[{"doi":"10.1038/s42003-022-03568-6","type":"journal_article","publication_identifier":{"eissn":["23993642"]},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","language":[{"iso":"eng"}],"publication":"Communications Biology","oa_version":"Published Version","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"publisher":"Springer Nature","intvolume":"         5","isi":1,"status":"public","quality_controlled":"1","file":[{"date_created":"2022-07-13T07:44:58Z","relation":"main_file","checksum":"965f88bbcef3fd0c3e121340555c4467","creator":"kschuh","file_id":"11571","content_type":"application/pdf","access_level":"open_access","file_size":2335369,"date_updated":"2022-07-13T07:44:58Z","file_name":"2022_communicationsbiology_Molina-Granada.pdf","success":1}],"abstract":[{"text":"Imbalanced mitochondrial dNTP pools are known players in the pathogenesis of multiple human diseases. Here we show that, even under physiological conditions, dGTP is largely overrepresented among other dNTPs in mitochondria of mouse tissues and human cultured cells. In addition, a vast majority of mitochondrial dGTP is tightly bound to NDUFA10, an accessory subunit of complex I of the mitochondrial respiratory chain. NDUFA10 shares a deoxyribonucleoside kinase (dNK) domain with deoxyribonucleoside kinases in the nucleotide salvage pathway, though no specific function beyond stabilizing the complex I holoenzyme has been described for this subunit. We mutated the dNK domain of NDUFA10 in human HEK-293T cells while preserving complex I assembly and activity. The NDUFA10E160A/R161A shows reduced dGTP binding capacity in vitro and leads to a 50% reduction in mitochondrial dGTP content, proving that most dGTP is directly bound to the dNK domain of NDUFA10. This interaction may represent a hitherto unknown mechanism regulating mitochondrial dNTP availability and linking oxidative metabolism to DNA maintenance.","lang":"eng"}],"ddc":["570"],"date_published":"2022-06-23T00:00:00Z","scopus_import":"1","article_processing_charge":"No","month":"06","author":[{"first_name":"David","last_name":"Molina-Granada","full_name":"Molina-Granada, David"},{"last_name":"González-Vioque","full_name":"González-Vioque, Emiliano","first_name":"Emiliano"},{"first_name":"Marris G.","full_name":"Dibley, Marris G.","last_name":"Dibley"},{"full_name":"Cabrera-Pérez, Raquel","last_name":"Cabrera-Pérez","first_name":"Raquel"},{"full_name":"Vallbona-Garcia, Antoni","last_name":"Vallbona-Garcia","first_name":"Antoni"},{"first_name":"Javier","last_name":"Torres-Torronteras","full_name":"Torres-Torronteras, Javier"},{"first_name":"Leonid A","id":"338D39FE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0977-7989","last_name":"Sazanov","full_name":"Sazanov, Leonid A"},{"last_name":"Ryan","full_name":"Ryan, Michael T.","first_name":"Michael T."},{"full_name":"Cámara, Yolanda","last_name":"Cámara","first_name":"Yolanda"},{"first_name":"Ramon","full_name":"Martí, Ramon","last_name":"Martí"}],"has_accepted_license":"1","article_number":"620","date_updated":"2023-08-03T11:51:58Z","_id":"11551","file_date_updated":"2022-07-13T07:44:58Z","department":[{"_id":"LeSa"}],"citation":{"ieee":"D. Molina-Granada <i>et al.</i>, “Most mitochondrial dGTP is tightly bound to respiratory complex I through the NDUFA10 subunit,” <i>Communications Biology</i>, vol. 5, no. 1. Springer Nature, 2022.","short":"D. Molina-Granada, E. González-Vioque, M.G. Dibley, R. Cabrera-Pérez, A. Vallbona-Garcia, J. Torres-Torronteras, L.A. Sazanov, M.T. Ryan, Y. Cámara, R. Martí, Communications Biology 5 (2022).","ista":"Molina-Granada D, González-Vioque E, Dibley MG, Cabrera-Pérez R, Vallbona-Garcia A, Torres-Torronteras J, Sazanov LA, Ryan MT, Cámara Y, Martí R. 2022. Most mitochondrial dGTP is tightly bound to respiratory complex I through the NDUFA10 subunit. Communications Biology. 5(1), 620.","apa":"Molina-Granada, D., González-Vioque, E., Dibley, M. G., Cabrera-Pérez, R., Vallbona-Garcia, A., Torres-Torronteras, J., … Martí, R. (2022). Most mitochondrial dGTP is tightly bound to respiratory complex I through the NDUFA10 subunit. <i>Communications Biology</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s42003-022-03568-6\">https://doi.org/10.1038/s42003-022-03568-6</a>","chicago":"Molina-Granada, David, Emiliano González-Vioque, Marris G. Dibley, Raquel Cabrera-Pérez, Antoni Vallbona-Garcia, Javier Torres-Torronteras, Leonid A Sazanov, Michael T. Ryan, Yolanda Cámara, and Ramon Martí. “Most Mitochondrial DGTP Is Tightly Bound to Respiratory Complex I through the NDUFA10 Subunit.” <i>Communications Biology</i>. Springer Nature, 2022. <a href=\"https://doi.org/10.1038/s42003-022-03568-6\">https://doi.org/10.1038/s42003-022-03568-6</a>.","mla":"Molina-Granada, David, et al. “Most Mitochondrial DGTP Is Tightly Bound to Respiratory Complex I through the NDUFA10 Subunit.” <i>Communications Biology</i>, vol. 5, no. 1, 620, Springer Nature, 2022, doi:<a href=\"https://doi.org/10.1038/s42003-022-03568-6\">10.1038/s42003-022-03568-6</a>.","ama":"Molina-Granada D, González-Vioque E, Dibley MG, et al. Most mitochondrial dGTP is tightly bound to respiratory complex I through the NDUFA10 subunit. <i>Communications Biology</i>. 2022;5(1). doi:<a href=\"https://doi.org/10.1038/s42003-022-03568-6\">10.1038/s42003-022-03568-6</a>"},"publication_status":"published","date_created":"2022-07-10T22:01:52Z","pmid":1,"external_id":{"isi":["000815098500002"],"pmid":[" 35739187"]},"title":"Most mitochondrial dGTP is tightly bound to respiratory complex I through the NDUFA10 subunit","day":"23","acknowledgement":"We thank Dr, Luke Formosa (Department of Biochemistry and Molecular Biology, Monash Biomedicine Discovery Institute, Monash University, Melbourne, Australia) for his valuable advice and assistance on NDUFA10 molecular studies and Dr. Francesc Canals and his team (Proteomics Laboratory, Vall d’Hebron Institute of Oncology [VHIO], Universitat Autònoma de Barcelona, Barcelona, Spain) for their assistance with LC-MS/MS analyses. This work was supported by the Spanish Ministry of Industry, Economy and Competitiveness [grants BFU2014-52618-R, SAF2017-87506, and PID2020-112929RB-I00 to Y.C.], by the Spanish Instituto de Salud Carlos III [grants PI21/00554 and PMP15/00025 to R.M.], co-financed by the European Regional Development Fund (ERDF), and by an NHMRC Project grant to M.R. (GNT1164459).\r\n","volume":5,"year":"2022","issue":"1"},{"type":"journal_article","publication_identifier":{"issn":["00319007"],"eissn":["10797114"]},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","doi":"10.1103/PhysRevLett.128.243201","ec_funded":1,"language":[{"iso":"eng"}],"oa_version":"Submitted Version","arxiv":1,"publication":"Physical Review Letters","intvolume":"       128","isi":1,"publisher":"American Physical Society","oa":1,"quality_controlled":"1","status":"public","abstract":[{"text":"Rotational dynamics of D2 molecules inside helium nanodroplets is induced by a moderately intense femtosecond pump pulse and measured as a function of time by recording the yield of HeD+ ions, created through strong-field dissociative ionization with a delayed femtosecond probe pulse. The yield oscillates with a period of 185 fs, reflecting field-free rotational wave packet dynamics, and the oscillation persists for more than 500 periods. Within the experimental uncertainty, the rotational constant BHe of the in-droplet D2 molecule, determined by Fourier analysis, is the same as Bgas for an isolated D2 molecule. Our observations show that the D2 molecules inside helium nanodroplets essentially rotate as free D2 molecules.","lang":"eng"}],"date_published":"2022-06-16T00:00:00Z","month":"06","author":[{"last_name":"Qiang","full_name":"Qiang, Junjie","first_name":"Junjie"},{"first_name":"Lianrong","full_name":"Zhou, Lianrong","last_name":"Zhou"},{"first_name":"Peifen","last_name":"Lu","full_name":"Lu, Peifen"},{"full_name":"Lin, Kang","last_name":"Lin","first_name":"Kang"},{"first_name":"Yongzhe","last_name":"Ma","full_name":"Ma, Yongzhe"},{"full_name":"Pan, Shengzhe","last_name":"Pan","first_name":"Shengzhe"},{"first_name":"Chenxu","last_name":"Lu","full_name":"Lu, Chenxu"},{"first_name":"Wenyu","full_name":"Jiang, Wenyu","last_name":"Jiang"},{"first_name":"Fenghao","last_name":"Sun","full_name":"Sun, Fenghao"},{"first_name":"Wenbin","last_name":"Zhang","full_name":"Zhang, Wenbin"},{"last_name":"Li","full_name":"Li, Hui","first_name":"Hui"},{"full_name":"Gong, Xiaochun","last_name":"Gong","first_name":"Xiaochun"},{"last_name":"Averbukh","full_name":"Averbukh, Ilya Sh","first_name":"Ilya Sh"},{"last_name":"Prior","full_name":"Prior, Yehiam","first_name":"Yehiam"},{"first_name":"Constant A.","last_name":"Schouder","full_name":"Schouder, Constant A."},{"last_name":"Stapelfeldt","full_name":"Stapelfeldt, Henrik","first_name":"Henrik"},{"first_name":"Igor","id":"339C7E5A-F248-11E8-B48F-1D18A9856A87","last_name":"Cherepanov","full_name":"Cherepanov, Igor"},{"first_name":"Mikhail","orcid":"0000-0002-6990-7802","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","last_name":"Lemeshko","full_name":"Lemeshko, Mikhail"},{"first_name":"Wolfgang","last_name":"Jäger","full_name":"Jäger, Wolfgang"},{"last_name":"Wu","full_name":"Wu, Jian","first_name":"Jian"}],"article_processing_charge":"No","scopus_import":"1","article_number":"243201","project":[{"grant_number":"801770","_id":"2688CF98-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Angulon: physics and applications of a new quasiparticle"},{"grant_number":"665385","call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","name":"International IST Doctoral Program"}],"date_updated":"2023-08-03T11:54:14Z","_id":"11552","department":[{"_id":"MiLe"}],"citation":{"apa":"Qiang, J., Zhou, L., Lu, P., Lin, K., Ma, Y., Pan, S., … Wu, J. (2022). Femtosecond rotational dynamics of D2 molecules in superfluid helium nanodroplets. <i>Physical Review Letters</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevLett.128.243201\">https://doi.org/10.1103/PhysRevLett.128.243201</a>","ista":"Qiang J, Zhou L, Lu P, Lin K, Ma Y, Pan S, Lu C, Jiang W, Sun F, Zhang W, Li H, Gong X, Averbukh IS, Prior Y, Schouder CA, Stapelfeldt H, Cherepanov I, Lemeshko M, Jäger W, Wu J. 2022. Femtosecond rotational dynamics of D2 molecules in superfluid helium nanodroplets. Physical Review Letters. 128(24), 243201.","short":"J. Qiang, L. Zhou, P. Lu, K. Lin, Y. Ma, S. Pan, C. Lu, W. Jiang, F. Sun, W. Zhang, H. Li, X. Gong, I.S. Averbukh, Y. Prior, C.A. Schouder, H. Stapelfeldt, I. Cherepanov, M. Lemeshko, W. Jäger, J. Wu, Physical Review Letters 128 (2022).","ama":"Qiang J, Zhou L, Lu P, et al. Femtosecond rotational dynamics of D2 molecules in superfluid helium nanodroplets. <i>Physical Review Letters</i>. 2022;128(24). doi:<a href=\"https://doi.org/10.1103/PhysRevLett.128.243201\">10.1103/PhysRevLett.128.243201</a>","mla":"Qiang, Junjie, et al. “Femtosecond Rotational Dynamics of D2 Molecules in Superfluid Helium Nanodroplets.” <i>Physical Review Letters</i>, vol. 128, no. 24, 243201, American Physical Society, 2022, doi:<a href=\"https://doi.org/10.1103/PhysRevLett.128.243201\">10.1103/PhysRevLett.128.243201</a>.","chicago":"Qiang, Junjie, Lianrong Zhou, Peifen Lu, Kang Lin, Yongzhe Ma, Shengzhe Pan, Chenxu Lu, et al. “Femtosecond Rotational Dynamics of D2 Molecules in Superfluid Helium Nanodroplets.” <i>Physical Review Letters</i>. American Physical Society, 2022. <a href=\"https://doi.org/10.1103/PhysRevLett.128.243201\">https://doi.org/10.1103/PhysRevLett.128.243201</a>.","ieee":"J. Qiang <i>et al.</i>, “Femtosecond rotational dynamics of D2 molecules in superfluid helium nanodroplets,” <i>Physical Review Letters</i>, vol. 128, no. 24. American Physical Society, 2022."},"main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2201.09281","open_access":"1"}],"publication_status":"published","date_created":"2022-07-10T22:01:52Z","title":"Femtosecond rotational dynamics of D2 molecules in superfluid helium nanodroplets","day":"16","external_id":{"isi":["000820659700002"],"arxiv":["2201.09281"]},"volume":128,"year":"2022","issue":"24"},{"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"publisher":"Springer Nature","intvolume":"         8","doi":"10.1007/s40598-022-00200-7","page":"319-410","publication_identifier":{"issn":["2199-6792"],"eissn":["2199-6806"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"journal_article","related_material":{"link":[{"relation":"erratum","url":"https://doi.org/10.1007/s40598-022-00209-y"},{"relation":"erratum","url":"https://doi.org/10.1007/s40598-022-00218-x"}]},"oa_version":"None","publication":"Arnold Mathematical Journal","ec_funded":1,"language":[{"iso":"eng"}],"scopus_import":"1","article_processing_charge":"No","author":[{"first_name":"Trevor","full_name":"Clark, Trevor","last_name":"Clark"},{"first_name":"Kostiantyn","id":"fe8209e2-906f-11eb-847d-950f8fc09115","orcid":"0000-0002-9156-8616","last_name":"Drach","full_name":"Drach, Kostiantyn"},{"first_name":"Oleg","full_name":"Kozlovski, Oleg","last_name":"Kozlovski"},{"last_name":"Strien","full_name":"Strien, Sebastian Van","first_name":"Sebastian Van"}],"month":"06","has_accepted_license":"1","article_type":"original","status":"public","quality_controlled":"1","file":[{"date_updated":"2022-07-12T10:04:55Z","file_name":"2022_ArnoldMathematicalJournal_Clark.pdf","success":1,"content_type":"application/pdf","file_id":"11559","file_size":2509915,"access_level":"open_access","checksum":"16e7c659dee9073c6c8aeb87316ef201","creator":"kschuh","relation":"main_file","date_created":"2022-07-12T10:04:55Z"}],"date_published":"2022-06-01T00:00:00Z","ddc":["500"],"abstract":[{"text":"In holomorphic dynamics, complex box mappings arise as first return maps to wellchosen domains. They are a generalization of polynomial-like mapping, where the domain of the return map can have infinitely many components. They turned out to be extremely useful in tackling diverse problems. The purpose of this paper is:\r\n• To illustrate some pathologies that can occur when a complex box mapping is not induced by a globally defined map and when its domain has infinitely many components, and to give conditions to avoid these issues.\r\n• To show that once one has a box mapping for a rational map, these conditions can be assumed to hold in a very natural setting. Thus, we call such complex box mappings dynamically natural. Having such box mappings is the first step in tackling many problems in one-dimensional dynamics.\r\n• Many results in holomorphic dynamics rely on an interplay between combinatorial and analytic techniques. In this setting, some of these tools are:\r\n  • the Enhanced Nest (a nest of puzzle pieces around critical points) from Kozlovski, Shen, van Strien (AnnMath 165:749–841, 2007), referred to below as KSS;\r\n  • the Covering Lemma (which controls the moduli of pullbacks of annuli) from Kahn and Lyubich (Ann Math 169(2):561–593, 2009);\r\n   • the QC-Criterion and the Spreading Principle from KSS.\r\nThe purpose of this paper is to make these tools more accessible so that they can be used as a ‘black box’, so one does not have to redo the proofs in new settings.\r\n• To give an intuitive, but also rather detailed, outline of the proof from KSS and Kozlovski and van Strien (Proc Lond Math Soc (3) 99:275–296, 2009) of the following results for non-renormalizable dynamically natural complex box mappings:\r\n   • puzzle pieces shrink to points,\r\n   • (under some assumptions) topologically conjugate non-renormalizable polynomials and box mappings are quasiconformally conjugate.\r\n• We prove the fundamental ergodic properties for dynamically natural box mappings. This leads to some necessary conditions for when such a box mapping supports a measurable invariant line field on its filled Julia set. These mappings\r\nare the analogues of Lattès maps in this setting.\r\n• We prove a version of Mañé’s Theorem for complex box mappings concerning expansion along orbits of points that avoid a neighborhood of the set of critical points.","lang":"eng"}],"publication_status":"published","date_created":"2022-07-10T22:01:53Z","_id":"11553","date_updated":"2023-02-16T10:02:12Z","project":[{"grant_number":"885707","name":"Spectral rigidity and integrability for billiards and geodesic flows","call_identifier":"H2020","_id":"9B8B92DE-BA93-11EA-9121-9846C619BF3A"}],"file_date_updated":"2022-07-12T10:04:55Z","citation":{"ama":"Clark T, Drach K, Kozlovski O, Strien SV. The dynamics of complex box mappings. <i>Arnold Mathematical Journal</i>. 2022;8(2):319-410. doi:<a href=\"https://doi.org/10.1007/s40598-022-00200-7\">10.1007/s40598-022-00200-7</a>","mla":"Clark, Trevor, et al. “The Dynamics of Complex Box Mappings.” <i>Arnold Mathematical Journal</i>, vol. 8, no. 2, Springer Nature, 2022, pp. 319–410, doi:<a href=\"https://doi.org/10.1007/s40598-022-00200-7\">10.1007/s40598-022-00200-7</a>.","chicago":"Clark, Trevor, Kostiantyn Drach, Oleg Kozlovski, and Sebastian Van Strien. “The Dynamics of Complex Box Mappings.” <i>Arnold Mathematical Journal</i>. Springer Nature, 2022. <a href=\"https://doi.org/10.1007/s40598-022-00200-7\">https://doi.org/10.1007/s40598-022-00200-7</a>.","ista":"Clark T, Drach K, Kozlovski O, Strien SV. 2022. The dynamics of complex box mappings. Arnold Mathematical Journal. 8(2), 319–410.","apa":"Clark, T., Drach, K., Kozlovski, O., &#38; Strien, S. V. (2022). The dynamics of complex box mappings. <i>Arnold Mathematical Journal</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s40598-022-00200-7\">https://doi.org/10.1007/s40598-022-00200-7</a>","short":"T. Clark, K. Drach, O. Kozlovski, S.V. Strien, Arnold Mathematical Journal 8 (2022) 319–410.","ieee":"T. Clark, K. Drach, O. Kozlovski, and S. V. Strien, “The dynamics of complex box mappings,” <i>Arnold Mathematical Journal</i>, vol. 8, no. 2. Springer Nature, pp. 319–410, 2022."},"department":[{"_id":"VaKa"}],"issue":"2","year":"2022","day":"01","title":"The dynamics of complex box mappings","volume":8,"acknowledgement":"We would also like to thank Dzmitry Dudko and Dierk Schleicher for many stimulating discussions and encouragement during our work on this project, and Weixiao Shen, Mikhail Hlushchanka and the referee for helpful comments. We are grateful to Leon Staresinic who carefully read the revised version of the manuscript and provided many helpful suggestions."},{"date_created":"2022-07-11T12:19:59Z","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2103.09481"}],"publication_status":"published","citation":{"chicago":"Kalinov, Aleksei, A.I. Osinskiy, S.A. Matveev, W. Otieno, and N.V. Brilliantov. “Direct Simulation Monte Carlo for New Regimes in Aggregation-Fragmentation Kinetics.” <i>Journal of Computational Physics</i>. Elsevier, 2022. <a href=\"https://doi.org/10.1016/j.jcp.2022.111439\">https://doi.org/10.1016/j.jcp.2022.111439</a>.","mla":"Kalinov, Aleksei, et al. “Direct Simulation Monte Carlo for New Regimes in Aggregation-Fragmentation Kinetics.” <i>Journal of Computational Physics</i>, vol. 467, 111439, Elsevier, 2022, doi:<a href=\"https://doi.org/10.1016/j.jcp.2022.111439\">10.1016/j.jcp.2022.111439</a>.","ama":"Kalinov A, Osinskiy AI, Matveev SA, Otieno W, Brilliantov NV. Direct simulation Monte Carlo for new regimes in aggregation-fragmentation kinetics. <i>Journal of Computational Physics</i>. 2022;467. doi:<a href=\"https://doi.org/10.1016/j.jcp.2022.111439\">10.1016/j.jcp.2022.111439</a>","short":"A. Kalinov, A.I. Osinskiy, S.A. Matveev, W. Otieno, N.V. Brilliantov, Journal of Computational Physics 467 (2022).","apa":"Kalinov, A., Osinskiy, A. I., Matveev, S. A., Otieno, W., &#38; Brilliantov, N. V. (2022). Direct simulation Monte Carlo for new regimes in aggregation-fragmentation kinetics. <i>Journal of Computational Physics</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.jcp.2022.111439\">https://doi.org/10.1016/j.jcp.2022.111439</a>","ista":"Kalinov A, Osinskiy AI, Matveev SA, Otieno W, Brilliantov NV. 2022. Direct simulation Monte Carlo for new regimes in aggregation-fragmentation kinetics. Journal of Computational Physics. 467, 111439.","ieee":"A. Kalinov, A. I. Osinskiy, S. A. Matveev, W. Otieno, and N. V. Brilliantov, “Direct simulation Monte Carlo for new regimes in aggregation-fragmentation kinetics,” <i>Journal of Computational Physics</i>, vol. 467. Elsevier, 2022."},"department":[{"_id":"GradSch"},{"_id":"ChWo"}],"_id":"11556","date_updated":"2023-08-03T11:55:06Z","year":"2022","volume":467,"acknowledgement":"Zhores supercomputer of Skolkovo Institute of Science and Technology [68] has been used in the present research. S.A.M. was supported by Moscow Center for Fundamental and Applied Mathematics (the agreement with the Ministry of Education and Science of the Russian Federation No. 075-15-2019-1624). A.I.O. acknowledges RFBR project No. 20-31-90022. N.V.B. acknowledges the support of the Analytical Center (subsidy agreement 000000D730321P5Q0002, Grant No. 70-2021-00145 02.11.2021).","external_id":{"isi":["000917225500013"],"arxiv":["2103.09481"]},"day":"15","title":"Direct simulation Monte Carlo for new regimes in aggregation-fragmentation kinetics","publisher":"Elsevier","oa":1,"isi":1,"intvolume":"       467","publication":"Journal of Computational Physics","oa_version":"Preprint","arxiv":1,"language":[{"iso":"eng"}],"doi":"10.1016/j.jcp.2022.111439","publication_identifier":{"issn":["0021-9991"]},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","keyword":["Computer Science Applications","Physics and Astronomy (miscellaneous)","Applied Mathematics","Computational Mathematics","Modeling and Simulation","Numerical Analysis"],"type":"journal_article","article_number":"111439","article_processing_charge":"No","author":[{"last_name":"Kalinov","full_name":"Kalinov, Aleksei","first_name":"Aleksei","id":"44b7120e-eb97-11eb-a6c2-e1557aa81d02","orcid":"0000-0003-2189-3904"},{"first_name":"A.I.","full_name":"Osinskiy, A.I.","last_name":"Osinskiy"},{"first_name":"S.A.","last_name":"Matveev","full_name":"Matveev, S.A."},{"last_name":"Otieno","full_name":"Otieno, W.","first_name":"W."},{"full_name":"Brilliantov, N.V.","last_name":"Brilliantov","first_name":"N.V."}],"month":"10","date_published":"2022-10-15T00:00:00Z","ddc":["518"],"abstract":[{"lang":"eng","text":"We revisit two basic Direct Simulation Monte Carlo Methods to model aggregation kinetics and extend them for aggregation processes with collisional fragmentation (shattering). We test the performance and accuracy of the extended methods and compare their performance with efficient deterministic finite-difference method applied to the same model. We validate the stochastic methods on the test problems and apply them to verify the existence of oscillating regimes in the aggregation-fragmentation kinetics recently detected in deterministic simulations. We confirm the emergence of steady oscillations of densities in such systems and prove the stability of the\r\noscillations with respect to fluctuations and noise."}],"article_type":"original","status":"public","quality_controlled":"1"},{"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publication_identifier":{"eissn":["1474-760X"]},"type":"journal_article","doi":"10.1186/s13059-022-02711-0","oa_version":"Published Version","publication":"Genome Biology","language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"isi":1,"intvolume":"        23","oa":1,"publisher":"BioMed Central","quality_controlled":"1","article_type":"original","status":"public","date_published":"2022-07-07T00:00:00Z","abstract":[{"text":"Background: Accurate and comprehensive annotation of transcript sequences is essential for transcript quantification and differential gene and transcript expression analysis. Single-molecule long-read sequencing technologies provide improved integrity of transcript structures including alternative splicing, and transcription start and polyadenylation sites. However, accuracy is significantly affected by sequencing errors, mRNA degradation, or incomplete cDNA synthesis.\r\nResults: We present a new and comprehensive Arabidopsis thaliana Reference Transcript Dataset 3 (AtRTD3). AtRTD3 contains over 169,000 transcripts—twice that of the best current Arabidopsis transcriptome and including over 1500 novel genes. Seventy-eight percent of transcripts are from Iso-seq with accurately defined splice junctions and transcription start and end sites. We develop novel methods to determine splice junctions and transcription start and end sites accurately. Mismatch profiles around splice junctions provide a powerful feature to distinguish correct splice junctions and remove false splice junctions. Stratified approaches identify high-confidence transcription start and end sites and remove fragmentary transcripts due to degradation. AtRTD3 is a major improvement over existing transcriptomes as demonstrated by analysis of an Arabidopsis cold response RNA-seq time-series. AtRTD3 provides higher resolution of transcript expression profiling and identifies cold-induced differential transcription start and polyadenylation site usage.\r\nConclusions: AtRTD3 is the most comprehensive Arabidopsis transcriptome currently. It improves the precision of differential gene and transcript expression, differential alternative splicing, and transcription start/end site usage analysis from RNA-seq data. The novel methods for identifying accurate splice junctions and transcription start/end sites are widely applicable and will improve single-molecule sequencing analysis from any species.","lang":"eng"}],"ddc":["570"],"file":[{"success":1,"date_updated":"2022-07-18T08:15:24Z","file_name":"2022_GenomeBiology_Zhang.pdf","access_level":"open_access","file_size":3146207,"file_id":"11597","content_type":"application/pdf","creator":"dernst","checksum":"2c30ef84151d257a6b835b4e069b70ac","date_created":"2022-07-18T08:15:24Z","relation":"main_file"}],"author":[{"first_name":"Runxuan","full_name":"Zhang, Runxuan","last_name":"Zhang"},{"full_name":"Kuo, Richard","last_name":"Kuo","first_name":"Richard"},{"first_name":"Max","last_name":"Coulter","full_name":"Coulter, Max"},{"last_name":"Calixto","full_name":"Calixto, Cristiane P.G.","first_name":"Cristiane P.G."},{"last_name":"Entizne","full_name":"Entizne, Juan Carlos","first_name":"Juan Carlos"},{"full_name":"Guo, Wenbin","last_name":"Guo","first_name":"Wenbin"},{"full_name":"Marquez, Yamile","last_name":"Marquez","first_name":"Yamile"},{"last_name":"Milne","full_name":"Milne, Linda","first_name":"Linda"},{"last_name":"Riegler","full_name":"Riegler, Stefan","first_name":"Stefan","id":"FF6018E0-D806-11E9-8E43-0B14E6697425","orcid":"0000-0003-3413-1343"},{"last_name":"Matsui","full_name":"Matsui, Akihiro","first_name":"Akihiro"},{"last_name":"Tanaka","full_name":"Tanaka, Maho","first_name":"Maho"},{"full_name":"Harvey, Sarah","last_name":"Harvey","first_name":"Sarah"},{"first_name":"Yubang","full_name":"Gao, Yubang","last_name":"Gao"},{"full_name":"Wießner-Kroh, Theresa","last_name":"Wießner-Kroh","first_name":"Theresa"},{"first_name":"Alejandro","last_name":"Paniagua","full_name":"Paniagua, Alejandro"},{"first_name":"Martin","last_name":"Crespi","full_name":"Crespi, Martin"},{"full_name":"Denby, Katherine","last_name":"Denby","first_name":"Katherine"},{"last_name":"Hur","full_name":"Hur, Asa Ben","first_name":"Asa Ben"},{"first_name":"Enamul","last_name":"Huq","full_name":"Huq, Enamul"},{"first_name":"Michael","last_name":"Jantsch","full_name":"Jantsch, Michael"},{"first_name":"Artur","full_name":"Jarmolowski, Artur","last_name":"Jarmolowski"},{"full_name":"Koester, Tino","last_name":"Koester","first_name":"Tino"},{"first_name":"Sascha","last_name":"Laubinger","full_name":"Laubinger, Sascha"},{"first_name":"Qingshun Quinn","last_name":"Li","full_name":"Li, Qingshun Quinn"},{"last_name":"Gu","full_name":"Gu, Lianfeng","first_name":"Lianfeng"},{"last_name":"Seki","full_name":"Seki, Motoaki","first_name":"Motoaki"},{"full_name":"Staiger, Dorothee","last_name":"Staiger","first_name":"Dorothee"},{"last_name":"Sunkar","full_name":"Sunkar, Ramanjulu","first_name":"Ramanjulu"},{"last_name":"Szweykowska-Kulinska","full_name":"Szweykowska-Kulinska, Zofia","first_name":"Zofia"},{"last_name":"Tu","full_name":"Tu, Shih Long","first_name":"Shih Long"},{"first_name":"Andreas","full_name":"Wachter, Andreas","last_name":"Wachter"},{"first_name":"Robbie","last_name":"Waugh","full_name":"Waugh, Robbie"},{"last_name":"Xiong","full_name":"Xiong, Liming","first_name":"Liming"},{"full_name":"Zhang, Xiao Ning","last_name":"Zhang","first_name":"Xiao Ning"},{"first_name":"Ana","last_name":"Conesa","full_name":"Conesa, Ana"},{"first_name":"Anireddy S.N.","full_name":"Reddy, Anireddy S.N.","last_name":"Reddy"},{"last_name":"Barta","full_name":"Barta, Andrea","first_name":"Andrea"},{"full_name":"Kalyna, Maria","last_name":"Kalyna","first_name":"Maria"},{"full_name":"Brown, John W.S.","last_name":"Brown","first_name":"John W.S."}],"month":"07","article_processing_charge":"No","scopus_import":"1","article_number":"149","has_accepted_license":"1","file_date_updated":"2022-07-18T08:15:24Z","_id":"11587","date_updated":"2023-08-03T12:04:18Z","citation":{"ama":"Zhang R, Kuo R, Coulter M, et al. A high-resolution single-molecule sequencing-based Arabidopsis transcriptome using novel methods of Iso-seq analysis. <i>Genome Biology</i>. 2022;23. doi:<a href=\"https://doi.org/10.1186/s13059-022-02711-0\">10.1186/s13059-022-02711-0</a>","mla":"Zhang, Runxuan, et al. “A High-Resolution Single-Molecule Sequencing-Based Arabidopsis Transcriptome Using Novel Methods of Iso-Seq Analysis.” <i>Genome Biology</i>, vol. 23, 149, BioMed Central, 2022, doi:<a href=\"https://doi.org/10.1186/s13059-022-02711-0\">10.1186/s13059-022-02711-0</a>.","chicago":"Zhang, Runxuan, Richard Kuo, Max Coulter, Cristiane P.G. Calixto, Juan Carlos Entizne, Wenbin Guo, Yamile Marquez, et al. “A High-Resolution Single-Molecule Sequencing-Based Arabidopsis Transcriptome Using Novel Methods of Iso-Seq Analysis.” <i>Genome Biology</i>. BioMed Central, 2022. <a href=\"https://doi.org/10.1186/s13059-022-02711-0\">https://doi.org/10.1186/s13059-022-02711-0</a>.","ista":"Zhang R, Kuo R, Coulter M, Calixto CPG, Entizne JC, Guo W, Marquez Y, Milne L, Riegler S, Matsui A, Tanaka M, Harvey S, Gao Y, Wießner-Kroh T, Paniagua A, Crespi M, Denby K, Hur AB, Huq E, Jantsch M, Jarmolowski A, Koester T, Laubinger S, Li QQ, Gu L, Seki M, Staiger D, Sunkar R, Szweykowska-Kulinska Z, Tu SL, Wachter A, Waugh R, Xiong L, Zhang XN, Conesa A, Reddy ASN, Barta A, Kalyna M, Brown JWS. 2022. A high-resolution single-molecule sequencing-based Arabidopsis transcriptome using novel methods of Iso-seq analysis. Genome Biology. 23, 149.","apa":"Zhang, R., Kuo, R., Coulter, M., Calixto, C. P. G., Entizne, J. C., Guo, W., … Brown, J. W. S. (2022). A high-resolution single-molecule sequencing-based Arabidopsis transcriptome using novel methods of Iso-seq analysis. <i>Genome Biology</i>. BioMed Central. <a href=\"https://doi.org/10.1186/s13059-022-02711-0\">https://doi.org/10.1186/s13059-022-02711-0</a>","short":"R. Zhang, R. Kuo, M. Coulter, C.P.G. Calixto, J.C. Entizne, W. Guo, Y. Marquez, L. Milne, S. Riegler, A. Matsui, M. Tanaka, S. Harvey, Y. Gao, T. Wießner-Kroh, A. Paniagua, M. Crespi, K. Denby, A.B. Hur, E. Huq, M. Jantsch, A. Jarmolowski, T. Koester, S. Laubinger, Q.Q. Li, L. Gu, M. Seki, D. Staiger, R. Sunkar, Z. Szweykowska-Kulinska, S.L. Tu, A. Wachter, R. Waugh, L. Xiong, X.N. Zhang, A. Conesa, A.S.N. Reddy, A. Barta, M. Kalyna, J.W.S. Brown, Genome Biology 23 (2022).","ieee":"R. Zhang <i>et al.</i>, “A high-resolution single-molecule sequencing-based Arabidopsis transcriptome using novel methods of Iso-seq analysis,” <i>Genome Biology</i>, vol. 23. BioMed Central, 2022."},"department":[{"_id":"FyKo"}],"publication_status":"published","date_created":"2022-07-17T22:01:53Z","day":"07","title":"A high-resolution single-molecule sequencing-based Arabidopsis transcriptome using novel methods of Iso-seq analysis","external_id":{"isi":["000821915500002"]},"volume":23,"acknowledgement":"This work was jointly supported by funding from the Biotechnology and Biological Sciences Research Council (BBSRC) BB/P009751/1 to JB; BB/R014582/1 to RW and RZ; BB/S020160/1 to RZ; BB/S004610/1 (16 ERA-CAPS BARN) to RW; the Scottish Government Rural and Environment Science and Analytical Services division (RESAS) [to RZ, RW, and JB]; the\r\nNational Science Foundation (MCB-2014408) and the National Institute of Health (NIH) (GM-114297) to E.H.; S. H. was supported by funding to K.D. from the University of York; the Austrian Science Fund (FWF) SFB F43 to AB and MJ and [P26333] to MK; The French Agence Nationale de la Recherche grant ANR-16-CE12-0032 to MC; the Japan Science and\r\nTechnology Agency (JST), the Core Research for Evolutionary Science and Technology (CREST; Grant Number JPMJCR13B4) to M.S.; the National Science Foundation (Grant No. DBI1949036 to A.b.H and A.S.N.R, and Grant No. MCB 2014542 to E.H. and A.S.N.R.); and the DOE Office of Science, Office of Biological and Environmental Research (Grant\r\nNo. DE-SC0010733) to A.S.N.R and A.b.H.; the Deutsche Forschungsgemeinschaft (DFG) STA653/14-1 and STA653/15-1 to DS; the National Science Foundation grant (IOS-154173) to Q.Q.L.; the German Research Foundation (DFG) WA2167/8-1 to AW and SFB1101/C03 to AW and TWK; the Research Grants Council (RGC) of Hong Kong (GRF 12103020) to LX. NSF grant IOS-1849708 and NSF EPSCoR grant 1826836 to RS; the Academia Sinica to S.-L. T.","year":"2022"},{"issue":"7","year":"2022","volume":107,"acknowledgement":"This study was supported by the Deutsche Forschungsgemeinschaft (DFG) SFB 914 ( to SM [B02 and Z01]), the DFG SFB 1123 (to SM [B06]), the DFG FOR 2033 (to SM), the German\r\nCenter for Cardiovascular Research (DZHK) (Clinician Scientist Programme), MHA 1.4VD (to SM), Postdoc Start-up Grant, 81X3600213 (to FG), 81X3600222 (to LN), the FP7 program\r\n(project 260309, PRESTIGE [to SM]). This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement No. 83344, ERC-2018-ADG “IMMUNOTHROMBOSIS” [to SM] and the Marie Skłodowska Curie Individual Fellowship (EU project 747687, LamelliActin [to FG]). ","day":"01","title":"Single platelet and megakaryocyte morpho-dynamics uncovered by multicolor reporter mouse strains in vitro and in vivo","external_id":{"isi":["000823746100018"]},"license":"https://creativecommons.org/licenses/by-nc/4.0/","date_created":"2022-07-17T22:01:54Z","publication_status":"published","citation":{"ieee":"L. Nicolai <i>et al.</i>, “Single platelet and megakaryocyte morpho-dynamics uncovered by multicolor reporter mouse strains in vitro and in vivo,” <i>Haematologica</i>, vol. 107, no. 7. Ferrata Storti Foundation, pp. 1669–1680, 2022.","apa":"Nicolai, L., Kaiser, R., Escaig, R., Hoffknecht, M. L., Anjum, A., Leunig, A., … Gärtner, F. R. (2022). Single platelet and megakaryocyte morpho-dynamics uncovered by multicolor reporter mouse strains in vitro and in vivo. <i>Haematologica</i>. Ferrata Storti Foundation. <a href=\"https://doi.org/10.3324/haematol.2021.278896\">https://doi.org/10.3324/haematol.2021.278896</a>","ista":"Nicolai L, Kaiser R, Escaig R, Hoffknecht ML, Anjum A, Leunig A, Pircher J, Ehrlich A, Lorenz M, Ishikawa-Ankerhold H, Aird WC, Massberg S, Gärtner FR. 2022. Single platelet and megakaryocyte morpho-dynamics uncovered by multicolor reporter mouse strains in vitro and in vivo. Haematologica. 107(7), 1669–1680.","short":"L. Nicolai, R. Kaiser, R. Escaig, M.L. Hoffknecht, A. Anjum, A. Leunig, J. Pircher, A. Ehrlich, M. Lorenz, H. Ishikawa-Ankerhold, W.C. Aird, S. Massberg, F.R. Gärtner, Haematologica 107 (2022) 1669–1680.","mla":"Nicolai, Leo, et al. “Single Platelet and Megakaryocyte Morpho-Dynamics Uncovered by Multicolor Reporter Mouse Strains in Vitro and in Vivo.” <i>Haematologica</i>, vol. 107, no. 7, Ferrata Storti Foundation, 2022, pp. 1669–80, doi:<a href=\"https://doi.org/10.3324/haematol.2021.278896\">10.3324/haematol.2021.278896</a>.","ama":"Nicolai L, Kaiser R, Escaig R, et al. Single platelet and megakaryocyte morpho-dynamics uncovered by multicolor reporter mouse strains in vitro and in vivo. <i>Haematologica</i>. 2022;107(7):1669-1680. doi:<a href=\"https://doi.org/10.3324/haematol.2021.278896\">10.3324/haematol.2021.278896</a>","chicago":"Nicolai, Leo, Rainer Kaiser, Raphael Escaig, Marie Louise Hoffknecht, Afra Anjum, Alexander Leunig, Joachim Pircher, et al. “Single Platelet and Megakaryocyte Morpho-Dynamics Uncovered by Multicolor Reporter Mouse Strains in Vitro and in Vivo.” <i>Haematologica</i>. Ferrata Storti Foundation, 2022. <a href=\"https://doi.org/10.3324/haematol.2021.278896\">https://doi.org/10.3324/haematol.2021.278896</a>."},"department":[{"_id":"MiSi"}],"file_date_updated":"2022-07-18T07:51:55Z","project":[{"grant_number":"747687","name":"Mechanical Adaptation of Lamellipodial Actin Networks in Migrating Cells","_id":"260AA4E2-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"_id":"11588","date_updated":"2023-08-03T12:01:01Z","has_accepted_license":"1","author":[{"last_name":"Nicolai","full_name":"Nicolai, Leo","first_name":"Leo"},{"full_name":"Kaiser, Rainer","last_name":"Kaiser","first_name":"Rainer"},{"full_name":"Escaig, Raphael","last_name":"Escaig","first_name":"Raphael"},{"first_name":"Marie Louise","full_name":"Hoffknecht, Marie Louise","last_name":"Hoffknecht"},{"full_name":"Anjum, Afra","last_name":"Anjum","first_name":"Afra"},{"last_name":"Leunig","full_name":"Leunig, Alexander","first_name":"Alexander"},{"first_name":"Joachim","last_name":"Pircher","full_name":"Pircher, Joachim"},{"first_name":"Andreas","last_name":"Ehrlich","full_name":"Ehrlich, Andreas"},{"first_name":"Michael","last_name":"Lorenz","full_name":"Lorenz, Michael"},{"first_name":"Hellen","last_name":"Ishikawa-Ankerhold","full_name":"Ishikawa-Ankerhold, Hellen"},{"last_name":"Aird","full_name":"Aird, William C.","first_name":"William C."},{"first_name":"Steffen","full_name":"Massberg, Steffen","last_name":"Massberg"},{"full_name":"Gärtner, Florian R","last_name":"Gärtner","orcid":"0000-0001-6120-3723","id":"397A88EE-F248-11E8-B48F-1D18A9856A87","first_name":"Florian R"}],"month":"07","scopus_import":"1","article_processing_charge":"No","date_published":"2022-07-01T00:00:00Z","abstract":[{"lang":"eng","text":"Visualizing cell behavior and effector function on a single cell level has been crucial for understanding key aspects of mammalian biology. Due to their small size, large number and rapid recruitment into thrombi, there is a lack of data on fate and behavior of individual platelets in thrombosis and hemostasis. Here we report the use of platelet lineage restricted multi-color reporter mouse strains to delineate platelet function on a single cell level. We show that genetic labeling allows for single platelet and megakaryocyte (MK) tracking and morphological analysis in vivo and in vitro, while not affecting lineage functions. Using Cre-driven Confetti expression, we provide insights into temporal gene expression patterns as well as spatial clustering of MK in the bone marrow. In the vasculature, shape analysis of activated platelets recruited to thrombi identifies ubiquitous filopodia formation with no evidence of lamellipodia formation. Single cell tracking in complex thrombi reveals prominent myosin-dependent motility of platelets and highlights thrombus formation as a highly dynamic process amenable to modification and intervention of the acto-myosin cytoskeleton. Platelet function assays combining flow cytrometry, as well as in vivo, ex vivo and in vitro imaging show unaltered platelet functions of multicolor reporter mice compared to wild-type controls. In conclusion, platelet lineage multicolor reporter mice prove useful in furthering our understanding of platelet and MK biology on a single cell level."}],"ddc":["570"],"file":[{"creator":"dernst","checksum":"9b47830945f3c30428fe9cfee2dc4a8a","date_created":"2022-07-18T07:51:55Z","relation":"main_file","success":1,"date_updated":"2022-07-18T07:51:55Z","file_name":"2022_Haematologica_Nicolai.pdf","access_level":"open_access","file_size":1722094,"file_id":"11595","content_type":"application/pdf"}],"quality_controlled":"1","article_type":"original","status":"public","isi":1,"intvolume":"       107","publisher":"Ferrata Storti Foundation","oa":1,"tmp":{"name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","image":"/images/cc_by_nc.png","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","short":"CC BY-NC (4.0)"},"publication":"Haematologica","oa_version":"Published Version","language":[{"iso":"eng"}],"ec_funded":1,"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publication_identifier":{"issn":["0390-6078"],"eissn":["1592-8721"]},"type":"journal_article","doi":"10.3324/haematol.2021.278896","page":"1669-1680"},{"year":"2022","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.","volume":13,"external_id":{"pmid":["35783951"],"isi":["000819250500001"]},"title":"Constitutive active CPK30 interferes with root growth and endomembrane trafficking in Arabidopsis thaliana","day":"16","date_created":"2022-07-17T22:01:54Z","pmid":1,"publication_status":"published","department":[{"_id":"JiFr"}],"citation":{"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.","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>","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>.","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>.","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>","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.","short":"R. Wang, E. Himschoot, J. Chen, M. Boudsocq, D. Geelen, J. Friml, T. Beeckman, S. Vanneste, Frontiers in Plant Science 13 (2022)."},"date_updated":"2023-08-03T12:01:47Z","_id":"11589","file_date_updated":"2022-07-18T08:05:15Z","article_number":"862398","has_accepted_license":"1","scopus_import":"1","article_processing_charge":"No","month":"06","author":[{"first_name":"Ren","full_name":"Wang, Ren","last_name":"Wang"},{"last_name":"Himschoot","full_name":"Himschoot, Ellie","first_name":"Ellie"},{"first_name":"Jian","full_name":"Chen, Jian","last_name":"Chen"},{"full_name":"Boudsocq, Marie","last_name":"Boudsocq","first_name":"Marie"},{"first_name":"Danny","full_name":"Geelen, Danny","last_name":"Geelen"},{"full_name":"Friml, Jiří","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","first_name":"Jiří"},{"last_name":"Beeckman","full_name":"Beeckman, Tom","first_name":"Tom"},{"last_name":"Vanneste","full_name":"Vanneste, Steffen","first_name":"Steffen"}],"file":[{"file_id":"11596","content_type":"application/pdf","access_level":"open_access","file_size":5040638,"file_name":"2022_FrontiersPlantScience_Wang.pdf","date_updated":"2022-07-18T08:05:15Z","success":1,"date_created":"2022-07-18T08:05:15Z","relation":"main_file","checksum":"95313515637c0f84de591d204375d764","creator":"dernst"}],"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"],"date_published":"2022-06-16T00:00:00Z","status":"public","article_type":"original","quality_controlled":"1","oa":1,"publisher":"Frontiers","intvolume":"        13","isi":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"related_material":{"link":[{"relation":"erratum","url":"https://doi.org/10.3389/fpls.2022.1100792"}]},"language":[{"iso":"eng"}],"oa_version":"Published Version","publication":"Frontiers in Plant Science","doi":"10.3389/fpls.2022.862398","type":"journal_article","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publication_identifier":{"eissn":["1664-462X"]}},{"doi":"10.1088/1367-2630/ac78d8","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publication_identifier":{"issn":["1367-2630"]},"type":"journal_article","oa_version":"Published Version","publication":"New Journal of Physics","ec_funded":1,"language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"publisher":"IOP Publishing","isi":1,"intvolume":"        24","article_type":"original","status":"public","quality_controlled":"1","file":[{"date_created":"2022-07-18T06:33:13Z","relation":"main_file","checksum":"dc67b60f2e50e9ef2bd820ca0d7333d2","creator":"dernst","file_id":"11594","content_type":"application/pdf","access_level":"open_access","file_size":3415721,"file_name":"2022_NewJournalPhysics_Brauneis.pdf","date_updated":"2022-07-18T06:33:13Z","success":1}],"date_published":"2022-06-01T00:00:00Z","ddc":["530"],"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."}],"scopus_import":"1","article_processing_charge":"No","author":[{"full_name":"Brauneis, Fabian","last_name":"Brauneis","first_name":"Fabian"},{"first_name":"Timothy G.","last_name":"Backert","full_name":"Backert, Timothy G."},{"first_name":"Simeon I.","full_name":"Mistakidis, Simeon I.","last_name":"Mistakidis"},{"first_name":"Mikhail","orcid":"0000-0002-6990-7802","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","last_name":"Lemeshko","full_name":"Lemeshko, Mikhail"},{"first_name":"Hans Werner","last_name":"Hammer","full_name":"Hammer, Hans Werner"},{"full_name":"Volosniev, Artem","last_name":"Volosniev","orcid":"0000-0003-0393-5525","id":"37D278BC-F248-11E8-B48F-1D18A9856A87","first_name":"Artem"}],"month":"06","article_number":"063036","has_accepted_license":"1","_id":"11590","date_updated":"2023-08-03T11:57:41Z","file_date_updated":"2022-07-18T06:33:13Z","project":[{"grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425"},{"grant_number":"801770","name":"Angulon: physics and applications of a new quasiparticle","_id":"2688CF98-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"citation":{"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.","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>","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>.","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.","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)."},"department":[{"_id":"MiLe"}],"publication_status":"published","date_created":"2022-07-17T22:01:55Z","external_id":{"isi":["000818530000001"]},"day":"01","title":"Artificial atoms from cold bosons in one dimension","volume":24,"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.","issue":"6","year":"2022"},{"article_type":"original","status":"public","quality_controlled":"1","date_published":"2022-06-29T00:00:00Z","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"}],"scopus_import":"1","article_processing_charge":"No","author":[{"full_name":"Agustí, J.","last_name":"Agustí","first_name":"J."},{"first_name":"Y.","last_name":"Minoguchi","full_name":"Minoguchi, Y."},{"orcid":"0000-0001-8112-028X","id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","first_name":"Johannes M","full_name":"Fink, Johannes M","last_name":"Fink"},{"full_name":"Rabl, P.","last_name":"Rabl","first_name":"P."}],"month":"06","article_number":"062454","doi":"10.1103/PhysRevA.105.062454","publication_identifier":{"eissn":["2469-9934"],"issn":["2469-9926"]},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","type":"journal_article","arxiv":1,"oa_version":"Preprint","publication":"Physical Review A","ec_funded":1,"language":[{"iso":"eng"}],"oa":1,"publisher":"American Physical Society","isi":1,"intvolume":"       105","external_id":{"isi":["000824330200003"],"arxiv":["2204.02993"]},"day":"29","title":"Long-distance distribution of qubit-qubit entanglement using Gaussian-correlated photonic beams","volume":105,"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].","issue":"6","year":"2022","_id":"11591","date_updated":"2023-08-03T11:58:16Z","project":[{"grant_number":"899354","name":"Quantum Local Area Networks with Superconducting Qubits","call_identifier":"H2020","_id":"9B868D20-BA93-11EA-9121-9846C619BF3A"}],"citation":{"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>.","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>","short":"J. Agustí, Y. Minoguchi, J.M. Fink, P. Rabl, Physical Review A 105 (2022).","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>","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.","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."},"department":[{"_id":"JoFi"}],"publication_status":"published","main_file_link":[{"url":" https://doi.org/10.48550/arXiv.2204.02993","open_access":"1"}],"date_created":"2022-07-17T22:01:55Z"},{"article_type":"original","status":"public","quality_controlled":"1","date_published":"2022-06-30T00:00:00Z","abstract":[{"lang":"eng","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."}],"scopus_import":"1","article_processing_charge":"No","author":[{"orcid":"0000-0001-8823-9777","id":"4CA96FD4-F248-11E8-B48F-1D18A9856A87","first_name":"Giacomo","full_name":"Bighin, Giacomo","last_name":"Bighin"},{"last_name":"Cappellaro","full_name":"Cappellaro, Alberto","first_name":"Alberto","id":"9d13b3cb-30a2-11eb-80dc-f772505e8660","orcid":"0000-0001-6110-2359"},{"last_name":"Salasnich","full_name":"Salasnich, L.","first_name":"L."}],"month":"06","article_number":"063329","doi":"10.1103/PhysRevA.105.063329","publication_identifier":{"eissn":["2469-9934"],"issn":["2469-9926"]},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","type":"journal_article","publication":"Physical Review A","oa_version":"Preprint","arxiv":1,"language":[{"iso":"eng"}],"oa":1,"publisher":"American Physical Society","isi":1,"intvolume":"       105","external_id":{"arxiv":["2206.03924"],"isi":["000829758500010"]},"day":"30","title":"Unitary Fermi superfluid near the critical temperature: Thermodynamics and sound modes from elementary excitations","volume":105,"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).","issue":"6","year":"2022","_id":"11592","date_updated":"2023-08-03T12:00:11Z","citation":{"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.","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>.","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>","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>.","short":"G. Bighin, A. Cappellaro, L. Salasnich, Physical Review A 105 (2022).","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>","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."},"department":[{"_id":"MiLe"}],"publication_status":"published","main_file_link":[{"url":" https://doi.org/10.48550/arXiv.2206.03924","open_access":"1"}],"date_created":"2022-07-17T22:01:55Z"},{"citation":{"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>.","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>.","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>","short":"R. Fulek, J. Kynčl, Discrete and Computational Geometry 68 (2022) 425–447.","ista":"Fulek R, Kynčl J. 2022. The Z2-Genus of Kuratowski minors. Discrete and Computational Geometry. 68, 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>","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."},"department":[{"_id":"UlWa"}],"project":[{"_id":"261FA626-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Eliminating intersections in drawings of graphs","grant_number":"M02281"}],"_id":"11593","date_updated":"2023-08-14T12:43:52Z","date_created":"2022-07-17T22:01:56Z","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1803.05085"}],"publication_status":"published","volume":68,"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.","day":"01","title":"The Z2-Genus of Kuratowski minors","external_id":{"arxiv":["1803.05085"],"isi":["000825014500001"]},"year":"2022","arxiv":1,"publication":"Discrete and Computational Geometry","oa_version":"Preprint","language":[{"iso":"eng"}],"related_material":{"record":[{"status":"public","relation":"earlier_version","id":"186"}]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_identifier":{"eissn":["1432-0444"],"issn":["0179-5376"]},"type":"journal_article","page":"425-447","doi":"10.1007/s00454-022-00412-w","isi":1,"intvolume":"        68","publisher":"Springer Nature","oa":1,"date_published":"2022-09-01T00:00:00Z","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"}],"quality_controlled":"1","article_type":"original","status":"public","author":[{"full_name":"Fulek, Radoslav","last_name":"Fulek","orcid":"0000-0001-8485-1774","id":"39F3FFE4-F248-11E8-B48F-1D18A9856A87","first_name":"Radoslav"},{"first_name":"Jan","full_name":"Kynčl, Jan","last_name":"Kynčl"}],"month":"09","article_processing_charge":"No","scopus_import":"1"},{"has_accepted_license":"1","month":"07","author":[{"full_name":"Gallei, Michelle C","last_name":"Gallei","orcid":"0000-0003-1286-7368","id":"35A03822-F248-11E8-B48F-1D18A9856A87","first_name":"Michelle C"}],"article_processing_charge":"No","ddc":["575"],"abstract":[{"lang":"eng","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."}],"date_published":"2022-07-20T00:00:00Z","file":[{"relation":"main_file","date_created":"2022-07-25T09:08:47Z","creator":"mgallei","checksum":"bd7ac35403cf5b4b2607287d2a104b3a","file_size":9730864,"access_level":"open_access","content_type":"application/pdf","file_id":"11645","file_name":"Thesis_Gallei.pdf","date_updated":"2022-07-25T09:08:47Z"},{"access_level":"closed","file_size":19560720,"file_id":"11646","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_name":"Thesis_Gallei_source.docx","date_updated":"2022-07-25T09:39:58Z","date_created":"2022-07-25T09:09:09Z","relation":"source_file","creator":"mgallei","checksum":"a9e54fe5471ba25dc13c2150c1b8ccbb"},{"date_created":"2022-07-25T09:09:32Z","relation":"source_file","creator":"mgallei","checksum":"3994f7f20058941b5bb8a16886b21e71","access_level":"closed","file_size":24542837,"file_id":"11647","description":"This is the print version of the thesis including the full appendix","content_type":"application/pdf","date_updated":"2022-07-25T09:39:58Z","file_name":"Thesis_Gallei_to_print.pdf"},{"creator":"mgallei","checksum":"f24acd3c0d864f4c6676e8b0d7bfa76b","relation":"main_file","date_created":"2022-07-25T11:48:45Z","file_name":"Thesis_Gallei_Appendix.pdf","date_updated":"2022-07-25T11:48:45Z","file_size":15435966,"access_level":"open_access","content_type":"application/pdf","file_id":"11650"}],"status":"public","oa":1,"publisher":"Institute of Science and Technology Austria","ec_funded":1,"language":[{"iso":"eng"}],"oa_version":"Published Version","related_material":{"record":[{"relation":"part_of_dissertation","id":"9287","status":"public"},{"status":"public","relation":"part_of_dissertation","id":"7142"},{"status":"public","relation":"part_of_dissertation","id":"7465"},{"status":"public","relation":"part_of_dissertation","id":"8138"},{"status":"public","id":"6260","relation":"part_of_dissertation"},{"status":"public","relation":"part_of_dissertation","id":"8931"},{"status":"public","id":"10411","relation":"part_of_dissertation"}]},"type":"dissertation","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-019-0"]},"doi":"10.15479/at:ista:11626","degree_awarded":"PhD","page":"248","supervisor":[{"full_name":"Friml, Jiří","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","first_name":"Jiří"},{"last_name":"Benková","full_name":"Benková, Eva","first_name":"Eva","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8510-9739"},{"first_name":"Eilon","full_name":"Shani, Eilon","last_name":"Shani"}],"year":"2022","title":"Auxin and strigolactone non-canonical signaling regulating development in Arabidopsis thaliana","day":"20","date_created":"2022-07-20T11:21:53Z","publication_status":"published","alternative_title":["ISTA Thesis"],"department":[{"_id":"GradSch"},{"_id":"JiFr"}],"citation":{"short":"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.","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>.","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>.","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>","ieee":"M. C. Gallei, “Auxin and strigolactone non-canonical signaling regulating development in Arabidopsis thaliana,” Institute of Science and Technology Austria, 2022."},"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","date_updated":"2024-10-29T10:22:45Z","_id":"11626"},{"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"isi":1,"intvolume":"        83","publisher":"Elsevier","oa":1,"publication_identifier":{"eissn":["10902465"],"issn":["10715797"]},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","type":"journal_article","doi":"10.1016/j.ffa.2022.102085","arxiv":1,"oa_version":"Published Version","publication":"Finite Fields and their Applications","language":[{"iso":"eng"}],"author":[{"id":"c90670c9-0bf0-11ed-86f5-ed522ece2fac","first_name":"Philip","full_name":"Kmentt, Philip","last_name":"Kmentt"},{"last_name":"Shute","full_name":"Shute, Alec L","first_name":"Alec L","id":"440EB050-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-1812-2810"}],"month":"10","scopus_import":"1","article_processing_charge":"Yes (via OA deal)","has_accepted_license":"1","article_number":"102085","quality_controlled":"1","article_type":"original","status":"public","date_published":"2022-10-01T00:00:00Z","ddc":["510"],"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"}],"file":[{"creator":"dernst","checksum":"3ca88decb1011180dc6de7e0862153e1","relation":"main_file","date_created":"2023-02-02T07:56:34Z","success":1,"file_name":"2022_FiniteFields_Kmentt.pdf","date_updated":"2023-02-02T07:56:34Z","file_size":247615,"access_level":"open_access","content_type":"application/pdf","file_id":"12475"}],"publication_status":"published","date_created":"2022-07-24T22:01:41Z","file_date_updated":"2023-02-02T07:56:34Z","_id":"11636","date_updated":"2023-08-03T12:12:57Z","citation":{"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.","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>","ista":"Kmentt P, Shute AL. 2022. The Bertini irreducibility theorem for higher codimensional slices. Finite Fields and their Applications. 83(10), 102085.","short":"P. Kmentt, A.L. Shute, Finite Fields and Their Applications 83 (2022).","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>","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>.","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>."},"department":[{"_id":"TiBr"}],"issue":"10","year":"2022","day":"01","title":"The Bertini irreducibility theorem for higher codimensional slices","external_id":{"isi":["000835490600001"],"arxiv":["2111.06697"]},"volume":83},{"type":"journal_article","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publication_identifier":{"eissn":["1545-7885"]},"doi":"10.1371/journal.pbio.3001684","language":[{"iso":"eng"}],"publication":"PLoS Biology","oa_version":"Published Version","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"intvolume":"        20","isi":1,"oa":1,"publisher":"Public Library of Science","quality_controlled":"1","status":"public","article_type":"original","ddc":["570"],"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."}],"date_published":"2022-06-21T00:00:00Z","file":[{"access_level":"open_access","file_size":3721585,"file_id":"11643","content_type":"application/pdf","success":1,"file_name":"2022_PLoSBiology_Zhao.pdf","date_updated":"2022-07-25T07:38:49Z","date_created":"2022-07-25T07:38:49Z","relation":"main_file","creator":"dernst","checksum":"df4902f854ad76769d3203bfdc69f16c"}],"month":"06","author":[{"full_name":"Zhao, Lina","last_name":"Zhao","first_name":"Lina"},{"first_name":"Lorenz A.","last_name":"Fenk","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","full_name":"Amin-Wetzel, Niko Paresh","last_name":"Amin-Wetzel"},{"last_name":"Ramirez","full_name":"Ramirez, Nelson","first_name":"Nelson","id":"39831956-E4FE-11E9-85DE-0DC7E5697425"},{"first_name":"Mario","orcid":"0000-0001-8347-0443","id":"4E3FF80E-F248-11E8-B48F-1D18A9856A87","last_name":"De Bono","full_name":"De Bono, Mario"},{"last_name":"Chen","full_name":"Chen, Changchun","first_name":"Changchun"}],"article_processing_charge":"No","scopus_import":"1","has_accepted_license":"1","article_number":"e3001684","project":[{"name":"Molecular mechanisms of neural circuit function","_id":"23870BE8-32DE-11EA-91FC-C7463DDC885E","grant_number":"209504/A/17/Z"}],"file_date_updated":"2022-07-25T07:38:49Z","date_updated":"2023-08-03T12:11:44Z","_id":"11637","department":[{"_id":"MaDe"}],"citation":{"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.","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>.","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>","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>","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.","short":"L. Zhao, L.A. Fenk, L. Nilsson, N.P. Amin-Wetzel, N. Ramirez, M. de Bono, C. Chen, PLoS Biology 20 (2022)."},"publication_status":"published","pmid":1,"date_created":"2022-07-24T22:01:42Z","title":"ROS and cGMP signaling modulate persistent escape from hypoxia in Caenorhabditis elegans","day":"21","external_id":{"isi":["000828679600001"],"pmid":["35727855"]},"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.","volume":20,"year":"2022","issue":"6"},{"has_accepted_license":"1","article_number":"023240","author":[{"full_name":"Ngampruetikorn, Vudtiwat","last_name":"Ngampruetikorn","first_name":"Vudtiwat"},{"first_name":"Vedant","last_name":"Sachdeva","full_name":"Sachdeva, Vedant"},{"first_name":"Johanna","full_name":"Torrence, Johanna","last_name":"Torrence"},{"full_name":"Humplik, Jan","last_name":"Humplik","id":"2E9627A8-F248-11E8-B48F-1D18A9856A87","first_name":"Jan"},{"full_name":"Schwab, David J.","last_name":"Schwab","first_name":"David J."},{"last_name":"Palmer","full_name":"Palmer, Stephanie E.","first_name":"Stephanie E."}],"month":"06","article_processing_charge":"No","scopus_import":"1","date_published":"2022-06-24T00:00:00Z","ddc":["530"],"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."}],"file":[{"success":1,"file_name":"2022_PhysicalReviewResearch_Ngampruetikorn.pdf","date_updated":"2022-07-25T07:47:23Z","file_size":1379683,"access_level":"open_access","content_type":"application/pdf","file_id":"11644","creator":"dernst","checksum":"ed6fdc2a3a096df785fa5f7b17b716c6","relation":"main_file","date_created":"2022-07-25T07:47:23Z"}],"quality_controlled":"1","article_type":"original","status":"public","intvolume":"         4","publisher":"American Physical Society","oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"arxiv":1,"publication":"Physical Review Research","oa_version":"Published Version","language":[{"iso":"eng"}],"publication_identifier":{"issn":["2643-1564"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"journal_article","doi":"10.1103/PhysRevResearch.4.023240","funded_apc":"1","issue":"2","year":"2022","volume":4,"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).","day":"24","title":"Inferring couplings in networks across order-disorder phase transitions","external_id":{"arxiv":["2106.02349"]},"date_created":"2022-07-24T22:01:42Z","publication_status":"published","citation":{"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.","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).","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>.","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>","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."},"department":[{"_id":"GaTk"}],"file_date_updated":"2022-07-25T07:47:23Z","_id":"11638","date_updated":"2022-07-25T07:52:35Z"},{"quality_controlled":"1","status":"public","article_type":"original","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."}],"date_published":"2022-12-01T00:00:00Z","month":"12","author":[{"first_name":"Yihan","id":"2ce5da42-b2ea-11eb-bba5-9f264e9d002c","last_name":"Zhang","full_name":"Zhang, Yihan"},{"first_name":"Shashank","full_name":"Vatedka, Shashank","last_name":"Vatedka"}],"scopus_import":"1","article_processing_charge":"No","type":"journal_article","publication_identifier":{"eissn":["1557-9654"],"issn":["0018-9448"]},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","page":"7753-7786","doi":"10.1109/TIT.2022.3189542","language":[{"iso":"eng"}],"publication":"IEEE Transactions on Information Theory","arxiv":1,"oa_version":"Preprint","intvolume":"        68","isi":1,"oa":1,"publisher":"IEEE","title":"List decoding random Euclidean codes and Infinite constellations","day":"01","external_id":{"isi":["000891796100007"],"arxiv":["1901.03790"]},"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].","volume":68,"year":"2022","issue":"12","date_updated":"2023-08-03T12:12:19Z","_id":"11639","department":[{"_id":"MaMo"}],"citation":{"short":"Y. Zhang, S. Vatedka, IEEE Transactions on Information Theory 68 (2022) 7753–7786.","ista":"Zhang Y, Vatedka S. 2022. List decoding random Euclidean codes and Infinite constellations. IEEE Transactions on Information Theory. 68(12), 7753–7786.","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>.","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>.","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>","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."},"main_file_link":[{"url":"https://doi.org/10.48550/arXiv.1901.03790","open_access":"1"}],"publication_status":"published","date_created":"2022-07-24T22:01:42Z"},{"oa_version":"Published Version","publication":"Molecular Ecology Resources","language":[{"iso":"eng"}],"ec_funded":1,"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publication_identifier":{"eissn":["1755-0998"],"issn":["1755-098X"]},"type":"journal_article","doi":"10.1111/1755-0998.13676","page":"2941-2955","isi":1,"intvolume":"        22","publisher":"Wiley","oa":1,"tmp":{"name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","image":"/images/cc_by_nc.png","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","short":"CC BY-NC (4.0)"},"date_published":"2022-11-01T00:00:00Z","ddc":["570"],"abstract":[{"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.","lang":"eng"}],"file":[{"file_name":"2022_MolecularEcologyRes_Szep.pdf","date_updated":"2023-02-02T08:11:23Z","success":1,"content_type":"application/pdf","file_id":"12477","file_size":6431779,"access_level":"open_access","checksum":"3102e203e77b884bffffdbe8e548da88","creator":"dernst","relation":"main_file","date_created":"2023-02-02T08:11:23Z"}],"quality_controlled":"1","article_type":"original","status":"public","has_accepted_license":"1","author":[{"full_name":"Szep, Eniko","last_name":"Szep","id":"485BB5A4-F248-11E8-B48F-1D18A9856A87","first_name":"Eniko"},{"full_name":"Trubenova, Barbora","last_name":"Trubenova","id":"42302D54-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6873-2967","first_name":"Barbora"},{"last_name":"Csilléry","full_name":"Csilléry, Katalin","first_name":"Katalin"}],"month":"11","article_processing_charge":"Yes (via OA deal)","scopus_import":"1","citation":{"short":"E. Szep, B. Trubenova, K. Csilléry, Molecular Ecology Resources 22 (2022) 2941–2955.","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.","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>","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>.","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>.","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>","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."},"department":[{"_id":"NiBa"}],"file_date_updated":"2023-02-02T08:11:23Z","project":[{"grant_number":"704172","name":"Rate of Adaptation in Changing Environment","_id":"25AEDD42-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"_id":"11640","date_updated":"2023-08-03T12:11:01Z","date_created":"2022-07-24T22:01:43Z","publication_status":"published","volume":22,"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.","day":"01","title":"Using gridCoal to assess whether standard population genetic theory holds in the presence of spatio-temporal heterogeneity in population size","external_id":{"isi":["000825873600001"]},"issue":"8","year":"2022"},{"author":[{"first_name":"Christoph","full_name":"Gerle, Christoph","last_name":"Gerle"},{"first_name":"Jun-ichi","last_name":"Kishikawa","full_name":"Kishikawa, Jun-ichi"},{"first_name":"Tomoko","last_name":"Yamaguchi","full_name":"Yamaguchi, Tomoko"},{"first_name":"Atsuko","full_name":"Nakanishi, Atsuko","last_name":"Nakanishi"},{"first_name":"Mehmet Orkun","orcid":"0000-0002-3219-2022","id":"d25163e5-8d53-11eb-a251-e6dd8ea1b8ef","last_name":"Çoruh","full_name":"Çoruh, Mehmet Orkun"},{"first_name":"Fumiaki","last_name":"Makino","full_name":"Makino, Fumiaki"},{"last_name":"Miyata","full_name":"Miyata, Tomoko","first_name":"Tomoko"},{"first_name":"Akihiro","last_name":"Kawamoto","full_name":"Kawamoto, Akihiro"},{"first_name":"Ken","full_name":"Yokoyama, Ken","last_name":"Yokoyama"},{"first_name":"Keiichi","last_name":"Namba","full_name":"Namba, Keiichi"},{"last_name":"Kurisu","full_name":"Kurisu, Genji","first_name":"Genji"},{"first_name":"Takayuki","last_name":"Kato","full_name":"Kato, Takayuki"}],"month":"10","scopus_import":"1","article_processing_charge":"No","has_accepted_license":"1","quality_controlled":"1","article_type":"original","status":"public","date_published":"2022-10-01T00:00:00Z","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."}],"ddc":["570"],"file":[{"checksum":"23b51c163636bf9313f7f0818312e67e","creator":"dernst","relation":"main_file","date_created":"2023-02-03T08:34:48Z","date_updated":"2023-02-03T08:34:48Z","file_name":"2022_Microscopy_Gerle.pdf","success":1,"content_type":"application/pdf","file_id":"12498","file_size":7812696,"access_level":"open_access"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"isi":1,"intvolume":"        71","publisher":"Oxford University Press","oa":1,"publication_identifier":{"eissn":["2050-5701"],"issn":["2050-5698"]},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","keyword":["Radiology","Nuclear Medicine and imaging","Instrumentation","Structural Biology"],"type":"journal_article","doi":"10.1093/jmicro/dfac037","page":"249-261","oa_version":"Published Version","publication":"Microscopy","language":[{"iso":"eng"}],"issue":"5","year":"2022","day":"01","title":"Structures of multisubunit membrane complexes with the CRYO ARM 200","external_id":{"pmid":["35861182"],"isi":["000837950900001"]},"volume":71,"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.","publication_status":"published","pmid":1,"date_created":"2022-07-25T10:04:58Z","file_date_updated":"2023-02-03T08:34:48Z","_id":"11648","date_updated":"2023-08-03T12:13:37Z","citation":{"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.","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.","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>","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.","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>.","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>.","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>"},"department":[{"_id":"LeSa"}]},{"article_processing_charge":"No","month":"08","author":[{"id":"0B46FACA-A8E1-11E9-9BD3-79D1E5697425","orcid":"0000-0002-5328-7231","first_name":"Marwan N","full_name":"Elkrewi, Marwan N","last_name":"Elkrewi"}],"year":"2022","has_accepted_license":"1","status":"public","title":"Data from Elkrewi, Khauratovich, Toups et al. 2022, \"ZW sex-chromosome evolution and contagious parthenogenesis in Artemia brine shrimp\"","day":"05","file":[{"creator":"melkrewi","checksum":"5f1d7c6d7ab5375ed2564521432bed0c","embargo":"2022-08-07","relation":"main_file","date_created":"2022-07-26T12:37:52Z","title":"Supplementary Datasets","date_updated":"2022-08-08T22:30:04Z","file_name":"Data.zip","file_size":2209382998,"access_level":"open_access","content_type":"application/x-zip-compressed","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_id":"11655"}],"ddc":["570"],"abstract":[{"lang":"eng","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."}],"date_published":"2022-08-05T00:00:00Z","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"date_created":"2022-07-26T11:01:47Z","publisher":"Institute of Science and Technology Austria","oa":1,"date_updated":"2024-02-21T12:35:53Z","_id":"11653","doi":"10.15479/AT:ISTA:11653","contributor":[{"orcid":"0000-0002-5328-7231","id":"0B46FACA-A8E1-11E9-9BD3-79D1E5697425","first_name":"Marwan N","last_name":"Elkrewi"},{"first_name":"Uladzislava","last_name":"Khauratovich"},{"last_name":"Toups","id":"4E099E4E-F248-11E8-B48F-1D18A9856A87","first_name":"Melissa A"},{"first_name":"Vincent K","id":"57854184-AAE0-11E9-8D04-98D6E5697425","last_name":"Bett"},{"last_name":"Mrnjavac","first_name":"Andrea","id":"353FAC84-AE61-11E9-8BFC-00D3E5697425"},{"id":"2A0848E2-F248-11E8-B48F-1D18A9856A87","first_name":"Ariana","last_name":"Macon"},{"orcid":"0000-0001-8441-5075","id":"32DF5794-F248-11E8-B48F-1D18A9856A87","first_name":"Christelle","last_name":"Fraisse"},{"last_name":"Sax","first_name":"Luca"},{"id":"4C0A3874-F248-11E8-B48F-1D18A9856A87","first_name":"Ann K","last_name":"Huylmans"},{"last_name":"Hontoria ","first_name":"Francisco"},{"last_name":"Vicoso","first_name":"Beatriz","orcid":"0000-0002-4579-8306","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87"}],"file_date_updated":"2022-08-08T22:30:04Z","type":"research_data","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","related_material":{"record":[{"relation":"used_in_publication","id":"12248","status":"public"}]},"department":[{"_id":"GradSch"},{"_id":"BeVi"}],"oa_version":"Published Version","citation":{"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.","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>.","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>","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>.","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>.","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>","short":"M.N. Elkrewi, (2022)."}},{"oa_version":"Submitted Version","publication":"Leibniz International Proceedings on Mathematics","ec_funded":1,"language":[{"iso":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"journal_article","oa":1,"publisher":"Schloss Dagstuhl - Leibniz Zentrum für Informatik","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"date_published":"2022-07-27T00:00:00Z","abstract":[{"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.","lang":"eng"}],"ddc":["510"],"file":[{"creator":"scultrer","checksum":"b2f511e8b1cae5f1892b0cdec341acac","relation":"main_file","date_created":"2022-07-27T09:25:53Z","file_name":"D-S-E.pdf","date_updated":"2022-07-27T09:25:53Z","file_size":639266,"access_level":"open_access","content_type":"application/pdf","file_id":"11659"}],"quality_controlled":"1","status":"public","has_accepted_license":"1","author":[{"id":"3C2B033E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-5372-7890","first_name":"Ranita","full_name":"Biswas, Ranita","last_name":"Biswas"},{"last_name":"Cultrera di Montesano","full_name":"Cultrera di Montesano, Sebastiano","first_name":"Sebastiano","id":"34D2A09C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6249-0832"},{"first_name":"Herbert","orcid":"0000-0002-9823-6833","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","last_name":"Edelsbrunner","full_name":"Edelsbrunner, Herbert"},{"full_name":"Saghafian, Morteza","last_name":"Saghafian","id":"f86f7148-b140-11ec-9577-95435b8df824","first_name":"Morteza"}],"month":"07","article_processing_charge":"No","citation":{"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.","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.","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.","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.","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.","short":"R. Biswas, S. Cultrera di Montesano, H. Edelsbrunner, M. Saghafian, Leibniz International Proceedings on Mathematics (n.d.)."},"department":[{"_id":"GradSch"},{"_id":"HeEd"}],"project":[{"_id":"266A2E9E-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Alpha Shape Theory Extended","grant_number":"788183"},{"grant_number":"Z00342","name":"The Wittgenstein Prize","_id":"268116B8-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"grant_number":"I02979-N35","name":"Persistence and stability of geometric complexes","call_identifier":"FWF","_id":"2561EBF4-B435-11E9-9278-68D0E5697425"}],"file_date_updated":"2022-07-27T09:25:53Z","_id":"11658","date_updated":"2022-07-28T07:57:48Z","date_created":"2022-07-27T09:27:34Z","publication_status":"submitted","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.","day":"27","title":"Depth in arrangements: Dehn–Sommerville–Euler relations with applications","year":"2022"}]