[{"article_type":"original","month":"06","date_published":"2022-06-16T00:00:00Z","date_updated":"2023-08-03T12:01:47Z","publisher":"Frontiers","publication_status":"published","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","scopus_import":"1","day":"16","status":"public","article_number":"862398","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"volume":13,"title":"Constitutive active CPK30 interferes with root growth and endomembrane trafficking in Arabidopsis thaliana","file_date_updated":"2022-07-18T08:05:15Z","publication":"Frontiers in Plant Science","_id":"11589","article_processing_charge":"No","type":"journal_article","oa_version":"Published Version","date_created":"2022-07-17T22:01:54Z","department":[{"_id":"JiFr"}],"author":[{"last_name":"Wang","first_name":"Ren","full_name":"Wang, Ren"},{"first_name":"Ellie","last_name":"Himschoot","full_name":"Himschoot, Ellie"},{"first_name":"Jian","last_name":"Chen","full_name":"Chen, Jian"},{"first_name":"Marie","last_name":"Boudsocq","full_name":"Boudsocq, Marie"},{"first_name":"Danny","last_name":"Geelen","full_name":"Geelen, Danny"},{"first_name":"Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","orcid":"0000-0002-8302-7596","full_name":"Friml, Jiří"},{"full_name":"Beeckman, Tom","first_name":"Tom","last_name":"Beeckman"},{"full_name":"Vanneste, Steffen","last_name":"Vanneste","first_name":"Steffen"}],"file":[{"date_updated":"2022-07-18T08:05:15Z","file_size":5040638,"checksum":"95313515637c0f84de591d204375d764","creator":"dernst","content_type":"application/pdf","success":1,"relation":"main_file","file_name":"2022_FrontiersPlantScience_Wang.pdf","file_id":"11596","date_created":"2022-07-18T08:05:15Z","access_level":"open_access"}],"abstract":[{"lang":"eng","text":"Calcium-dependent protein kinases (CPK) are key components of a wide array of signaling pathways, translating stress and nutrient signaling into the modulation of cellular processes such as ion transport and transcription. However, not much is known about CPKs in endomembrane trafficking. Here, we screened for CPKs that impact on root growth and gravitropism, by overexpressing constitutively active forms of CPKs under the control of an inducible promoter in Arabidopsis thaliana. We found that inducible overexpression of an constitutive active CPK30 (CA-CPK30) resulted in a loss of root gravitropism and ectopic auxin accumulation in the root tip. Immunolocalization revealed that CA-CPK30 roots have reduced PIN protein levels, PIN1 polarity defects and impaired Brefeldin A (BFA)-sensitive trafficking. Moreover, FM4-64 uptake was reduced, indicative of a defect in endocytosis. The effects on BFA-sensitive trafficking were not specific to PINs, as BFA could not induce aggregation of ARF1- and CHC-labeled endosomes in CA-CPK30. Interestingly, the interference with BFA-body formation, could be reverted by increasing the extracellular pH, indicating a pH-dependence of this CA-CPK30 effect. Altogether, our data reveal an important role for CPK30 in root growth regulation and endomembrane trafficking in Arabidopsis thaliana."}],"ddc":["580"],"oa":1,"external_id":{"pmid":["35783951"],"isi":["000819250500001"]},"isi":1,"publication_identifier":{"eissn":["1664-462X"]},"language":[{"iso":"eng"}],"year":"2022","intvolume":"        13","pmid":1,"has_accepted_license":"1","quality_controlled":"1","citation":{"ama":"Wang R, Himschoot E, Chen J, et al. Constitutive active CPK30 interferes with root growth and endomembrane trafficking in Arabidopsis thaliana. <i>Frontiers in Plant Science</i>. 2022;13. doi:<a href=\"https://doi.org/10.3389/fpls.2022.862398\">10.3389/fpls.2022.862398</a>","apa":"Wang, R., Himschoot, E., Chen, J., Boudsocq, M., Geelen, D., Friml, J., … Vanneste, S. (2022). Constitutive active CPK30 interferes with root growth and endomembrane trafficking in Arabidopsis thaliana. <i>Frontiers in Plant Science</i>. Frontiers. <a href=\"https://doi.org/10.3389/fpls.2022.862398\">https://doi.org/10.3389/fpls.2022.862398</a>","short":"R. Wang, E. Himschoot, J. Chen, M. Boudsocq, D. Geelen, J. Friml, T. Beeckman, S. Vanneste, Frontiers in Plant Science 13 (2022).","chicago":"Wang, Ren, Ellie Himschoot, Jian Chen, Marie Boudsocq, Danny Geelen, Jiří Friml, Tom Beeckman, and Steffen Vanneste. “Constitutive Active CPK30 Interferes with Root Growth and Endomembrane Trafficking in Arabidopsis Thaliana.” <i>Frontiers in Plant Science</i>. Frontiers, 2022. <a href=\"https://doi.org/10.3389/fpls.2022.862398\">https://doi.org/10.3389/fpls.2022.862398</a>.","ista":"Wang R, Himschoot E, Chen J, Boudsocq M, Geelen D, Friml J, Beeckman T, Vanneste S. 2022. Constitutive active CPK30 interferes with root growth and endomembrane trafficking in Arabidopsis thaliana. Frontiers in Plant Science. 13, 862398.","ieee":"R. Wang <i>et al.</i>, “Constitutive active CPK30 interferes with root growth and endomembrane trafficking in Arabidopsis thaliana,” <i>Frontiers in Plant Science</i>, vol. 13. Frontiers, 2022.","mla":"Wang, Ren, et al. “Constitutive Active CPK30 Interferes with Root Growth and Endomembrane Trafficking in Arabidopsis Thaliana.” <i>Frontiers in Plant Science</i>, vol. 13, 862398, Frontiers, 2022, doi:<a href=\"https://doi.org/10.3389/fpls.2022.862398\">10.3389/fpls.2022.862398</a>."},"doi":"10.3389/fpls.2022.862398","acknowledgement":"RW and JC predoctoral fellows that were supported by the Chinese Science Counsil. The IPS2 benefits from the support of the LabEx Saclay Plant Sciences-SPS (ANR-10-LABX-0040-SPS).\r\nWe thank Jen Sheen for establishing and generously sharing the CKP family clone sets, and for providing useful feedback on the manuscript.","related_material":{"link":[{"relation":"erratum","url":"https://doi.org/10.3389/fpls.2022.1100792"}]}},{"external_id":{"isi":["000818530000001"]},"isi":1,"file":[{"content_type":"application/pdf","success":1,"relation":"main_file","file_name":"2022_NewJournalPhysics_Brauneis.pdf","file_id":"11594","access_level":"open_access","date_created":"2022-07-18T06:33:13Z","date_updated":"2022-07-18T06:33:13Z","file_size":3415721,"checksum":"dc67b60f2e50e9ef2bd820ca0d7333d2","creator":"dernst"}],"abstract":[{"lang":"eng","text":"We investigate the ground-state properties of weakly repulsive one-dimensional bosons in the presence of an attractive zero-range impurity potential. First, we derive mean-field solutions to the problem on a finite ring for the two asymptotic cases: (i) all bosons are bound to the impurity and (ii) all bosons are in a scattering state. Moreover, we derive the critical line that separates these regimes in the parameter space. In the thermodynamic limit, this critical line determines the maximum number of bosons that can be bound by the impurity potential, forming an artificial atom. Second, we validate the mean-field results using the flow equation approach and the multi-layer multi-configuration time-dependent Hartree method for atomic mixtures. While beyond-mean-field effects destroy long-range order in the Bose gas, the critical boson number is unaffected. Our findings are important for understanding such artificial atoms in low-density Bose gases with static and mobile impurities."}],"oa":1,"ddc":["530"],"ec_funded":1,"quality_controlled":"1","doi":"10.1088/1367-2630/ac78d8","citation":{"apa":"Brauneis, F., Backert, T. G., Mistakidis, S. I., Lemeshko, M., Hammer, H. W., &#38; Volosniev, A. (2022). Artificial atoms from cold bosons in one dimension. <i>New Journal of Physics</i>. IOP Publishing. <a href=\"https://doi.org/10.1088/1367-2630/ac78d8\">https://doi.org/10.1088/1367-2630/ac78d8</a>","short":"F. Brauneis, T.G. Backert, S.I. Mistakidis, M. Lemeshko, H.W. Hammer, A. Volosniev, New Journal of Physics 24 (2022).","chicago":"Brauneis, Fabian, Timothy G. Backert, Simeon I. Mistakidis, Mikhail Lemeshko, Hans Werner Hammer, and Artem Volosniev. “Artificial Atoms from Cold Bosons in One Dimension.” <i>New Journal of Physics</i>. IOP Publishing, 2022. <a href=\"https://doi.org/10.1088/1367-2630/ac78d8\">https://doi.org/10.1088/1367-2630/ac78d8</a>.","ista":"Brauneis F, Backert TG, Mistakidis SI, Lemeshko M, Hammer HW, Volosniev A. 2022. Artificial atoms from cold bosons in one dimension. New Journal of Physics. 24(6), 063036.","ieee":"F. Brauneis, T. G. Backert, S. I. Mistakidis, M. Lemeshko, H. W. Hammer, and A. Volosniev, “Artificial atoms from cold bosons in one dimension,” <i>New Journal of Physics</i>, vol. 24, no. 6. IOP Publishing, 2022.","mla":"Brauneis, Fabian, et al. “Artificial Atoms from Cold Bosons in One Dimension.” <i>New Journal of Physics</i>, vol. 24, no. 6, 063036, IOP Publishing, 2022, doi:<a href=\"https://doi.org/10.1088/1367-2630/ac78d8\">10.1088/1367-2630/ac78d8</a>.","ama":"Brauneis F, Backert TG, Mistakidis SI, Lemeshko M, Hammer HW, Volosniev A. Artificial atoms from cold bosons in one dimension. <i>New Journal of Physics</i>. 2022;24(6). doi:<a href=\"https://doi.org/10.1088/1367-2630/ac78d8\">10.1088/1367-2630/ac78d8</a>"},"acknowledgement":"This work has received funding from the DFG Project No. 413495248 [VO 2437/1-1] (FB, H-WH, AGV) and European Union's Horizon 2020 research and innovation programme under the Marie Skĺodowska-Curie Grant Agreement No. 754411 (AGV). ML acknowledges support by the European Research Council (ERC) Starting Grant No. 801770 (ANGULON). SIM acknowledges support from the NSF through a grant for ITAMP at Harvard University.","language":[{"iso":"eng"}],"publication_identifier":{"issn":["1367-2630"]},"year":"2022","intvolume":"        24","has_accepted_license":"1","scopus_import":"1","article_type":"original","date_published":"2022-06-01T00:00:00Z","month":"06","date_updated":"2023-08-03T11:57:41Z","publisher":"IOP Publishing","publication_status":"published","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publication":"New Journal of Physics","file_date_updated":"2022-07-18T06:33:13Z","_id":"11590","issue":"6","type":"journal_article","article_processing_charge":"No","date_created":"2022-07-17T22:01:55Z","oa_version":"Published Version","project":[{"_id":"260C2330-B435-11E9-9278-68D0E5697425","name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411","call_identifier":"H2020"},{"grant_number":"801770","call_identifier":"H2020","_id":"2688CF98-B435-11E9-9278-68D0E5697425","name":"Angulon: physics and applications of a new quasiparticle"}],"department":[{"_id":"MiLe"}],"author":[{"full_name":"Brauneis, Fabian","first_name":"Fabian","last_name":"Brauneis"},{"full_name":"Backert, Timothy G.","first_name":"Timothy G.","last_name":"Backert"},{"first_name":"Simeon I.","last_name":"Mistakidis","full_name":"Mistakidis, Simeon I."},{"full_name":"Lemeshko, Mikhail","orcid":"0000-0002-6990-7802","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","first_name":"Mikhail","last_name":"Lemeshko"},{"full_name":"Hammer, Hans Werner","first_name":"Hans Werner","last_name":"Hammer"},{"full_name":"Volosniev, Artem","orcid":"0000-0003-0393-5525","first_name":"Artem","id":"37D278BC-F248-11E8-B48F-1D18A9856A87","last_name":"Volosniev"}],"day":"01","status":"public","article_number":"063036","title":"Artificial atoms from cold bosons in one dimension","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"volume":24},{"month":"06","date_published":"2022-06-29T00:00:00Z","article_type":"original","publisher":"American Physical Society","date_updated":"2023-08-03T11:58:16Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publication_status":"published","main_file_link":[{"open_access":"1","url":" https://doi.org/10.48550/arXiv.2204.02993"}],"scopus_import":"1","day":"29","article_number":"062454","status":"public","volume":105,"title":"Long-distance distribution of qubit-qubit entanglement using Gaussian-correlated photonic beams","_id":"11591","type":"journal_article","article_processing_charge":"No","issue":"6","publication":"Physical Review A","project":[{"call_identifier":"H2020","grant_number":"899354","_id":"9B868D20-BA93-11EA-9121-9846C619BF3A","name":"Quantum Local Area Networks with Superconducting Qubits"}],"oa_version":"Preprint","date_created":"2022-07-17T22:01:55Z","department":[{"_id":"JoFi"}],"author":[{"first_name":"J.","last_name":"Agustí","full_name":"Agustí, J."},{"full_name":"Minoguchi, Y.","first_name":"Y.","last_name":"Minoguchi"},{"full_name":"Fink, Johannes M","orcid":"0000-0001-8112-028X","id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","first_name":"Johannes M","last_name":"Fink"},{"full_name":"Rabl, P.","first_name":"P.","last_name":"Rabl"}],"oa":1,"abstract":[{"text":"We investigate the deterministic generation and distribution of entanglement in large quantum networks by driving distant qubits with the output fields of a nondegenerate parametric amplifier. In this setting, the amplifier produces a continuous Gaussian two-mode squeezed state, which acts as a quantum-correlated reservoir for the qubits and relaxes them into a highly entangled steady state. Here we are interested in the maximal amount of entanglement and the optimal entanglement generation rates that can be achieved with this scheme under realistic conditions taking, in particular, the finite amplifier bandwidth, waveguide losses, and propagation delays into account. By combining exact numerical simulations of the full network with approximate analytic results, we predict the optimal working point for the amplifier and the corresponding qubit-qubit entanglement under various conditions. Our findings show that this passive conversion of Gaussian into discrete-variable entanglement offers a robust and experimentally very attractive approach for operating large optical, microwave, or hybrid quantum networks, for which efficient parametric amplifiers are currently developed.","lang":"eng"}],"external_id":{"isi":["000824330200003"],"arxiv":["2204.02993"]},"isi":1,"publication_identifier":{"issn":["2469-9926"],"eissn":["2469-9934"]},"language":[{"iso":"eng"}],"year":"2022","intvolume":"       105","arxiv":1,"citation":{"apa":"Agustí, J., Minoguchi, Y., Fink, J. M., &#38; Rabl, P. (2022). Long-distance distribution of qubit-qubit entanglement using Gaussian-correlated photonic beams. <i>Physical Review A</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevA.105.062454\">https://doi.org/10.1103/PhysRevA.105.062454</a>","short":"J. Agustí, Y. Minoguchi, J.M. Fink, P. Rabl, Physical Review A 105 (2022).","chicago":"Agustí, J., Y. Minoguchi, Johannes M Fink, and P. Rabl. “Long-Distance Distribution of Qubit-Qubit Entanglement Using Gaussian-Correlated Photonic Beams.” <i>Physical Review A</i>. American Physical Society, 2022. <a href=\"https://doi.org/10.1103/PhysRevA.105.062454\">https://doi.org/10.1103/PhysRevA.105.062454</a>.","ieee":"J. Agustí, Y. Minoguchi, J. M. Fink, and P. Rabl, “Long-distance distribution of qubit-qubit entanglement using Gaussian-correlated photonic beams,” <i>Physical Review A</i>, vol. 105, no. 6. American Physical Society, 2022.","ista":"Agustí J, Minoguchi Y, Fink JM, Rabl P. 2022. Long-distance distribution of qubit-qubit entanglement using Gaussian-correlated photonic beams. Physical Review A. 105(6), 062454.","mla":"Agustí, J., et al. “Long-Distance Distribution of Qubit-Qubit Entanglement Using Gaussian-Correlated Photonic Beams.” <i>Physical Review A</i>, vol. 105, no. 6, 062454, American Physical Society, 2022, doi:<a href=\"https://doi.org/10.1103/PhysRevA.105.062454\">10.1103/PhysRevA.105.062454</a>.","ama":"Agustí J, Minoguchi Y, Fink JM, Rabl P. Long-distance distribution of qubit-qubit entanglement using Gaussian-correlated photonic beams. <i>Physical Review A</i>. 2022;105(6). doi:<a href=\"https://doi.org/10.1103/PhysRevA.105.062454\">10.1103/PhysRevA.105.062454</a>"},"doi":"10.1103/PhysRevA.105.062454","ec_funded":1,"quality_controlled":"1","acknowledgement":"We thank T. Mavrogordatos and D. Zhu for initial contribution on the presented topic and K. Fedorov for stimulating discussions on entangled microwave beams. This work was supported by the Austrian Science Fund (FWF) through Grant No. P32299 (PHONED) and the European Union’s Horizon 2020 research and innovation programme under Grant Agreement No. 899354 (SuperQuLAN). Most of the computational results presented were obtained using the CLIP cluster [65]."},{"intvolume":"       105","arxiv":1,"publication_identifier":{"issn":["2469-9926"],"eissn":["2469-9934"]},"language":[{"iso":"eng"}],"year":"2022","acknowledgement":"The authors gratefully acknowledge stimulating discussions with T. Enss, and thank an anonymous referee for suggestions and remarks that allowed us to improve the original manuscript. This work is supported by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) under Germany’s Excellence Strategy EXC2181/1-390900948 (the Heidelberg STRUCTURES Excellence Cluster).","quality_controlled":"1","doi":"10.1103/PhysRevA.105.063329","citation":{"ama":"Bighin G, Cappellaro A, Salasnich L. Unitary Fermi superfluid near the critical temperature: Thermodynamics and sound modes from elementary excitations. <i>Physical Review A</i>. 2022;105(6). doi:<a href=\"https://doi.org/10.1103/PhysRevA.105.063329\">10.1103/PhysRevA.105.063329</a>","ista":"Bighin G, Cappellaro A, Salasnich L. 2022. Unitary Fermi superfluid near the critical temperature: Thermodynamics and sound modes from elementary excitations. Physical Review A. 105(6), 063329.","ieee":"G. Bighin, A. Cappellaro, and L. Salasnich, “Unitary Fermi superfluid near the critical temperature: Thermodynamics and sound modes from elementary excitations,” <i>Physical Review A</i>, vol. 105, no. 6. American Physical Society, 2022.","mla":"Bighin, Giacomo, et al. “Unitary Fermi Superfluid near the Critical Temperature: Thermodynamics and Sound Modes from Elementary Excitations.” <i>Physical Review A</i>, vol. 105, no. 6, 063329, American Physical Society, 2022, doi:<a href=\"https://doi.org/10.1103/PhysRevA.105.063329\">10.1103/PhysRevA.105.063329</a>.","apa":"Bighin, G., Cappellaro, A., &#38; Salasnich, L. (2022). Unitary Fermi superfluid near the critical temperature: Thermodynamics and sound modes from elementary excitations. <i>Physical Review A</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevA.105.063329\">https://doi.org/10.1103/PhysRevA.105.063329</a>","chicago":"Bighin, Giacomo, Alberto Cappellaro, and L. Salasnich. “Unitary Fermi Superfluid near the Critical Temperature: Thermodynamics and Sound Modes from Elementary Excitations.” <i>Physical Review A</i>. American Physical Society, 2022. <a href=\"https://doi.org/10.1103/PhysRevA.105.063329\">https://doi.org/10.1103/PhysRevA.105.063329</a>.","short":"G. Bighin, A. Cappellaro, L. Salasnich, Physical Review A 105 (2022)."},"abstract":[{"text":"We compare recent experimental results [Science 375, 528 (2022)] of the superfluid unitary Fermi gas near the critical temperature with a thermodynamic model based on the elementary excitations of the system. We find good agreement between experimental data and our theory for several quantities such as first sound, second sound, and superfluid fraction. We also show that mode mixing between first and second sound occurs. Finally, we characterize the response amplitude to a density perturbation: Close to the critical temperature both first and second sound can be excited through a density perturbation, whereas at lower temperatures only the first sound mode exhibits a significant response.","lang":"eng"}],"oa":1,"external_id":{"isi":["000829758500010"],"arxiv":["2206.03924"]},"isi":1,"status":"public","article_number":"063329","title":"Unitary Fermi superfluid near the critical temperature: Thermodynamics and sound modes from elementary excitations","volume":105,"day":"30","department":[{"_id":"MiLe"}],"author":[{"full_name":"Bighin, Giacomo","orcid":"0000-0001-8823-9777","id":"4CA96FD4-F248-11E8-B48F-1D18A9856A87","first_name":"Giacomo","last_name":"Bighin"},{"orcid":"0000-0001-6110-2359","full_name":"Cappellaro, Alberto","last_name":"Cappellaro","id":"9d13b3cb-30a2-11eb-80dc-f772505e8660","first_name":"Alberto"},{"full_name":"Salasnich, L.","last_name":"Salasnich","first_name":"L."}],"publication":"Physical Review A","type":"journal_article","_id":"11592","issue":"6","article_processing_charge":"No","oa_version":"Preprint","date_created":"2022-07-17T22:01:55Z","date_updated":"2023-08-03T12:00:11Z","publisher":"American Physical Society","publication_status":"published","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","article_type":"original","date_published":"2022-06-30T00:00:00Z","month":"06","scopus_import":"1","main_file_link":[{"url":" https://doi.org/10.48550/arXiv.2206.03924","open_access":"1"}]},{"date_published":"2022-09-01T00:00:00Z","month":"09","article_type":"original","publisher":"Springer Nature","date_updated":"2023-08-14T12:43:52Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_status":"published","main_file_link":[{"url":"https://arxiv.org/abs/1803.05085","open_access":"1"}],"scopus_import":"1","day":"01","status":"public","volume":68,"title":"The Z2-Genus of Kuratowski minors","article_processing_charge":"No","_id":"11593","type":"journal_article","publication":"Discrete and Computational Geometry","project":[{"call_identifier":"FWF","grant_number":"M02281","name":"Eliminating intersections in drawings of graphs","_id":"261FA626-B435-11E9-9278-68D0E5697425"}],"date_created":"2022-07-17T22:01:56Z","oa_version":"Preprint","department":[{"_id":"UlWa"}],"author":[{"last_name":"Fulek","id":"39F3FFE4-F248-11E8-B48F-1D18A9856A87","first_name":"Radoslav","orcid":"0000-0001-8485-1774","full_name":"Fulek, Radoslav"},{"full_name":"Kynčl, Jan","first_name":"Jan","last_name":"Kynčl"}],"oa":1,"abstract":[{"text":"A drawing of a graph on a surface is independently even if every pair of nonadjacent edges in the drawing crosses an even number of times. The Z2 -genus of a graph G is the minimum g such that G has an independently even drawing on the orientable surface of genus g. An unpublished result by Robertson and Seymour implies that for every t, every graph of sufficiently large genus contains as a minor a projective t×t grid or one of the following so-called t -Kuratowski graphs: K3,t, or t copies of K5 or K3,3 sharing at most two common vertices. We show that the Z2-genus of graphs in these families is unbounded in t; in fact, equal to their genus. Together, this implies that the genus of a graph is bounded from above by a function of its Z2-genus, solving a problem posed by Schaefer and Štefankovič, and giving an approximate version of the Hanani–Tutte theorem on orientable surfaces. We also obtain an analogous result for Euler genus and Euler Z2-genus of graphs.","lang":"eng"}],"external_id":{"isi":["000825014500001"],"arxiv":["1803.05085"]},"page":"425-447","isi":1,"publication_identifier":{"eissn":["1432-0444"],"issn":["0179-5376"]},"language":[{"iso":"eng"}],"year":"2022","arxiv":1,"intvolume":"        68","doi":"10.1007/s00454-022-00412-w","citation":{"ama":"Fulek R, Kynčl J. The Z2-Genus of Kuratowski minors. <i>Discrete and Computational Geometry</i>. 2022;68:425-447. doi:<a href=\"https://doi.org/10.1007/s00454-022-00412-w\">10.1007/s00454-022-00412-w</a>","mla":"Fulek, Radoslav, and Jan Kynčl. “The Z2-Genus of Kuratowski Minors.” <i>Discrete and Computational Geometry</i>, vol. 68, Springer Nature, 2022, pp. 425–47, doi:<a href=\"https://doi.org/10.1007/s00454-022-00412-w\">10.1007/s00454-022-00412-w</a>.","ista":"Fulek R, Kynčl J. 2022. The Z2-Genus of Kuratowski minors. Discrete and Computational Geometry. 68, 425–447.","ieee":"R. Fulek and J. Kynčl, “The Z2-Genus of Kuratowski minors,” <i>Discrete and Computational Geometry</i>, vol. 68. Springer Nature, pp. 425–447, 2022.","chicago":"Fulek, Radoslav, and Jan Kynčl. “The Z2-Genus of Kuratowski Minors.” <i>Discrete and Computational Geometry</i>. Springer Nature, 2022. <a href=\"https://doi.org/10.1007/s00454-022-00412-w\">https://doi.org/10.1007/s00454-022-00412-w</a>.","short":"R. Fulek, J. Kynčl, Discrete and Computational Geometry 68 (2022) 425–447.","apa":"Fulek, R., &#38; Kynčl, J. (2022). The Z2-Genus of Kuratowski minors. <i>Discrete and Computational Geometry</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s00454-022-00412-w\">https://doi.org/10.1007/s00454-022-00412-w</a>"},"quality_controlled":"1","acknowledgement":"We thank Zdeněk Dvořák, Xavier Goaoc, and Pavel Paták for helpful discussions. We also thank Bojan Mohar, Paul Seymour, Gelasio Salazar, Jim Geelen, and John Maharry for information about their unpublished results related to Conjecture 3.1. Finally we thank the reviewers for corrections and suggestions for improving the presentation.\r\nSupported by Austrian Science Fund (FWF): M2281-N35. Supported by project 19-04113Y of the Czech Science Foundation (GAČR), by the Czech-French collaboration project EMBEDS II (CZ: 7AMB17FR029, FR: 38087RM), and by Charles University project UNCE/SCI/004.","related_material":{"record":[{"relation":"earlier_version","id":"186","status":"public"}]}},{"month":"07","date_published":"2022-07-20T00:00:00Z","publication_status":"published","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","date_updated":"2024-10-29T10:22:45Z","publisher":"Institute of Science and Technology Austria","day":"20","title":"Auxin and strigolactone non-canonical signaling regulating development in Arabidopsis thaliana","status":"public","date_created":"2022-07-20T11:21:53Z","oa_version":"Published Version","project":[{"name":"Tracing Evolution of Auxin Transport and Polarity in Plants","_id":"261099A6-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"742985"}],"file_date_updated":"2022-07-25T11:48:45Z","_id":"11626","article_processing_charge":"No","type":"dissertation","author":[{"orcid":"0000-0003-1286-7368","full_name":"Gallei, Michelle C","last_name":"Gallei","first_name":"Michelle C","id":"35A03822-F248-11E8-B48F-1D18A9856A87"}],"department":[{"_id":"GradSch"},{"_id":"JiFr"}],"abstract":[{"text":"Plant growth and development is well known to be both, flexible and dynamic. The high capacity for post-embryonic organ formation and tissue regeneration requires tightly regulated intercellular communication and coordinated tissue polarization. One of the most important drivers for patterning and polarity in plant development is the phytohormone auxin. Auxin has the unique characteristic to establish polarized channels for its own active directional cell to cell transport. This fascinating phenomenon is called auxin canalization. Those auxin transport channels are characterized by the expression and polar, subcellular localization of PIN auxin efflux carriers. PIN proteins have the ability to dynamically change their localization and auxin itself can affect this by interfering with trafficking. Most of the underlying molecular mechanisms of canalization still remain enigmatic. What is known so far is that canonical auxin signaling is indispensable but also other non-canonical signaling components are thought to play a role. In order to shed light into the mysteries auf auxin canalization this study revisits the branches of auxin signaling in detail. Further a new auxin analogue, PISA, is developed which triggers auxin-like responses but does not directly activate canonical transcriptional auxin signaling. We revisit the direct auxin effect on PIN trafficking where we found that, contradictory to previous observations, auxin is very specifically promoting endocytosis of PIN2 but has no overall effect on endocytosis. Further, we evaluate which cellular processes related to PIN subcellular dynamics are involved in the establishment of auxin conducting channels and the formation of vascular tissue. We are re-evaluating the function of AUXIN BINDING PROTEIN 1 (ABP1) and provide a comprehensive picture about its developmental phneotypes and involvement in auxin signaling and canalization. Lastly, we are focusing on the crosstalk between the hormone strigolactone (SL) and auxin and found that SL is interfering with essentially all processes involved in auxin canalization in a non-transcriptional manner. Lastly we identify a new way of SL perception and signaling which is emanating from mitochondria, is independent of canonical SL signaling and is modulating primary root growth.","lang":"eng"}],"degree_awarded":"PhD","oa":1,"ddc":["575"],"file":[{"content_type":"application/pdf","file_name":"Thesis_Gallei.pdf","relation":"main_file","file_id":"11645","access_level":"open_access","date_created":"2022-07-25T09:08:47Z","date_updated":"2022-07-25T09:08:47Z","file_size":9730864,"checksum":"bd7ac35403cf5b4b2607287d2a104b3a","creator":"mgallei"},{"file_size":19560720,"checksum":"a9e54fe5471ba25dc13c2150c1b8ccbb","creator":"mgallei","date_updated":"2022-07-25T09:39:58Z","file_id":"11646","date_created":"2022-07-25T09:09:09Z","access_level":"closed","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_name":"Thesis_Gallei_source.docx","relation":"source_file"},{"access_level":"closed","date_created":"2022-07-25T09:09:32Z","file_id":"11647","file_name":"Thesis_Gallei_to_print.pdf","relation":"source_file","content_type":"application/pdf","description":"This is the print version of the thesis including the full appendix","creator":"mgallei","file_size":24542837,"checksum":"3994f7f20058941b5bb8a16886b21e71","date_updated":"2022-07-25T09:39:58Z"},{"date_updated":"2022-07-25T11:48:45Z","creator":"mgallei","file_size":15435966,"checksum":"f24acd3c0d864f4c6676e8b0d7bfa76b","file_name":"Thesis_Gallei_Appendix.pdf","relation":"main_file","content_type":"application/pdf","date_created":"2022-07-25T11:48:45Z","access_level":"open_access","file_id":"11650"}],"supervisor":[{"full_name":"Friml, Jiří","orcid":"0000-0002-8302-7596","last_name":"Friml","first_name":"Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Benková","first_name":"Eva","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8510-9739","full_name":"Benková, Eva"},{"full_name":"Shani, Eilon","first_name":"Eilon","last_name":"Shani"}],"alternative_title":["ISTA Thesis"],"page":"248","year":"2022","publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-019-0"]},"language":[{"iso":"eng"}],"has_accepted_license":"1","ec_funded":1,"doi":"10.15479/at:ista:11626","citation":{"ama":"Gallei MC. Auxin and strigolactone non-canonical signaling regulating development in Arabidopsis thaliana. 2022. doi:<a href=\"https://doi.org/10.15479/at:ista:11626\">10.15479/at:ista:11626</a>","apa":"Gallei, M. C. (2022). <i>Auxin and strigolactone non-canonical signaling regulating development in Arabidopsis thaliana</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:11626\">https://doi.org/10.15479/at:ista:11626</a>","chicago":"Gallei, Michelle C. “Auxin and Strigolactone Non-Canonical Signaling Regulating Development in Arabidopsis Thaliana.” Institute of Science and Technology Austria, 2022. <a href=\"https://doi.org/10.15479/at:ista:11626\">https://doi.org/10.15479/at:ista:11626</a>.","short":"M.C. Gallei, Auxin and Strigolactone Non-Canonical Signaling Regulating Development in Arabidopsis Thaliana, Institute of Science and Technology Austria, 2022.","ieee":"M. C. Gallei, “Auxin and strigolactone non-canonical signaling regulating development in Arabidopsis thaliana,” Institute of Science and Technology Austria, 2022.","ista":"Gallei MC. 2022. Auxin and strigolactone non-canonical signaling regulating development in Arabidopsis thaliana. Institute of Science and Technology Austria.","mla":"Gallei, Michelle C. <i>Auxin and Strigolactone Non-Canonical Signaling Regulating Development in Arabidopsis Thaliana</i>. Institute of Science and Technology Austria, 2022, doi:<a href=\"https://doi.org/10.15479/at:ista:11626\">10.15479/at:ista:11626</a>."},"related_material":{"record":[{"relation":"part_of_dissertation","id":"9287","status":"public"},{"status":"public","id":"7142","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","status":"public","id":"7465"},{"status":"public","id":"8138","relation":"part_of_dissertation"},{"id":"6260","status":"public","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","status":"public","id":"8931"},{"relation":"part_of_dissertation","status":"public","id":"10411"}]}},{"external_id":{"isi":["000835490600001"],"arxiv":["2111.06697"]},"isi":1,"file":[{"date_updated":"2023-02-02T07:56:34Z","checksum":"3ca88decb1011180dc6de7e0862153e1","file_size":247615,"creator":"dernst","content_type":"application/pdf","success":1,"relation":"main_file","file_name":"2022_FiniteFields_Kmentt.pdf","file_id":"12475","date_created":"2023-02-02T07:56:34Z","access_level":"open_access"}],"abstract":[{"text":"In [3], Poonen and Slavov recently developed a novel approach to Bertini irreducibility theorems over an arbitrary field, based on random hyperplane slicing. In this paper, we extend their work by proving an analogous bound for the dimension of the exceptional locus in the setting of linear subspaces of higher codimensions.","lang":"eng"}],"oa":1,"ddc":["510"],"quality_controlled":"1","citation":{"apa":"Kmentt, P., &#38; Shute, A. L. (2022). The Bertini irreducibility theorem for higher codimensional slices. <i>Finite Fields and Their Applications</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.ffa.2022.102085\">https://doi.org/10.1016/j.ffa.2022.102085</a>","short":"P. Kmentt, A.L. Shute, Finite Fields and Their Applications 83 (2022).","chicago":"Kmentt, Philip, and Alec L Shute. “The Bertini Irreducibility Theorem for Higher Codimensional Slices.” <i>Finite Fields and Their Applications</i>. Elsevier, 2022. <a href=\"https://doi.org/10.1016/j.ffa.2022.102085\">https://doi.org/10.1016/j.ffa.2022.102085</a>.","ista":"Kmentt P, Shute AL. 2022. The Bertini irreducibility theorem for higher codimensional slices. Finite Fields and their Applications. 83(10), 102085.","ieee":"P. Kmentt and A. L. Shute, “The Bertini irreducibility theorem for higher codimensional slices,” <i>Finite Fields and their Applications</i>, vol. 83, no. 10. Elsevier, 2022.","mla":"Kmentt, Philip, and Alec L. Shute. “The Bertini Irreducibility Theorem for Higher Codimensional Slices.” <i>Finite Fields and Their Applications</i>, vol. 83, no. 10, 102085, Elsevier, 2022, doi:<a href=\"https://doi.org/10.1016/j.ffa.2022.102085\">10.1016/j.ffa.2022.102085</a>.","ama":"Kmentt P, Shute AL. The Bertini irreducibility theorem for higher codimensional slices. <i>Finite Fields and their Applications</i>. 2022;83(10). doi:<a href=\"https://doi.org/10.1016/j.ffa.2022.102085\">10.1016/j.ffa.2022.102085</a>"},"doi":"10.1016/j.ffa.2022.102085","arxiv":1,"intvolume":"        83","has_accepted_license":"1","publication_identifier":{"issn":["10715797"],"eissn":["10902465"]},"language":[{"iso":"eng"}],"year":"2022","scopus_import":"1","date_updated":"2023-08-03T12:12:57Z","publisher":"Elsevier","publication_status":"published","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","article_type":"original","date_published":"2022-10-01T00:00:00Z","month":"10","department":[{"_id":"TiBr"}],"author":[{"last_name":"Kmentt","first_name":"Philip","id":"c90670c9-0bf0-11ed-86f5-ed522ece2fac","full_name":"Kmentt, Philip"},{"orcid":"0000-0002-1812-2810","full_name":"Shute, Alec L","last_name":"Shute","first_name":"Alec L","id":"440EB050-F248-11E8-B48F-1D18A9856A87"}],"publication":"Finite Fields and their Applications","file_date_updated":"2023-02-02T07:56:34Z","_id":"11636","article_processing_charge":"Yes (via OA deal)","issue":"10","type":"journal_article","oa_version":"Published Version","date_created":"2022-07-24T22:01:41Z","status":"public","article_number":"102085","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"title":"The Bertini irreducibility theorem for higher codimensional slices","volume":83,"day":"01"},{"day":"21","status":"public","article_number":"e3001684","title":"ROS and cGMP signaling modulate persistent escape from hypoxia in Caenorhabditis elegans","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"volume":20,"file_date_updated":"2022-07-25T07:38:49Z","publication":"PLoS Biology","_id":"11637","article_processing_charge":"No","issue":"6","type":"journal_article","oa_version":"Published Version","date_created":"2022-07-24T22:01:42Z","project":[{"grant_number":"209504/A/17/Z","_id":"23870BE8-32DE-11EA-91FC-C7463DDC885E","name":"Molecular mechanisms of neural circuit function"}],"department":[{"_id":"MaDe"}],"author":[{"first_name":"Lina","last_name":"Zhao","full_name":"Zhao, Lina"},{"last_name":"Fenk","first_name":"Lorenz A.","full_name":"Fenk, Lorenz A."},{"full_name":"Nilsson, Lars","last_name":"Nilsson","first_name":"Lars"},{"id":"E95D3014-9D8C-11E9-9C80-D2F8E5697425","first_name":"Niko Paresh","last_name":"Amin-Wetzel","full_name":"Amin-Wetzel, Niko Paresh"},{"full_name":"Ramirez, Nelson","id":"39831956-E4FE-11E9-85DE-0DC7E5697425","first_name":"Nelson","last_name":"Ramirez"},{"full_name":"De Bono, Mario","orcid":"0000-0001-8347-0443","id":"4E3FF80E-F248-11E8-B48F-1D18A9856A87","first_name":"Mario","last_name":"De Bono"},{"first_name":"Changchun","last_name":"Chen","full_name":"Chen, Changchun"}],"article_type":"original","date_published":"2022-06-21T00:00:00Z","month":"06","date_updated":"2023-08-03T12:11:44Z","publisher":"Public Library of Science","publication_status":"published","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","scopus_import":"1","publication_identifier":{"eissn":["1545-7885"]},"language":[{"iso":"eng"}],"year":"2022","intvolume":"        20","pmid":1,"has_accepted_license":"1","quality_controlled":"1","citation":{"mla":"Zhao, Lina, et al. “ROS and CGMP Signaling Modulate Persistent Escape from Hypoxia in Caenorhabditis Elegans.” <i>PLoS Biology</i>, vol. 20, no. 6, e3001684, Public Library of Science, 2022, doi:<a href=\"https://doi.org/10.1371/journal.pbio.3001684\">10.1371/journal.pbio.3001684</a>.","ista":"Zhao L, Fenk LA, Nilsson L, Amin-Wetzel NP, Ramirez N, de Bono M, Chen C. 2022. ROS and cGMP signaling modulate persistent escape from hypoxia in Caenorhabditis elegans. PLoS Biology. 20(6), e3001684.","ieee":"L. Zhao <i>et al.</i>, “ROS and cGMP signaling modulate persistent escape from hypoxia in Caenorhabditis elegans,” <i>PLoS Biology</i>, vol. 20, no. 6. Public Library of Science, 2022.","short":"L. Zhao, L.A. Fenk, L. Nilsson, N.P. Amin-Wetzel, N. Ramirez, M. de Bono, C. Chen, PLoS Biology 20 (2022).","chicago":"Zhao, Lina, Lorenz A. Fenk, Lars Nilsson, Niko Paresh Amin-Wetzel, Nelson Ramirez, Mario de Bono, and Changchun Chen. “ROS and CGMP Signaling Modulate Persistent Escape from Hypoxia in Caenorhabditis Elegans.” <i>PLoS Biology</i>. Public Library of Science, 2022. <a href=\"https://doi.org/10.1371/journal.pbio.3001684\">https://doi.org/10.1371/journal.pbio.3001684</a>.","apa":"Zhao, L., Fenk, L. A., Nilsson, L., Amin-Wetzel, N. P., Ramirez, N., de Bono, M., &#38; Chen, C. (2022). ROS and cGMP signaling modulate persistent escape from hypoxia in Caenorhabditis elegans. <i>PLoS Biology</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pbio.3001684\">https://doi.org/10.1371/journal.pbio.3001684</a>","ama":"Zhao L, Fenk LA, Nilsson L, et al. ROS and cGMP signaling modulate persistent escape from hypoxia in Caenorhabditis elegans. <i>PLoS Biology</i>. 2022;20(6). doi:<a href=\"https://doi.org/10.1371/journal.pbio.3001684\">10.1371/journal.pbio.3001684</a>"},"doi":"10.1371/journal.pbio.3001684","acknowledgement":" This work was funded by H2020 European Research Council (ERC Advanced grant, 269058 ACMO, https://erc.europa.eu/funding/advanced-grants) and Wellcome Trust UK (Wellcome Investigator Award, 209504/Z/17/Z, https://wellcome.org/grant-funding/people-and-projects/grants-awarded/molecular-mechanisms-neural-circuit-function-0) to M.d.B, and by H2020 European Research Council (ERC starting grant, 802653 OXYGEN SENSING, https://erc.europa.eu/funding/starting-grants) and Vetenskapsrådet (VR starting grant, 2018-02216, https://www.vr.se/english.html) to C.C. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.","file":[{"access_level":"open_access","date_created":"2022-07-25T07:38:49Z","file_id":"11643","relation":"main_file","file_name":"2022_PLoSBiology_Zhao.pdf","success":1,"content_type":"application/pdf","creator":"dernst","file_size":3721585,"checksum":"df4902f854ad76769d3203bfdc69f16c","date_updated":"2022-07-25T07:38:49Z"}],"abstract":[{"lang":"eng","text":"The ability to detect and respond to acute oxygen (O2) shortages is indispensable to aerobic life. The molecular mechanisms and circuits underlying this capacity are poorly understood. Here, we characterize the behavioral responses of feeding Caenorhabditis elegans to approximately 1% O2. Acute hypoxia triggers a bout of turning maneuvers followed by a persistent switch to rapid forward movement as animals seek to avoid and escape hypoxia. While the behavioral responses to 1% O2 closely resemble those evoked by 21% O2, they have distinct molecular and circuit underpinnings. Disrupting phosphodiesterases (PDEs), specific G proteins, or BBSome function inhibits escape from 1% O2 due to increased cGMP signaling. A primary source of cGMP is GCY-28, the ortholog of the atrial natriuretic peptide (ANP) receptor. cGMP activates the protein kinase G EGL-4 and enhances neuroendocrine secretion to inhibit acute responses to 1% O2. Triggering a rise in cGMP optogenetically in multiple neurons, including AIA interneurons, rapidly and reversibly inhibits escape from 1% O2. Ca2+ imaging reveals that a 7% to 1% O2 stimulus evokes a Ca2+ decrease in several neurons. Defects in mitochondrial complex I (MCI) and mitochondrial complex I (MCIII), which lead to persistently high reactive oxygen species (ROS), abrogate acute hypoxia responses. In particular, repressing the expression of isp-1, which encodes the iron sulfur protein of MCIII, inhibits escape from 1% O2 without affecting responses to 21% O2. Both genetic and pharmacological up-regulation of mitochondrial ROS increase cGMP levels, which contribute to the reduced hypoxia responses. Our results implicate ROS and precise regulation of intracellular cGMP in the modulation of acute responses to hypoxia by C. elegans."}],"oa":1,"ddc":["570"],"external_id":{"isi":["000828679600001"],"pmid":["35727855"]},"isi":1},{"abstract":[{"lang":"eng","text":"Statistical inference is central to many scientific endeavors, yet how it works remains unresolved. Answering this requires a quantitative understanding of the intrinsic interplay between statistical models, inference methods, and the structure in the data. To this end, we characterize the efficacy of direct coupling analysis (DCA)—a highly successful method for analyzing amino acid sequence data—in inferring pairwise interactions from samples of ferromagnetic Ising models on random graphs. Our approach allows for physically motivated exploration of qualitatively distinct data regimes separated by phase transitions. We show that inference quality depends strongly on the nature of data-generating distributions: optimal accuracy occurs at an intermediate temperature where the detrimental effects from macroscopic order and thermal noise are minimal. Importantly our results indicate that DCA does not always outperform its local-statistics-based predecessors; while DCA excels at low temperatures, it becomes inferior to simple correlation thresholding at virtually all temperatures when data are limited. Our findings offer insights into the regime in which DCA operates so successfully, and more broadly, how inference interacts with the structure in the data."}],"oa":1,"ddc":["530"],"file":[{"file_size":1379683,"checksum":"ed6fdc2a3a096df785fa5f7b17b716c6","creator":"dernst","date_updated":"2022-07-25T07:47:23Z","file_id":"11644","date_created":"2022-07-25T07:47:23Z","access_level":"open_access","success":1,"content_type":"application/pdf","file_name":"2022_PhysicalReviewResearch_Ngampruetikorn.pdf","relation":"main_file"}],"external_id":{"arxiv":["2106.02349"]},"funded_apc":"1","has_accepted_license":"1","arxiv":1,"intvolume":"         4","year":"2022","publication_identifier":{"issn":["2643-1564"]},"language":[{"iso":"eng"}],"acknowledgement":"This work was supported in part by the Alfred P. Sloan Foundation, the Simons Foundation, the National Institutes of Health under Award No. R01EB026943, and the National Science Foundation, through the Center for the Physics of Biological Function (PHY-1734030).","quality_controlled":"1","citation":{"ama":"Ngampruetikorn V, Sachdeva V, Torrence J, Humplik J, Schwab DJ, Palmer SE. Inferring couplings in networks across order-disorder phase transitions. <i>Physical Review Research</i>. 2022;4(2). doi:<a href=\"https://doi.org/10.1103/PhysRevResearch.4.023240\">10.1103/PhysRevResearch.4.023240</a>","apa":"Ngampruetikorn, V., Sachdeva, V., Torrence, J., Humplik, J., Schwab, D. J., &#38; Palmer, S. E. (2022). Inferring couplings in networks across order-disorder phase transitions. <i>Physical Review Research</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevResearch.4.023240\">https://doi.org/10.1103/PhysRevResearch.4.023240</a>","short":"V. Ngampruetikorn, V. Sachdeva, J. Torrence, J. Humplik, D.J. Schwab, S.E. Palmer, Physical Review Research 4 (2022).","chicago":"Ngampruetikorn, Vudtiwat, Vedant Sachdeva, Johanna Torrence, Jan Humplik, David J. Schwab, and Stephanie E. Palmer. “Inferring Couplings in Networks across Order-Disorder Phase Transitions.” <i>Physical Review Research</i>. American Physical Society, 2022. <a href=\"https://doi.org/10.1103/PhysRevResearch.4.023240\">https://doi.org/10.1103/PhysRevResearch.4.023240</a>.","ieee":"V. Ngampruetikorn, V. Sachdeva, J. Torrence, J. Humplik, D. J. Schwab, and S. E. Palmer, “Inferring couplings in networks across order-disorder phase transitions,” <i>Physical Review Research</i>, vol. 4, no. 2. American Physical Society, 2022.","ista":"Ngampruetikorn V, Sachdeva V, Torrence J, Humplik J, Schwab DJ, Palmer SE. 2022. Inferring couplings in networks across order-disorder phase transitions. Physical Review Research. 4(2), 023240.","mla":"Ngampruetikorn, Vudtiwat, et al. “Inferring Couplings in Networks across Order-Disorder Phase Transitions.” <i>Physical Review Research</i>, vol. 4, no. 2, 023240, American Physical Society, 2022, doi:<a href=\"https://doi.org/10.1103/PhysRevResearch.4.023240\">10.1103/PhysRevResearch.4.023240</a>."},"doi":"10.1103/PhysRevResearch.4.023240","publication_status":"published","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2022-07-25T07:52:35Z","publisher":"American Physical Society","article_type":"original","month":"06","date_published":"2022-06-24T00:00:00Z","scopus_import":"1","volume":4,"tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"title":"Inferring couplings in networks across order-disorder phase transitions","status":"public","article_number":"023240","day":"24","author":[{"full_name":"Ngampruetikorn, Vudtiwat","first_name":"Vudtiwat","last_name":"Ngampruetikorn"},{"full_name":"Sachdeva, Vedant","first_name":"Vedant","last_name":"Sachdeva"},{"last_name":"Torrence","first_name":"Johanna","full_name":"Torrence, Johanna"},{"full_name":"Humplik, Jan","id":"2E9627A8-F248-11E8-B48F-1D18A9856A87","first_name":"Jan","last_name":"Humplik"},{"full_name":"Schwab, David J.","last_name":"Schwab","first_name":"David J."},{"full_name":"Palmer, Stephanie E.","first_name":"Stephanie E.","last_name":"Palmer"}],"department":[{"_id":"GaTk"}],"oa_version":"Published Version","date_created":"2022-07-24T22:01:42Z","publication":"Physical Review Research","file_date_updated":"2022-07-25T07:47:23Z","type":"journal_article","_id":"11638","article_processing_charge":"No","issue":"2"},{"main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.1901.03790"}],"scopus_import":"1","article_type":"original","date_published":"2022-12-01T00:00:00Z","month":"12","publication_status":"published","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","date_updated":"2023-08-03T12:12:19Z","publisher":"IEEE","oa_version":"Preprint","date_created":"2022-07-24T22:01:42Z","publication":"IEEE Transactions on Information Theory","issue":"12","_id":"11639","type":"journal_article","article_processing_charge":"No","author":[{"full_name":"Zhang, Yihan","last_name":"Zhang","id":"2ce5da42-b2ea-11eb-bba5-9f264e9d002c","first_name":"Yihan"},{"full_name":"Vatedka, Shashank","last_name":"Vatedka","first_name":"Shashank"}],"department":[{"_id":"MaMo"}],"day":"01","title":"List decoding random Euclidean codes and Infinite constellations","volume":68,"status":"public","isi":1,"page":"7753-7786","external_id":{"isi":["000891796100007"],"arxiv":["1901.03790"]},"abstract":[{"lang":"eng","text":"We study the list decodability of different ensembles of codes over the real alphabet under the assumption of an omniscient adversary. It is a well-known result that when the source and the adversary have power constraints P and N respectively, the list decoding capacity is equal to 1/2logP/N. Random spherical codes achieve constant list sizes, and the goal of the present paper is to obtain a better understanding of the smallest achievable list size as a function of the gap to capacity. We show a reduction from arbitrary codes to spherical codes, and derive a lower bound on the list size of typical random spherical codes. We also give an upper bound on the list size achievable using nested Construction-A lattices and infinite Construction-A lattices. We then define and study a class of infinite constellations that generalize Construction-A lattices and prove upper and lower bounds for the same. Other goodness properties such as packing goodness and AWGN goodness of infinite constellations are proved along the way. Finally, we consider random lattices sampled from the Haar distribution and show that if a certain conjecture that originates in analytic number theory is true, then the list size grows as a polynomial function of the gap-to-capacity."}],"oa":1,"quality_controlled":"1","doi":"10.1109/TIT.2022.3189542","citation":{"ama":"Zhang Y, Vatedka S. List decoding random Euclidean codes and Infinite constellations. <i>IEEE Transactions on Information Theory</i>. 2022;68(12):7753-7786. doi:<a href=\"https://doi.org/10.1109/TIT.2022.3189542\">10.1109/TIT.2022.3189542</a>","ista":"Zhang Y, Vatedka S. 2022. List decoding random Euclidean codes and Infinite constellations. IEEE Transactions on Information Theory. 68(12), 7753–7786.","ieee":"Y. Zhang and S. Vatedka, “List decoding random Euclidean codes and Infinite constellations,” <i>IEEE Transactions on Information Theory</i>, vol. 68, no. 12. IEEE, pp. 7753–7786, 2022.","mla":"Zhang, Yihan, and Shashank Vatedka. “List Decoding Random Euclidean Codes and Infinite Constellations.” <i>IEEE Transactions on Information Theory</i>, vol. 68, no. 12, IEEE, 2022, pp. 7753–86, doi:<a href=\"https://doi.org/10.1109/TIT.2022.3189542\">10.1109/TIT.2022.3189542</a>.","apa":"Zhang, Y., &#38; Vatedka, S. (2022). List decoding random Euclidean codes and Infinite constellations. <i>IEEE Transactions on Information Theory</i>. IEEE. <a href=\"https://doi.org/10.1109/TIT.2022.3189542\">https://doi.org/10.1109/TIT.2022.3189542</a>","chicago":"Zhang, Yihan, and Shashank Vatedka. “List Decoding Random Euclidean Codes and Infinite Constellations.” <i>IEEE Transactions on Information Theory</i>. IEEE, 2022. <a href=\"https://doi.org/10.1109/TIT.2022.3189542\">https://doi.org/10.1109/TIT.2022.3189542</a>.","short":"Y. Zhang, S. Vatedka, IEEE Transactions on Information Theory 68 (2022) 7753–7786."},"acknowledgement":"This work was done when Shashank Vatedka was at the Chinese University of Hong Kong, where he was supported in part by CUHK Direct Grants 4055039 and 4055077. He would like to acknowledge funding from a seed grant offered by IIT Hyderabad and the Start-up Research Grant (SRG/2020/000910) from the Science and Engineering Board, India. Yihan Zhang has received funding from the European Union’s Horizon 2020 research and innovation programme\r\nunder grant agreement No 682203-ERC-[Inf-Speed-Tradeoff].","year":"2022","language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1557-9654"],"issn":["0018-9448"]},"arxiv":1,"intvolume":"        68"},{"scopus_import":"1","publisher":"Wiley","date_updated":"2023-08-03T12:11:01Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publication_status":"published","month":"11","date_published":"2022-11-01T00:00:00Z","article_type":"original","department":[{"_id":"NiBa"}],"author":[{"id":"485BB5A4-F248-11E8-B48F-1D18A9856A87","first_name":"Eniko","last_name":"Szep","full_name":"Szep, Eniko"},{"first_name":"Barbora","id":"42302D54-F248-11E8-B48F-1D18A9856A87","last_name":"Trubenova","orcid":"0000-0002-6873-2967","full_name":"Trubenova, Barbora"},{"last_name":"Csilléry","first_name":"Katalin","full_name":"Csilléry, Katalin"}],"article_processing_charge":"Yes (via OA deal)","_id":"11640","issue":"8","type":"journal_article","publication":"Molecular Ecology Resources","file_date_updated":"2023-02-02T08:11:23Z","project":[{"grant_number":"704172","call_identifier":"H2020","_id":"25AEDD42-B435-11E9-9278-68D0E5697425","name":"Rate of Adaptation in Changing Environment"}],"date_created":"2022-07-24T22:01:43Z","oa_version":"Published Version","status":"public","tmp":{"image":"/images/cc_by_nc.png","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","short":"CC BY-NC (4.0)","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)"},"volume":22,"title":"Using gridCoal to assess whether standard population genetic theory holds in the presence of spatio-temporal heterogeneity in population size","day":"01","external_id":{"isi":["000825873600001"]},"isi":1,"page":"2941-2955","file":[{"file_id":"12477","date_created":"2023-02-02T08:11:23Z","access_level":"open_access","success":1,"content_type":"application/pdf","relation":"main_file","file_name":"2022_MolecularEcologyRes_Szep.pdf","checksum":"3102e203e77b884bffffdbe8e548da88","file_size":6431779,"creator":"dernst","date_updated":"2023-02-02T08:11:23Z"}],"oa":1,"ddc":["570"],"abstract":[{"lang":"eng","text":"Spatially explicit population genetic models have long been developed, yet have rarely been used to test hypotheses about the spatial distribution of genetic diversity or the genetic divergence between populations. Here, we use spatially explicit coalescence simulations to explore the properties of the island and the two-dimensional stepping stone models under a wide range of scenarios with spatio-temporal variation in deme size. We avoid the simulation of genetic data, using the fact that under the studied models, summary statistics of genetic diversity and divergence can be approximated from coalescence times. We perform the simulations using gridCoal, a flexible spatial wrapper for the software msprime (Kelleher et al., 2016, Theoretical Population Biology, 95, 13) developed herein. In gridCoal, deme sizes can change arbitrarily across space and time, as well as migration rates between individual demes. We identify different factors that can cause a deviation from theoretical expectations, such as the simulation time in comparison to the effective deme size and the spatio-temporal autocorrelation across the grid. Our results highlight that FST, a measure of the strength of population structure, principally depends on recent demography, which makes it robust to temporal variation in deme size. In contrast, the amount of genetic diversity is dependent on the distant past when Ne is large, therefore longer run times are needed to estimate Ne than FST. Finally, we illustrate the use of gridCoal on a real-world example, the range expansion of silver fir (Abies alba Mill.) since the last glacial maximum, using different degrees of spatio-temporal variation in deme size."}],"acknowledgement":"ES was supported by an IST studentship provided by IST Austria. BT was funded by the European Union's Horizon 2020 research and innovation programme under the Marie Sklodowska-Curie Independent Fellowship (704172, RACE). This project received further funding awarded to KC from the Swiss National Science Foundation (SNSF CRSK-3_190288) and the Swiss Federal Research Institute WSL. We thank Nick Barton for many invaluable discussions and his comments on the thesis chapter and this manuscript. We thank Peter Ralph and Jerome Kelleher for useful discussions and Bisschop Gertjan for comments on this manuscript. We thank Fortunat Joos for providing us with the raw data from the LPX-Bern model for silver fir, and Willy Tinner for helpful insights about the demographic history of silver fir. We also thank the editor Alana Alexander for useful comments and advice on the manuscript. Open access funding provided by Eidgenossische Technische Hochschule Zurich.","citation":{"ama":"Szep E, Trubenova B, Csilléry K. Using gridCoal to assess whether standard population genetic theory holds in the presence of spatio-temporal heterogeneity in population size. <i>Molecular Ecology Resources</i>. 2022;22(8):2941-2955. doi:<a href=\"https://doi.org/10.1111/1755-0998.13676\">10.1111/1755-0998.13676</a>","mla":"Szep, Eniko, et al. “Using GridCoal to Assess Whether Standard Population Genetic Theory Holds in the Presence of Spatio-Temporal Heterogeneity in Population Size.” <i>Molecular Ecology Resources</i>, vol. 22, no. 8, Wiley, 2022, pp. 2941–55, doi:<a href=\"https://doi.org/10.1111/1755-0998.13676\">10.1111/1755-0998.13676</a>.","ieee":"E. Szep, B. Trubenova, and K. Csilléry, “Using gridCoal to assess whether standard population genetic theory holds in the presence of spatio-temporal heterogeneity in population size,” <i>Molecular Ecology Resources</i>, vol. 22, no. 8. Wiley, pp. 2941–2955, 2022.","ista":"Szep E, Trubenova B, Csilléry K. 2022. Using gridCoal to assess whether standard population genetic theory holds in the presence of spatio-temporal heterogeneity in population size. Molecular Ecology Resources. 22(8), 2941–2955.","short":"E. Szep, B. Trubenova, K. Csilléry, Molecular Ecology Resources 22 (2022) 2941–2955.","chicago":"Szep, Eniko, Barbora Trubenova, and Katalin Csilléry. “Using GridCoal to Assess Whether Standard Population Genetic Theory Holds in the Presence of Spatio-Temporal Heterogeneity in Population Size.” <i>Molecular Ecology Resources</i>. Wiley, 2022. <a href=\"https://doi.org/10.1111/1755-0998.13676\">https://doi.org/10.1111/1755-0998.13676</a>.","apa":"Szep, E., Trubenova, B., &#38; Csilléry, K. (2022). Using gridCoal to assess whether standard population genetic theory holds in the presence of spatio-temporal heterogeneity in population size. <i>Molecular Ecology Resources</i>. Wiley. <a href=\"https://doi.org/10.1111/1755-0998.13676\">https://doi.org/10.1111/1755-0998.13676</a>"},"doi":"10.1111/1755-0998.13676","ec_funded":1,"quality_controlled":"1","intvolume":"        22","has_accepted_license":"1","publication_identifier":{"issn":["1755-098X"],"eissn":["1755-0998"]},"language":[{"iso":"eng"}],"year":"2022"},{"scopus_import":"1","publication_status":"published","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","date_updated":"2023-08-03T12:13:37Z","publisher":"Oxford University Press","article_type":"original","month":"10","date_published":"2022-10-01T00:00:00Z","author":[{"first_name":"Christoph","last_name":"Gerle","full_name":"Gerle, Christoph"},{"first_name":"Jun-ichi","last_name":"Kishikawa","full_name":"Kishikawa, Jun-ichi"},{"full_name":"Yamaguchi, Tomoko","first_name":"Tomoko","last_name":"Yamaguchi"},{"first_name":"Atsuko","last_name":"Nakanishi","full_name":"Nakanishi, Atsuko"},{"last_name":"Çoruh","id":"d25163e5-8d53-11eb-a251-e6dd8ea1b8ef","first_name":"Mehmet Orkun","full_name":"Çoruh, Mehmet Orkun","orcid":"0000-0002-3219-2022"},{"full_name":"Makino, Fumiaki","last_name":"Makino","first_name":"Fumiaki"},{"full_name":"Miyata, Tomoko","last_name":"Miyata","first_name":"Tomoko"},{"first_name":"Akihiro","last_name":"Kawamoto","full_name":"Kawamoto, Akihiro"},{"full_name":"Yokoyama, Ken","last_name":"Yokoyama","first_name":"Ken"},{"first_name":"Keiichi","last_name":"Namba","full_name":"Namba, Keiichi"},{"last_name":"Kurisu","first_name":"Genji","full_name":"Kurisu, Genji"},{"full_name":"Kato, Takayuki","first_name":"Takayuki","last_name":"Kato"}],"department":[{"_id":"LeSa"}],"oa_version":"Published Version","date_created":"2022-07-25T10:04:58Z","publication":"Microscopy","file_date_updated":"2023-02-03T08:34:48Z","_id":"11648","type":"journal_article","article_processing_charge":"No","issue":"5","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"volume":71,"title":"Structures of multisubunit membrane complexes with the CRYO ARM 200","status":"public","day":"01","isi":1,"page":"249-261","external_id":{"isi":["000837950900001"],"pmid":["35861182"]},"abstract":[{"lang":"eng","text":"Progress in structural membrane biology has been significantly accelerated by the ongoing 'Resolution Revolution' in cryo electron microscopy (cryo-EM). In particular, structure determination by single particle analysis has evolved into the most powerful method for atomic model building of multisubunit membrane protein complexes. This has created an ever increasing demand in cryo-EM machine time, which to satisfy is in need of new and affordable cryo electron microscopes. Here, we review our experience in using the JEOL CRYO ARM 200 prototype for the structure determination by single particle analysis of three different multisubunit membrane complexes: the Thermus thermophilus V-type ATPase VO complex, the Thermosynechococcus elongatus photosystem I monomer and the flagellar motor LP-ring from Salmonella enterica."}],"keyword":["Radiology","Nuclear Medicine and imaging","Instrumentation","Structural Biology"],"oa":1,"ddc":["570"],"file":[{"access_level":"open_access","date_created":"2023-02-03T08:34:48Z","file_id":"12498","file_name":"2022_Microscopy_Gerle.pdf","relation":"main_file","success":1,"content_type":"application/pdf","creator":"dernst","checksum":"23b51c163636bf9313f7f0818312e67e","file_size":7812696,"date_updated":"2023-02-03T08:34:48Z"}],"acknowledgement":"Cyclic Innovation for Clinical Empowerment (JP17pc0101020 from Japan Agency for Medical Research and Development (AMED) to K.N. and G.K.); Platform Project for Supporting Drug Discovery and Life Science Research (Basis for Supporting Innovative Drug Discovery and Life Science Research) from AMED (JP20am0101117 to K.N., JP16K07266 to Atsunori Oshima and C.G., JP22ama121001j0001 to Masaki Yamamoto, G.K., T.K. and C.G.); a JSPS KAHKENHI\r\ngrant (20K06514 to J.K.) and a Grant-in-aid for JSPS fellows (20J00162 to A.N.).\r\nWe are grateful for initiation and scientific support from Matthias Rogner, Marc M. Nowaczyk, Anna Frank and ̈Yuko Misumi for the PSI monomer project and also would like to thank Hideki Shigematsu for critical reading of the manuscript. And we are indebted to the two anonymous reviewers who helped us to improve our manuscript.","quality_controlled":"1","citation":{"mla":"Gerle, Christoph, et al. “Structures of Multisubunit Membrane Complexes with the CRYO ARM 200.” <i>Microscopy</i>, vol. 71, no. 5, Oxford University Press, 2022, pp. 249–61, doi:<a href=\"https://doi.org/10.1093/jmicro/dfac037\">10.1093/jmicro/dfac037</a>.","ieee":"C. Gerle <i>et al.</i>, “Structures of multisubunit membrane complexes with the CRYO ARM 200,” <i>Microscopy</i>, vol. 71, no. 5. Oxford University Press, pp. 249–261, 2022.","ista":"Gerle C, Kishikawa J, Yamaguchi T, Nakanishi A, Çoruh MO, Makino F, Miyata T, Kawamoto A, Yokoyama K, Namba K, Kurisu G, Kato T. 2022. Structures of multisubunit membrane complexes with the CRYO ARM 200. Microscopy. 71(5), 249–261.","short":"C. Gerle, J. Kishikawa, T. Yamaguchi, A. Nakanishi, M.O. Çoruh, F. Makino, T. Miyata, A. Kawamoto, K. Yokoyama, K. Namba, G. Kurisu, T. Kato, Microscopy 71 (2022) 249–261.","chicago":"Gerle, Christoph, Jun-ichi Kishikawa, Tomoko Yamaguchi, Atsuko Nakanishi, Mehmet Orkun Çoruh, Fumiaki Makino, Tomoko Miyata, et al. “Structures of Multisubunit Membrane Complexes with the CRYO ARM 200.” <i>Microscopy</i>. Oxford University Press, 2022. <a href=\"https://doi.org/10.1093/jmicro/dfac037\">https://doi.org/10.1093/jmicro/dfac037</a>.","apa":"Gerle, C., Kishikawa, J., Yamaguchi, T., Nakanishi, A., Çoruh, M. O., Makino, F., … Kato, T. (2022). Structures of multisubunit membrane complexes with the CRYO ARM 200. <i>Microscopy</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/jmicro/dfac037\">https://doi.org/10.1093/jmicro/dfac037</a>","ama":"Gerle C, Kishikawa J, Yamaguchi T, et al. Structures of multisubunit membrane complexes with the CRYO ARM 200. <i>Microscopy</i>. 2022;71(5):249-261. doi:<a href=\"https://doi.org/10.1093/jmicro/dfac037\">10.1093/jmicro/dfac037</a>"},"doi":"10.1093/jmicro/dfac037","has_accepted_license":"1","intvolume":"        71","pmid":1,"year":"2022","publication_identifier":{"issn":["2050-5698"],"eissn":["2050-5701"]},"language":[{"iso":"eng"}]},{"year":"2022","day":"05","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"title":"Data from Elkrewi, Khauratovich, Toups et al. 2022, \"ZW sex-chromosome evolution and contagious parthenogenesis in Artemia brine shrimp\"","has_accepted_license":"1","status":"public","citation":{"ama":"Elkrewi MN. Data from Elkrewi, Khauratovich, Toups et al. 2022, “ZW sex-chromosome evolution and contagious parthenogenesis in Artemia brine shrimp.” 2022. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:11653\">10.15479/AT:ISTA:11653</a>","short":"M.N. Elkrewi, (2022).","chicago":"Elkrewi, Marwan N. “Data from Elkrewi, Khauratovich, Toups et Al. 2022, ‘ZW Sex-Chromosome Evolution and Contagious Parthenogenesis in Artemia Brine Shrimp.’” Institute of Science and Technology Austria, 2022. <a href=\"https://doi.org/10.15479/AT:ISTA:11653\">https://doi.org/10.15479/AT:ISTA:11653</a>.","apa":"Elkrewi, M. N. (2022). Data from Elkrewi, Khauratovich, Toups et al. 2022, “ZW sex-chromosome evolution and contagious parthenogenesis in Artemia brine shrimp.” Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:11653\">https://doi.org/10.15479/AT:ISTA:11653</a>","mla":"Elkrewi, Marwan N. <i>Data from Elkrewi, Khauratovich, Toups et Al. 2022, “ZW Sex-Chromosome Evolution and Contagious Parthenogenesis in Artemia Brine Shrimp.”</i> Institute of Science and Technology Austria, 2022, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:11653\">10.15479/AT:ISTA:11653</a>.","ista":"Elkrewi MN. 2022. Data from Elkrewi, Khauratovich, Toups et al. 2022, ‘ZW sex-chromosome evolution and contagious parthenogenesis in Artemia brine shrimp’, Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:11653\">10.15479/AT:ISTA:11653</a>.","ieee":"M. N. Elkrewi, “Data from Elkrewi, Khauratovich, Toups et al. 2022, ‘ZW sex-chromosome evolution and contagious parthenogenesis in Artemia brine shrimp.’” Institute of Science and Technology Austria, 2022."},"doi":"10.15479/AT:ISTA:11653","date_created":"2022-07-26T11:01:47Z","oa_version":"Published Version","article_processing_charge":"No","_id":"11653","type":"research_data","file_date_updated":"2022-08-08T22:30:04Z","related_material":{"record":[{"status":"public","id":"12248","relation":"used_in_publication"}]},"author":[{"id":"0B46FACA-A8E1-11E9-9BD3-79D1E5697425","first_name":"Marwan N","last_name":"Elkrewi","full_name":"Elkrewi, Marwan N","orcid":"0000-0002-5328-7231"}],"department":[{"_id":"GradSch"},{"_id":"BeVi"}],"oa":1,"ddc":["570"],"abstract":[{"text":"Eurasian brine shrimp (genus Artemia) have closely related sexual and asexual lineages of parthenogenetic females, which produce rare males at low frequencies. Although they are known to have ZW chromosomes, these are not well characterized, and it is unclear whether they are shared across the clade. Furthermore, the underlying genetic architecture of the transmission of asexuality, which can occur when rare males mate with closely related sexual females, is not well understood. We produced a chromosome-level assembly for the sexual Eurasian species A. sinica and characterized in detail the pair of sex chromosomes of this species. We combined this new assembly with short-read genomic data for the sexual species A. sp. Kazakhstan and several asexual lineages of A. parthenogenetica, allowing us to perform an in-depth characterization of sex-chromosome evolution across the genus. We identified a small differentiated region of the ZW pair that is shared by all sexual and asexual lineages, supporting the shared ancestry of the sex chromosomes. We also inferred that recombination suppression has spread to larger sections of the chromosome independently in the American and Eurasian lineages. Finally, we took advantage of a rare male, which we backcrossed to sexual females, to explore the genetic basis of asexuality. Our results suggest that parthenogenesis is likely partly controlled by a locus on the Z chromosome, highlighting the interplay between sex determination and asexuality.","lang":"eng"}],"date_published":"2022-08-05T00:00:00Z","month":"08","file":[{"date_created":"2022-07-26T12:37:52Z","access_level":"open_access","file_id":"11655","file_name":"Data.zip","relation":"main_file","content_type":"application/x-zip-compressed","creator":"melkrewi","description":"The folder contains the following datasets (fasta files, and text files):\nSup. Dataset 1: Genome assemblies: A. sinica male high quality assembly, A. sp. Kazakhstan\nmale draft assembly\nSup. Dataset 2: Male transcriptome assemblies for A. sinica and A. franciscana\nSup. Dataset 3: Male and female coverage for A. sinica, A. sp. Kazakhstan, A. urmiana, and\nA. parthenogenetica females and rare male.\nSup. Dataset 4: Artemia sinica Male:female FST per 1Kb window\nSup. Dataset 5: FASTA file with candidate W scaffolds\nSup. Dataset 6: Candidate W-derived transcripts and alignments\nSup. Dataset 7: Gene expression with genomic location\nSup. Dataset 8: VCF for asexual female and rare male\nSup. Dataset 9: FST between backcrossed asexual and control females (pooled analysis)\nSup. Dataset 10: VCF of backcrossed asexual and control females (individual analysis using\nA. sp. Kazakhstan as the reference), and inferred ancestry\nSup. Dataset 11: GO and DE annotations of all the Artemia sinica transcripts and their\nlocations in the Artemia sinica male genome.\n","file_size":2209382998,"embargo":"2022-08-07","checksum":"5f1d7c6d7ab5375ed2564521432bed0c","title":"Supplementary Datasets","date_updated":"2022-08-08T22:30:04Z"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Institute of Science and Technology Austria","contributor":[{"last_name":"Elkrewi","id":"0B46FACA-A8E1-11E9-9BD3-79D1E5697425","first_name":"Marwan N","orcid":"0000-0002-5328-7231"},{"last_name":"Khauratovich","first_name":"Uladzislava"},{"id":"4E099E4E-F248-11E8-B48F-1D18A9856A87","first_name":"Melissa A","last_name":"Toups"},{"last_name":"Bett","first_name":"Vincent K","id":"57854184-AAE0-11E9-8D04-98D6E5697425"},{"last_name":"Mrnjavac","id":"353FAC84-AE61-11E9-8BFC-00D3E5697425","first_name":"Andrea"},{"last_name":"Macon","first_name":"Ariana","id":"2A0848E2-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Fraisse","first_name":"Christelle","id":"32DF5794-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8441-5075"},{"first_name":"Luca","last_name":"Sax"},{"last_name":"Huylmans","id":"4C0A3874-F248-11E8-B48F-1D18A9856A87","first_name":"Ann K"},{"first_name":"Francisco","last_name":"Hontoria "},{"first_name":"Beatriz","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","last_name":"Vicoso","orcid":"0000-0002-4579-8306"}],"date_updated":"2024-02-21T12:35:53Z"},{"author":[{"full_name":"Biswas, Ranita","orcid":"0000-0002-5372-7890","last_name":"Biswas","id":"3C2B033E-F248-11E8-B48F-1D18A9856A87","first_name":"Ranita"},{"id":"34D2A09C-F248-11E8-B48F-1D18A9856A87","first_name":"Sebastiano","last_name":"Cultrera di Montesano","orcid":"0000-0001-6249-0832","full_name":"Cultrera di Montesano, Sebastiano"},{"last_name":"Edelsbrunner","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","first_name":"Herbert","full_name":"Edelsbrunner, Herbert","orcid":"0000-0002-9823-6833"},{"full_name":"Saghafian, Morteza","last_name":"Saghafian","id":"f86f7148-b140-11ec-9577-95435b8df824","first_name":"Morteza"}],"department":[{"_id":"GradSch"},{"_id":"HeEd"}],"date_created":"2022-07-27T09:27:34Z","oa_version":"Submitted Version","project":[{"call_identifier":"H2020","grant_number":"788183","name":"Alpha Shape Theory Extended","_id":"266A2E9E-B435-11E9-9278-68D0E5697425"},{"grant_number":"Z00342","call_identifier":"FWF","name":"The Wittgenstein Prize","_id":"268116B8-B435-11E9-9278-68D0E5697425"},{"grant_number":"I02979-N35","call_identifier":"FWF","_id":"2561EBF4-B435-11E9-9278-68D0E5697425","name":"Persistence and stability of geometric complexes"}],"publication":"Leibniz International Proceedings on Mathematics","file_date_updated":"2022-07-27T09:25:53Z","_id":"11658","type":"journal_article","article_processing_charge":"No","title":"Depth in arrangements: Dehn–Sommerville–Euler relations with applications","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"status":"public","day":"27","publication_status":"submitted","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2022-07-28T07:57:48Z","publisher":"Schloss Dagstuhl - Leibniz Zentrum für Informatik","date_published":"2022-07-27T00:00:00Z","month":"07","acknowledgement":"This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme, grant no. 788183, from the Wittgenstein Prize, Austrian Science Fund (FWF), grant no. Z 342-N31, and from the DFG Collaborative Research Center TRR 109, ‘Discretization in Geometry and Dynamics’, Austrian Science Fund (FWF), grant no. I 02979-N35.","ec_funded":1,"quality_controlled":"1","citation":{"ama":"Biswas R, Cultrera di Montesano S, Edelsbrunner H, Saghafian M. Depth in arrangements: Dehn–Sommerville–Euler relations with applications. <i>Leibniz International Proceedings on Mathematics</i>.","mla":"Biswas, Ranita, et al. “Depth in Arrangements: Dehn–Sommerville–Euler Relations with Applications.” <i>Leibniz International Proceedings on Mathematics</i>, Schloss Dagstuhl - Leibniz Zentrum für Informatik.","ieee":"R. Biswas, S. Cultrera di Montesano, H. Edelsbrunner, and M. Saghafian, “Depth in arrangements: Dehn–Sommerville–Euler relations with applications,” <i>Leibniz International Proceedings on Mathematics</i>. Schloss Dagstuhl - Leibniz Zentrum für Informatik.","ista":"Biswas R, Cultrera di Montesano S, Edelsbrunner H, Saghafian M. Depth in arrangements: Dehn–Sommerville–Euler relations with applications. Leibniz International Proceedings on Mathematics.","chicago":"Biswas, Ranita, Sebastiano Cultrera di Montesano, Herbert Edelsbrunner, and Morteza Saghafian. “Depth in Arrangements: Dehn–Sommerville–Euler Relations with Applications.” <i>Leibniz International Proceedings on Mathematics</i>. Schloss Dagstuhl - Leibniz Zentrum für Informatik, n.d.","short":"R. Biswas, S. Cultrera di Montesano, H. Edelsbrunner, M. Saghafian, Leibniz International Proceedings on Mathematics (n.d.).","apa":"Biswas, R., Cultrera di Montesano, S., Edelsbrunner, H., &#38; Saghafian, M. (n.d.). Depth in arrangements: Dehn–Sommerville–Euler relations with applications. <i>Leibniz International Proceedings on Mathematics</i>. Schloss Dagstuhl - Leibniz Zentrum für Informatik."},"has_accepted_license":"1","year":"2022","language":[{"iso":"eng"}],"abstract":[{"lang":"eng","text":"The depth of a cell in an arrangement of n (non-vertical) great-spheres in Sd is the number of great-spheres that pass above the cell. We prove Euler-type relations, which imply extensions of the classic Dehn–Sommerville relations for convex polytopes to sublevel sets of the depth function, and we use the relations to extend the expressions for the number of faces of neighborly polytopes to the number of cells of levels in neighborly arrangements."}],"oa":1,"ddc":["510"],"file":[{"access_level":"open_access","date_created":"2022-07-27T09:25:53Z","file_id":"11659","file_name":"D-S-E.pdf","relation":"main_file","content_type":"application/pdf","creator":"scultrer","checksum":"b2f511e8b1cae5f1892b0cdec341acac","file_size":639266,"date_updated":"2022-07-27T09:25:53Z"}]},{"project":[{"name":"Alpha Shape Theory Extended","_id":"266A2E9E-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"788183"},{"grant_number":"Z00342","call_identifier":"FWF","name":"The Wittgenstein Prize","_id":"268116B8-B435-11E9-9278-68D0E5697425"},{"name":"Persistence and stability of geometric complexes","_id":"2561EBF4-B435-11E9-9278-68D0E5697425","grant_number":"I02979-N35","call_identifier":"FWF"}],"date_created":"2022-07-27T09:31:15Z","oa_version":"Submitted Version","article_processing_charge":"No","_id":"11660","type":"journal_article","publication":"LIPIcs","file_date_updated":"2022-07-27T09:30:30Z","author":[{"orcid":"0000-0002-5372-7890","full_name":"Biswas, Ranita","first_name":"Ranita","id":"3C2B033E-F248-11E8-B48F-1D18A9856A87","last_name":"Biswas"},{"full_name":"Cultrera di Montesano, Sebastiano","orcid":"0000-0001-6249-0832","id":"34D2A09C-F248-11E8-B48F-1D18A9856A87","first_name":"Sebastiano","last_name":"Cultrera di Montesano"},{"first_name":"Herbert","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","last_name":"Edelsbrunner","full_name":"Edelsbrunner, Herbert","orcid":"0000-0002-9823-6833"},{"first_name":"Morteza","last_name":"Saghafian","full_name":"Saghafian, Morteza"}],"department":[{"_id":"GradSch"},{"_id":"HeEd"}],"day":"25","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"title":"A window to the persistence of 1D maps. I: Geometric characterization of critical point pairs","status":"public","month":"07","date_published":"2022-07-25T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_status":"submitted","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","date_updated":"2022-07-28T08:05:34Z","citation":{"ama":"Biswas R, Cultrera di Montesano S, Edelsbrunner H, Saghafian M. A window to the persistence of 1D maps. I: Geometric characterization of critical point pairs. <i>LIPIcs</i>.","apa":"Biswas, R., Cultrera di Montesano, S., Edelsbrunner, H., &#38; Saghafian, M. (n.d.). A window to the persistence of 1D maps. I: Geometric characterization of critical point pairs. <i>LIPIcs</i>. Schloss Dagstuhl - Leibniz-Zentrum für Informatik.","chicago":"Biswas, Ranita, Sebastiano Cultrera di Montesano, Herbert Edelsbrunner, and Morteza Saghafian. “A Window to the Persistence of 1D Maps. I: Geometric Characterization of Critical Point Pairs.” <i>LIPIcs</i>. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, n.d.","short":"R. Biswas, S. Cultrera di Montesano, H. Edelsbrunner, M. Saghafian, LIPIcs (n.d.).","ista":"Biswas R, Cultrera di Montesano S, Edelsbrunner H, Saghafian M. A window to the persistence of 1D maps. I: Geometric characterization of critical point pairs. LIPIcs.","ieee":"R. Biswas, S. Cultrera di Montesano, H. Edelsbrunner, and M. Saghafian, “A window to the persistence of 1D maps. I: Geometric characterization of critical point pairs,” <i>LIPIcs</i>. Schloss Dagstuhl - Leibniz-Zentrum für Informatik.","mla":"Biswas, Ranita, et al. “A Window to the Persistence of 1D Maps. I: Geometric Characterization of Critical Point Pairs.” <i>LIPIcs</i>, Schloss Dagstuhl - Leibniz-Zentrum für Informatik."},"quality_controlled":"1","ec_funded":1,"acknowledgement":"This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme, grant no. 788183, from the Wittgenstein Prize, Austrian Science Fund (FWF), grant no. Z 342-N31, and from the DFG Collaborative Research Center TRR 109, ‘Discretization in Geometry and Dynamics’, Austrian Science Fund (FWF), grant no. I 02979-N35. ","year":"2022","language":[{"iso":"eng"}],"has_accepted_license":"1","alternative_title":["LIPIcs"],"ddc":["510"],"oa":1,"abstract":[{"text":"We characterize critical points of 1-dimensional maps paired in persistent homology geometrically and this way get elementary proofs of theorems about the symmetry of persistence diagrams and the variation of such maps. In particular, we identify branching points and endpoints of networks as the sole source of asymmetry and relate the cycle basis in persistent homology with a version of the stable marriage problem. Our analysis provides the foundations of fast algorithms for maintaining collections of interrelated sorted lists together with their persistence diagrams. ","lang":"eng"}],"file":[{"file_id":"11661","access_level":"open_access","date_created":"2022-07-27T09:30:30Z","content_type":"application/pdf","file_name":"window 1.pdf","relation":"main_file","checksum":"95903f9d1649e8e437a967b6f2f64730","file_size":564836,"creator":"scultrer","date_updated":"2022-07-27T09:30:30Z"}]},{"title":"Wolbachia frequency data from: Why did the Wolbachia transinfection cross the road? Drift, deterministic dynamics and disease control","tmp":{"image":"/images/cc_0.png","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","name":"Creative Commons Public Domain Dedication (CC0 1.0)","short":"CC0 (1.0)"},"status":"public","day":"06","year":"2022","related_material":{"record":[{"id":"10604","status":"public","relation":"used_in_publication"}]},"author":[{"full_name":"Turelli, Michael","first_name":"Michael","last_name":"Turelli"},{"last_name":"Barton","first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240"}],"department":[{"_id":"NiBa"}],"acknowledgement":"Bill and Melinda Gates Foundation, Award: OPP1180815","doi":"10.25338/B81931","citation":{"ama":"Turelli M, Barton NH. Wolbachia frequency data from: Why did the Wolbachia transinfection cross the road? Drift, deterministic dynamics and disease control. 2022. doi:<a href=\"https://doi.org/10.25338/B81931\">10.25338/B81931</a>","ista":"Turelli M, Barton NH. 2022. Wolbachia frequency data from: Why did the Wolbachia transinfection cross the road? Drift, deterministic dynamics and disease control, Dryad, <a href=\"https://doi.org/10.25338/B81931\">10.25338/B81931</a>.","ieee":"M. Turelli and N. H. Barton, “Wolbachia frequency data from: Why did the Wolbachia transinfection cross the road? Drift, deterministic dynamics and disease control.” Dryad, 2022.","mla":"Turelli, Michael, and Nicholas H. Barton. <i>Wolbachia Frequency Data from: Why Did the Wolbachia Transinfection Cross the Road? Drift, Deterministic Dynamics and Disease Control</i>. Dryad, 2022, doi:<a href=\"https://doi.org/10.25338/B81931\">10.25338/B81931</a>.","apa":"Turelli, M., &#38; Barton, N. H. (2022). Wolbachia frequency data from: Why did the Wolbachia transinfection cross the road? Drift, deterministic dynamics and disease control. Dryad. <a href=\"https://doi.org/10.25338/B81931\">https://doi.org/10.25338/B81931</a>","short":"M. Turelli, N.H. Barton, (2022).","chicago":"Turelli, Michael, and Nicholas H Barton. “Wolbachia Frequency Data from: Why Did the Wolbachia Transinfection Cross the Road? Drift, Deterministic Dynamics and Disease Control.” Dryad, 2022. <a href=\"https://doi.org/10.25338/B81931\">https://doi.org/10.25338/B81931</a>."},"oa_version":"Published Version","date_created":"2022-07-29T06:45:41Z","_id":"11686","article_processing_charge":"No","type":"research_data_reference","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","publisher":"Dryad","date_updated":"2023-08-02T13:50:08Z","oa":1,"ddc":["570"],"abstract":[{"text":"Maternally inherited Wolbachia transinfections are being introduced into natural mosquito populations to reduce the transmission of dengue, Zika and other arboviruses. Wolbachia-induced cytoplasmic incompatibility provides a frequency-dependent reproductive advantage to infected females that can spread transinfections within and among populations. However, because transinfections generally reduce host fitness, they tend to spread within populations only after their frequency exceeds a critical threshold. This produces bistability with stable equilibrium frequencies at both 0 and 1, analogous to the bistability produced by underdominance between alleles or karyotypes and by population dynamics under Allee effects. Here, we analyze how stochastic frequency variation produced by finite population size can facilitate the local spread of variants with bistable dynamics into areas where invasion is unexpected from deterministic models. Our exemplar is the establishment of wMel Wolbachia in the Aedes aegypti population of Pyramid Estates (PE), a small community in far north Queensland, Australia. In 2011, wMel was stably introduced into Gordonvale, separated from PE by barriers to Ae. aegypti dispersal. After nearly six years during which wMel was observed only at low frequencies in PE, corresponding to an apparent equilibrium between immigration and selection, wMel rose to fixation by 2018. Using analytic approximations and statistical analyses, we demonstrate that the observed fixation of wMel at PE is consistent with both stochastic transition past an unstable threshold frequency and deterministic transformation produced by steady immigration at a rate just above the threshold required for deterministic invasion. The indeterminacy results from a delicate balance of parameters needed to produce the delayed transition observed. Our analyses suggest that once Wolbachia transinfections are established locally through systematic introductions, stochastic “threshold crossing” is likely to only minimally enhance spatial spread, providing a local ratchet that slightly – but systematically – aids area-wide transformation of disease-vector populations in heterogeneous landscapes.","lang":"eng"}],"keyword":["Biological sciences"],"month":"01","date_published":"2022-01-06T00:00:00Z","license":"https://creativecommons.org/publicdomain/zero/1.0/","main_file_link":[{"url":"https://doi.org/10.25338/B81931","open_access":"1"}]},{"author":[{"full_name":"Parvizian, Mahsa","last_name":"Parvizian","first_name":"Mahsa"},{"full_name":"Duran Balsa, Alejandra","first_name":"Alejandra","last_name":"Duran Balsa"},{"first_name":"Rohan","last_name":"Pokratath","full_name":"Pokratath, Rohan"},{"full_name":"Kalha, Curran","last_name":"Kalha","first_name":"Curran"},{"last_name":"Lee","first_name":"Seungho","full_name":"Lee, Seungho"},{"full_name":"Van den Eynden, Dietger","first_name":"Dietger","last_name":"Van den Eynden"},{"last_name":"Ibáñez","id":"43C61214-F248-11E8-B48F-1D18A9856A87","first_name":"Maria","orcid":"0000-0001-5013-2843","full_name":"Ibáñez, Maria"},{"last_name":"Regoutz","first_name":"Anna","full_name":"Regoutz, Anna"},{"last_name":"De Roo","first_name":"Jonathan","full_name":"De Roo, Jonathan"}],"related_material":{"record":[{"status":"public","id":"11451","relation":"used_in_publication"}]},"department":[{"_id":"MaIb"}],"oa_version":"Published Version","date_created":"2022-07-29T09:31:13Z","citation":{"ama":"Parvizian M, Duran Balsa A, Pokratath R, et al. Data for “The chemistry of Cu3N and Cu3PdN nanocrystals.” 2022. doi:<a href=\"https://doi.org/10.5281/ZENODO.6542908\">10.5281/ZENODO.6542908</a>","ieee":"M. Parvizian <i>et al.</i>, “Data for ‘The chemistry of Cu3N and Cu3PdN nanocrystals.’” Zenodo, 2022.","ista":"Parvizian M, Duran Balsa A, Pokratath R, Kalha C, Lee S, Van den Eynden D, Ibáñez M, Regoutz A, De Roo J. 2022. Data for ‘The chemistry of Cu3N and Cu3PdN nanocrystals’, Zenodo, <a href=\"https://doi.org/10.5281/ZENODO.6542908\">10.5281/ZENODO.6542908</a>.","mla":"Parvizian, Mahsa, et al. <i>Data for “The Chemistry of Cu3N and Cu3PdN Nanocrystals.”</i> Zenodo, 2022, doi:<a href=\"https://doi.org/10.5281/ZENODO.6542908\">10.5281/ZENODO.6542908</a>.","apa":"Parvizian, M., Duran Balsa, A., Pokratath, R., Kalha, C., Lee, S., Van den Eynden, D., … De Roo, J. (2022). Data for “The chemistry of Cu3N and Cu3PdN nanocrystals.” Zenodo. <a href=\"https://doi.org/10.5281/ZENODO.6542908\">https://doi.org/10.5281/ZENODO.6542908</a>","chicago":"Parvizian, Mahsa, Alejandra Duran Balsa, Rohan Pokratath, Curran Kalha, Seungho Lee, Dietger Van den Eynden, Maria Ibáñez, Anna Regoutz, and Jonathan De Roo. “Data for ‘The Chemistry of Cu3N and Cu3PdN Nanocrystals.’” Zenodo, 2022. <a href=\"https://doi.org/10.5281/ZENODO.6542908\">https://doi.org/10.5281/ZENODO.6542908</a>.","short":"M. Parvizian, A. Duran Balsa, R. Pokratath, C. Kalha, S. Lee, D. Van den Eynden, M. Ibáñez, A. Regoutz, J. De Roo, (2022)."},"doi":"10.5281/ZENODO.6542908","article_processing_charge":"No","_id":"11695","type":"research_data_reference","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"title":"Data for \"The chemistry of Cu3N and Cu3PdN nanocrystals\"","status":"public","year":"2022","day":"12","main_file_link":[{"open_access":"1","url":"https://doi.org/10.5281/ZENODO.6542908"}],"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","date_updated":"2023-08-03T07:19:12Z","publisher":"Zenodo","abstract":[{"lang":"eng","text":"Data underlying the figures in the publication \"The chemistry of Cu3N and Cu3PdN nanocrystals\" "}],"oa":1,"ddc":["540"],"month":"05","date_published":"2022-05-12T00:00:00Z"},{"volume":17,"title":"Gradient flow formulation of diffusion equations in the Wasserstein space over a metric graph","status":"public","day":"01","author":[{"full_name":"Erbar, Matthias","last_name":"Erbar","first_name":"Matthias"},{"full_name":"Forkert, Dominik L","last_name":"Forkert","id":"35C79D68-F248-11E8-B48F-1D18A9856A87","first_name":"Dominik L"},{"last_name":"Maas","first_name":"Jan","id":"4C5696CE-F248-11E8-B48F-1D18A9856A87","full_name":"Maas, Jan","orcid":"0000-0002-0845-1338"},{"last_name":"Mugnolo","first_name":"Delio","full_name":"Mugnolo, Delio"}],"department":[{"_id":"JaMa"}],"project":[{"call_identifier":"H2020","grant_number":"716117","_id":"256E75B8-B435-11E9-9278-68D0E5697425","name":"Optimal Transport and Stochastic Dynamics"},{"_id":"fc31cba2-9c52-11eb-aca3-ff467d239cd2","name":"Taming Complexity in Partial Differential Systems","grant_number":"F6504"}],"date_created":"2022-07-31T22:01:46Z","oa_version":"Preprint","type":"journal_article","_id":"11700","article_processing_charge":"No","issue":"5","publication":"Networks and Heterogeneous Media","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publication_status":"published","publisher":"American Institute of Mathematical Sciences","date_updated":"2023-08-03T12:25:49Z","month":"10","date_published":"2022-10-01T00:00:00Z","article_type":"original","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2105.05677"}],"arxiv":1,"intvolume":"        17","year":"2022","publication_identifier":{"eissn":["1556-181X"],"issn":["1556-1801"]},"language":[{"iso":"eng"}],"acknowledgement":"ME acknowledges funding by the Deutsche Forschungsgemeinschaft (DFG), Grant SFB 1283/2 2021 – 317210226. DF and JM were supported by the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement No 716117). JM also acknowledges support by the Austrian Science Fund (FWF), Project SFB F65. The work of DM was partially supported by the Deutsche Forschungsgemeinschaft\r\n(DFG), Grant 397230547. This article is based upon work from COST Action\r\n18232 MAT-DYN-NET, supported by COST (European Cooperation in Science\r\nand Technology), www.cost.eu. We wish to thank Martin Burger and Jan-Frederik\r\nPietschmann for useful discussions. We are grateful to the anonymous referees for\r\ntheir careful reading and useful suggestions.","citation":{"ista":"Erbar M, Forkert DL, Maas J, Mugnolo D. 2022. Gradient flow formulation of diffusion equations in the Wasserstein space over a metric graph. Networks and Heterogeneous Media. 17(5), 687–717.","ieee":"M. Erbar, D. L. Forkert, J. Maas, and D. Mugnolo, “Gradient flow formulation of diffusion equations in the Wasserstein space over a metric graph,” <i>Networks and Heterogeneous Media</i>, vol. 17, no. 5. American Institute of Mathematical Sciences, pp. 687–717, 2022.","mla":"Erbar, Matthias, et al. “Gradient Flow Formulation of Diffusion Equations in the Wasserstein Space over a Metric Graph.” <i>Networks and Heterogeneous Media</i>, vol. 17, no. 5, American Institute of Mathematical Sciences, 2022, pp. 687–717, doi:<a href=\"https://doi.org/10.3934/nhm.2022023\">10.3934/nhm.2022023</a>.","apa":"Erbar, M., Forkert, D. L., Maas, J., &#38; Mugnolo, D. (2022). Gradient flow formulation of diffusion equations in the Wasserstein space over a metric graph. <i>Networks and Heterogeneous Media</i>. American Institute of Mathematical Sciences. <a href=\"https://doi.org/10.3934/nhm.2022023\">https://doi.org/10.3934/nhm.2022023</a>","short":"M. Erbar, D.L. Forkert, J. Maas, D. 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Firstly, we prove a Benamou–Brenier formula for the Wasserstein distance, which establishes the equivalence of static and dynamical optimal transport. Secondly, in the spirit of Jordan–Kinderlehrer–Otto, we show that McKean–Vlasov equations can be formulated as gradient flow of the free energy in the Wasserstein space of probability measures. 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A second part in preparation is on blow-up criteria and regularization. Our theory is formulated in an Lp-setting, and because of this we can deal with nonlinearities in a very efficient way. Applications to several concrete problems and their quasilinear variants are given. This includes Burgers' equation, the Allen–Cahn equation, the Cahn–Hilliard equation, reaction–diffusion equations, and the porous media equation. The interplay of the nonlinearities and the critical spaces of initial data leads to new results and insights for these SPDEs. The proofs are based on recent developments in maximal regularity theory for the linearized problem for deterministic and stochastic evolution equations. In particular, our theory can be seen as a stochastic version of the theory of critical spaces due to Prüss–Simonett–Wilke (2018). Sharp weighted time-regularity allow us to deal with rough initial values and obtain instantaneous regularization results. 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The ‘New Synthesis’. Proceedings of the National Academy of Sciences of the United States of America. 119(30), e2122147119.","ieee":"N. H. Barton, “The ‘New Synthesis,’” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 119, no. 30. Proceedings of the National Academy of Sciences, 2022.","chicago":"Barton, Nicholas H. “The ‘New Synthesis.’” <i>Proceedings of the National Academy of Sciences of the United States of America</i>. Proceedings of the National Academy of Sciences, 2022. <a href=\"https://doi.org/10.1073/pnas.2122147119\">https://doi.org/10.1073/pnas.2122147119</a>.","short":"N.H. Barton, Proceedings of the National Academy of Sciences of the United States of America 119 (2022).","apa":"Barton, N. H. (2022). The “New Synthesis.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>. Proceedings of the National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.2122147119\">https://doi.org/10.1073/pnas.2122147119</a>","ama":"Barton NH. The “New Synthesis.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>. 2022;119(30). doi:<a href=\"https://doi.org/10.1073/pnas.2122147119\">10.1073/pnas.2122147119</a>"},"doi":"10.1073/pnas.2122147119","acknowledgement":"I thank Laura Hayward, Jitka Polechova, and Anja Westram for discussions and comments.","file":[{"date_updated":"2022-08-01T10:58:28Z","creator":"dernst","checksum":"06c866196a8957f0c37b8a121771c885","file_size":848511,"relation":"main_file","file_name":"2022_PNAS_Barton.pdf","content_type":"application/pdf","success":1,"date_created":"2022-08-01T10:58:28Z","access_level":"open_access","file_id":"11716"}],"abstract":[{"text":"When Mendel’s work was rediscovered in 1900, and extended to establish classical genetics, it was initially seen in opposition to Darwin’s theory of evolution by natural selection on continuous variation, as represented by the biometric research program that was the foundation of quantitative genetics. As Fisher, Haldane, and Wright established a century ago, Mendelian inheritance is exactly what is needed for natural selection to work efficiently. Yet, the synthesis remains unfinished. We do not understand why sexual reproduction and a fair meiosis predominate in eukaryotes, or how far these are responsible for their diversity and complexity. Moreover, although quantitative geneticists have long known that adaptive variation is highly polygenic, and that this is essential for efficient selection, this is only now becoming appreciated by molecular biologists—and we still do not have a good framework for understanding polygenic variation or diffuse function.","lang":"eng"}],"ddc":["570"],"oa":1,"external_id":{"pmid":["35858408"]}}]