuracy of the method over a rich set of relevant signals. This new approach surpasses current state-of-the-art demodulation techniques apt to wideband signals in computational efficiency by up to many orders of magnitude with no sacrifice in quality. Such performance opens the door for applications of the amplitude demodulation procedure in new contexts. In particular, the new method makes online and large-scale offline data processing feasible, including the calculation of modulator-carrier pairs in higher dimensions and poor sampling conditions, independent of the signal bandwidth. We illustrate the utility and specifics of applications of the new method in practice by using natural speech and synthetic signals."}],"publication":"IEEE Transactions on Signal Processing","doi":"10.1109/TSP.2021.3087899","acknowledgement":"The author thanks his colleagues K. Huszár and G. Tkačik for valuable discussions and comments on the manuscript.","volume":69,"_id":"9828","date_created":"2021-08-08T22:01:31Z","author":[{"first_name":"Mantas","last_name":"Gabrielaitis","id":"4D5B0CBC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7758-2016","full_name":"Gabrielaitis, Mantas"}],"article_type":"original","date_updated":"2023-08-10T14:19:33Z","day":"09","intvolume":"        69","arxiv":1,"month":"06","department":[{"_id":"GaTk"}],"isi":1,"external_id":{"arxiv":["2102.04832"],"isi":["000682123900002"]},"citation":{"short":"M. Gabrielaitis, IEEE Transactions on Signal Processing 69 (2021) 4039–4054.","apa":"Gabrielaitis, M. (2021). Fast and accurate amplitude demodulation of wideband signals. <i>IEEE Transactions on Signal Processing</i>. Institute of Electrical and Electronics Engineers. <a href=\"https://doi.org/10.1109/TSP.2021.3087899\">https://doi.org/10.1109/TSP.2021.3087899</a>","mla":"Gabrielaitis, Mantas. “Fast and Accurate Amplitude Demodulation of Wideband Signals.” <i>IEEE Transactions on Signal Processing</i>, vol. 69, Institute of Electrical and Electronics Engineers, 2021, pp. 4039–54, doi:<a href=\"https://doi.org/10.1109/TSP.2021.3087899\">10.1109/TSP.2021.3087899</a>.","ama":"Gabrielaitis M. Fast and accurate amplitude demodulation of wideband signals. <i>IEEE Transactions on Signal Processing</i>. 2021;69:4039-4054. doi:<a href=\"https://doi.org/10.1109/TSP.2021.3087899\">10.1109/TSP.2021.3087899</a>","chicago":"Gabrielaitis, Mantas. “Fast and Accurate Amplitude Demodulation of Wideband Signals.” <i>IEEE Transactions on Signal Processing</i>. Institute of Electrical and Electronics Engineers, 2021. <a href=\"https://doi.org/10.1109/TSP.2021.3087899\">https://doi.org/10.1109/TSP.2021.3087899</a>.","ista":"Gabrielaitis M. 2021. Fast and accurate amplitude demodulation of wideband signals. IEEE Transactions on Signal Processing. 69, 4039–4054.","ieee":"M. Gabrielaitis, “Fast and accurate amplitude demodulation of wideband signals,” <i>IEEE Transactions on Signal Processing</i>, vol. 69. Institute of Electrical and Electronics Engineers, pp. 4039–4054, 2021."},"scopus_import":"1"},{"publication":"ACS Nano","abstract":[{"text":"In 2020, many in-person scientific events were canceled due to the COVID-19 pandemic, creating a vacuum in networking and knowledge exchange between scientists. To fill this void in scientific communication, a group of early career nanocrystal enthusiasts launched the virtual seminar series, News in Nanocrystals, in the summer of 2020. By the end of the year, the series had attracted over 850 participants from 46 countries. In this Nano Focus, we describe the process of organizing the News in Nanocrystals seminar series; discuss its growth, emphasizing what the organizers have learned in terms of diversity and accessibility; and provide an outlook for the next steps and future opportunities. This summary and analysis of experiences and learned lessons are intended to inform the broader scientific community, especially those who are looking for avenues to continue fostering discussion and scientific engagement virtually, both during the pandemic and after.","lang":"eng"}],"doi":"10.1021/acsnano.1c03276","main_file_link":[{"url":"https://doi.org/10.1021/acsnano.1c03276","open_access":"1"}],"title":"News in Nanocrystals seminar: Self-assembly of early career researchers toward globally accessible nanoscience","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","type":"journal_article","page":"10743–10747","quality_controlled":"1","publisher":"American Chemical Society","date_published":"2021-07-06T00:00:00Z","year":"2021","publication_identifier":{"eissn":["1936086X"],"issn":["19360851"]},"publication_status":"published","oa":1,"oa_version":"Published Version","status":"public","language":[{"iso":"eng"}],"article_processing_charge":"No","external_id":{"isi":["000679406500002"],"pmid":["34228432"]},"scopus_import":"1","citation":{"ieee":"D. Baranov <i>et al.</i>, “News in Nanocrystals seminar: Self-assembly of early career researchers toward globally accessible nanoscience,” <i>ACS Nano</i>, vol. 15, no. 7. American Chemical Society, pp. 10743–10747, 2021.","apa":"Baranov, D., Šverko, T., Moot, T., Keller, H. R., Klein, M. D., Vishnu, E. K., … Shulenberger, K. E. (2021). News in Nanocrystals seminar: Self-assembly of early career researchers toward globally accessible nanoscience. <i>ACS Nano</i>. American Chemical Society. <a href=\"https://doi.org/10.1021/acsnano.1c03276\">https://doi.org/10.1021/acsnano.1c03276</a>","mla":"Baranov, Dmitry, et al. “News in Nanocrystals Seminar: Self-Assembly of Early Career Researchers toward Globally Accessible Nanoscience.” <i>ACS Nano</i>, vol. 15, no. 7, American Chemical Society, 2021, pp. 10743–10747, doi:<a href=\"https://doi.org/10.1021/acsnano.1c03276\">10.1021/acsnano.1c03276</a>.","short":"D. Baranov, T. Šverko, T. Moot, H.R. Keller, M.D. Klein, E.K. Vishnu, D. Balazs, K.E. Shulenberger, ACS Nano 15 (2021) 10743–10747.","ama":"Baranov D, Šverko T, Moot T, et al. News in Nanocrystals seminar: Self-assembly of early career researchers toward globally accessible nanoscience. <i>ACS Nano</i>. 2021;15(7):10743–10747. doi:<a href=\"https://doi.org/10.1021/acsnano.1c03276\">10.1021/acsnano.1c03276</a>","ista":"Baranov D, Šverko T, Moot T, Keller HR, Klein MD, Vishnu EK, Balazs D, Shulenberger KE. 2021. News in Nanocrystals seminar: Self-assembly of early career researchers toward globally accessible nanoscience. ACS Nano. 15(7), 10743–10747.","chicago":"Baranov, Dmitry, Tara Šverko, Taylor Moot, Helena R. Keller, Megan D. Klein, E. K. Vishnu, Daniel Balazs, and Katherine E. Shulenberger. “News in Nanocrystals Seminar: Self-Assembly of Early Career Researchers toward Globally Accessible Nanoscience.” <i>ACS Nano</i>. American Chemical Society, 2021. <a href=\"https://doi.org/10.1021/acsnano.1c03276\">https://doi.org/10.1021/acsnano.1c03276</a>."},"intvolume":"        15","day":"06","pmid":1,"isi":1,"department":[{"_id":"MaIb"}],"month":"07","article_type":"original","author":[{"last_name":"Baranov","first_name":"Dmitry","full_name":"Baranov, Dmitry"},{"first_name":"Tara","last_name":"Šverko","full_name":"Šverko, Tara"},{"full_name":"Moot, Taylor","last_name":"Moot","first_name":"Taylor"},{"full_name":"Keller, Helena R.","last_name":"Keller","first_name":"Helena R."},{"last_name":"Klein","first_name":"Megan D.","full_name":"Klein, Megan D."},{"full_name":"Vishnu, E. K.","first_name":"E. K.","last_name":"Vishnu"},{"first_name":"Daniel","last_name":"Balazs","id":"302BADF6-85FC-11EA-9E3B-B9493DDC885E","orcid":"0000-0001-7597-043X","full_name":"Balazs, Daniel"},{"first_name":"Katherine E.","last_name":"Shulenberger","full_name":"Shulenberger, Katherine E."}],"date_updated":"2023-08-11T10:55:08Z","volume":15,"acknowledgement":"K. E. Shulenberger, M. D. Klein, T. Šverko, and H. R. Keller would like to thank Professors Moungi Bawendi (MIT) and Gordana Dukovic (CU Boulder) for their feedback and support of the News in Nanocrystals initiative. The authors thank Madison Jilek (CU Boulder) and Dhananjeya Kumaar (ETH Zurich) for their help in the organization of the seminar, and Professors Brandi Cossairt (University of Washington) and Gordana Dukovic for their feedback on an earlier version of this manuscript. The authors thank all the seminar speakers and attendees for their interest and continuing participation in the seminar series.","issue":"7","date_created":"2021-08-08T22:01:31Z","_id":"9829"},{"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":"2023-08-11T10:27:03Z","article_type":"original","author":[{"last_name":"Raso","first_name":"Andrea","full_name":"Raso, Andrea"},{"full_name":"Dirkx, Ellen","last_name":"Dirkx","first_name":"Ellen"},{"full_name":"Sampaio-Pinto, Vasco","first_name":"Vasco","last_name":"Sampaio-Pinto"},{"full_name":"el Azzouzi, Hamid","first_name":"Hamid","last_name":"el Azzouzi"},{"orcid":"0000-0003-0002-1867","full_name":"Cubero, Ryan J","first_name":"Ryan J","last_name":"Cubero","id":"850B2E12-9CD4-11E9-837F-E719E6697425"},{"full_name":"Sorensen, Daniel W.","last_name":"Sorensen","first_name":"Daniel W."},{"first_name":"Lara","last_name":"Ottaviani","full_name":"Ottaviani, Lara"},{"full_name":"Olieslagers, Servé","first_name":"Servé","last_name":"Olieslagers"},{"full_name":"Huibers, Manon M.","last_name":"Huibers","first_name":"Manon M."},{"last_name":"de Weger","first_name":"Roel","full_name":"de Weger, Roel"},{"first_name":"Sailay","last_name":"Siddiqi","full_name":"Siddiqi, Sailay"},{"full_name":"Moimas, Silvia","last_name":"Moimas","first_name":"Silvia"},{"full_name":"Torrini, Consuelo","last_name":"Torrini","first_name":"Consuelo"},{"first_name":"Lorena","last_name":"Zentillin","full_name":"Zentillin, Lorena"},{"first_name":"Luca","last_name":"Braga","full_name":"Braga, Luca"},{"full_name":"Nascimento, Diana S.","first_name":"Diana S.","last_name":"Nascimento"},{"full_name":"da Costa Martins, Paula A.","last_name":"da Costa Martins","first_name":"Paula A."},{"full_name":"van Berlo, Jop H.","last_name":"van Berlo","first_name":"Jop H."},{"full_name":"Zacchigna, Serena","last_name":"Zacchigna","first_name":"Serena"},{"first_name":"Mauro","last_name":"Giacca","full_name":"Giacca, Mauro"},{"full_name":"De Windt, Leon J.","first_name":"Leon J.","last_name":"De Windt"}],"_id":"9874","date_created":"2021-08-10T11:49:20Z","file_date_updated":"2021-08-10T12:29:59Z","acknowledgement":"E.D. is supported by a VENI award 916-150-16 from the Netherlands Organization for Health Research and Development (ZonMW), an EMBO Long-term Fellowship (EMBO ALTF 848-2013) and a FP7 Marie Curie Intra-European Fellowship (Project number 627539). V.S.P. was funded by a fellowship from the FCT/ Ministério da Ciência, Tecnologia e Inovação SFRH/BD/111799/2015. P.D.C.M. is an Established Investigator of the Dutch Heart Foundation. L.D.W. acknowledges support from the Dutch CardioVascular Alliance (ARENA-PRIME). L.D.W. was further supported by grant 311549 from the European Research Council (ERC), a VICI award 918-156-47 from the Dutch Research Council and Marie Sklodowska-Curie grant agreement no. 813716 (TRAIN-HEART).","volume":12,"citation":{"short":"A. Raso, E. Dirkx, V. Sampaio-Pinto, H. el Azzouzi, R.J. Cubero, D.W. Sorensen, L. Ottaviani, S. Olieslagers, M.M. Huibers, R. de Weger, S. Siddiqi, S. Moimas, C. Torrini, L. Zentillin, L. Braga, D.S. Nascimento, P.A. da Costa Martins, J.H. van Berlo, S. Zacchigna, M. Giacca, L.J. De Windt, Nature Communications 12 (2021).","mla":"Raso, Andrea, et al. “A MicroRNA Program Regulates the Balance between Cardiomyocyte Hyperplasia and Hypertrophy and Stimulates Cardiac Regeneration.” <i>Nature Communications</i>, vol. 12, 4808, Springer Nature, 2021, doi:<a href=\"https://doi.org/10.1038/s41467-021-25211-4\">10.1038/s41467-021-25211-4</a>.","apa":"Raso, A., Dirkx, E., Sampaio-Pinto, V., el Azzouzi, H., Cubero, R. J., Sorensen, D. W., … De Windt, L. J. (2021). A microRNA program regulates the balance between cardiomyocyte hyperplasia and hypertrophy and stimulates cardiac regeneration. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-021-25211-4\">https://doi.org/10.1038/s41467-021-25211-4</a>","ista":"Raso A, Dirkx E, Sampaio-Pinto V, el Azzouzi H, Cubero RJ, Sorensen DW, Ottaviani L, Olieslagers S, Huibers MM, de Weger R, Siddiqi S, Moimas S, Torrini C, Zentillin L, Braga L, Nascimento DS, da Costa Martins PA, van Berlo JH, Zacchigna S, Giacca M, De Windt LJ. 2021. A microRNA program regulates the balance between cardiomyocyte hyperplasia and hypertrophy and stimulates cardiac regeneration. Nature Communications. 12, 4808.","chicago":"Raso, Andrea, Ellen Dirkx, Vasco Sampaio-Pinto, Hamid el Azzouzi, Ryan J Cubero, Daniel W. Sorensen, Lara Ottaviani, et al. “A MicroRNA Program Regulates the Balance between Cardiomyocyte Hyperplasia and Hypertrophy and Stimulates Cardiac Regeneration.” <i>Nature Communications</i>. Springer Nature, 2021. <a href=\"https://doi.org/10.1038/s41467-021-25211-4\">https://doi.org/10.1038/s41467-021-25211-4</a>.","ama":"Raso A, Dirkx E, Sampaio-Pinto V, et al. A microRNA program regulates the balance between cardiomyocyte hyperplasia and hypertrophy and stimulates cardiac regeneration. <i>Nature Communications</i>. 2021;12. doi:<a href=\"https://doi.org/10.1038/s41467-021-25211-4\">10.1038/s41467-021-25211-4</a>","ieee":"A. Raso <i>et al.</i>, “A microRNA program regulates the balance between cardiomyocyte hyperplasia and hypertrophy and stimulates cardiac regeneration,” <i>Nature Communications</i>, vol. 12. Springer Nature, 2021."},"scopus_import":"1","external_id":{"isi":["000683910200042"],"pmid":["34376683"]},"department":[{"_id":"SaSi"}],"month":"08","isi":1,"pmid":1,"day":"10","intvolume":"        12","publication_status":"published","publication_identifier":{"eissn":["2041-1723"]},"year":"2021","date_published":"2021-08-10T00:00:00Z","publisher":"Springer Nature","quality_controlled":"1","article_processing_charge":"Yes","article_number":"4808","language":[{"iso":"eng"}],"related_material":{"link":[{"relation":"erratum","url":"https://doi.org/10.1038/s41467-022-32785-0"}]},"status":"public","genbank":["GSE178867"],"oa_version":"Published Version","oa":1,"has_accepted_license":"1","doi":"10.1038/s41467-021-25211-4","abstract":[{"text":"Myocardial regeneration is restricted to early postnatal life, when mammalian cardiomyocytes still retain the ability to proliferate. The molecular cues that induce cell cycle arrest of neonatal cardiomyocytes towards terminally differentiated adult heart muscle cells remain obscure. Here we report that the miR-106b~25 cluster is higher expressed in the early postnatal myocardium and decreases in expression towards adulthood, especially under conditions of overload, and orchestrates the transition of cardiomyocyte hyperplasia towards cell cycle arrest and hypertrophy by virtue of its targetome. In line, gene delivery of miR-106b~25 to the mouse heart provokes cardiomyocyte proliferation by targeting a network of negative cell cycle regulators including E2f5, Cdkn1c, Ccne1 and Wee1. Conversely, gene-targeted miR-106b~25 null mice display spontaneous hypertrophic remodeling and exaggerated remodeling to overload by derepression of the prohypertrophic transcription factors Hand2 and Mef2d. Taking advantage of the regulatory function of miR-106b~25 on cardiomyocyte hyperplasia and hypertrophy, viral gene delivery of miR-106b~25 provokes nearly complete regeneration of the adult myocardium after ischemic injury. Our data demonstrate that exploitation of conserved molecular programs can enhance the regenerative capacity of the injured heart.","lang":"eng"}],"publication":"Nature Communications","file":[{"file_size":4364333,"file_id":"9876","file_name":"2021_NatureCommunications_Raso.pdf","success":1,"date_updated":"2021-08-10T12:29:59Z","content_type":"application/pdf","access_level":"open_access","creator":"asandaue","checksum":"48d8562e8229e4282f3f354b329722c5","relation":"main_file","date_created":"2021-08-10T12:29:59Z"}],"ddc":["610","570"],"type":"journal_article","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","title":"A microRNA program regulates the balance between cardiomyocyte hyperplasia and hypertrophy and stimulates cardiac regeneration"},{"issue":"29","file_date_updated":"2021-08-11T09:31:41Z","acknowledgement":"We thank W. Schackwitz, M. Joel, and the Joint Genome Institute sequencing team for generating the IR64 genome sequence and initial analysis; L. Bartley and E. Marvinney for genomic DNA preparation for IR64 resequencing; and the University of California (UC), Berkeley Sanger sequencing team for technical advice and service. This work was partially funded by NSF Grant IOS-1025890 (to R.L.F. and D.Z.), NIH Grant GM69415 (to R.L.F. and D.Z.), NIH Grant GM122968 (to P.C.R.), a Young Investigator Grant from the Arnold and Mabel Beckman Foundation (to D.Z.), an International Fulbright Science and Technology Award (to J.A.R.), and a Taiwan Ministry of Education Studying Abroad Scholarship (to P.-H.H.). This work used the Vincent J. Coates Genomics Sequencing Laboratory at UC Berkeley, supported by NIH Instrumentation Grant S10 OD018174.","volume":118,"_id":"9877","date_created":"2021-08-10T19:30:41Z","article_type":"original","author":[{"first_name":"Jessica A.","last_name":"Rodrigues","full_name":"Rodrigues, Jessica A."},{"full_name":"Hsieh, Ping-Hung","first_name":"Ping-Hung","last_name":"Hsieh"},{"full_name":"Ruan, Deling","first_name":"Deling","last_name":"Ruan"},{"last_name":"Nishimura","first_name":"Toshiro","full_name":"Nishimura, Toshiro"},{"first_name":"Manoj K.","last_name":"Sharma","full_name":"Sharma, Manoj K."},{"full_name":"Sharma, Rita","last_name":"Sharma","first_name":"Rita"},{"first_name":"XinYi","last_name":"Ye","full_name":"Ye, XinYi"},{"last_name":"Nguyen","first_name":"Nicholas D.","full_name":"Nguyen, Nicholas D."},{"full_name":"Nijjar, Sukhranjan","first_name":"Sukhranjan","last_name":"Nijjar"},{"full_name":"Ronald, Pamela C.","last_name":"Ronald","first_name":"Pamela C."},{"full_name":"Fischer, Robert L.","last_name":"Fischer","first_name":"Robert L."},{"orcid":"0000-0002-0123-8649","full_name":"Zilberman, Daniel","last_name":"Zilberman","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","first_name":"Daniel"}],"date_updated":"2023-08-11T10:28:10Z","tmp":{"short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)"},"day":"16","intvolume":"       118","month":"07","department":[{"_id":"DaZi"}],"pmid":1,"isi":1,"external_id":{"pmid":["34272287"],"isi":["000685037700012"]},"citation":{"ista":"Rodrigues JA, Hsieh P-H, Ruan D, Nishimura T, Sharma MK, Sharma R, Ye X, Nguyen ND, Nijjar S, Ronald PC, Fischer RL, Zilberman D. 2021. Divergence among rice cultivars reveals roles for transposition and epimutation in ongoing evolution of genomic imprinting. Proceedings of the National Academy of Sciences. 118(29), e2104445118.","ama":"Rodrigues JA, Hsieh P-H, Ruan D, et al. Divergence among rice cultivars reveals roles for transposition and epimutation in ongoing evolution of genomic imprinting. <i>Proceedings of the National Academy of Sciences</i>. 2021;118(29). doi:<a href=\"https://doi.org/10.1073/pnas.2104445118\">10.1073/pnas.2104445118</a>","chicago":"Rodrigues, Jessica A., Ping-Hung Hsieh, Deling Ruan, Toshiro Nishimura, Manoj K. Sharma, Rita Sharma, XinYi Ye, et al. “Divergence among Rice Cultivars Reveals Roles for Transposition and Epimutation in Ongoing Evolution of Genomic Imprinting.” <i>Proceedings of the National Academy of Sciences</i>. National Academy of Sciences, 2021. <a href=\"https://doi.org/10.1073/pnas.2104445118\">https://doi.org/10.1073/pnas.2104445118</a>.","mla":"Rodrigues, Jessica A., et al. “Divergence among Rice Cultivars Reveals Roles for Transposition and Epimutation in Ongoing Evolution of Genomic Imprinting.” <i>Proceedings of the National Academy of Sciences</i>, vol. 118, no. 29, e2104445118, National Academy of Sciences, 2021, doi:<a href=\"https://doi.org/10.1073/pnas.2104445118\">10.1073/pnas.2104445118</a>.","apa":"Rodrigues, J. A., Hsieh, P.-H., Ruan, D., Nishimura, T., Sharma, M. K., Sharma, R., … Zilberman, D. (2021). Divergence among rice cultivars reveals roles for transposition and epimutation in ongoing evolution of genomic imprinting. <i>Proceedings of the National Academy of Sciences</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.2104445118\">https://doi.org/10.1073/pnas.2104445118</a>","short":"J.A. Rodrigues, P.-H. Hsieh, D. Ruan, T. Nishimura, M.K. Sharma, R. Sharma, X. Ye, N.D. Nguyen, S. Nijjar, P.C. Ronald, R.L. Fischer, D. Zilberman, Proceedings of the National Academy of Sciences 118 (2021).","ieee":"J. A. Rodrigues <i>et al.</i>, “Divergence among rice cultivars reveals roles for transposition and epimutation in ongoing evolution of genomic imprinting,” <i>Proceedings of the National Academy of Sciences</i>, vol. 118, no. 29. National Academy of Sciences, 2021."},"scopus_import":"1","status":"public","oa_version":"Published Version","oa":1,"has_accepted_license":"1","article_processing_charge":"Yes (in subscription journal)","article_number":"e2104445118","language":[{"iso":"eng"}],"publisher":"National Academy of Sciences","quality_controlled":"1","year":"2021","publication_status":"published","publication_identifier":{"eissn":["1091-6490"],"issn":["0027-8424"]},"date_published":"2021-07-16T00:00:00Z","type":"journal_article","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","title":"Divergence among rice cultivars reveals roles for transposition and epimutation in ongoing evolution of genomic imprinting","ddc":["580","570"],"file":[{"file_id":"9879","success":1,"file_name":"2021_ProceedingsOfTheNationalAcademyOfSciences_Rodrigues.pdf","date_updated":"2021-08-11T09:31:41Z","file_size":1898360,"relation":"main_file","date_created":"2021-08-11T09:31:41Z","creator":"asandaue","access_level":"open_access","content_type":"application/pdf","checksum":"19e84ad8c03c60222744ee8e16cd6998"}],"abstract":[{"lang":"eng","text":"Parent-of-origin–dependent gene expression in mammals and flowering plants results from differing chromatin imprints (genomic imprinting) between maternally and paternally inherited alleles. Imprinted gene expression in the endosperm of seeds is associated with localized hypomethylation of maternally but not paternally inherited DNA, with certain small RNAs also displaying parent-of-origin–specific expression. To understand the evolution of imprinting mechanisms in Oryza sativa (rice), we analyzed imprinting divergence among four cultivars that span both japonica and indica subspecies: Nipponbare, Kitaake, 93-11, and IR64. Most imprinted genes are imprinted across cultivars and enriched for functions in chromatin and transcriptional regulation, development, and signaling. However, 4 to 11% of imprinted genes display divergent imprinting. Analyses of DNA methylation and small RNAs revealed that endosperm-specific 24-nt small RNA–producing loci show weak RNA-directed DNA methylation, frequently overlap genes, and are imprinted four times more often than genes. However, imprinting divergence most often correlated with local DNA methylation epimutations (9 of 17 assessable loci), which were largely stable within subspecies. Small insertion/deletion events and transposable element insertions accompanied 4 of the 9 locally epimutated loci and associated with imprinting divergence at another 4 of the remaining 8 loci. Correlating epigenetic and genetic variation occurred at key regulatory regions—the promoter and transcription start site of maternally biased genes, and the promoter and gene body of paternally biased genes. Our results reinforce models for the role of maternal-specific DNA hypomethylation in imprinting of both maternally and paternally biased genes, and highlight the role of transposition and epimutation in rice imprinting evolution."}],"publication":"Proceedings of the National Academy of Sciences","doi":"10.1073/pnas.2104445118"}]