[{"publisher":"Elsevier","issue":"10","_id":"12239","publication_status":"published","external_id":{"pmid":["36081349"],"isi":["000882769800009"]},"file":[{"file_name":"2022_MolecularPlant_Johnson.pdf","relation":"main_file","creator":"dernst","file_id":"12435","date_updated":"2023-01-30T07:46:51Z","content_type":"application/pdf","access_level":"open_access","date_created":"2023-01-30T07:46:51Z","checksum":"04d5c12490052d03e4dc4412338a43dd","file_size":2307251,"success":1}],"type":"journal_article","oa_version":"Published Version","ddc":["580"],"month":"10","year":"2022","project":[{"grant_number":"I03630","call_identifier":"FWF","name":"Molecular mechanisms of endocytic cargo recognition in plants","_id":"26538374-B435-11E9-9278-68D0E5697425"}],"isi":1,"publication_identifier":{"issn":["1674-2052"]},"article_type":"original","department":[{"_id":"JiFr"},{"_id":"EM-Fac"},{"_id":"Bio"}],"language":[{"iso":"eng"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","date_updated":"2023-08-04T09:39:24Z","scopus_import":"1","abstract":[{"lang":"eng","text":"Biological systems are the sum of their dynamic three-dimensional (3D) parts. Therefore, it is critical to study biological structures in 3D and at high resolution to gain insights into their physiological functions. Electron microscopy of metal replicas of unroofed cells and isolated organelles has been a key technique to visualize intracellular structures at nanometer resolution. However, many of these methods require specialized equipment and personnel to complete them. Here, we present novel accessible methods to analyze biological structures in unroofed cells and biochemically isolated organelles in 3D and at nanometer resolution, focusing on Arabidopsis clathrin-coated vesicles (CCVs). While CCVs are essential trafficking organelles, their detailed structural information is lacking due to their poor preservation when observed via classical electron microscopy protocols experiments. First, we establish a method to visualize CCVs in unroofed cells using scanning transmission electron microscopy tomography, providing sufficient resolution to define the clathrin coat arrangements. Critically, the samples are prepared directly on electron microscopy grids, removing the requirement to use extremely corrosive acids, thereby enabling the use of this method in any electron microscopy lab. Secondly, we demonstrate that this standardized sample preparation allows the direct comparison of isolated CCV samples with those visualized in cells. Finally, to facilitate the high-throughput and robust screening of metal replicated samples, we provide a deep learning analysis method to screen the “pseudo 3D” morphologies of CCVs imaged with 2D modalities. Collectively, our work establishes accessible ways to examine the 3D structure of biological samples and provide novel insights into the structure of plant CCVs."}],"keyword":["Plant Science","Molecular Biology"],"author":[{"orcid":"0000-0002-2739-8843","full_name":"Johnson, Alexander J","last_name":"Johnson","first_name":"Alexander J","id":"46A62C3A-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Walter","id":"3F99E422-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9735-5315","last_name":"Kaufmann","full_name":"Kaufmann, Walter"},{"first_name":"Christoph M","id":"4DF26D8C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1216-9105","full_name":"Sommer, Christoph M","last_name":"Sommer"},{"id":"D93824F4-D9BA-11E9-BB12-F207E6697425","first_name":"Tommaso","orcid":"0000-0001-9732-3815","full_name":"Costanzo, Tommaso","last_name":"Costanzo"},{"full_name":"Dahhan, Dana A.","last_name":"Dahhan","first_name":"Dana A."},{"last_name":"Bednarek","full_name":"Bednarek, Sebastian Y.","first_name":"Sebastian Y."},{"first_name":"Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","full_name":"Friml, Jiří","orcid":"0000-0002-8302-7596"}],"status":"public","oa":1,"quality_controlled":"1","date_created":"2023-01-16T09:51:49Z","acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"LifeSc"},{"_id":"Bio"}],"citation":{"ista":"Johnson AJ, Kaufmann W, Sommer CM, Costanzo T, Dahhan DA, Bednarek SY, Friml J. 2022. Three-dimensional visualization of planta clathrin-coated vesicles at ultrastructural resolution. Molecular Plant. 15(10), 1533–1542.","short":"A.J. Johnson, W. Kaufmann, C.M. Sommer, T. Costanzo, D.A. Dahhan, S.Y. Bednarek, J. Friml, Molecular Plant 15 (2022) 1533–1542.","ieee":"A. J. Johnson <i>et al.</i>, “Three-dimensional visualization of planta clathrin-coated vesicles at ultrastructural resolution,” <i>Molecular Plant</i>, vol. 15, no. 10. Elsevier, pp. 1533–1542, 2022.","ama":"Johnson AJ, Kaufmann W, Sommer CM, et al. Three-dimensional visualization of planta clathrin-coated vesicles at ultrastructural resolution. <i>Molecular Plant</i>. 2022;15(10):1533-1542. doi:<a href=\"https://doi.org/10.1016/j.molp.2022.09.003\">10.1016/j.molp.2022.09.003</a>","chicago":"Johnson, Alexander J, Walter Kaufmann, Christoph M Sommer, Tommaso Costanzo, Dana A. Dahhan, Sebastian Y. Bednarek, and Jiří Friml. “Three-Dimensional Visualization of Planta Clathrin-Coated Vesicles at Ultrastructural Resolution.” <i>Molecular Plant</i>. Elsevier, 2022. <a href=\"https://doi.org/10.1016/j.molp.2022.09.003\">https://doi.org/10.1016/j.molp.2022.09.003</a>.","apa":"Johnson, A. J., Kaufmann, W., Sommer, C. M., Costanzo, T., Dahhan, D. A., Bednarek, S. Y., &#38; Friml, J. (2022). Three-dimensional visualization of planta clathrin-coated vesicles at ultrastructural resolution. <i>Molecular Plant</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.molp.2022.09.003\">https://doi.org/10.1016/j.molp.2022.09.003</a>","mla":"Johnson, Alexander J., et al. “Three-Dimensional Visualization of Planta Clathrin-Coated Vesicles at Ultrastructural Resolution.” <i>Molecular Plant</i>, vol. 15, no. 10, Elsevier, 2022, pp. 1533–42, doi:<a href=\"https://doi.org/10.1016/j.molp.2022.09.003\">10.1016/j.molp.2022.09.003</a>."},"page":"1533-1542","title":"Three-dimensional visualization of planta clathrin-coated vesicles at ultrastructural resolution","pmid":1,"volume":15,"day":"03","acknowledgement":"A.J. is supported by funding from the Austrian Science Fund I3630B25 (to J.F.). This research was supported by the Scientific Service Units of Institute of Science and Technology Austria (ISTA) through resources provided by the Electron Microscopy Facility, Lab Support Facility, and the Imaging and Optics Facility. We acknowledge Prof. David Robinson (Heidelberg) and Prof. Jan Traas (Lyon) for making us aware of previously published classical on-grid preparation methods. No conflict of interest declared.","publication":"Molecular Plant","date_published":"2022-10-03T00:00:00Z","has_accepted_license":"1","intvolume":"        15","file_date_updated":"2023-01-30T07:46:51Z","doi":"10.1016/j.molp.2022.09.003","article_processing_charge":"Yes (via OA deal)","tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"}},{"publication_identifier":{"eissn":["1089-7658"],"issn":["0022-2488"]},"isi":1,"project":[{"grant_number":"101020331","name":"Random matrices beyond Wigner-Dyson-Mehta","call_identifier":"H2020","_id":"62796744-2b32-11ec-9570-940b20777f1d"}],"year":"2022","month":"10","department":[{"_id":"LaEr"}],"article_type":"original","publisher":"AIP Publishing","file":[{"date_updated":"2023-01-30T08:01:10Z","content_type":"application/pdf","access_level":"open_access","date_created":"2023-01-30T08:01:10Z","file_size":7356807,"checksum":"2db278ae5b07f345a7e3fec1f92b5c33","success":1,"file_name":"2022_JourMathPhysics_Cipolloni2.pdf","relation":"main_file","creator":"dernst","file_id":"12436"}],"type":"journal_article","ddc":["510","530"],"oa_version":"Published Version","publication_status":"published","external_id":{"arxiv":["2206.04443"],"isi":["000869715800001"]},"_id":"12243","issue":"10","status":"public","author":[{"orcid":"0000-0002-4901-7992","last_name":"Cipolloni","full_name":"Cipolloni, Giorgio","first_name":"Giorgio","id":"42198EFA-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Erdös","full_name":"Erdös, László","orcid":"0000-0001-5366-9603","first_name":"László","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Schröder","full_name":"Schröder, Dominik J","orcid":"0000-0002-2904-1856","id":"408ED176-F248-11E8-B48F-1D18A9856A87","first_name":"Dominik J"},{"full_name":"Xu, Yuanyuan","last_name":"Xu","first_name":"Yuanyuan","id":"7902bdb1-a2a4-11eb-a164-c9216f71aea3"}],"date_updated":"2023-08-04T09:40:02Z","language":[{"iso":"eng"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","keyword":["Mathematical Physics","Statistical and Nonlinear Physics"],"abstract":[{"lang":"eng","text":"We consider the eigenvalues of a large dimensional real or complex Ginibre matrix in the region of the complex plane where their real parts reach their maximum value. This maximum follows the Gumbel distribution and that these extreme eigenvalues form a Poisson point process as the dimension asymptotically tends to infinity. In the complex case, these facts have already been established by Bender [Probab. Theory Relat. Fields 147, 241 (2010)] and in the real case by Akemann and Phillips [J. Stat. Phys. 155, 421 (2014)] even for the more general elliptic ensemble with a sophisticated saddle point analysis. The purpose of this article is to give a very short direct proof in the Ginibre case with an effective error term. Moreover, our estimates on the correlation kernel in this regime serve as a key input for accurately locating [Formula: see text] for any large matrix X with i.i.d. entries in the companion paper [G. Cipolloni et al., arXiv:2206.04448 (2022)]. "}],"scopus_import":"1","title":"Directional extremal statistics for Ginibre eigenvalues","oa":1,"article_number":"103303","citation":{"ieee":"G. Cipolloni, L. Erdös, D. J. Schröder, and Y. Xu, “Directional extremal statistics for Ginibre eigenvalues,” <i>Journal of Mathematical Physics</i>, vol. 63, no. 10. AIP Publishing, 2022.","short":"G. Cipolloni, L. Erdös, D.J. Schröder, Y. Xu, Journal of Mathematical Physics 63 (2022).","ista":"Cipolloni G, Erdös L, Schröder DJ, Xu Y. 2022. Directional extremal statistics for Ginibre eigenvalues. Journal of Mathematical Physics. 63(10), 103303.","ama":"Cipolloni G, Erdös L, Schröder DJ, Xu Y. Directional extremal statistics for Ginibre eigenvalues. <i>Journal of Mathematical Physics</i>. 2022;63(10). doi:<a href=\"https://doi.org/10.1063/5.0104290\">10.1063/5.0104290</a>","chicago":"Cipolloni, Giorgio, László Erdös, Dominik J Schröder, and Yuanyuan Xu. “Directional Extremal Statistics for Ginibre Eigenvalues.” <i>Journal of Mathematical Physics</i>. AIP Publishing, 2022. <a href=\"https://doi.org/10.1063/5.0104290\">https://doi.org/10.1063/5.0104290</a>.","apa":"Cipolloni, G., Erdös, L., Schröder, D. J., &#38; Xu, Y. (2022). Directional extremal statistics for Ginibre eigenvalues. <i>Journal of Mathematical Physics</i>. AIP Publishing. <a href=\"https://doi.org/10.1063/5.0104290\">https://doi.org/10.1063/5.0104290</a>","mla":"Cipolloni, Giorgio, et al. “Directional Extremal Statistics for Ginibre Eigenvalues.” <i>Journal of Mathematical Physics</i>, vol. 63, no. 10, 103303, AIP Publishing, 2022, doi:<a href=\"https://doi.org/10.1063/5.0104290\">10.1063/5.0104290</a>."},"date_created":"2023-01-16T09:52:58Z","quality_controlled":"1","arxiv":1,"doi":"10.1063/5.0104290","file_date_updated":"2023-01-30T08:01:10Z","tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"article_processing_charge":"Yes (via OA deal)","ec_funded":1,"acknowledgement":"The authors are grateful to G. Akemann for bringing Refs. 19 and 24–26 to their attention. Discussions with Guillaume Dubach on a preliminary version of this project are acknowledged.\r\nL.E. and Y.X. were supported by the ERC Advanced Grant “RMTBeyond” under Grant No. 101020331. D.S. was supported by Dr. Max Rössler, the Walter Haefner Foundation, and the ETH Zürich Foundation.","day":"14","publication":"Journal of Mathematical Physics","volume":63,"has_accepted_license":"1","intvolume":"        63","date_published":"2022-10-14T00:00:00Z"},{"date_created":"2023-01-16T09:53:07Z","citation":{"ista":"Colombo G, Cubero RJ, Kanari L, Venturino A, Schulz R, Scolamiero M, Agerberg J, Mathys H, Tsai L-H, Chachólski W, Hess K, Siegert S. 2022. A tool for mapping microglial morphology, morphOMICs, reveals brain-region and sex-dependent phenotypes. Nature Neuroscience. 25(10), 1379–1393.","short":"G. Colombo, R.J. Cubero, L. Kanari, A. Venturino, R. Schulz, M. Scolamiero, J. Agerberg, H. Mathys, L.-H. Tsai, W. Chachólski, K. Hess, S. Siegert, Nature Neuroscience 25 (2022) 1379–1393.","ieee":"G. Colombo <i>et al.</i>, “A tool for mapping microglial morphology, morphOMICs, reveals brain-region and sex-dependent phenotypes,” <i>Nature Neuroscience</i>, vol. 25, no. 10. Springer Nature, pp. 1379–1393, 2022.","ama":"Colombo G, Cubero RJ, Kanari L, et al. A tool for mapping microglial morphology, morphOMICs, reveals brain-region and sex-dependent phenotypes. <i>Nature Neuroscience</i>. 2022;25(10):1379-1393. doi:<a href=\"https://doi.org/10.1038/s41593-022-01167-6\">10.1038/s41593-022-01167-6</a>","mla":"Colombo, Gloria, et al. “A Tool for Mapping Microglial Morphology, MorphOMICs, Reveals Brain-Region and Sex-Dependent Phenotypes.” <i>Nature Neuroscience</i>, vol. 25, no. 10, Springer Nature, 2022, pp. 1379–93, doi:<a href=\"https://doi.org/10.1038/s41593-022-01167-6\">10.1038/s41593-022-01167-6</a>.","chicago":"Colombo, Gloria, Ryan J Cubero, Lida Kanari, Alessandro Venturino, Rouven Schulz, Martina Scolamiero, Jens Agerberg, et al. “A Tool for Mapping Microglial Morphology, MorphOMICs, Reveals Brain-Region and Sex-Dependent Phenotypes.” <i>Nature Neuroscience</i>. Springer Nature, 2022. <a href=\"https://doi.org/10.1038/s41593-022-01167-6\">https://doi.org/10.1038/s41593-022-01167-6</a>.","apa":"Colombo, G., Cubero, R. J., Kanari, L., Venturino, A., Schulz, R., Scolamiero, M., … Siegert, S. (2022). A tool for mapping microglial morphology, morphOMICs, reveals brain-region and sex-dependent phenotypes. <i>Nature Neuroscience</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41593-022-01167-6\">https://doi.org/10.1038/s41593-022-01167-6</a>"},"acknowledged_ssus":[{"_id":"PreCl"},{"_id":"Bio"},{"_id":"ScienComp"}],"quality_controlled":"1","oa":1,"title":"A tool for mapping microglial morphology, morphOMICs, reveals brain-region and sex-dependent phenotypes","page":"1379-1393","has_accepted_license":"1","intvolume":"        25","date_published":"2022-10-01T00:00:00Z","volume":25,"publication":"Nature Neuroscience","day":"01","acknowledgement":"We thank the scientific service units at ISTA, in particular M. Schunn’s team at the preclinical facility, and especially our colony manager S. Haslinger, for excellent support. We are also grateful to the ISTA Imaging & Optics Facility, and in particular C. Sommer for helping with the data file conversions. We thank R. Erhart from the ISTA Scientific Computing Unit for improving the script performance. We thank M. Maes, B. Nagy, S. Oakeley and M. Benevento and all members of the Siegert group for constant feedback on the project and on the manuscript. This research was supported by the European Union Horizon 2020 research and innovation program under the Marie Skłodowska-Curie Actions program (754411 to R.J.A.C.), and by the European Research Council (grant no. 715571 to S.S.). L.K. was supported by funding to the Blue Brain Project, a research center of the École polytechnique fédérale de Lausanne, from the Swiss government’s ETH Board of the Swiss Federal Institutes of Technology. L.-H.T. was supported by NIH (grant no. R37NS051874) and by the JPB Foundation. The funders had no role in study design, data collection and analysis, decision to publish or preparation of the manuscript.","pmid":1,"article_processing_charge":"No","ec_funded":1,"tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"doi":"10.1038/s41593-022-01167-6","file_date_updated":"2023-01-30T08:06:56Z","ddc":["570"],"oa_version":"Published Version","type":"journal_article","file":[{"file_name":"2022_NatureNeuroscience_Colombo.pdf","relation":"main_file","file_id":"12437","creator":"dernst","date_updated":"2023-01-30T08:06:56Z","access_level":"open_access","content_type":"application/pdf","date_created":"2023-01-30T08:06:56Z","checksum":"28431146873096f52e0107b534f178c9","file_size":23789835,"success":1}],"_id":"12244","issue":"10","external_id":{"pmid":["36180790"],"isi":["000862214700001"]},"publication_status":"published","publisher":"Springer Nature","department":[{"_id":"SaSi"}],"article_type":"original","isi":1,"publication_identifier":{"issn":["1097-6256"],"eissn":["1546-1726"]},"month":"10","year":"2022","project":[{"_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411"},{"grant_number":"715571","_id":"25D4A630-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Microglia action towards neuronal circuit formation and function in health and disease"}],"abstract":[{"lang":"eng","text":"Environmental cues influence the highly dynamic morphology of microglia. Strategies to characterize these changes usually involve user-selected morphometric features, which preclude the identification of a spectrum of context-dependent morphological phenotypes. Here we develop MorphOMICs, a topological data analysis approach, which enables semiautomatic mapping of microglial morphology into an atlas of cue-dependent phenotypes and overcomes feature-selection biases and biological variability. We extract spatially heterogeneous and sexually dimorphic morphological phenotypes for seven adult mouse brain regions. This sex-specific phenotype declines with maturation but increases over the disease trajectories in two neurodegeneration mouse models, with females showing a faster morphological shift in affected brain regions. Remarkably, microglia morphologies reflect an adaptation upon repeated exposure to ketamine anesthesia and do not recover to control morphologies. Finally, we demonstrate that both long primary processes and short terminal processes provide distinct insights to morphological phenotypes. MorphOMICs opens a new perspective to characterize microglial morphology."}],"keyword":["General Neuroscience"],"related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"12378"}],"link":[{"url":"https://ista.ac.at/en/news/morphomics-revealing-the-hidden-meaning-of-microglia-shape/","relation":"press_release","description":"News on ISTA website"}]},"scopus_import":"1","date_updated":"2024-03-25T23:30:10Z","language":[{"iso":"eng"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","author":[{"orcid":"0000-0001-9434-8902","full_name":"Colombo, Gloria","last_name":"Colombo","id":"3483CF6C-F248-11E8-B48F-1D18A9856A87","first_name":"Gloria"},{"last_name":"Cubero","full_name":"Cubero, Ryan J","orcid":"0000-0003-0002-1867","id":"850B2E12-9CD4-11E9-837F-E719E6697425","first_name":"Ryan J"},{"full_name":"Kanari, Lida","last_name":"Kanari","first_name":"Lida"},{"id":"41CB84B2-F248-11E8-B48F-1D18A9856A87","first_name":"Alessandro","orcid":"0000-0003-2356-9403","full_name":"Venturino, Alessandro","last_name":"Venturino"},{"id":"4C5E7B96-F248-11E8-B48F-1D18A9856A87","first_name":"Rouven","last_name":"Schulz","full_name":"Schulz, Rouven","orcid":"0000-0001-5297-733X"},{"full_name":"Scolamiero, Martina","last_name":"Scolamiero","first_name":"Martina"},{"last_name":"Agerberg","full_name":"Agerberg, Jens","first_name":"Jens"},{"first_name":"Hansruedi","full_name":"Mathys, Hansruedi","last_name":"Mathys"},{"first_name":"Li-Huei","full_name":"Tsai, Li-Huei","last_name":"Tsai"},{"first_name":"Wojciech","full_name":"Chachólski, Wojciech","last_name":"Chachólski"},{"last_name":"Hess","full_name":"Hess, Kathryn","first_name":"Kathryn"},{"orcid":"0000-0001-8635-0877","last_name":"Siegert","full_name":"Siegert, Sandra","first_name":"Sandra","id":"36ACD32E-F248-11E8-B48F-1D18A9856A87"}],"status":"public"},{"status":"public","author":[{"last_name":"Soto","full_name":"Soto, Ximena","first_name":"Ximena"},{"first_name":"Joshua","last_name":"Burton","full_name":"Burton, Joshua"},{"last_name":"Manning","full_name":"Manning, Cerys S.","first_name":"Cerys S."},{"last_name":"Minchington","full_name":"Minchington, Thomas","first_name":"Thomas","id":"7d1648cb-19e9-11eb-8e7a-f8c037fb3e3f"},{"last_name":"Lea","full_name":"Lea, Robert","first_name":"Robert"},{"first_name":"Jessica","full_name":"Lee, Jessica","last_name":"Lee"},{"first_name":"Jochen","full_name":"Kursawe, Jochen","last_name":"Kursawe"},{"full_name":"Rattray, Magnus","last_name":"Rattray","first_name":"Magnus"},{"first_name":"Nancy","last_name":"Papalopulu","full_name":"Papalopulu, Nancy"}],"date_updated":"2023-08-04T09:41:08Z","language":[{"iso":"eng"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","related_material":{"link":[{"url":" https://github.com/burtonjosh/StepwiseMir9","relation":"software"}]},"keyword":["Developmental Biology","Molecular Biology"],"abstract":[{"text":"MicroRNAs (miRs) have an important role in tuning dynamic gene expression. However, the mechanism by which they are quantitatively controlled is unknown. We show that the amount of mature miR-9, a key regulator of neuronal development, increases during zebrafish neurogenesis in a sharp stepwise manner. We characterize the spatiotemporal profile of seven distinct microRNA primary transcripts (pri-mir)-9s that produce the same mature miR-9 and show that they are sequentially expressed during hindbrain neurogenesis. Expression of late-onset pri-mir-9-1 is added on to, rather than replacing, the expression of early onset pri-mir-9-4 and -9-5 in single cells. CRISPR/Cas9 mutation of the late-onset pri-mir-9-1 prevents the developmental increase of mature miR-9, reduces late neuronal differentiation and fails to downregulate Her6 at late stages. Mathematical modelling shows that an adaptive network containing Her6 is insensitive to linear increases in miR-9 but responds to stepwise increases of miR-9. We suggest that a sharp stepwise increase of mature miR-9 is created by sequential and additive temporal activation of distinct loci. This may be a strategy to overcome adaptation and facilitate a transition of Her6 to a new dynamic regime or steady state.","lang":"eng"}],"scopus_import":"1","publication_identifier":{"issn":["0950-1991"],"eissn":["1477-9129"]},"isi":1,"year":"2022","month":"10","department":[{"_id":"AnKi"}],"article_type":"original","publisher":"The Company of Biologists","oa_version":"Published Version","type":"journal_article","file":[{"date_updated":"2023-01-30T08:35:44Z","access_level":"open_access","content_type":"application/pdf","date_created":"2023-01-30T08:35:44Z","file_size":9348839,"checksum":"d7c29b74e9e4032308228cc704a30e88","success":1,"file_name":"2022_Development_Soto.pdf","relation":"main_file","file_id":"12438","creator":"dernst"}],"ddc":["570"],"external_id":{"isi":["000918161000003"],"pmid":["36189829"]},"publication_status":"published","_id":"12245","issue":"19","doi":"10.1242/dev.200474","file_date_updated":"2023-01-30T08:35:44Z","tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"article_processing_charge":"No","acknowledgement":"We are grateful to Dr Tom Pettini for the advice on smiFISH technique and Dr Laure Bally-Cuif for sharing plasmids. The authors also thank the Biological Services Facility, Bioimaging and Systems Microscopy Facilities of the University of Manchester for technical support.\r\nThis work was supported by a Wellcome Trust Senior Research Fellowship (090868/Z/09/Z) and a Wellcome Trust Investigator Award (224394/Z/21/Z) to N.P. and a Medical Research Council Career Development Award to C.S.M. (MR/V032534/1). J.B. was supported by a Wellcome Trust Four-Year PhD Studentship in Basic Science (219992/Z/19/Z). Open Access funding provided by The University of Manchester. Deposited in PMC for immediate release.","day":"01","publication":"Development","volume":149,"pmid":1,"has_accepted_license":"1","intvolume":"       149","date_published":"2022-10-01T00:00:00Z","title":"Sequential and additive expression of miR-9 precursors control timing of neurogenesis","oa":1,"article_number":"dev200474","citation":{"short":"X. Soto, J. Burton, C.S. Manning, T. Minchington, R. Lea, J. Lee, J. Kursawe, M. Rattray, N. Papalopulu, Development 149 (2022).","ieee":"X. Soto <i>et al.</i>, “Sequential and additive expression of miR-9 precursors control timing of neurogenesis,” <i>Development</i>, vol. 149, no. 19. The Company of Biologists, 2022.","ista":"Soto X, Burton J, Manning CS, Minchington T, Lea R, Lee J, Kursawe J, Rattray M, Papalopulu N. 2022. Sequential and additive expression of miR-9 precursors control timing of neurogenesis. Development. 149(19), dev200474.","ama":"Soto X, Burton J, Manning CS, et al. Sequential and additive expression of miR-9 precursors control timing of neurogenesis. <i>Development</i>. 2022;149(19). doi:<a href=\"https://doi.org/10.1242/dev.200474\">10.1242/dev.200474</a>","mla":"Soto, Ximena, et al. “Sequential and Additive Expression of MiR-9 Precursors Control Timing of Neurogenesis.” <i>Development</i>, vol. 149, no. 19, dev200474, The Company of Biologists, 2022, doi:<a href=\"https://doi.org/10.1242/dev.200474\">10.1242/dev.200474</a>.","chicago":"Soto, Ximena, Joshua Burton, Cerys S. Manning, Thomas Minchington, Robert Lea, Jessica Lee, Jochen Kursawe, Magnus Rattray, and Nancy Papalopulu. “Sequential and Additive Expression of MiR-9 Precursors Control Timing of Neurogenesis.” <i>Development</i>. The Company of Biologists, 2022. <a href=\"https://doi.org/10.1242/dev.200474\">https://doi.org/10.1242/dev.200474</a>.","apa":"Soto, X., Burton, J., Manning, C. S., Minchington, T., Lea, R., Lee, J., … Papalopulu, N. (2022). Sequential and additive expression of miR-9 precursors control timing of neurogenesis. <i>Development</i>. The Company of Biologists. <a href=\"https://doi.org/10.1242/dev.200474\">https://doi.org/10.1242/dev.200474</a>"},"date_created":"2023-01-16T09:53:17Z","quality_controlled":"1"},{"title":"Improved Lieb–Oxford bound on the indirect and exchange energies","arxiv":1,"quality_controlled":"1","citation":{"ama":"Lewin M, Lieb EH, Seiringer R. Improved Lieb–Oxford bound on the indirect and exchange energies. <i>Letters in Mathematical Physics</i>. 2022;112(5). doi:<a href=\"https://doi.org/10.1007/s11005-022-01584-5\">10.1007/s11005-022-01584-5</a>","ieee":"M. Lewin, E. H. Lieb, and R. Seiringer, “Improved Lieb–Oxford bound on the indirect and exchange energies,” <i>Letters in Mathematical Physics</i>, vol. 112, no. 5. Springer Nature, 2022.","ista":"Lewin M, Lieb EH, Seiringer R. 2022. Improved Lieb–Oxford bound on the indirect and exchange energies. Letters in Mathematical Physics. 112(5), 92.","short":"M. Lewin, E.H. Lieb, R. Seiringer, Letters in Mathematical Physics 112 (2022).","apa":"Lewin, M., Lieb, E. H., &#38; Seiringer, R. (2022). Improved Lieb–Oxford bound on the indirect and exchange energies. <i>Letters in Mathematical Physics</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s11005-022-01584-5\">https://doi.org/10.1007/s11005-022-01584-5</a>","chicago":"Lewin, Mathieu, Elliott H. Lieb, and Robert Seiringer. “Improved Lieb–Oxford Bound on the Indirect and Exchange Energies.” <i>Letters in Mathematical Physics</i>. Springer Nature, 2022. <a href=\"https://doi.org/10.1007/s11005-022-01584-5\">https://doi.org/10.1007/s11005-022-01584-5</a>.","mla":"Lewin, Mathieu, et al. “Improved Lieb–Oxford Bound on the Indirect and Exchange Energies.” <i>Letters in Mathematical Physics</i>, vol. 112, no. 5, 92, Springer Nature, 2022, doi:<a href=\"https://doi.org/10.1007/s11005-022-01584-5\">10.1007/s11005-022-01584-5</a>."},"date_created":"2023-01-16T09:53:54Z","article_number":"92","oa":1,"article_processing_charge":"No","ec_funded":1,"doi":"10.1007/s11005-022-01584-5","date_published":"2022-09-15T00:00:00Z","intvolume":"       112","volume":112,"publication":"Letters in Mathematical Physics","day":"15","acknowledgement":"We would like to thank David Gontier for useful advice on the numerical simulations. This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (Grant Agreements MDFT No. 725528 of M.L. and AQUAMS No. 694227 of R.S.). We are thankful for the hospitality of the Institut Henri Poincaré in Paris, where part of this work was done.","article_type":"original","department":[{"_id":"RoSe"}],"year":"2022","month":"09","project":[{"grant_number":"694227","_id":"25C6DC12-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Analysis of quantum many-body systems"}],"isi":1,"publication_identifier":{"eissn":["1573-0530"],"issn":["0377-9017"]},"_id":"12246","issue":"5","publication_status":"published","external_id":{"isi":["000854762600001"],"arxiv":["2203.12473"]},"oa_version":"Preprint","type":"journal_article","publisher":"Springer Nature","author":[{"last_name":"Lewin","full_name":"Lewin, Mathieu","first_name":"Mathieu"},{"full_name":"Lieb, Elliott H.","last_name":"Lieb","first_name":"Elliott H."},{"first_name":"Robert","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","full_name":"Seiringer, Robert","last_name":"Seiringer","orcid":"0000-0002-6781-0521"}],"status":"public","scopus_import":"1","abstract":[{"text":"The Lieb–Oxford inequality provides a lower bound on the Coulomb energy of a classical system of N identical charges only in terms of their one-particle density. We prove here a new estimate on the best constant in this inequality. Numerical evaluation provides the value 1.58, which is a significant improvement to the previously known value 1.64. The best constant has recently been shown to be larger than 1.44. In a second part, we prove that the constant can be reduced to 1.25 when the inequality is restricted to Hartree–Fock states. This is the first proof that the exchange term is always much lower than the full indirect Coulomb energy.","lang":"eng"}],"keyword":["Mathematical Physics","Statistical and Nonlinear Physics"],"main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2203.12473","open_access":"1"}],"language":[{"iso":"eng"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","date_updated":"2023-09-05T15:17:34Z"},{"publisher":"Wiley","external_id":{"isi":["000848449100001"],"pmid":["35994296"]},"publication_status":"published","issue":"10","_id":"12247","file":[{"file_id":"12439","creator":"dernst","relation":"main_file","file_name":"2022_Evolution_Koch.pdf","checksum":"defd8a4bea61cf00a3c88d4a30e2728c","file_size":2990581,"success":1,"date_created":"2023-01-30T08:45:35Z","access_level":"open_access","content_type":"application/pdf","date_updated":"2023-01-30T08:45:35Z"}],"type":"journal_article","ddc":["570"],"oa_version":"Published Version","year":"2022","month":"10","publication_identifier":{"issn":["0014-3820"],"eissn":["1558-5646"]},"isi":1,"article_type":"original","department":[{"_id":"NiBa"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","language":[{"iso":"eng"}],"date_updated":"2023-08-04T09:42:11Z","scopus_import":"1","related_material":{"record":[{"id":"13066","status":"public","relation":"research_data"}]},"keyword":["General Agricultural and Biological Sciences","Genetics","Ecology","Evolution","Behavior and Systematics"],"abstract":[{"lang":"eng","text":"Chromosomal inversions have been shown to play a major role in a local adaptation by suppressing recombination between alternative arrangements and maintaining beneficial allele combinations. However, so far, their importance relative to the remaining genome remains largely unknown. Understanding the genetic architecture of adaptation requires better estimates of how loci of different effect sizes contribute to phenotypic variation. Here, we used three Swedish islands where the marine snail Littorina saxatilis has repeatedly evolved into two distinct ecotypes along a habitat transition. We estimated the contribution of inversion polymorphisms to phenotypic divergence while controlling for polygenic effects in the remaining genome using a quantitative genetics framework. We confirmed the importance of inversions but showed that contributions of loci outside inversions are of similar magnitude, with variable proportions dependent on the trait and the population. Some inversions showed consistent effects across all sites, whereas others exhibited site-specific effects, indicating that the genomic basis for replicated phenotypic divergence is only partly shared. The contributions of sexual dimorphism as well as environmental factors to phenotypic variation were significant but minor compared to inversions and polygenic background. Overall, this integrated approach provides insight into the multiple mechanisms contributing to parallel phenotypic divergence."}],"status":"public","author":[{"first_name":"Eva L.","full_name":"Koch, Eva L.","last_name":"Koch"},{"first_name":"Mark","last_name":"Ravinet","full_name":"Ravinet, Mark"},{"last_name":"Westram","full_name":"Westram, Anja M","orcid":"0000-0003-1050-4969","id":"3C147470-F248-11E8-B48F-1D18A9856A87","first_name":"Anja M"},{"first_name":"Kerstin","full_name":"Johannesson, Kerstin","last_name":"Johannesson"},{"first_name":"Roger K.","last_name":"Butlin","full_name":"Butlin, Roger K."}],"oa":1,"quality_controlled":"1","date_created":"2023-01-16T09:54:15Z","citation":{"mla":"Koch, Eva L., et al. “Genetic Architecture of Repeated Phenotypic Divergence in Littorina Saxatilis Evolution.” <i>Evolution</i>, vol. 76, no. 10, Wiley, 2022, pp. 2332–46, doi:<a href=\"https://doi.org/10.1111/evo.14602\">10.1111/evo.14602</a>.","chicago":"Koch, Eva L., Mark Ravinet, Anja M Westram, Kerstin Johannesson, and Roger K. Butlin. “Genetic Architecture of Repeated Phenotypic Divergence in Littorina Saxatilis Evolution.” <i>Evolution</i>. Wiley, 2022. <a href=\"https://doi.org/10.1111/evo.14602\">https://doi.org/10.1111/evo.14602</a>.","apa":"Koch, E. L., Ravinet, M., Westram, A. M., Johannesson, K., &#38; Butlin, R. K. (2022). Genetic architecture of repeated phenotypic divergence in Littorina saxatilis evolution. <i>Evolution</i>. Wiley. <a href=\"https://doi.org/10.1111/evo.14602\">https://doi.org/10.1111/evo.14602</a>","short":"E.L. Koch, M. Ravinet, A.M. Westram, K. Johannesson, R.K. Butlin, Evolution 76 (2022) 2332–2346.","ieee":"E. L. Koch, M. Ravinet, A. M. Westram, K. Johannesson, and R. K. Butlin, “Genetic architecture of repeated phenotypic divergence in Littorina saxatilis evolution,” <i>Evolution</i>, vol. 76, no. 10. Wiley, pp. 2332–2346, 2022.","ista":"Koch EL, Ravinet M, Westram AM, Johannesson K, Butlin RK. 2022. Genetic architecture of repeated phenotypic divergence in Littorina saxatilis evolution. Evolution. 76(10), 2332–2346.","ama":"Koch EL, Ravinet M, Westram AM, Johannesson K, Butlin RK. Genetic architecture of repeated phenotypic divergence in Littorina saxatilis evolution. <i>Evolution</i>. 2022;76(10):2332-2346. doi:<a href=\"https://doi.org/10.1111/evo.14602\">10.1111/evo.14602</a>"},"page":"2332-2346","title":"Genetic architecture of repeated phenotypic divergence in Littorina saxatilis evolution","pmid":1,"day":"01","acknowledgement":"We thank everyone who helped with fieldwork, snail processing, and DNA extractions, particularly Laura Brettell, Mårten Duvetorp, Juan Galindo, Anne-Lise Liabot, Irena Senčić, and Zuzanna Zagrodzka. We also thank Rui Faria and Jenny Larsson for their contributions, with inversions and shell shape respectively. KJ was funded by the Swedish research council Vetenskapsrådet, grant number 2017-03798. R.K.B. and E.K. were funded by the European Research Council (ERC-2015-AdG-693030-BARRIERS). R.K.B. was also funded by the Natural Environment Research Council and the Swedish Research Council Vetenskapsrådet.","publication":"Evolution","volume":76,"date_published":"2022-10-01T00:00:00Z","intvolume":"        76","has_accepted_license":"1","file_date_updated":"2023-01-30T08:45:35Z","doi":"10.1111/evo.14602","tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"article_processing_charge":"No"},{"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","language":[{"iso":"eng"}],"date_updated":"2024-03-25T23:30:26Z","scopus_import":"1","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 Artemia 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 Artemia sp. Kazakhstan and several asexual lineages of Artemia 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."}],"keyword":["Genetics"],"related_material":{"record":[{"relation":"research_data","status":"public","id":"11653"}]},"author":[{"orcid":"0000-0002-5328-7231","full_name":"Elkrewi, Marwan N","last_name":"Elkrewi","first_name":"Marwan N","id":"0B46FACA-A8E1-11E9-9BD3-79D1E5697425"},{"full_name":"Khauratovich, Uladzislava","last_name":"Khauratovich","first_name":"Uladzislava","id":"5eba06f4-97d8-11ed-9f8f-d826ebdd9434"},{"orcid":"0000-0002-9752-7380","last_name":"Toups","full_name":"Toups, Melissa A","first_name":"Melissa A","id":"4E099E4E-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Bett","full_name":"Bett, Vincent K","id":"57854184-AAE0-11E9-8D04-98D6E5697425","first_name":"Vincent K"},{"last_name":"Mrnjavac","full_name":"Mrnjavac, Andrea","id":"353FAC84-AE61-11E9-8BFC-00D3E5697425","first_name":"Andrea"},{"id":"2A0848E2-F248-11E8-B48F-1D18A9856A87","first_name":"Ariana","last_name":"Macon","full_name":"Macon, Ariana"},{"full_name":"Fraisse, Christelle","last_name":"Fraisse","orcid":"0000-0001-8441-5075","first_name":"Christelle","id":"32DF5794-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Luca","id":"701c5602-97d8-11ed-96b5-b52773c70189","full_name":"Sax, Luca","last_name":"Sax"},{"orcid":"0000-0001-8871-4961","last_name":"Huylmans","full_name":"Huylmans, Ann K","id":"4C0A3874-F248-11E8-B48F-1D18A9856A87","first_name":"Ann K"},{"first_name":"Francisco","last_name":"Hontoria","full_name":"Hontoria, Francisco"},{"id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","first_name":"Beatriz","full_name":"Vicoso, Beatriz","last_name":"Vicoso","orcid":"0000-0002-4579-8306"}],"status":"public","publisher":"Oxford University Press","_id":"12248","issue":"2","publication_status":"published","external_id":{"isi":["000850270300001"],"pmid":["35977389"]},"ddc":["570"],"file":[{"relation":"main_file","file_id":"12440","creator":"dernst","file_name":"2022_Genetics_Elkrewi.pdf","date_created":"2023-01-30T08:59:58Z","checksum":"f79ff5383e882ea3f95f3da47a78029d","file_size":1347136,"success":1,"date_updated":"2023-01-30T08:59:58Z","access_level":"open_access","content_type":"application/pdf"}],"oa_version":"Published Version","type":"journal_article","year":"2022","month":"10","project":[{"grant_number":"715257","name":"Prevalence and Influence of Sexual Antagonism on Genome Evolution","call_identifier":"H2020","_id":"250BDE62-B435-11E9-9278-68D0E5697425"},{"grant_number":"F8810","_id":"34ae1506-11ca-11ed-8bc3-c14f4c474396","name":"The highjacking of meiosis for asexual reproduction"}],"isi":1,"publication_identifier":{"issn":["1943-2631"]},"article_type":"original","department":[{"_id":"BeVi"}],"pmid":1,"volume":222,"publication":"Genetics","acknowledgement":"This work was supported by the European Research Council under the European Union’s Horizon 2020 research and innovation program (grant agreement no. 715257) and by the Austrian Science Foundation (FWF SFB F88-10).\r\nWe thank the Vicoso group for comments on the manuscript and the ISTA Scientific computing team and the Vienna Biocenter Sequencing facility for technical support.","day":"01","date_published":"2022-10-01T00:00:00Z","intvolume":"       222","has_accepted_license":"1","file_date_updated":"2023-01-30T08:59:58Z","doi":"10.1093/genetics/iyac123","article_processing_charge":"No","ec_funded":1,"tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"article_number":"iyac123","oa":1,"quality_controlled":"1","citation":{"ama":"Elkrewi MN, Khauratovich U, Toups MA, et al. ZW sex-chromosome evolution and contagious parthenogenesis in Artemia brine shrimp. <i>Genetics</i>. 2022;222(2). doi:<a href=\"https://doi.org/10.1093/genetics/iyac123\">10.1093/genetics/iyac123</a>","short":"M.N. Elkrewi, U. Khauratovich, M.A. Toups, V.K. Bett, A. Mrnjavac, A. Macon, C. Fraisse, L. Sax, A.K. Huylmans, F. Hontoria, B. Vicoso, Genetics 222 (2022).","ista":"Elkrewi MN, Khauratovich U, Toups MA, Bett VK, Mrnjavac A, Macon A, Fraisse C, Sax L, Huylmans AK, Hontoria F, Vicoso B. 2022. ZW sex-chromosome evolution and contagious parthenogenesis in Artemia brine shrimp. Genetics. 222(2), iyac123.","ieee":"M. N. Elkrewi <i>et al.</i>, “ZW sex-chromosome evolution and contagious parthenogenesis in Artemia brine shrimp,” <i>Genetics</i>, vol. 222, no. 2. Oxford University Press, 2022.","apa":"Elkrewi, M. N., Khauratovich, U., Toups, M. A., Bett, V. K., Mrnjavac, A., Macon, A., … Vicoso, B. (2022). ZW sex-chromosome evolution and contagious parthenogenesis in Artemia brine shrimp. <i>Genetics</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/genetics/iyac123\">https://doi.org/10.1093/genetics/iyac123</a>","chicago":"Elkrewi, Marwan N, Uladzislava Khauratovich, Melissa A Toups, Vincent K Bett, Andrea Mrnjavac, Ariana Macon, Christelle Fraisse, et al. “ZW Sex-Chromosome Evolution and Contagious Parthenogenesis in Artemia Brine Shrimp.” <i>Genetics</i>. Oxford University Press, 2022. <a href=\"https://doi.org/10.1093/genetics/iyac123\">https://doi.org/10.1093/genetics/iyac123</a>.","mla":"Elkrewi, Marwan N., et al. “ZW Sex-Chromosome Evolution and Contagious Parthenogenesis in Artemia Brine Shrimp.” <i>Genetics</i>, vol. 222, no. 2, iyac123, Oxford University Press, 2022, doi:<a href=\"https://doi.org/10.1093/genetics/iyac123\">10.1093/genetics/iyac123</a>."},"acknowledged_ssus":[{"_id":"ScienComp"}],"date_created":"2023-01-16T09:56:10Z","title":"ZW sex-chromosome evolution and contagious parthenogenesis in Artemia brine shrimp"},{"title":"Computing chemical potentials of solutions from structure factors","quality_controlled":"1","date_created":"2023-01-16T09:56:20Z","citation":{"chicago":"Cheng, Bingqing. “Computing Chemical Potentials of Solutions from Structure Factors.” <i>The Journal of Chemical Physics</i>. AIP Publishing, 2022. <a href=\"https://doi.org/10.1063/5.0107059\">https://doi.org/10.1063/5.0107059</a>.","apa":"Cheng, B. (2022). Computing chemical potentials of solutions from structure factors. <i>The Journal of Chemical Physics</i>. AIP Publishing. <a href=\"https://doi.org/10.1063/5.0107059\">https://doi.org/10.1063/5.0107059</a>","mla":"Cheng, Bingqing. “Computing Chemical Potentials of Solutions from Structure Factors.” <i>The Journal of Chemical Physics</i>, vol. 157, no. 12, 121101, AIP Publishing, 2022, doi:<a href=\"https://doi.org/10.1063/5.0107059\">10.1063/5.0107059</a>.","short":"B. Cheng, The Journal of Chemical Physics 157 (2022).","ista":"Cheng B. 2022. Computing chemical potentials of solutions from structure factors. The Journal of Chemical Physics. 157(12), 121101.","ieee":"B. Cheng, “Computing chemical potentials of solutions from structure factors,” <i>The Journal of Chemical Physics</i>, vol. 157, no. 12. AIP Publishing, 2022.","ama":"Cheng B. Computing chemical potentials of solutions from structure factors. <i>The Journal of Chemical Physics</i>. 2022;157(12). doi:<a href=\"https://doi.org/10.1063/5.0107059\">10.1063/5.0107059</a>"},"oa":1,"article_number":"121101","tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"article_processing_charge":"No","file_date_updated":"2023-01-30T09:07:00Z","doi":"10.1063/5.0107059","date_published":"2022-09-30T00:00:00Z","intvolume":"       157","has_accepted_license":"1","day":"30","acknowledgement":"I thank Daan Frenkel for providing feedback on an early draft and for stimulating discussions, Debashish Mukherji and Robinson Cortes-Huerto for sharing the trajectories for urea–water mixtures, and Aleks Reinhardt for useful suggestions on the manuscript.","publication":"The Journal of Chemical Physics","volume":157,"article_type":"original","department":[{"_id":"BiCh"}],"month":"09","year":"2022","publication_identifier":{"eissn":["1089-7690"],"issn":["0021-9606"]},"isi":1,"external_id":{"isi":["000862856000003"]},"publication_status":"published","issue":"12","_id":"12249","type":"journal_article","file":[{"creator":"dernst","file_id":"12441","relation":"main_file","file_name":"2022_JourChemPhysics_Cheng.pdf","checksum":"b0915b706568a663a9a372fca24adf35","success":1,"file_size":4402384,"date_created":"2023-01-30T09:07:00Z","content_type":"application/pdf","access_level":"open_access","date_updated":"2023-01-30T09:07:00Z"}],"oa_version":"Published Version","ddc":["530","540"],"publisher":"AIP Publishing","status":"public","author":[{"orcid":"0000-0002-3584-9632","full_name":"Cheng, Bingqing","last_name":"Cheng","first_name":"Bingqing","id":"cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9"}],"scopus_import":"1","related_material":{"link":[{"url":"https://github.com/ BingqingCheng/S0","relation":"software"}]},"keyword":["Physical and Theoretical Chemistry","General Physics and Astronomy"],"abstract":[{"text":"The chemical potential of a component in a solution is defined as the free energy change as the amount of that component changes. Computing this fundamental thermodynamic property from atomistic simulations is notoriously difficult because of the convergence issues involved in free energy methods and finite size effects. This Communication presents the so-called S0 method, which can be used to obtain chemical potentials from static structure factors computed from equilibrium molecular dynamics simulations under the isothermal–isobaric ensemble. This new method is demonstrated on the systems of binary Lennard-Jones particles, urea–water mixtures, a NaCl aqueous solution, and a high-pressure carbon–hydrogen mixture. ","lang":"eng"}],"language":[{"iso":"eng"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","date_updated":"2023-08-04T09:43:11Z"},{"article_number":"943355","oa":1,"quality_controlled":"1","citation":{"mla":"Weiffert, Tanja, et al. “Influence of Denaturants on Amyloid Β42 Aggregation Kinetics.” <i>Frontiers in Neuroscience</i>, vol. 16, 943355, Frontiers Media, 2022, doi:<a href=\"https://doi.org/10.3389/fnins.2022.943355\">10.3389/fnins.2022.943355</a>.","chicago":"Weiffert, Tanja, Georg Meisl, Samo Curk, Risto Cukalevski, Anđela Šarić, Tuomas P. J. Knowles, and Sara Linse. “Influence of Denaturants on Amyloid Β42 Aggregation Kinetics.” <i>Frontiers in Neuroscience</i>. Frontiers Media, 2022. <a href=\"https://doi.org/10.3389/fnins.2022.943355\">https://doi.org/10.3389/fnins.2022.943355</a>.","apa":"Weiffert, T., Meisl, G., Curk, S., Cukalevski, R., Šarić, A., Knowles, T. P. J., &#38; Linse, S. (2022). Influence of denaturants on amyloid β42 aggregation kinetics. <i>Frontiers in Neuroscience</i>. Frontiers Media. <a href=\"https://doi.org/10.3389/fnins.2022.943355\">https://doi.org/10.3389/fnins.2022.943355</a>","short":"T. Weiffert, G. Meisl, S. Curk, R. Cukalevski, A. Šarić, T.P.J. Knowles, S. Linse, Frontiers in Neuroscience 16 (2022).","ieee":"T. Weiffert <i>et al.</i>, “Influence of denaturants on amyloid β42 aggregation kinetics,” <i>Frontiers in Neuroscience</i>, vol. 16. Frontiers Media, 2022.","ista":"Weiffert T, Meisl G, Curk S, Cukalevski R, Šarić A, Knowles TPJ, Linse S. 2022. Influence of denaturants on amyloid β42 aggregation kinetics. Frontiers in Neuroscience. 16, 943355.","ama":"Weiffert T, Meisl G, Curk S, et al. Influence of denaturants on amyloid β42 aggregation kinetics. <i>Frontiers in Neuroscience</i>. 2022;16. doi:<a href=\"https://doi.org/10.3389/fnins.2022.943355\">10.3389/fnins.2022.943355</a>"},"date_created":"2023-01-16T09:56:43Z","title":"Influence of denaturants on amyloid β42 aggregation kinetics","volume":16,"acknowledgement":"This work was supported by grants from the Swedish Research Council (grant no. 2015-00143) and the European Research Council (grant no. 340890).","publication":"Frontiers in Neuroscience","day":"20","date_published":"2022-09-20T00:00:00Z","intvolume":"        16","has_accepted_license":"1","file_date_updated":"2023-01-30T09:15:13Z","doi":"10.3389/fnins.2022.943355","article_processing_charge":"No","tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"publisher":"Frontiers Media","_id":"12251","external_id":{"isi":["000866287100001"]},"publication_status":"published","file":[{"file_size":19798610,"checksum":"e67d16113ffb4fb4fa38a183d169f210","success":1,"date_created":"2023-01-30T09:15:13Z","access_level":"open_access","content_type":"application/pdf","date_updated":"2023-01-30T09:15:13Z","file_id":"12442","creator":"dernst","relation":"main_file","file_name":"2022_FrontiersNeuroscience_Weiffert2.pdf"}],"oa_version":"Published Version","ddc":["570"],"type":"journal_article","year":"2022","month":"09","isi":1,"publication_identifier":{"issn":["1662-453X"]},"article_type":"original","department":[{"_id":"AnSa"}],"language":[{"iso":"eng"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","date_updated":"2023-08-04T09:48:56Z","scopus_import":"1","abstract":[{"text":"Amyloid formation is linked to devastating neurodegenerative diseases, motivating detailed studies of the mechanisms of amyloid formation. For Aβ, the peptide associated with Alzheimer’s disease, the mechanism and rate of aggregation have been established for a range of variants and conditions <jats:italic>in vitro</jats:italic> and in bodily fluids. A key outstanding question is how the relative stabilities of monomers, fibrils and intermediates affect each step in the fibril formation process. By monitoring the kinetics of aggregation of Aβ42, in the presence of urea or guanidinium hydrochloride (GuHCl), we here determine the rates of the underlying microscopic steps and establish the importance of changes in relative stability induced by the presence of denaturant for each individual step. Denaturants shift the equilibrium towards the unfolded state of each species. We find that a non-ionic denaturant, urea, reduces the overall aggregation rate, and that the effect on nucleation is stronger than the effect on elongation. Urea reduces the rate of secondary nucleation by decreasing the coverage of fibril surfaces and the rate of nucleus formation. It also reduces the rate of primary nucleation, increasing its reaction order. The ionic denaturant, GuHCl, accelerates the aggregation at low denaturant concentrations and decelerates the aggregation at high denaturant concentrations. Below approximately 0.25 M GuHCl, the screening of repulsive electrostatic interactions between peptides by the charged denaturant dominates, leading to an increased aggregation rate. At higher GuHCl concentrations, the electrostatic repulsion is completely screened, and the denaturing effect dominates. The results illustrate how the differential effects of denaturants on stability of monomer, oligomer and fibril translate to differential effects on microscopic steps, with the rate of nucleation being most strongly reduced.","lang":"eng"}],"keyword":["General Neuroscience"],"author":[{"full_name":"Weiffert, Tanja","last_name":"Weiffert","first_name":"Tanja"},{"first_name":"Georg","full_name":"Meisl, Georg","last_name":"Meisl"},{"last_name":"Curk","full_name":"Curk, Samo","first_name":"Samo"},{"last_name":"Cukalevski","full_name":"Cukalevski, Risto","first_name":"Risto"},{"full_name":"Šarić, Anđela","last_name":"Šarić","orcid":"0000-0002-7854-2139","id":"bf63d406-f056-11eb-b41d-f263a6566d8b","first_name":"Anđela"},{"first_name":"Tuomas P. J.","last_name":"Knowles","full_name":"Knowles, Tuomas P. J."},{"last_name":"Linse","full_name":"Linse, Sara","first_name":"Sara"}],"status":"public"},{"doi":"10.3389/fimmu.2022.965446","file_date_updated":"2023-01-30T09:22:26Z","article_processing_charge":"No","tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"volume":13,"acknowledgement":"The authors declare that this study received funding from Immunofusion. The funder was not involved in the study design, collection, analysis, interpretation of data, the writing of this article or the decision to submit it for publication.","publication":"Frontiers in Immunology","day":"16","intvolume":"        13","has_accepted_license":"1","date_published":"2022-09-16T00:00:00Z","title":"Isolation of an escape-resistant SARS-CoV-2 neutralizing nanobody from a novel synthetic nanobody library","article_number":"965446","oa":1,"citation":{"mla":"Dormeshkin, Dmitri, et al. “Isolation of an Escape-Resistant SARS-CoV-2 Neutralizing Nanobody from a Novel Synthetic Nanobody Library.” <i>Frontiers in Immunology</i>, vol. 13, 965446, Frontiers Media, 2022, doi:<a href=\"https://doi.org/10.3389/fimmu.2022.965446\">10.3389/fimmu.2022.965446</a>.","apa":"Dormeshkin, D., Shapira, M., Dubovik, S., Kavaleuski, A., Katsin, M., Migas, A., … Semyonov, S. (2022). Isolation of an escape-resistant SARS-CoV-2 neutralizing nanobody from a novel synthetic nanobody library. <i>Frontiers in Immunology</i>. Frontiers Media. <a href=\"https://doi.org/10.3389/fimmu.2022.965446\">https://doi.org/10.3389/fimmu.2022.965446</a>","chicago":"Dormeshkin, Dmitri, Michail Shapira, Simon Dubovik, Anton Kavaleuski, Mikalai Katsin, Alexandr Migas, Alexander Meleshko, and Sergei Semyonov. “Isolation of an Escape-Resistant SARS-CoV-2 Neutralizing Nanobody from a Novel Synthetic Nanobody Library.” <i>Frontiers in Immunology</i>. Frontiers Media, 2022. <a href=\"https://doi.org/10.3389/fimmu.2022.965446\">https://doi.org/10.3389/fimmu.2022.965446</a>.","ama":"Dormeshkin D, Shapira M, Dubovik S, et al. Isolation of an escape-resistant SARS-CoV-2 neutralizing nanobody from a novel synthetic nanobody library. <i>Frontiers in Immunology</i>. 2022;13. doi:<a href=\"https://doi.org/10.3389/fimmu.2022.965446\">10.3389/fimmu.2022.965446</a>","ista":"Dormeshkin D, Shapira M, Dubovik S, Kavaleuski A, Katsin M, Migas A, Meleshko A, Semyonov S. 2022. Isolation of an escape-resistant SARS-CoV-2 neutralizing nanobody from a novel synthetic nanobody library. Frontiers in Immunology. 13, 965446.","short":"D. Dormeshkin, M. Shapira, S. Dubovik, A. Kavaleuski, M. Katsin, A. Migas, A. Meleshko, S. Semyonov, Frontiers in Immunology 13 (2022).","ieee":"D. Dormeshkin <i>et al.</i>, “Isolation of an escape-resistant SARS-CoV-2 neutralizing nanobody from a novel synthetic nanobody library,” <i>Frontiers in Immunology</i>, vol. 13. Frontiers Media, 2022."},"date_created":"2023-01-16T09:56:57Z","quality_controlled":"1","author":[{"first_name":"Dmitri","full_name":"Dormeshkin, Dmitri","last_name":"Dormeshkin"},{"full_name":"Shapira, Michail","last_name":"Shapira","first_name":"Michail"},{"full_name":"Dubovik, Simon","last_name":"Dubovik","first_name":"Simon"},{"first_name":"Anton","id":"4968f7ad-eb97-11eb-a6c2-8ed382e8912c","orcid":"0000-0003-2091-526X","full_name":"Kavaleuski, Anton","last_name":"Kavaleuski"},{"first_name":"Mikalai","full_name":"Katsin, Mikalai","last_name":"Katsin"},{"last_name":"Migas","full_name":"Migas, Alexandr","first_name":"Alexandr"},{"last_name":"Meleshko","full_name":"Meleshko, Alexander","first_name":"Alexander"},{"first_name":"Sergei","full_name":"Semyonov, Sergei","last_name":"Semyonov"}],"status":"public","date_updated":"2023-08-04T09:49:24Z","language":[{"iso":"eng"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","abstract":[{"text":"The COVID−19 pandemic not only resulted in a global crisis, but also accelerated vaccine development and antibody discovery. Herein we report a synthetic humanized VHH library development pipeline for nanomolar-range affinity VHH binders to SARS-CoV-2 variants of concern (VoC) receptor binding domains (RBD) isolation. Trinucleotide-based randomization of CDRs by Kunkel mutagenesis with the subsequent rolling-cycle amplification resulted in more than 10<jats:sup>11</jats:sup> diverse phage display library in a manageable for a single person number of electroporation reactions. We identified a number of nanomolar-range affinity VHH binders to SARS-CoV-2 variants of concern (VoC) receptor binding domains (RBD) by screening a novel synthetic humanized antibody library. In order to explore the most robust and fast method for affinity improvement, we performed affinity maturation by CDR1 and CDR2 shuffling and avidity engineering by multivalent trimeric VHH fusion protein construction. As a result, H7-Fc and G12x3-Fc binders were developed with the affinities in nM and pM range respectively. Importantly, these affinities are weakly influenced by most of SARS-CoV-2 VoC mutations and they retain moderate binding to BA.4\\5. The plaque reduction neutralization test (PRNT) resulted in IC50 = 100 ng\\ml and 9.6 ng\\ml for H7-Fc and G12x3-Fc antibodies, respectively, for the emerging Omicron BA.1 variant. Therefore, these VHH could expand the present landscape of SARS-CoV-2 neutralization binders with the therapeutic potential for present and future SARS-CoV-2 variants.","lang":"eng"}],"keyword":["Immunology","Immunology and Allergy","COVID-19","SARS-CoV-2","synthetic library","RBD","neutralization nanobody","VHH"],"scopus_import":"1","isi":1,"publication_identifier":{"issn":["1664-3224"]},"year":"2022","month":"09","department":[{"_id":"LeSa"}],"article_type":"original","publisher":"Frontiers Media","type":"journal_article","ddc":["570"],"oa_version":"Published Version","file":[{"creator":"dernst","file_id":"12443","relation":"main_file","file_name":"2022_FrontiersImmunology_Dormeshkin.pdf","success":1,"checksum":"f8f5d8110710033d0532e7e08bf9dad4","file_size":5695892,"date_created":"2023-01-30T09:22:26Z","content_type":"application/pdf","access_level":"open_access","date_updated":"2023-01-30T09:22:26Z"}],"_id":"12252","publication_status":"published","external_id":{"isi":["000862479100001"]}},{"quality_controlled":"1","citation":{"ieee":"J. Stock, T. Kazmar, F. Schlumm, E. B. Hannezo, and A. Pauli, “A self-generated Toddler gradient guides mesodermal cell migration,” <i>Science Advances</i>, vol. 8, no. 37. American Association for the Advancement of Science, 2022.","short":"J. Stock, T. Kazmar, F. Schlumm, E.B. Hannezo, A. Pauli, Science Advances 8 (2022).","ista":"Stock J, Kazmar T, Schlumm F, Hannezo EB, Pauli A. 2022. A self-generated Toddler gradient guides mesodermal cell migration. Science Advances. 8(37), eadd2488.","ama":"Stock J, Kazmar T, Schlumm F, Hannezo EB, Pauli A. A self-generated Toddler gradient guides mesodermal cell migration. <i>Science Advances</i>. 2022;8(37). doi:<a href=\"https://doi.org/10.1126/sciadv.add2488\">10.1126/sciadv.add2488</a>","mla":"Stock, Jessica, et al. “A Self-Generated Toddler Gradient Guides Mesodermal Cell Migration.” <i>Science Advances</i>, vol. 8, no. 37, eadd2488, American Association for the Advancement of Science, 2022, doi:<a href=\"https://doi.org/10.1126/sciadv.add2488\">10.1126/sciadv.add2488</a>.","chicago":"Stock, Jessica, Tomas Kazmar, Friederike Schlumm, Edouard B Hannezo, and Andrea Pauli. “A Self-Generated Toddler Gradient Guides Mesodermal Cell Migration.” <i>Science Advances</i>. American Association for the Advancement of Science, 2022. <a href=\"https://doi.org/10.1126/sciadv.add2488\">https://doi.org/10.1126/sciadv.add2488</a>.","apa":"Stock, J., Kazmar, T., Schlumm, F., Hannezo, E. B., &#38; Pauli, A. (2022). A self-generated Toddler gradient guides mesodermal cell migration. <i>Science Advances</i>. American Association for the Advancement of Science. <a href=\"https://doi.org/10.1126/sciadv.add2488\">https://doi.org/10.1126/sciadv.add2488</a>"},"date_created":"2023-01-16T09:57:10Z","oa":1,"article_number":"eadd2488","title":"A self-generated Toddler gradient guides mesodermal cell migration","date_published":"2022-09-14T00:00:00Z","has_accepted_license":"1","intvolume":"         8","pmid":1,"day":"14","publication":"Science Advances","acknowledgement":"We thank K. Aumayer and the team of the biooptics facility at the Vienna Biocenter, particularly P. Pasierbek and T. Müller, for support with microscopy; K. Panser, C. Pribitzer, and the animal facility personnel for taking care of zebrafish; M. Binner and A. Bandura for help with genotyping; M. Codina Tobias for help with establishing the conditions for the Toddler overexpression compensation experiment; T. Lubiana Alves for sharing the code for scRNA-Seq analyses; the Heisenberg laboratory, particularly D. Pinheiro, for joint laboratory meetings, discussions on the project, and providing the tg(gsc:CAAX-GFP) fish line; the Raz laboratory for providing the Lifeact-GFP plasmid; A. Andersen, A. Schier, C.-P. Heisenberg, and E. Tanaka for comments on the manuscript; and the entire Pauli laboratory, particularly K. Gert and V. Deneke, for valuable discussions and feedback on the manuscript. Funding: Work in A.P.’s laboratory has been supported by the IMP, which receives institutional funding from Boehringer Ingelheim and the Austrian Research Promotion Agency (Headquarter grant FFG-852936), as well as the FWF START program (Y 1031-B28 to A.P.), the Human Frontier Science Program (HFSP) Career Development Award (CDA00066/2015 to A.P.) and Young Investigator Grant (RGY0079/2020 to A.P.), the SFB RNA-Deco (project number F 80 to A.P.), a Whitman Center Fellowship from the Marine Biological Laboratory (to A.P.), and EMBO-YIP funds (to A.P.). This work was supported by the European Union (European Research Council Starting Grant 851288 to E.H.). For the purpose of Open Access, the authors have applied a CC BY public copyright license to any Author Accepted Manuscript (AAM) version arising from this submission.","volume":8,"tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"ec_funded":1,"article_processing_charge":"No","file_date_updated":"2023-01-30T09:27:49Z","doi":"10.1126/sciadv.add2488","external_id":{"isi":["000888875000009"],"pmid":["36103529"]},"publication_status":"published","_id":"12253","issue":"37","ddc":["570"],"file":[{"file_name":"2022_ScienceAdvances_Stock.pdf","file_id":"12444","creator":"dernst","relation":"main_file","access_level":"open_access","content_type":"application/pdf","date_updated":"2023-01-30T09:27:49Z","success":1,"checksum":"f59cdb824e5d4221045def81f46f6c65","file_size":1636732,"date_created":"2023-01-30T09:27:49Z"}],"oa_version":"Published Version","type":"journal_article","publisher":"American Association for the Advancement of Science","article_type":"original","department":[{"_id":"EdHa"}],"project":[{"grant_number":"851288","_id":"05943252-7A3F-11EA-A408-12923DDC885E","name":"Design Principles of Branching Morphogenesis","call_identifier":"H2020"}],"month":"09","year":"2022","publication_identifier":{"issn":["2375-2548"]},"isi":1,"scopus_import":"1","abstract":[{"lang":"eng","text":"The sculpting of germ layers during gastrulation relies on the coordinated migration of progenitor cells, yet the cues controlling these long-range directed movements remain largely unknown. While directional migration often relies on a chemokine gradient generated from a localized source, we find that zebrafish ventrolateral mesoderm is guided by a self-generated gradient of the initially uniformly expressed and secreted protein Toddler/ELABELA/Apela. We show that the Apelin receptor, which is specifically expressed in mesodermal cells, has a dual role during gastrulation, acting as a scavenger receptor to generate a Toddler gradient, and as a chemokine receptor to sense this guidance cue. Thus, we uncover a single receptor–based self-generated gradient as the enigmatic guidance cue that can robustly steer the directional migration of mesoderm through the complex and continuously changing environment of the gastrulating embryo."}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","language":[{"iso":"eng"}],"date_updated":"2023-08-04T09:49:59Z","status":"public","author":[{"first_name":"Jessica","last_name":"Stock","full_name":"Stock, Jessica"},{"first_name":"Tomas","full_name":"Kazmar, Tomas","last_name":"Kazmar"},{"first_name":"Friederike","full_name":"Schlumm, Friederike","last_name":"Schlumm"},{"orcid":"0000-0001-6005-1561","full_name":"Hannezo, Edouard B","last_name":"Hannezo","first_name":"Edouard B","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Andrea","last_name":"Pauli","full_name":"Pauli, Andrea"}]},{"scopus_import":"1","abstract":[{"lang":"eng","text":"Structural balance theory is an established framework for studying social relationships of friendship and enmity. These relationships are modeled by a signed network whose energy potential measures the level of imbalance, while stochastic dynamics drives the network toward a state of minimum energy that captures social balance. It is known that this energy landscape has local minima that can trap socially aware dynamics, preventing it from reaching balance. Here we first study the robustness and attractor properties of these local minima. We show that a stochastic process can reach them from an abundance of initial states and that some local minima cannot be escaped by mild perturbations of the network. Motivated by these anomalies, we introduce best-edge dynamics (BED), a new plausible stochastic process. We prove that BED always reaches balance and that it does so fast in various interesting settings."}],"main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2210.02394","open_access":"1"}],"language":[{"iso":"eng"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","date_updated":"2025-07-14T09:09:49Z","author":[{"orcid":"0000-0002-4561-241X","last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu"},{"last_name":"Svoboda","full_name":"Svoboda, Jakub","orcid":"0000-0002-1419-3267","id":"130759D2-D7DD-11E9-87D2-DE0DE6697425","first_name":"Jakub"},{"orcid":"0000-0002-4681-1699","full_name":"Zikelic, Dorde","last_name":"Zikelic","first_name":"Dorde","id":"294AA7A6-F248-11E8-B48F-1D18A9856A87"},{"id":"49704004-F248-11E8-B48F-1D18A9856A87","first_name":"Andreas","orcid":"0000-0002-8943-0722","full_name":"Pavlogiannis, Andreas","last_name":"Pavlogiannis"},{"last_name":"Tkadlec","full_name":"Tkadlec, Josef","orcid":"0000-0002-1097-9684","id":"3F24CCC8-F248-11E8-B48F-1D18A9856A87","first_name":"Josef"}],"status":"public","issue":"3","_id":"12257","publication_status":"published","external_id":{"isi":["000870243100001"],"arxiv":["2210.02394"]},"oa_version":"Preprint","type":"journal_article","publisher":"American Physical Society","article_type":"original","department":[{"_id":"KrCh"}],"year":"2022","month":"09","project":[{"call_identifier":"FP7","name":"Quantitative Graph Games: Theory and Applications","_id":"2581B60A-B435-11E9-9278-68D0E5697425","grant_number":"279307"},{"call_identifier":"H2020","name":"Formal Methods for Stochastic Models: Algorithms and Applications","_id":"0599E47C-7A3F-11EA-A408-12923DDC885E","grant_number":"863818"},{"grant_number":"P 23499-N23","name":"Modern Graph Algorithmic Techniques in Formal Verification","call_identifier":"FWF","_id":"2584A770-B435-11E9-9278-68D0E5697425"},{"grant_number":"S11407","_id":"25863FF4-B435-11E9-9278-68D0E5697425","name":"Game Theory","call_identifier":"FWF"},{"name":"International IST Doctoral Program","call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385"}],"isi":1,"publication_identifier":{"eissn":["2470-0053"],"issn":["2470-0045"]},"date_published":"2022-09-29T00:00:00Z","intvolume":"       106","volume":106,"acknowledgement":"K.C. acknowledges support from ERC Start Grant No. (279307: Graph Games), ERC Consolidator Grant No. (863818: ForM-SMart), and Austrian Science Fund (FWF)\r\nGrants No. P23499-N23 and No. S11407-N23 (RiSE). This project has received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie\r\nSkłodowska-Curie Grant Agreement No. 665385.","day":"29","publication":"Physical Review E","ec_funded":1,"article_processing_charge":"No","doi":"10.1103/physreve.106.034321","quality_controlled":"1","arxiv":1,"date_created":"2023-01-16T09:57:57Z","citation":{"apa":"Chatterjee, K., Svoboda, J., Zikelic, D., Pavlogiannis, A., &#38; Tkadlec, J. (2022). Social balance on networks: Local minima and best-edge dynamics. <i>Physical Review E</i>. American Physical Society. <a href=\"https://doi.org/10.1103/physreve.106.034321\">https://doi.org/10.1103/physreve.106.034321</a>","chicago":"Chatterjee, Krishnendu, Jakub Svoboda, Dorde Zikelic, Andreas Pavlogiannis, and Josef Tkadlec. “Social Balance on Networks: Local Minima and Best-Edge Dynamics.” <i>Physical Review E</i>. American Physical Society, 2022. <a href=\"https://doi.org/10.1103/physreve.106.034321\">https://doi.org/10.1103/physreve.106.034321</a>.","mla":"Chatterjee, Krishnendu, et al. “Social Balance on Networks: Local Minima and Best-Edge Dynamics.” <i>Physical Review E</i>, vol. 106, no. 3, 034321, American Physical Society, 2022, doi:<a href=\"https://doi.org/10.1103/physreve.106.034321\">10.1103/physreve.106.034321</a>.","ama":"Chatterjee K, Svoboda J, Zikelic D, Pavlogiannis A, Tkadlec J. Social balance on networks: Local minima and best-edge dynamics. <i>Physical Review E</i>. 2022;106(3). doi:<a href=\"https://doi.org/10.1103/physreve.106.034321\">10.1103/physreve.106.034321</a>","short":"K. Chatterjee, J. Svoboda, D. Zikelic, A. Pavlogiannis, J. Tkadlec, Physical Review E 106 (2022).","ista":"Chatterjee K, Svoboda J, Zikelic D, Pavlogiannis A, Tkadlec J. 2022. Social balance on networks: Local minima and best-edge dynamics. Physical Review E. 106(3), 034321.","ieee":"K. Chatterjee, J. Svoboda, D. Zikelic, A. Pavlogiannis, and J. Tkadlec, “Social balance on networks: Local minima and best-edge dynamics,” <i>Physical Review E</i>, vol. 106, no. 3. American Physical Society, 2022."},"article_number":"034321","oa":1,"title":"Social balance on networks: Local minima and best-edge dynamics"},{"day":"26","acknowledgement":"This work was partially funded by the Institute of Science and Technology Austria Interdisciplinary Project Committee Grant “Pilot-Wave Hydrodynamics: Chaos and Quantum Analogies.”","publication":"Chaos: An Interdisciplinary Journal of Nonlinear Science","volume":32,"date_published":"2022-09-26T00:00:00Z","intvolume":"        32","has_accepted_license":"1","file_date_updated":"2023-01-30T09:41:12Z","doi":"10.1063/5.0102904","tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"article_processing_charge":"No","oa":1,"article_number":"093138","quality_controlled":"1","arxiv":1,"date_created":"2023-01-16T09:58:16Z","citation":{"ieee":"G. H. Choueiri, B. Suri, J. Merrin, M. Serbyn, B. Hof, and N. B. Budanur, “Crises and chaotic scattering in hydrodynamic pilot-wave experiments,” <i>Chaos: An Interdisciplinary Journal of Nonlinear Science</i>, vol. 32, no. 9. AIP Publishing, 2022.","short":"G.H. Choueiri, B. Suri, J. Merrin, M. Serbyn, B. Hof, N.B. Budanur, Chaos: An Interdisciplinary Journal of Nonlinear Science 32 (2022).","ista":"Choueiri GH, Suri B, Merrin J, Serbyn M, Hof B, Budanur NB. 2022. Crises and chaotic scattering in hydrodynamic pilot-wave experiments. Chaos: An Interdisciplinary Journal of Nonlinear Science. 32(9), 093138.","ama":"Choueiri GH, Suri B, Merrin J, Serbyn M, Hof B, Budanur NB. Crises and chaotic scattering in hydrodynamic pilot-wave experiments. <i>Chaos: An Interdisciplinary Journal of Nonlinear Science</i>. 2022;32(9). doi:<a href=\"https://doi.org/10.1063/5.0102904\">10.1063/5.0102904</a>","chicago":"Choueiri, George H, Balachandra Suri, Jack Merrin, Maksym Serbyn, Björn Hof, and Nazmi B Budanur. “Crises and Chaotic Scattering in Hydrodynamic Pilot-Wave Experiments.” <i>Chaos: An Interdisciplinary Journal of Nonlinear Science</i>. AIP Publishing, 2022. <a href=\"https://doi.org/10.1063/5.0102904\">https://doi.org/10.1063/5.0102904</a>.","apa":"Choueiri, G. H., Suri, B., Merrin, J., Serbyn, M., Hof, B., &#38; Budanur, N. B. (2022). Crises and chaotic scattering in hydrodynamic pilot-wave experiments. <i>Chaos: An Interdisciplinary Journal of Nonlinear Science</i>. AIP Publishing. <a href=\"https://doi.org/10.1063/5.0102904\">https://doi.org/10.1063/5.0102904</a>","mla":"Choueiri, George H., et al. “Crises and Chaotic Scattering in Hydrodynamic Pilot-Wave Experiments.” <i>Chaos: An Interdisciplinary Journal of Nonlinear Science</i>, vol. 32, no. 9, 093138, AIP Publishing, 2022, doi:<a href=\"https://doi.org/10.1063/5.0102904\">10.1063/5.0102904</a>."},"title":"Crises and chaotic scattering in hydrodynamic pilot-wave experiments","language":[{"iso":"eng"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","date_updated":"2023-08-04T09:51:17Z","scopus_import":"1","keyword":["Applied Mathematics","General Physics and Astronomy","Mathematical Physics","Statistical and Nonlinear Physics"],"abstract":[{"lang":"eng","text":"Theoretical foundations of chaos have been predominantly laid out for finite-dimensional dynamical systems, such as the three-body problem in classical mechanics and the Lorenz model in dissipative systems. In contrast, many real-world chaotic phenomena, e.g., weather, arise in systems with many (formally infinite) degrees of freedom, which limits direct quantitative analysis of such systems using chaos theory. In the present work, we demonstrate that the hydrodynamic pilot-wave systems offer a bridge between low- and high-dimensional chaotic phenomena by allowing for a systematic study of how the former connects to the latter. Specifically, we present experimental results, which show the formation of low-dimensional chaotic attractors upon destabilization of regular dynamics and a final transition to high-dimensional chaos via the merging of distinct chaotic regions through a crisis bifurcation. Moreover, we show that the post-crisis dynamics of the system can be rationalized as consecutive scatterings from the nonattracting chaotic sets with lifetimes following exponential distributions. "}],"status":"public","author":[{"last_name":"Choueiri","full_name":"Choueiri, George H","id":"448BD5BC-F248-11E8-B48F-1D18A9856A87","first_name":"George H"},{"full_name":"Suri, Balachandra","last_name":"Suri","first_name":"Balachandra","id":"47A5E706-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Jack","id":"4515C308-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5145-4609","full_name":"Merrin, Jack","last_name":"Merrin"},{"first_name":"Maksym","id":"47809E7E-F248-11E8-B48F-1D18A9856A87","last_name":"Serbyn","full_name":"Serbyn, Maksym","orcid":"0000-0002-2399-5827"},{"orcid":"0000-0003-2057-2754","full_name":"Hof, Björn","last_name":"Hof","id":"3A374330-F248-11E8-B48F-1D18A9856A87","first_name":"Björn"},{"orcid":"0000-0003-0423-5010","full_name":"Budanur, Nazmi B","last_name":"Budanur","id":"3EA1010E-F248-11E8-B48F-1D18A9856A87","first_name":"Nazmi B"}],"publisher":"AIP Publishing","publication_status":"published","external_id":{"arxiv":["2206.01531"],"isi":["000861009600005"]},"_id":"12259","issue":"9","type":"journal_article","oa_version":"Published Version","ddc":["530"],"file":[{"creator":"dernst","file_id":"12445","relation":"main_file","file_name":"2022_Chaos_Choueiri.pdf","success":1,"file_size":3209644,"checksum":"17881eff8b21969359a2dd64620120ba","date_created":"2023-01-30T09:41:12Z","content_type":"application/pdf","access_level":"open_access","date_updated":"2023-01-30T09:41:12Z"}],"month":"09","year":"2022","publication_identifier":{"issn":["1054-1500"],"eissn":["1089-7682"]},"isi":1,"article_type":"original","department":[{"_id":"MaSe"},{"_id":"BjHo"},{"_id":"NanoFab"}]},{"status":"public","author":[{"orcid":"0000-0001-8619-2223","last_name":"Angermayr","full_name":"Angermayr, Andreas","first_name":"Andreas","id":"4677C796-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Tin Yau","full_name":"Pang, Tin Yau","last_name":"Pang"},{"first_name":"Guillaume","last_name":"Chevereau","full_name":"Chevereau, Guillaume"},{"last_name":"Mitosch","full_name":"Mitosch, Karin","id":"39B66846-F248-11E8-B48F-1D18A9856A87","first_name":"Karin"},{"first_name":"Martin J","last_name":"Lercher","full_name":"Lercher, Martin J"},{"orcid":"0000-0003-4398-476X","full_name":"Bollenbach, Mark Tobias","last_name":"Bollenbach","id":"3E6DB97A-F248-11E8-B48F-1D18A9856A87","first_name":"Mark Tobias"}],"keyword":["Applied Mathematics","Computational Theory and Mathematics","General Agricultural and Biological Sciences","General Immunology and Microbiology","General Biochemistry","Genetics and Molecular Biology","Information Systems"],"abstract":[{"text":"Dose–response relationships are a general concept for quantitatively describing biological systems across multiple scales, from the molecular to the whole-cell level. A clinically relevant example is the bacterial growth response to antibiotics, which is routinely characterized by dose–response curves. The shape of the dose–response curve varies drastically between antibiotics and plays a key role in treatment, drug interactions, and resistance evolution. However, the mechanisms shaping the dose–response curve remain largely unclear. Here, we show in Escherichia coli that the distinctively shallow dose–response curve of the antibiotic trimethoprim is caused by a negative growth-mediated feedback loop: Trimethoprim slows growth, which in turn weakens the effect of this antibiotic. At the molecular level, this feedback is caused by the upregulation of the drug target dihydrofolate reductase (FolA/DHFR). We show that this upregulation is not a specific response to trimethoprim but follows a universal trend line that depends primarily on the growth rate, irrespective of its cause. Rewiring the feedback loop alters the dose–response curve in a predictable manner, which we corroborate using a mathematical model of cellular resource allocation and growth. Our results indicate that growth-mediated feedback loops may shape drug responses more generally and could be exploited to design evolutionary traps that enable selection against drug resistance.","lang":"eng"}],"scopus_import":"1","date_updated":"2023-08-04T09:51:49Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","language":[{"iso":"eng"}],"department":[{"_id":"ToBo"}],"article_type":"original","publication_identifier":{"eissn":["1744-4292"]},"isi":1,"month":"09","year":"2022","oa_version":"Published Version","file":[{"creator":"dernst","file_id":"12446","relation":"main_file","file_name":"2022_MolecularSystemsBio_Angermayr.pdf","checksum":"8b1d8f5ea20c8408acf466435fb6ae01","success":1,"file_size":1098812,"date_created":"2023-01-30T09:49:55Z","content_type":"application/pdf","access_level":"open_access","date_updated":"2023-01-30T09:49:55Z"}],"ddc":["570"],"type":"journal_article","external_id":{"isi":["000856482800001"]},"publication_status":"published","_id":"12261","issue":"9","publisher":"Embo Press","tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"article_processing_charge":"No","doi":"10.15252/msb.202110490","file_date_updated":"2023-01-30T09:49:55Z","intvolume":"        18","has_accepted_license":"1","date_published":"2022-09-01T00:00:00Z","acknowledgement":"This work was in part supported by Human Frontier Science Program GrantRGP0042/2013, Marie Curie Career Integration Grant303507, AustrianScience Fund (FWF) Grant P27201-B22, and German Research Foundation(DFG) Collaborative Research Center (SFB)1310to TB. SAA was supportedby the European Union’s Horizon2020Research and Innovation Programunder the Marie Skłodowska-Curie Grant agreement No707352. We wouldlike to thank the Bollenbach group for regular fruitful discussions. We areparticularly thankful for the technical assistance of Booshini Fernando andfor discussions of the theoretical aspects with Gerrit Ansmann. We areindebted to Bor Kavˇciˇc for invaluable advice, help with setting up theluciferase-based growth monitoring system, and for sharing plasmids. Weacknowledge the IST Austria Miba Machine Shop for their support inbuilding a housing for the stacker of the plate reader, which enabled thehigh-throughput luciferase-based experiments. We are grateful to RosalindAllen, Bor Kavˇciˇc and Dor Russ for feedback on the manuscript. Open Accessfunding enabled and organized by Projekt DEAL.","publication":"Molecular Systems Biology","day":"01","volume":18,"title":"Growth‐mediated negative feedback shapes quantitative antibiotic response","date_created":"2023-01-16T09:58:34Z","acknowledged_ssus":[{"_id":"M-Shop"}],"citation":{"short":"A. Angermayr, T.Y. Pang, G. Chevereau, K. Mitosch, M.J. Lercher, M.T. Bollenbach, Molecular Systems Biology 18 (2022).","ieee":"A. Angermayr, T. Y. Pang, G. Chevereau, K. Mitosch, M. J. Lercher, and M. T. Bollenbach, “Growth‐mediated negative feedback shapes quantitative antibiotic response,” <i>Molecular Systems Biology</i>, vol. 18, no. 9. Embo Press, 2022.","ista":"Angermayr A, Pang TY, Chevereau G, Mitosch K, Lercher MJ, Bollenbach MT. 2022. Growth‐mediated negative feedback shapes quantitative antibiotic response. Molecular Systems Biology. 18(9), e10490.","ama":"Angermayr A, Pang TY, Chevereau G, Mitosch K, Lercher MJ, Bollenbach MT. Growth‐mediated negative feedback shapes quantitative antibiotic response. <i>Molecular Systems Biology</i>. 2022;18(9). doi:<a href=\"https://doi.org/10.15252/msb.202110490\">10.15252/msb.202110490</a>","mla":"Angermayr, Andreas, et al. “Growth‐mediated Negative Feedback Shapes Quantitative Antibiotic Response.” <i>Molecular Systems Biology</i>, vol. 18, no. 9, e10490, Embo Press, 2022, doi:<a href=\"https://doi.org/10.15252/msb.202110490\">10.15252/msb.202110490</a>.","chicago":"Angermayr, Andreas, Tin Yau Pang, Guillaume Chevereau, Karin Mitosch, Martin J Lercher, and Mark Tobias Bollenbach. “Growth‐mediated Negative Feedback Shapes Quantitative Antibiotic Response.” <i>Molecular Systems Biology</i>. Embo Press, 2022. <a href=\"https://doi.org/10.15252/msb.202110490\">https://doi.org/10.15252/msb.202110490</a>.","apa":"Angermayr, A., Pang, T. Y., Chevereau, G., Mitosch, K., Lercher, M. J., &#38; Bollenbach, M. T. (2022). Growth‐mediated negative feedback shapes quantitative antibiotic response. <i>Molecular Systems Biology</i>. Embo Press. <a href=\"https://doi.org/10.15252/msb.202110490\">https://doi.org/10.15252/msb.202110490</a>"},"quality_controlled":"1","oa":1,"article_number":"e10490"},{"tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"article_processing_charge":"Yes (via OA deal)","doi":"10.1111/jeb.14005","file_date_updated":"2023-01-30T10:05:31Z","intvolume":"        35","has_accepted_license":"1","date_published":"2022-09-01T00:00:00Z","day":"01","acknowledgement":"We are grateful to the participants of the ESEB satellite symposium ‘Understanding reproductive isolation: bridging conceptual barriers in  speciation  research’  in  2021  for  the  interesting  discussions  that  helped  us  clarify  the  thoughts  presented  in  this  article.  We  thank  Roger Butlin, Michael Turelli and two anonymous reviewers for their thoughtful comments on this manuscript. We are also very grateful to Roger Butlin and the Barton Group for the continued conversa-tions about RI. In addition, we thank all participants of the speciation survey. Part of this work was funded by the Austrian Science Fund FWF (grant P 32166)","publication":"Journal of Evolutionary Biology","volume":35,"pmid":1,"title":"What is reproductive isolation?","page":"1143-1164","citation":{"ama":"Westram AM, Stankowski S, Surendranadh P, Barton NH. What is reproductive isolation? <i>Journal of Evolutionary Biology</i>. 2022;35(9):1143-1164. doi:<a href=\"https://doi.org/10.1111/jeb.14005\">10.1111/jeb.14005</a>","ieee":"A. M. Westram, S. Stankowski, P. Surendranadh, and N. H. Barton, “What is reproductive isolation?,” <i>Journal of Evolutionary Biology</i>, vol. 35, no. 9. Wiley, pp. 1143–1164, 2022.","short":"A.M. Westram, S. Stankowski, P. Surendranadh, N.H. Barton, Journal of Evolutionary Biology 35 (2022) 1143–1164.","ista":"Westram AM, Stankowski S, Surendranadh P, Barton NH. 2022. What is reproductive isolation? Journal of Evolutionary Biology. 35(9), 1143–1164.","apa":"Westram, A. M., Stankowski, S., Surendranadh, P., &#38; Barton, N. H. (2022). What is reproductive isolation? <i>Journal of Evolutionary Biology</i>. Wiley. <a href=\"https://doi.org/10.1111/jeb.14005\">https://doi.org/10.1111/jeb.14005</a>","chicago":"Westram, Anja M, Sean Stankowski, Parvathy Surendranadh, and Nicholas H Barton. “What Is Reproductive Isolation?” <i>Journal of Evolutionary Biology</i>. Wiley, 2022. <a href=\"https://doi.org/10.1111/jeb.14005\">https://doi.org/10.1111/jeb.14005</a>.","mla":"Westram, Anja M., et al. “What Is Reproductive Isolation?” <i>Journal of Evolutionary Biology</i>, vol. 35, no. 9, Wiley, 2022, pp. 1143–64, doi:<a href=\"https://doi.org/10.1111/jeb.14005\">10.1111/jeb.14005</a>."},"date_created":"2023-01-16T09:59:24Z","quality_controlled":"1","oa":1,"status":"public","author":[{"first_name":"Anja M","id":"3C147470-F248-11E8-B48F-1D18A9856A87","full_name":"Westram, Anja M","last_name":"Westram","orcid":"0000-0003-1050-4969"},{"full_name":"Stankowski, Sean","last_name":"Stankowski","first_name":"Sean","id":"43161670-5719-11EA-8025-FABC3DDC885E"},{"first_name":"Parvathy","id":"455235B8-F248-11E8-B48F-1D18A9856A87","full_name":"Surendranadh, Parvathy","last_name":"Surendranadh"},{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H","orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H","last_name":"Barton"}],"related_material":{"record":[{"id":"12265","status":"public","relation":"other"}]},"keyword":["Ecology","Evolution","Behavior and Systematics"],"abstract":[{"lang":"eng","text":"Reproductive isolation (RI) is a core concept in evolutionary biology. It has been the central focus of speciation research since the modern synthesis and is the basis by which biological species are defined. Despite this, the term is used in seemingly different ways, and attempts to quantify RI have used very different approaches. After showing that the field lacks a clear definition of the term, we attempt to clarify key issues, including what RI is, how it can be quantified in principle, and how it can be measured in practice. Following other definitions with a genetic focus, we propose that RI is a quantitative measure of the effect that genetic differences between populations have on gene flow. Specifically, RI compares the flow of neutral alleles in the presence of these genetic differences to the flow without any such differences. RI is thus greater than zero when genetic differences between populations reduce the flow of neutral alleles between populations. We show how RI can be quantified in a range of scenarios. A key conclusion is that RI depends strongly on circumstances—including the spatial, temporal and genomic context—making it difficult to compare across systems. After reviewing methods for estimating RI from data, we conclude that it is difficult to measure in practice. We discuss our findings in light of the goals of speciation research and encourage the use of methods for estimating RI that integrate organismal and genetic approaches."}],"scopus_import":"1","date_updated":"2023-08-04T09:53:40Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","language":[{"iso":"eng"}],"department":[{"_id":"NiBa"}],"article_type":"review","publication_identifier":{"issn":["1010-061X"],"eissn":["1420-9101"]},"isi":1,"project":[{"grant_number":"P32166","name":"The maintenance of alternative adaptive peaks in snapdragons","_id":"05959E1C-7A3F-11EA-A408-12923DDC885E"}],"year":"2022","month":"09","type":"journal_article","file":[{"date_updated":"2023-01-30T10:05:31Z","access_level":"open_access","content_type":"application/pdf","date_created":"2023-01-30T10:05:31Z","checksum":"f08de57112330a7ee88d2e1b20576a1e","file_size":3146793,"success":1,"file_name":"2022_JourEvoBiology_Westram.pdf","relation":"main_file","file_id":"12448","creator":"dernst"}],"ddc":["570"],"oa_version":"Published Version","publication_status":"published","external_id":{"pmid":["36063156"],"isi":["000849851100002"]},"issue":"9","_id":"12264","publisher":"Wiley"},{"file_date_updated":"2023-01-30T10:14:09Z","doi":"10.1111/jeb.14082","article_processing_charge":"Yes (via OA deal)","tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"volume":35,"acknowledgement":"We  are  very  grateful  to  the  authors  of  the  commentaries  for  the  interesting discussion and to Luke Holman for handling this set of manuscripts. Part of this work was funded by the Austrian Science Fund FWF (grant P 32166).","day":"01","publication":"Journal of Evolutionary Biology","date_published":"2022-09-01T00:00:00Z","intvolume":"        35","has_accepted_license":"1","page":"1200-1205","title":"Reproductive isolation, speciation, and the value of disagreement: A reply to the commentaries on ‘What is reproductive isolation?’","oa":1,"quality_controlled":"1","date_created":"2023-01-16T09:59:37Z","citation":{"mla":"Westram, Anja M., et al. “Reproductive Isolation, Speciation, and the Value of Disagreement: A Reply to the Commentaries on ‘What Is Reproductive Isolation?’” <i>Journal of Evolutionary Biology</i>, vol. 35, no. 9, Wiley, 2022, pp. 1200–05, doi:<a href=\"https://doi.org/10.1111/jeb.14082\">10.1111/jeb.14082</a>.","chicago":"Westram, Anja M, Sean Stankowski, Parvathy Surendranadh, and Nicholas H Barton. “Reproductive Isolation, Speciation, and the Value of Disagreement: A Reply to the Commentaries on ‘What Is Reproductive Isolation?’” <i>Journal of Evolutionary Biology</i>. Wiley, 2022. <a href=\"https://doi.org/10.1111/jeb.14082\">https://doi.org/10.1111/jeb.14082</a>.","apa":"Westram, A. M., Stankowski, S., Surendranadh, P., &#38; Barton, N. H. (2022). Reproductive isolation, speciation, and the value of disagreement: A reply to the commentaries on ‘What is reproductive isolation?’ <i>Journal of Evolutionary Biology</i>. Wiley. <a href=\"https://doi.org/10.1111/jeb.14082\">https://doi.org/10.1111/jeb.14082</a>","ista":"Westram AM, Stankowski S, Surendranadh P, Barton NH. 2022. Reproductive isolation, speciation, and the value of disagreement: A reply to the commentaries on ‘What is reproductive isolation?’ Journal of Evolutionary Biology. 35(9), 1200–1205.","ieee":"A. M. Westram, S. Stankowski, P. Surendranadh, and N. H. Barton, “Reproductive isolation, speciation, and the value of disagreement: A reply to the commentaries on ‘What is reproductive isolation?,’” <i>Journal of Evolutionary Biology</i>, vol. 35, no. 9. Wiley, pp. 1200–1205, 2022.","short":"A.M. Westram, S. Stankowski, P. Surendranadh, N.H. Barton, Journal of Evolutionary Biology 35 (2022) 1200–1205.","ama":"Westram AM, Stankowski S, Surendranadh P, Barton NH. Reproductive isolation, speciation, and the value of disagreement: A reply to the commentaries on ‘What is reproductive isolation?’ <i>Journal of Evolutionary Biology</i>. 2022;35(9):1200-1205. doi:<a href=\"https://doi.org/10.1111/jeb.14082\">10.1111/jeb.14082</a>"},"author":[{"full_name":"Westram, Anja M","last_name":"Westram","orcid":"0000-0003-1050-4969","id":"3C147470-F248-11E8-B48F-1D18A9856A87","first_name":"Anja M"},{"full_name":"Stankowski, Sean","last_name":"Stankowski","first_name":"Sean","id":"43161670-5719-11EA-8025-FABC3DDC885E"},{"last_name":"Surendranadh","full_name":"Surendranadh, Parvathy","id":"455235B8-F248-11E8-B48F-1D18A9856A87","first_name":"Parvathy"},{"full_name":"Barton, Nicholas H","last_name":"Barton","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H"}],"status":"public","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","language":[{"iso":"eng"}],"date_updated":"2023-08-04T09:53:41Z","scopus_import":"1","related_material":{"record":[{"id":"12264","status":"public","relation":"other"}]},"keyword":["Ecology","Evolution","Behavior and Systematics"],"year":"2022","month":"09","project":[{"grant_number":"P32166","_id":"05959E1C-7A3F-11EA-A408-12923DDC885E","name":"The maintenance of alternative adaptive peaks in snapdragons"}],"isi":1,"publication_identifier":{"eissn":["1420-9101"],"issn":["1010-061X"]},"article_type":"letter_note","department":[{"_id":"NiBa"}],"publisher":"Wiley","issue":"9","_id":"12265","publication_status":"published","external_id":{"isi":["000849851100009"]},"ddc":["570"],"type":"journal_article","oa_version":"Published Version","file":[{"success":1,"checksum":"27268009e5eec030bc10667a4ac5ed4c","file_size":349603,"date_created":"2023-01-30T10:14:09Z","content_type":"application/pdf","access_level":"open_access","date_updated":"2023-01-30T10:14:09Z","creator":"dernst","file_id":"12449","relation":"main_file","file_name":"2022_JourEvoBiology_Westram_Response.pdf"}]},{"date_published":"2022-08-25T00:00:00Z","has_accepted_license":"1","intvolume":"        12","pmid":1,"day":"25","publication":"Frontiers in Oncology","acknowledgement":"The research leading to these results has received funding from AIRC under IG 2021 - ID. 26328 project – P.I. Cortese Barbara and AIRC under MFAG 2015 - ID. 16803 project – “P.I. Cortese Barbara”. The authors are also grateful to the ”Tecnopolo per la medicina di precisione” (TecnoMed Puglia) - Regione Puglia: DGR n.2117 del 21/11/2018, CUP: B84I18000540002 and “Tecnopolo di Nanotecnologia e Fotonica per la medicina di precisione” (TECNOMED) - FISR/MIUR-CNR: delibera CIPE n.3449 del 7-08-2017, CUP: B83B17000010001.\r\nWe thank Dr. Francesca Pagani for useful technical support. We thank also Irene Iacuitto, Giovanna Loffredo and Manuela Marchetti for practical administrative support.","volume":12,"tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"article_processing_charge":"No","file_date_updated":"2023-01-30T10:25:21Z","doi":"10.3389/fonc.2022.983507","quality_controlled":"1","date_created":"2023-01-16T10:00:28Z","citation":{"ista":"Basilico B, Palamà IE, D’Amone S, Lauro C, Rosito M, Grieco M, Ratano P, Cordella F, Sanchini C, Di Angelantonio S, Ragozzino D, Cascione M, Gigli G, Cortese B. 2022. Substrate stiffness effect on molecular crosstalk of epithelial-mesenchymal transition mediators of human glioblastoma cells. Frontiers in Oncology. 12, 983507.","short":"B. Basilico, I.E. Palamà, S. D’Amone, C. Lauro, M. Rosito, M. Grieco, P. Ratano, F. Cordella, C. Sanchini, S. Di Angelantonio, D. Ragozzino, M. Cascione, G. Gigli, B. Cortese, Frontiers in Oncology 12 (2022).","ieee":"B. Basilico <i>et al.</i>, “Substrate stiffness effect on molecular crosstalk of epithelial-mesenchymal transition mediators of human glioblastoma cells,” <i>Frontiers in Oncology</i>, vol. 12. Frontiers Media, 2022.","ama":"Basilico B, Palamà IE, D’Amone S, et al. Substrate stiffness effect on molecular crosstalk of epithelial-mesenchymal transition mediators of human glioblastoma cells. <i>Frontiers in Oncology</i>. 2022;12. doi:<a href=\"https://doi.org/10.3389/fonc.2022.983507\">10.3389/fonc.2022.983507</a>","chicago":"Basilico, Bernadette, Ilaria Elena Palamà, Stefania D’Amone, Clotilde Lauro, Maria Rosito, Maddalena Grieco, Patrizia Ratano, et al. “Substrate Stiffness Effect on Molecular Crosstalk of Epithelial-Mesenchymal Transition Mediators of Human Glioblastoma Cells.” <i>Frontiers in Oncology</i>. Frontiers Media, 2022. <a href=\"https://doi.org/10.3389/fonc.2022.983507\">https://doi.org/10.3389/fonc.2022.983507</a>.","apa":"Basilico, B., Palamà, I. E., D’Amone, S., Lauro, C., Rosito, M., Grieco, M., … Cortese, B. (2022). Substrate stiffness effect on molecular crosstalk of epithelial-mesenchymal transition mediators of human glioblastoma cells. <i>Frontiers in Oncology</i>. Frontiers Media. <a href=\"https://doi.org/10.3389/fonc.2022.983507\">https://doi.org/10.3389/fonc.2022.983507</a>","mla":"Basilico, Bernadette, et al. “Substrate Stiffness Effect on Molecular Crosstalk of Epithelial-Mesenchymal Transition Mediators of Human Glioblastoma Cells.” <i>Frontiers in Oncology</i>, vol. 12, 983507, Frontiers Media, 2022, doi:<a href=\"https://doi.org/10.3389/fonc.2022.983507\">10.3389/fonc.2022.983507</a>."},"oa":1,"article_number":"983507","title":"Substrate stiffness effect on molecular crosstalk of epithelial-mesenchymal transition mediators of human glioblastoma cells","scopus_import":"1","keyword":["Cancer Research","Oncology"],"abstract":[{"text":"The complexity of the microenvironment effects on cell response, show accumulating evidence that glioblastoma (GBM) migration and invasiveness are influenced by the mechanical rigidity of their surroundings. The epithelial–mesenchymal transition (EMT) is a well-recognized driving force of the invasive behavior of cancer. However, the primary mechanisms of EMT initiation and progression remain unclear. We have previously showed that certain substrate stiffness can selectively stimulate human GBM U251-MG and GL15 glioblastoma cell lines motility. The present study unifies several known EMT mediators to uncover the reason of the regulation and response to these stiffnesses. Our results revealed that changing the rigidity of the mechanical environment tuned the response of both cell lines through change in morphological features, epithelial-mesenchymal markers (E-, N-Cadherin), EGFR and ROS expressions in an interrelated manner. Specifically, a stiffer microenvironment induced a mesenchymal cell shape, a more fragmented morphology, higher intracellular cytosolic ROS expression and lower mitochondrial ROS. Finally, we observed that cells more motile showed a more depolarized mitochondrial membrane potential. Unravelling the process that regulates GBM cells’ infiltrative behavior could provide new opportunities for identification of new targets and less invasive approaches for treatment.","lang":"eng"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","language":[{"iso":"eng"}],"date_updated":"2023-08-04T09:54:16Z","status":"public","author":[{"id":"36035796-5ACA-11E9-A75E-7AF2E5697425","first_name":"Bernadette","last_name":"Basilico","full_name":"Basilico, Bernadette","orcid":"0000-0003-1843-3173"},{"full_name":"Palamà, Ilaria Elena","last_name":"Palamà","first_name":"Ilaria Elena"},{"last_name":"D’Amone","full_name":"D’Amone, Stefania","first_name":"Stefania"},{"last_name":"Lauro","full_name":"Lauro, Clotilde","first_name":"Clotilde"},{"first_name":"Maria","last_name":"Rosito","full_name":"Rosito, Maria"},{"last_name":"Grieco","full_name":"Grieco, Maddalena","first_name":"Maddalena"},{"full_name":"Ratano, Patrizia","last_name":"Ratano","first_name":"Patrizia"},{"first_name":"Federica","full_name":"Cordella, Federica","last_name":"Cordella"},{"full_name":"Sanchini, Caterina","last_name":"Sanchini","first_name":"Caterina"},{"last_name":"Di Angelantonio","full_name":"Di Angelantonio, Silvia","first_name":"Silvia"},{"last_name":"Ragozzino","full_name":"Ragozzino, Davide","first_name":"Davide"},{"first_name":"Mariafrancesca","last_name":"Cascione","full_name":"Cascione, Mariafrancesca"},{"full_name":"Gigli, Giuseppe","last_name":"Gigli","first_name":"Giuseppe"},{"first_name":"Barbara","full_name":"Cortese, Barbara","last_name":"Cortese"}],"publication_status":"published","external_id":{"isi":["000856524900001"],"pmid":["36091138"]},"_id":"12268","oa_version":"Published Version","type":"journal_article","file":[{"relation":"main_file","file_id":"12450","creator":"dernst","file_name":"2022_FrontiersOntology_Basilico.pdf","date_created":"2023-01-30T10:25:21Z","checksum":"efc7edf9f626af31853790c5b598a68c","file_size":13588502,"success":1,"date_updated":"2023-01-30T10:25:21Z","access_level":"open_access","content_type":"application/pdf"}],"ddc":["570"],"publisher":"Frontiers Media","article_type":"original","department":[{"_id":"GaNo"}],"year":"2022","month":"08","publication_identifier":{"issn":["2234-943X"]},"isi":1},{"title":"Absence of thermalization of free systems coupled to gapped interacting reservoirs","oa":1,"article_number":"054314","arxiv":1,"quality_controlled":"1","date_created":"2023-01-16T10:00:39Z","citation":{"apa":"Ljubotina, M., Roy, D., &#38; Prosen, T. (2022). Absence of thermalization of free systems coupled to gapped interacting reservoirs. <i>Physical Review B</i>. American Physical Society. <a href=\"https://doi.org/10.1103/physrevb.106.054314\">https://doi.org/10.1103/physrevb.106.054314</a>","chicago":"Ljubotina, Marko, Dibyendu Roy, and Tomaž Prosen. “Absence of Thermalization of Free Systems Coupled to Gapped Interacting Reservoirs.” <i>Physical Review B</i>. American Physical Society, 2022. <a href=\"https://doi.org/10.1103/physrevb.106.054314\">https://doi.org/10.1103/physrevb.106.054314</a>.","mla":"Ljubotina, Marko, et al. “Absence of Thermalization of Free Systems Coupled to Gapped Interacting Reservoirs.” <i>Physical Review B</i>, vol. 106, no. 5, 054314, American Physical Society, 2022, doi:<a href=\"https://doi.org/10.1103/physrevb.106.054314\">10.1103/physrevb.106.054314</a>.","ama":"Ljubotina M, Roy D, Prosen T. Absence of thermalization of free systems coupled to gapped interacting reservoirs. <i>Physical Review B</i>. 2022;106(5). doi:<a href=\"https://doi.org/10.1103/physrevb.106.054314\">10.1103/physrevb.106.054314</a>","short":"M. Ljubotina, D. Roy, T. Prosen, Physical Review B 106 (2022).","ista":"Ljubotina M, Roy D, Prosen T. 2022. Absence of thermalization of free systems coupled to gapped interacting reservoirs. Physical Review B. 106(5), 054314.","ieee":"M. Ljubotina, D. Roy, and T. Prosen, “Absence of thermalization of free systems coupled to gapped interacting reservoirs,” <i>Physical Review B</i>, vol. 106, no. 5. American Physical Society, 2022."},"doi":"10.1103/physrevb.106.054314","article_processing_charge":"No","ec_funded":1,"acknowledgement":"M.L. and T.P. acknowledge support from the European Research Council (ERC) through the advanced grant 694544 – OMNES and the grant P1-0402 of Slovenian Research Agency (ARRS). M.L. acknowledges support from the European Research Council (ERC) through the starting grant 850899 – NEQuM. D.R. acknowledges support from the Ministry of Electronics & Information Technology (MeitY), India under the grant for “Centre for Excellence in Quantum\r\nTechnologies” with Ref. No. 4(7)/2020-ITEA. ","publication":"Physical Review B","day":"31","volume":106,"date_published":"2022-08-31T00:00:00Z","intvolume":"       106","project":[{"name":"Non-Ergodic Quantum Matter: Universality, Dynamics and Control","call_identifier":"H2020","_id":"23841C26-32DE-11EA-91FC-C7463DDC885E","grant_number":"850899"}],"year":"2022","month":"08","publication_identifier":{"eissn":["2469-9969"],"issn":["2469-9950"]},"isi":1,"article_type":"original","department":[{"_id":"MaSe"}],"publisher":"American Physical Society","external_id":{"isi":["000861332900005"],"arxiv":["2106.08373"]},"publication_status":"published","_id":"12269","issue":"5","oa_version":"Preprint","type":"journal_article","status":"public","author":[{"full_name":"Ljubotina, Marko","last_name":"Ljubotina","id":"F75EE9BE-5C90-11EA-905D-16643DDC885E","first_name":"Marko"},{"first_name":"Dibyendu","last_name":"Roy","full_name":"Roy, Dibyendu"},{"first_name":"Tomaž","full_name":"Prosen, Tomaž","last_name":"Prosen"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","language":[{"iso":"eng"}],"date_updated":"2023-08-04T10:07:33Z","scopus_import":"1","main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2106.08373","open_access":"1"}],"abstract":[{"text":"We study the thermalization of a small XX chain coupled to long, gapped XXZ leads at either side by observing the relaxation dynamics of the whole system. Using extensive tensor network simulations, we show that such systems, although not integrable, appear to show either extremely slow thermalization or even lack thereof since the two cannot be distinguished within the accuracy of our numerics. We show that the persistent oscillations observed in the spin current in the middle of the XX chain are related to eigenstates of the entire system located within the gap of the boundary chains. We find from exact diagonalization that some of these states remain strictly localized within the XX chain and do not hybridize with the rest of the system. The frequencies of the persistent oscillations determined by numerical simulations of dynamics match the energy differences between these states exactly. This has important implications for open systems, where the strongly interacting leads are often assumed to thermalize the central system. Our results suggest that, if we employ gapped systems for the leads, this assumption does not hold.","lang":"eng"}]},{"citation":{"mla":"Stopp, Julian A., and Michael K. Sixt. “Plan Your Trip before You Leave: The Neutrophils’ Search-and-Run Journey.” <i>Journal of Cell Biology</i>, vol. 221, no. 8, e202206127, Rockefeller University Press, 2022, doi:<a href=\"https://doi.org/10.1083/jcb.202206127\">10.1083/jcb.202206127</a>.","chicago":"Stopp, Julian A, and Michael K Sixt. “Plan Your Trip before You Leave: The Neutrophils’ Search-and-Run Journey.” <i>Journal of Cell Biology</i>. Rockefeller University Press, 2022. <a href=\"https://doi.org/10.1083/jcb.202206127\">https://doi.org/10.1083/jcb.202206127</a>.","apa":"Stopp, J. A., &#38; Sixt, M. K. (2022). Plan your trip before you leave: The neutrophils’ search-and-run journey. <i>Journal of Cell Biology</i>. Rockefeller University Press. <a href=\"https://doi.org/10.1083/jcb.202206127\">https://doi.org/10.1083/jcb.202206127</a>","short":"J.A. Stopp, M.K. Sixt, Journal of Cell Biology 221 (2022).","ieee":"J. A. Stopp and M. K. Sixt, “Plan your trip before you leave: The neutrophils’ search-and-run journey,” <i>Journal of Cell Biology</i>, vol. 221, no. 8. Rockefeller University Press, 2022.","ista":"Stopp JA, Sixt MK. 2022. Plan your trip before you leave: The neutrophils’ search-and-run journey. Journal of Cell Biology. 221(8), e202206127.","ama":"Stopp JA, Sixt MK. Plan your trip before you leave: The neutrophils’ search-and-run journey. <i>Journal of Cell Biology</i>. 2022;221(8). doi:<a href=\"https://doi.org/10.1083/jcb.202206127\">10.1083/jcb.202206127</a>"},"date_created":"2023-01-16T10:01:08Z","quality_controlled":"1","oa":1,"article_number":"e202206127","title":"Plan your trip before you leave: The neutrophils’ search-and-run journey","intvolume":"       221","has_accepted_license":"1","date_published":"2022-07-20T00:00:00Z","publication":"Journal of Cell Biology","day":"20","volume":221,"pmid":1,"tmp":{"short":"CC BY-NC-SA (4.0)","image":"/images/cc_by_nc_sa.png","name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode"},"article_processing_charge":"No","doi":"10.1083/jcb.202206127","file_date_updated":"2023-01-30T10:39:34Z","type":"journal_article","oa_version":"Published Version","ddc":["570"],"file":[{"checksum":"6b1620743669679b48b9389bb40f5a11","success":1,"file_size":969969,"date_created":"2023-01-30T10:39:34Z","content_type":"application/pdf","access_level":"open_access","date_updated":"2023-01-30T10:39:34Z","creator":"dernst","file_id":"12451","relation":"main_file","file_name":"2022_JourCellBiology_Stopp.pdf"}],"publication_status":"published","external_id":{"pmid":["35856919"],"isi":["000874717200001"]},"_id":"12272","issue":"8","publisher":"Rockefeller University Press","department":[{"_id":"MiSi"}],"article_type":"original","publication_identifier":{"eissn":["1540-8140"],"issn":["0021-9525"]},"isi":1,"month":"07","year":"2022","keyword":["Cell Biology"],"related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"14697"}]},"abstract":[{"lang":"eng","text":"Reading, interpreting and crawling along gradients of chemotactic cues is one of the most complex questions in cell biology. In this issue, Georgantzoglou et al. (2022. J. Cell. Biol.https://doi.org/10.1083/jcb.202103207) use in vivo models to map the temporal sequence of how neutrophils respond to an acutely arising gradient of chemoattractant."}],"scopus_import":"1","date_updated":"2023-12-21T14:30:01Z","language":[{"iso":"eng"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","status":"public","author":[{"id":"489E3F00-F248-11E8-B48F-1D18A9856A87","first_name":"Julian A","last_name":"Stopp","full_name":"Stopp, Julian A"},{"first_name":"Michael K","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","full_name":"Sixt, Michael K","last_name":"Sixt","orcid":"0000-0002-6620-9179"}],"license":"https://creativecommons.org/licenses/by-nc-sa/4.0/"},{"title":"Quadratically constrained myopic adversarial channels","page":"4901-4948","quality_controlled":"1","arxiv":1,"citation":{"chicago":"Zhang, Yihan, Shashank Vatedka, Sidharth Jaggi, and Anand D. Sarwate. “Quadratically Constrained Myopic Adversarial Channels.” <i>IEEE Transactions on Information Theory</i>. Institute of Electrical and Electronics Engineers, 2022. <a href=\"https://doi.org/10.1109/tit.2022.3167554\">https://doi.org/10.1109/tit.2022.3167554</a>.","apa":"Zhang, Y., Vatedka, S., Jaggi, S., &#38; Sarwate, A. D. (2022). Quadratically constrained myopic adversarial channels. <i>IEEE Transactions on Information Theory</i>. Institute of Electrical and Electronics Engineers. <a href=\"https://doi.org/10.1109/tit.2022.3167554\">https://doi.org/10.1109/tit.2022.3167554</a>","mla":"Zhang, Yihan, et al. “Quadratically Constrained Myopic Adversarial Channels.” <i>IEEE Transactions on Information Theory</i>, vol. 68, no. 8, Institute of Electrical and Electronics Engineers, 2022, pp. 4901–48, doi:<a href=\"https://doi.org/10.1109/tit.2022.3167554\">10.1109/tit.2022.3167554</a>.","ista":"Zhang Y, Vatedka S, Jaggi S, Sarwate AD. 2022. Quadratically constrained myopic adversarial channels. IEEE Transactions on Information Theory. 68(8), 4901–4948.","ieee":"Y. Zhang, S. Vatedka, S. Jaggi, and A. D. Sarwate, “Quadratically constrained myopic adversarial channels,” <i>IEEE Transactions on Information Theory</i>, vol. 68, no. 8. Institute of Electrical and Electronics Engineers, pp. 4901–4948, 2022.","short":"Y. Zhang, S. Vatedka, S. Jaggi, A.D. Sarwate, IEEE Transactions on Information Theory 68 (2022) 4901–4948.","ama":"Zhang Y, Vatedka S, Jaggi S, Sarwate AD. Quadratically constrained myopic adversarial channels. <i>IEEE Transactions on Information Theory</i>. 2022;68(8):4901-4948. doi:<a href=\"https://doi.org/10.1109/tit.2022.3167554\">10.1109/tit.2022.3167554</a>"},"date_created":"2023-01-16T10:01:19Z","oa":1,"article_processing_charge":"No","doi":"10.1109/tit.2022.3167554","date_published":"2022-08-01T00:00:00Z","intvolume":"        68","day":"01","publication":"IEEE Transactions on Information Theory","volume":68,"article_type":"original","department":[{"_id":"MaMo"}],"month":"08","year":"2022","publication_identifier":{"eissn":["1557-9654"],"issn":["0018-9448"]},"isi":1,"external_id":{"arxiv":["1801.05951"],"isi":["000838527100004"]},"publication_status":"published","issue":"8","_id":"12273","type":"journal_article","oa_version":"Preprint","publisher":"Institute of Electrical and Electronics Engineers","status":"public","author":[{"first_name":"Yihan","id":"2ce5da42-b2ea-11eb-bba5-9f264e9d002c","full_name":"Zhang, Yihan","last_name":"Zhang"},{"first_name":"Shashank","full_name":"Vatedka, Shashank","last_name":"Vatedka"},{"full_name":"Jaggi, Sidharth","last_name":"Jaggi","first_name":"Sidharth"},{"first_name":"Anand D.","last_name":"Sarwate","full_name":"Sarwate, Anand D."}],"scopus_import":"1","main_file_link":[{"url":"https://doi.org/10.48550/arXiv.1801.05951","open_access":"1"}],"abstract":[{"lang":"eng","text":"We study communication in the presence of a jamming adversary where quadratic power constraints are imposed on the transmitter and the jammer. The jamming signal is allowed to be a function of the codebook, and a noncausal but noisy observation of the transmitted codeword. For a certain range of the noise-to-signal ratios (NSRs) of the transmitter and the jammer, we are able to characterize the capacity of this channel under deterministic encoding or stochastic encoding, i.e., with no common randomness between the encoder/decoder pair. For the remaining NSR regimes, we determine the capacity under the assumption of a small amount of common randomness (at most 2log(n) bits in one sub-regime, and at most Ω(n) bits in the other sub-regime) available to the encoder-decoder pair. Our proof techniques involve a novel myopic list-decoding result for achievability, and a Plotkin-type push attack for the converse in a subregion of the NSRs, both of which may be of independent interest. We also give bounds on the strong secrecy capacity of this channel assuming that the jammer is simultaneously eavesdropping."}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","language":[{"iso":"eng"}],"date_updated":"2023-08-04T10:08:49Z"}]