[{"department":[{"_id":"MiLe"}],"article_processing_charge":"No","author":[{"full_name":"Bighin, Giacomo","last_name":"Bighin","orcid":"0000-0001-8823-9777","first_name":"Giacomo","id":"4CA96FD4-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Luca","full_name":"Salasnich, Luca","last_name":"Salasnich"}],"scopus_import":"1","oa":1,"language":[{"iso":"eng"}],"fulldoi":"https://doi.org/10.1142/S0217979218400222","issue":"17","intvolume":"        32","date_updated":"2025-06-04T07:52:34Z","date_created":"2018-12-11T11:46:22Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"World Scientific Publishing","oa_version":"Preprint","volume":32,"external_id":{"isi":["000438217300007"],"arxiv":["1710.11171"]},"arxiv":1,"doi":"10.1142/S0217979218400222","date_published":"2018-07-10T00:00:00Z","publist_id":"7402","month":"07","isi":1,"page":"1840022","type":"journal_article","main_file_link":[{"url":"https://arxiv.org/abs/1710.11171","open_access":"1"}],"status":"public","title":"Renormalization of the superfluid density in the two-dimensional BCS-BEC crossover","year":"2018","abstract":[{"lang":"eng","text":"We analyze the theoretical derivation of the beyond-mean-field equation of state for two-dimensional gas of dilute, ultracold alkali-metal atoms in the Bardeen–Cooper–Schrieffer (BCS) to Bose–Einstein condensate (BEC) crossover. We show that at zero temperature our theory — considering Gaussian fluctuations on top of the mean-field equation of state — is in very good agreement with experimental data. Subsequently, we investigate the superfluid density at finite temperature and its renormalization due to the proliferation of vortex–antivortex pairs. By doing so, we determine the Berezinskii–Kosterlitz–Thouless (BKT) critical temperature — at which the renormalized superfluid density jumps to zero — as a function of the inter-atomic potential strength. We find that the Nelson–Kosterlitz criterion overestimates the BKT temperature with respect to the renormalization group equations, this effect being particularly relevant in the intermediate regime of the crossover."}],"publication_status":"published","publication":"International Journal of Modern Physics B","quality_controlled":"1","citation":{"ista":"Bighin G, Salasnich L. 2018. Renormalization of the superfluid density in the two-dimensional BCS-BEC crossover. International Journal of Modern Physics B. 32(17), 1840022.","short":"G. Bighin, L. Salasnich, International Journal of Modern Physics B 32 (2018) 1840022.","chicago":"Bighin, Giacomo, and Luca Salasnich. “Renormalization of the Superfluid Density in the Two-Dimensional BCS-BEC Crossover.” <i>International Journal of Modern Physics B</i>. World Scientific Publishing, 2018. <a href=\"https://doi.org/10.1142/S0217979218400222\">https://doi.org/10.1142/S0217979218400222</a>.","mla":"Bighin, Giacomo, and Luca Salasnich. “Renormalization of the Superfluid Density in the Two-Dimensional BCS-BEC Crossover.” <i>International Journal of Modern Physics B</i>, vol. 32, no. 17, World Scientific Publishing, 2018, p. 1840022, doi:<a href=\"https://doi.org/10.1142/S0217979218400222\">10.1142/S0217979218400222</a>.","apa":"Bighin, G., &#38; Salasnich, L. (2018). Renormalization of the superfluid density in the two-dimensional BCS-BEC crossover. <i>International Journal of Modern Physics B</i>. World Scientific Publishing. <a href=\"https://doi.org/10.1142/S0217979218400222\">https://doi.org/10.1142/S0217979218400222</a>","ama":"Bighin G, Salasnich L. Renormalization of the superfluid density in the two-dimensional BCS-BEC crossover. <i>International Journal of Modern Physics B</i>. 2018;32(17):1840022. doi:<a href=\"https://doi.org/10.1142/S0217979218400222\">10.1142/S0217979218400222</a>","ieee":"G. Bighin and L. Salasnich, “Renormalization of the superfluid density in the two-dimensional BCS-BEC crossover,” <i>International Journal of Modern Physics B</i>, vol. 32, no. 17. World Scientific Publishing, p. 1840022, 2018."},"day":"10","_id":"420"},{"date_created":"2018-12-11T11:46:23Z","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","date_updated":"2023-09-19T10:13:55Z","volume":114,"publisher":"Biophysical Society","oa_version":"Submitted Version","article_processing_charge":"No","author":[{"first_name":"Kinjal","full_name":"Dasbiswas, Kinjal","last_name":"Dasbiswas"},{"first_name":"Claude-Edouard B","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6005-1561","full_name":"Hannezo, Claude-Edouard B","last_name":"Hannezo"},{"full_name":"Gov, Nir","last_name":"Gov","first_name":"Nir"}],"department":[{"_id":"EdHa"}],"oa":1,"scopus_import":"1","fulldoi":"https://doi.org/10.1016/j.bpj.2017.12.022","issue":"4","intvolume":"       114","language":[{"iso":"eng"}],"title":"Theory of eppithelial cell shape transitions induced by mechanoactive chemical gradients","status":"public","year":"2018","abstract":[{"text":"Cell shape is determined by a balance of intrinsic properties of the cell as well as its mechanochemical environment. Inhomogeneous shape changes underlie many morphogenetic events and involve spatial gradients in active cellular forces induced by complex chemical signaling. Here, we introduce a mechanochemical model based on the notion that cell shape changes may be induced by external diffusible biomolecules that influence cellular contractility (or equivalently, adhesions) in a concentration-dependent manner—and whose spatial profile in turn is affected by cell shape. We map out theoretically the possible interplay between chemical concentration and cellular structure. Besides providing a direct route to spatial gradients in cell shape profiles in tissues, we show that the dependence on cell shape helps create robust mechanochemical gradients.","lang":"eng"}],"publication":"Biophysical Journal","quality_controlled":"1","day":"27","citation":{"short":"K. Dasbiswas, E.B. Hannezo, N. Gov, Biophysical Journal 114 (2018) 968–977.","ista":"Dasbiswas K, Hannezo EB, Gov N. 2018. Theory of eppithelial cell shape transitions induced by mechanoactive chemical gradients. Biophysical Journal. 114(4), 968–977.","mla":"Dasbiswas, Kinjal, et al. “Theory of Eppithelial Cell Shape Transitions Induced by Mechanoactive Chemical Gradients.” <i>Biophysical Journal</i>, vol. 114, no. 4, Biophysical Society, 2018, pp. 968–77, doi:<a href=\"https://doi.org/10.1016/j.bpj.2017.12.022\">10.1016/j.bpj.2017.12.022</a>.","chicago":"Dasbiswas, Kinjal, Edouard B Hannezo, and Nir Gov. “Theory of Eppithelial Cell Shape Transitions Induced by Mechanoactive Chemical Gradients.” <i>Biophysical Journal</i>. Biophysical Society, 2018. <a href=\"https://doi.org/10.1016/j.bpj.2017.12.022\">https://doi.org/10.1016/j.bpj.2017.12.022</a>.","apa":"Dasbiswas, K., Hannezo, E. B., &#38; Gov, N. (2018). Theory of eppithelial cell shape transitions induced by mechanoactive chemical gradients. <i>Biophysical Journal</i>. Biophysical Society. <a href=\"https://doi.org/10.1016/j.bpj.2017.12.022\">https://doi.org/10.1016/j.bpj.2017.12.022</a>","ieee":"K. Dasbiswas, E. B. Hannezo, and N. Gov, “Theory of eppithelial cell shape transitions induced by mechanoactive chemical gradients,” <i>Biophysical Journal</i>, vol. 114, no. 4. Biophysical Society, pp. 968–977, 2018.","ama":"Dasbiswas K, Hannezo EB, Gov N. Theory of eppithelial cell shape transitions induced by mechanoactive chemical gradients. <i>Biophysical Journal</i>. 2018;114(4):968-977. doi:<a href=\"https://doi.org/10.1016/j.bpj.2017.12.022\">10.1016/j.bpj.2017.12.022</a>"},"_id":"421","publication_status":"published","arxiv":1,"doi":"10.1016/j.bpj.2017.12.022","date_published":"2018-02-27T00:00:00Z","external_id":{"isi":["000428016700021"],"arxiv":["1709.01486"]},"page":"968 - 977","type":"journal_article","main_file_link":[{"url":"https://arxiv.org/abs/1709.01486","open_access":"1"}],"month":"02","publist_id":"7403","isi":1},{"acknowledgement":"We are grateful to Remy Chait for his help and assistance with establishing our experimental setups and to Tobias Bergmiller for valuable insights into some specific experimental details. We thank Luciano Marraffini for donating us the pCas9 plasmid used in this study. We also want to express our gratitude to Seth Barribeau, Andrea Betancourt, Călin Guet, Mato Lagator, Tiago Paixão and Maroš Pleška for valuable discussions on the manuscript. Finally, we would like to thank the \r\neditors and reviewers for their helpful comments and suggestions.","year":"2018","abstract":[{"lang":"eng","text":"Herd immunity, a process in which resistant individuals limit the spread of a pathogen among susceptible hosts has been extensively studied in eukaryotes. Even though bacteria have evolved multiple immune systems against their phage pathogens, herd immunity in bacteria remains unexplored. Here we experimentally demonstrate that herd immunity arises during phage epidemics in structured and unstructured Escherichia coli populations consisting of differing frequencies of susceptible and resistant cells harboring CRISPR immunity. In addition, we develop a mathematical model that quantifies how herd immunity is affected by spatial population structure, bacterial growth rate, and phage replication rate. Using our model we infer a general epidemiological rule describing the relative speed of an epidemic in partially resistant spatially structured populations. Our experimental and theoretical findings indicate that herd immunity may be important in bacterial communities, allowing for stable coexistence of bacteria and their phages and the maintenance of polymorphism in bacterial immunity."}],"status":"public","title":"CRISPR-based herd immunity can limit phage epidemics in bacterial populations","publication_status":"published","has_accepted_license":"1","file":[{"checksum":"447cf6e680bdc3c01062a8737d876569","relation":"main_file","file_id":"5689","file_name":"2018_eLife_Payne.pdf","date_updated":"2020-07-14T12:46:25Z","file_size":3533881,"date_created":"2018-12-17T10:36:07Z","access_level":"open_access","creator":"dernst","content_type":"application/pdf"}],"tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"_id":"423","publication":"eLife","quality_controlled":"1","day":"09","citation":{"ama":"Payne P, Geyrhofer L, Barton NH, Bollback JP. CRISPR-based herd immunity can limit phage epidemics in bacterial populations. <i>eLife</i>. 2018;7. doi:<a href=\"https://doi.org/10.7554/eLife.32035\">10.7554/eLife.32035</a>","ieee":"P. Payne, L. Geyrhofer, N. H. Barton, and J. P. Bollback, “CRISPR-based herd immunity can limit phage epidemics in bacterial populations,” <i>eLife</i>, vol. 7. eLife Sciences Publications, 2018.","apa":"Payne, P., Geyrhofer, L., Barton, N. H., &#38; Bollback, J. P. (2018). CRISPR-based herd immunity can limit phage epidemics in bacterial populations. <i>ELife</i>. eLife Sciences Publications. <a href=\"https://doi.org/10.7554/eLife.32035\">https://doi.org/10.7554/eLife.32035</a>","chicago":"Payne, Pavel, Lukas Geyrhofer, Nicholas H Barton, and Jonathan P Bollback. “CRISPR-Based Herd Immunity Can Limit Phage Epidemics in Bacterial Populations.” <i>ELife</i>. eLife Sciences Publications, 2018. <a href=\"https://doi.org/10.7554/eLife.32035\">https://doi.org/10.7554/eLife.32035</a>.","mla":"Payne, Pavel, et al. “CRISPR-Based Herd Immunity Can Limit Phage Epidemics in Bacterial Populations.” <i>ELife</i>, vol. 7, e32035, eLife Sciences Publications, 2018, doi:<a href=\"https://doi.org/10.7554/eLife.32035\">10.7554/eLife.32035</a>.","short":"P. Payne, L. Geyrhofer, N.H. Barton, J.P. Bollback, ELife 7 (2018).","ista":"Payne P, Geyrhofer L, Barton NH, Bollback JP. 2018. CRISPR-based herd immunity can limit phage epidemics in bacterial populations. eLife. 7, e32035."},"external_id":{"isi":["000431035800001"]},"doi":"10.7554/eLife.32035","date_published":"2018-03-09T00:00:00Z","publist_id":"7400","month":"03","isi":1,"type":"journal_article","ec_funded":1,"related_material":{"record":[{"relation":"research_data","id":"9840","status":"public"}]},"date_updated":"2025-03-31T16:00:24Z","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","date_created":"2018-12-11T11:46:23Z","oa_version":"Published Version","publisher":"eLife Sciences Publications","file_date_updated":"2020-07-14T12:46:25Z","ddc":["576"],"volume":7,"article_number":"e32035","oa":1,"scopus_import":"1","article_processing_charge":"No","department":[{"_id":"NiBa"},{"_id":"JoBo"}],"author":[{"orcid":"0000-0002-2711-9453","id":"35F78294-F248-11E8-B48F-1D18A9856A87","first_name":"Pavel","last_name":"Payne","full_name":"Payne, Pavel"},{"full_name":"Geyrhofer, Lukas","last_name":"Geyrhofer","first_name":"Lukas"},{"orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H","last_name":"Barton","full_name":"Barton, Nicholas H"},{"full_name":"Bollback, Jonathan P","last_name":"Bollback","first_name":"Jonathan P","id":"2C6FA9CC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4624-4612"}],"language":[{"iso":"eng"}],"intvolume":"         7","project":[{"grant_number":"648440","name":"Selective Barriers to Horizontal Gene Transfer","_id":"2578D616-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"fulldoi":"https://doi.org/10.7554/eLife.32035"},{"author":[{"first_name":"Jiří","full_name":"Matoušek, Jiří","last_name":"Matoušek"},{"first_name":"Eric","full_name":"Sedgwick, Eric","last_name":"Sedgwick"},{"orcid":"0000-0002-1191-6714","first_name":"Martin","id":"38AC689C-F248-11E8-B48F-1D18A9856A87","full_name":"Tancer, Martin","last_name":"Tancer"},{"orcid":"0000-0002-1494-0568","first_name":"Uli","id":"36690CA2-F248-11E8-B48F-1D18A9856A87","full_name":"Wagner, Uli","last_name":"Wagner"}],"article_processing_charge":"No","department":[{"_id":"UlWa"}],"scopus_import":"1","oa":1,"article_number":"5","project":[{"name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734"}],"fulldoi":"https://doi.org/10.1145/3078632","issue":"1","intvolume":"        65","language":[{"iso":"eng"}],"date_created":"2018-12-11T11:46:24Z","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","date_updated":"2025-06-11T07:59:02Z","related_material":{"record":[{"status":"public","id":"2157","relation":"earlier_version"}]},"volume":65,"publisher":"ACM","article_type":"original","oa_version":"Preprint","arxiv":1,"doi":"10.1145/3078632","date_published":"2018-01-01T00:00:00Z","external_id":{"arxiv":["1402.0815"],"isi":["000425685900006"]},"ec_funded":1,"type":"journal_article","main_file_link":[{"url":"https://arxiv.org/abs/1402.0815","open_access":"1"}],"month":"01","publist_id":"7398","isi":1,"title":"Embeddability in the 3-Sphere is decidable","status":"public","abstract":[{"lang":"eng","text":"We show that the following algorithmic problem is decidable: given a 2-dimensional simplicial complex, can it be embedded (topologically, or equivalently, piecewise linearly) in R3? By a known reduction, it suffices to decide the embeddability of a given triangulated 3-manifold X into the 3-sphere S3. The main step, which allows us to simplify X and recurse, is in proving that if X can be embedded in S3, then there is also an embedding in which X has a short meridian, that is, an essential curve in the boundary of X bounding a disk in S3 \\ X with length bounded by a computable function of the number of tetrahedra of X."}],"year":"2018","quality_controlled":"1","publication":"Journal of the ACM","citation":{"ieee":"J. Matoušek, E. Sedgwick, M. Tancer, and U. Wagner, “Embeddability in the 3-Sphere is decidable,” <i>Journal of the ACM</i>, vol. 65, no. 1. ACM, 2018.","ama":"Matoušek J, Sedgwick E, Tancer M, Wagner U. Embeddability in the 3-Sphere is decidable. <i>Journal of the ACM</i>. 2018;65(1). doi:<a href=\"https://doi.org/10.1145/3078632\">10.1145/3078632</a>","apa":"Matoušek, J., Sedgwick, E., Tancer, M., &#38; Wagner, U. (2018). Embeddability in the 3-Sphere is decidable. <i>Journal of the ACM</i>. ACM. <a href=\"https://doi.org/10.1145/3078632\">https://doi.org/10.1145/3078632</a>","chicago":"Matoušek, Jiří, Eric Sedgwick, Martin Tancer, and Uli Wagner. “Embeddability in the 3-Sphere Is Decidable.” <i>Journal of the ACM</i>. ACM, 2018. <a href=\"https://doi.org/10.1145/3078632\">https://doi.org/10.1145/3078632</a>.","mla":"Matoušek, Jiří, et al. “Embeddability in the 3-Sphere Is Decidable.” <i>Journal of the ACM</i>, vol. 65, no. 1, 5, ACM, 2018, doi:<a href=\"https://doi.org/10.1145/3078632\">10.1145/3078632</a>.","ista":"Matoušek J, Sedgwick E, Tancer M, Wagner U. 2018. Embeddability in the 3-Sphere is decidable. Journal of the ACM. 65(1), 5.","short":"J. Matoušek, E. Sedgwick, M. Tancer, U. Wagner, Journal of the ACM 65 (2018)."},"day":"01","_id":"425","publication_status":"published"},{"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","date_created":"2018-12-11T11:46:25Z","date_updated":"2024-10-09T20:58:28Z","volume":107,"oa_version":"None","publisher":"Elsevier","scopus_import":"1","author":[{"id":"48204546-F248-11E8-B48F-1D18A9856A87","first_name":"Sina","orcid":"0000-0002-9547-2494","last_name":"Metzler","full_name":"Metzler, Sina"},{"first_name":"Alexandra","full_name":"Schrempf, Alexandra","last_name":"Schrempf"},{"first_name":"Jürgen","full_name":"Heinze, Jürgen","last_name":"Heinze"}],"department":[{"_id":"SyCr"}],"article_processing_charge":"No","intvolume":"       107","fulldoi":"https://doi.org/10.1016/j.jinsphys.2017.12.003","language":[{"iso":"eng"}],"year":"2018","abstract":[{"text":"Sperm cells are the most morphologically diverse cells across animal taxa. Within species, sperm and ejaculate traits have been suggested to vary with the male's competitive environment, e.g., level of sperm competition, female mating status and quality, and also with male age, body mass, physiological condition, and resource availability. Most previous studies have based their conclusions on the analysis of only one or a few ejaculates per male without investigating differences among the ejaculates of the same individual. This masks potential ejaculate-specific traits. Here, we provide data on the length, quantity, and viability of sperm ejaculated by wingless males of the ant Cardiocondyla obscurior. Males of this ant species are relatively long-lived and can mate with large numbers of female sexuals throughout their lives. We analyzed all ejaculates across the individuals' lifespan and manipulated the availability of mating partners. Our study shows that both the number and size of sperm cells transferred during copulations differ among individuals and also among ejaculates of the same male. Sperm quality does not decrease with male age, but the variation in sperm number between ejaculates indicates that males need considerable time to replenish their sperm supplies. Producing many ejaculates in a short time appears to be traded-off against male longevity rather than sperm quality.","lang":"eng"}],"status":"public","title":"Individual- and ejaculate-specific sperm traits in ant males","corr_author":"1","acknowledgement":"Research with C. obscurior from Brazil was permitted by Instituto Brasileiro do Meio Ambiente e dos Recursos Naturais Renováveis, IBAMA (permit no. 20324-1). We thank the German Science Foundation ( DFG ) for funding ( Schr1135/2-1 ), T. Suckert for help with sperm length measurements and A.K. Huylmans for advice concerning graphs. One referee made helpful comments on the manuscript.\r\n","_id":"426","citation":{"ista":"Metzler S, Schrempf A, Heinze J. 2018. Individual- and ejaculate-specific sperm traits in ant males. Journal of Insect Physiology. 107, 284–290.","short":"S. Metzler, A. Schrempf, J. Heinze, Journal of Insect Physiology 107 (2018) 284–290.","mla":"Metzler, Sina, et al. “Individual- and Ejaculate-Specific Sperm Traits in Ant Males.” <i>Journal of Insect Physiology</i>, vol. 107, Elsevier, 2018, pp. 284–90, doi:<a href=\"https://doi.org/10.1016/j.jinsphys.2017.12.003\">10.1016/j.jinsphys.2017.12.003</a>.","chicago":"Metzler, Sina, Alexandra Schrempf, and Jürgen Heinze. “Individual- and Ejaculate-Specific Sperm Traits in Ant Males.” <i>Journal of Insect Physiology</i>. Elsevier, 2018. <a href=\"https://doi.org/10.1016/j.jinsphys.2017.12.003\">https://doi.org/10.1016/j.jinsphys.2017.12.003</a>.","apa":"Metzler, S., Schrempf, A., &#38; Heinze, J. (2018). Individual- and ejaculate-specific sperm traits in ant males. <i>Journal of Insect Physiology</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.jinsphys.2017.12.003\">https://doi.org/10.1016/j.jinsphys.2017.12.003</a>","ieee":"S. Metzler, A. Schrempf, and J. Heinze, “Individual- and ejaculate-specific sperm traits in ant males,” <i>Journal of Insect Physiology</i>, vol. 107. Elsevier, pp. 284–290, 2018.","ama":"Metzler S, Schrempf A, Heinze J. Individual- and ejaculate-specific sperm traits in ant males. <i>Journal of Insect Physiology</i>. 2018;107:284-290. doi:<a href=\"https://doi.org/10.1016/j.jinsphys.2017.12.003\">10.1016/j.jinsphys.2017.12.003</a>"},"day":"01","publication":"Journal of Insect Physiology","quality_controlled":"1","publication_status":"published","doi":"10.1016/j.jinsphys.2017.12.003","date_published":"2018-05-01T00:00:00Z","external_id":{"isi":["000434751100034"]},"type":"journal_article","page":"284-290","isi":1,"month":"05","publist_id":"7397"},{"ddc":["580"],"file_date_updated":"2020-07-14T12:46:26Z","volume":115,"oa_version":"Published Version","publisher":"National Academy of Sciences","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2018-12-11T11:46:25Z","date_updated":"2025-06-03T11:21:29Z","issue":"14","intvolume":"       115","fulldoi":"https://doi.org/10.1073/pnas.1721760115","project":[{"grant_number":"282300","call_identifier":"FP7","_id":"25716A02-B435-11E9-9278-68D0E5697425","name":"Polarity and subcellular dynamics in plants"}],"language":[{"iso":"eng"}],"scopus_import":"1","oa":1,"author":[{"first_name":"Yuliya","id":"46DAAE7E-F248-11E8-B48F-1D18A9856A87","full_name":"Salanenka, Yuliya","last_name":"Salanenka"},{"orcid":"0000-0001-7241-2328","first_name":"Inge","id":"362BF7FE-F248-11E8-B48F-1D18A9856A87","full_name":"Verstraeten, Inge","last_name":"Verstraeten"},{"last_name":"Löfke","full_name":"Löfke, Christian","first_name":"Christian"},{"id":"7DAAEDA4-02D0-11E9-B11A-A5A4D7DFFFD0","first_name":"Kaori","last_name":"Tabata","full_name":"Tabata, Kaori"},{"full_name":"Naramoto, Satoshi","last_name":"Naramoto","first_name":"Satoshi"},{"last_name":"Glanc","full_name":"Glanc, Matous","id":"1AE1EA24-02D0-11E9-9BAA-DAF4881429F2","first_name":"Matous","orcid":"0000-0003-0619-7783"},{"full_name":"Friml, Jirí","last_name":"Friml","orcid":"0000-0002-8302-7596","first_name":"Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87"}],"article_processing_charge":"No","department":[{"_id":"JiFr"}],"_id":"428","quality_controlled":"1","publication":"Proceedings of the National Academy of Sciences of the United States of America","day":"03","citation":{"apa":"Salanenka, Y., Verstraeten, I., Löfke, C., Tabata, K., Naramoto, S., Glanc, M., &#38; Friml, J. (2018). Gibberellin DELLA signaling targets the retromer complex to redirect protein trafficking to the plasma membrane. <i>Proceedings of the National Academy of Sciences of the United States of America</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1721760115\">https://doi.org/10.1073/pnas.1721760115</a>","ieee":"Y. Salanenka <i>et al.</i>, “Gibberellin DELLA signaling targets the retromer complex to redirect protein trafficking to the plasma membrane,” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 115, no. 14. National Academy of Sciences, pp. 3716–3721, 2018.","ama":"Salanenka Y, Verstraeten I, Löfke C, et al. Gibberellin DELLA signaling targets the retromer complex to redirect protein trafficking to the plasma membrane. <i>Proceedings of the National Academy of Sciences of the United States of America</i>. 2018;115(14):3716-3721. doi:<a href=\"https://doi.org/10.1073/pnas.1721760115\">10.1073/pnas.1721760115</a>","ista":"Salanenka Y, Verstraeten I, Löfke C, Tabata K, Naramoto S, Glanc M, Friml J. 2018. Gibberellin DELLA signaling targets the retromer complex to redirect protein trafficking to the plasma membrane. Proceedings of the National Academy of Sciences of the United States of America. 115(14), 3716–3721.","short":"Y. Salanenka, I. Verstraeten, C. Löfke, K. Tabata, S. Naramoto, M. Glanc, J. Friml, Proceedings of the National Academy of Sciences of the United States of America 115 (2018) 3716–3721.","chicago":"Salanenka, Yuliya, Inge Verstraeten, Christian Löfke, Kaori Tabata, Satoshi Naramoto, Matous Glanc, and Jiří Friml. “Gibberellin DELLA Signaling Targets the Retromer Complex to Redirect Protein Trafficking to the Plasma Membrane.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>. National Academy of Sciences, 2018. <a href=\"https://doi.org/10.1073/pnas.1721760115\">https://doi.org/10.1073/pnas.1721760115</a>.","mla":"Salanenka, Yuliya, et al. “Gibberellin DELLA Signaling Targets the Retromer Complex to Redirect Protein Trafficking to the Plasma Membrane.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 115, no. 14, National Academy of Sciences, 2018, pp. 3716–21, doi:<a href=\"https://doi.org/10.1073/pnas.1721760115\">10.1073/pnas.1721760115</a>."},"has_accepted_license":"1","publication_status":"published","file":[{"date_created":"2018-12-17T12:30:14Z","access_level":"open_access","content_type":"application/pdf","creator":"dernst","date_updated":"2020-07-14T12:46:26Z","file_size":1924101,"file_id":"5700","file_name":"2018_PNAS_Salanenka.pdf","checksum":"1fcf7223fb8f99559cfa80bd6f24ce44","relation":"main_file"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","image":"/images/cc_by_nc_nd.png"},"abstract":[{"text":"The plant hormone gibberellic acid (GA) is a crucial regulator of growth and development. The main paradigm of GA signaling puts forward transcriptional regulation via the degradation of DELLA transcriptional repressors. GA has also been shown to regulate tropic responses by modulation of the plasma membrane incidence of PIN auxin transporters by an unclear mechanism. Here we uncovered the cellular and molecular mechanisms by which GA redirects protein trafficking and thus regulates cell surface functionality. Photoconvertible reporters revealed that GA balances the protein traffic between the vacuole degradation route and recycling back to the cell surface. Low GA levels promote vacuolar delivery and degradation of multiple cargos, including PIN proteins, whereas high GA levels promote their recycling to the plasma membrane. This GA effect requires components of the retromer complex, such as Sorting Nexin 1 (SNX1) and its interacting, microtubule (MT)-associated protein, the Cytoplasmic Linker-Associated Protein (CLASP1). Accordingly, GA regulates the subcellular distribution of SNX1 and CLASP1, and the intact MT cytoskeleton is essential for the GA effect on trafficking. This GA cellular action occurs through DELLA proteins that regulate the MT and retromer presumably via their interaction partners Prefoldins (PFDs). Our study identified a branching of the GA signaling pathway at the level of DELLA proteins, which, in parallel to regulating transcription, also target by a nontranscriptional mechanism the retromer complex acting at the intersection of the degradation and recycling trafficking routes. By this mechanism, GA can redirect receptors and transporters to the cell surface, thus coregulating multiple processes, including PIN-dependent auxin fluxes during tropic responses.","lang":"eng"}],"year":"2018","corr_author":"1","status":"public","title":"Gibberellin DELLA signaling targets the retromer complex to redirect protein trafficking to the plasma membrane","acknowledgement":"We gratefully acknowledge M. Blázquez (Instituto de Biología Molecular y Celular de Plantas), M. Fendrych, C. Cuesta Moliner (Institute of Science and Technology Austria), M. Vanstraelen, M. Nowack (Center for Plant Systems Biology, Ghent), C. Luschnig (Universitat fur Bodenkultur Wien, Vienna), S. Simon (Central European Institute of Technology, Brno), C. Sommerville (Carnegie Institution for Science), and Y. Gu (Penn State University) for making available the materials used in this study;\r\n...funding from the European Research Council (ERC) under the European Union’s Seventh Framework Programme (FP7/2007-2013)/ERC Grant Agreement 282300.\r\nCC BY NC ND","type":"journal_article","page":" 3716 - 3721","ec_funded":1,"month":"04","publist_id":"7395","isi":1,"doi":"10.1073/pnas.1721760115","date_published":"2018-04-03T00:00:00Z","external_id":{"isi":["000429012500073"]}},{"isi":1,"publist_id":"8011","month":"10","ec_funded":1,"page":"10690 - 10695","type":"journal_article","publication_identifier":{"eissn":["1091-6490"],"issn":["0027-8424"]},"external_id":{"isi":["000447491300057"]},"date_published":"2018-10-02T00:00:00Z","doi":"10.1073/pnas.1721061115","file":[{"relation":"main_file","checksum":"df7ac544a587c06b75692653b9fabd18","file_id":"6258","file_name":"2018_PNAS_Rybicki.pdf","file_size":4070777,"date_updated":"2020-07-14T12:46:26Z","access_level":"open_access","date_created":"2019-04-09T08:02:50Z","content_type":"application/pdf","creator":"dernst"}],"has_accepted_license":"1","publication_status":"published","citation":{"apa":"Rybicki, J., Kisdi, E., &#38; Anttila, J. (2018). Model of bacterial toxin-dependent pathogenesis explains infective dose. <i>Proceedings of the National Academy of Sciences of the United States of America</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1721061115\">https://doi.org/10.1073/pnas.1721061115</a>","ama":"Rybicki J, Kisdi E, Anttila J. Model of bacterial toxin-dependent pathogenesis explains infective dose. <i>Proceedings of the National Academy of Sciences of the United States of America</i>. 2018;115(42):10690-10695. doi:<a href=\"https://doi.org/10.1073/pnas.1721061115\">10.1073/pnas.1721061115</a>","ieee":"J. Rybicki, E. Kisdi, and J. Anttila, “Model of bacterial toxin-dependent pathogenesis explains infective dose,” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 115, no. 42. National Academy of Sciences, pp. 10690–10695, 2018.","ista":"Rybicki J, Kisdi E, Anttila J. 2018. Model of bacterial toxin-dependent pathogenesis explains infective dose. Proceedings of the National Academy of Sciences of the United States of America. 115(42), 10690–10695.","short":"J. Rybicki, E. Kisdi, J. Anttila, Proceedings of the National Academy of Sciences of the United States of America 115 (2018) 10690–10695.","mla":"Rybicki, Joel, et al. “Model of Bacterial Toxin-Dependent Pathogenesis Explains Infective Dose.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 115, no. 42, National Academy of Sciences, 2018, pp. 10690–95, doi:<a href=\"https://doi.org/10.1073/pnas.1721061115\">10.1073/pnas.1721061115</a>.","chicago":"Rybicki, Joel, Eva Kisdi, and Jani Anttila. “Model of Bacterial Toxin-Dependent Pathogenesis Explains Infective Dose.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>. National Academy of Sciences, 2018. <a href=\"https://doi.org/10.1073/pnas.1721061115\">https://doi.org/10.1073/pnas.1721061115</a>."},"day":"02","quality_controlled":"1","publication":"Proceedings of the National Academy of Sciences of the United States of America","_id":"43","acknowledgement":"J.R. and J.V.A. were also supported by the Academy of Finland Grants 1273253 and 267541.","status":"public","title":"Model of bacterial toxin-dependent pathogenesis explains infective dose","abstract":[{"lang":"eng","text":"The initial amount of pathogens required to start an infection within a susceptible host is called the infective dose and is known to vary to a large extent between different pathogen species. We investigate the hypothesis that the differences in infective doses are explained by the mode of action in the underlying mechanism of pathogenesis: Pathogens with locally acting mechanisms tend to have smaller infective doses than pathogens with distantly acting mechanisms. While empirical evidence tends to support the hypothesis, a formal theoretical explanation has been lacking. We give simple analytical models to gain insight into this phenomenon and also investigate a stochastic, spatially explicit, mechanistic within-host model for toxin-dependent bacterial infections. The model shows that pathogens secreting locally acting toxins have smaller infective doses than pathogens secreting diffusive toxins, as hypothesized. While local pathogenetic mechanisms require smaller infective doses, pathogens with distantly acting toxins tend to spread faster and may cause more damage to the host. The proposed model can serve as a basis for the spatially explicit analysis of various virulence factors also in the context of other problems in infection dynamics."}],"year":"2018","language":[{"iso":"eng"}],"project":[{"grant_number":"754411","call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425","name":"ISTplus - Postdoctoral Fellowships"}],"fulldoi":"https://doi.org/10.1073/pnas.1721061115","pubrep_id":"1063","intvolume":"       115","issue":"42","author":[{"id":"334EFD2E-F248-11E8-B48F-1D18A9856A87","first_name":"Joel","orcid":"0000-0002-6432-6646","last_name":"Rybicki","full_name":"Rybicki, Joel"},{"full_name":"Kisdi, Eva","last_name":"Kisdi","first_name":"Eva"},{"last_name":"Anttila","full_name":"Anttila, Jani","first_name":"Jani"}],"article_processing_charge":"No","department":[{"_id":"DaAl"}],"scopus_import":"1","oa":1,"publisher":"National Academy of Sciences","oa_version":"Submitted Version","volume":115,"file_date_updated":"2020-07-14T12:46:26Z","ddc":["570","577"],"date_updated":"2025-06-03T11:16:28Z","date_created":"2018-12-11T11:44:19Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"year":"2018","abstract":[{"lang":"eng","text":"In this issue of GENETICS, a new method for detecting natural selection on polygenic traits is developed and applied to sev- eral human examples ( Racimo et al. 2018 ). By de fi nition, many loci contribute to variation in polygenic traits, and a challenge for evolutionary ge neticists has been that these traits can evolve by small, nearly undetectable shifts in allele frequencies across each of many, typically unknown, loci. Recently, a helpful remedy has arisen. Genome-wide associ- ation studies (GWAS) have been illuminating sets of loci that can be interrogated jointly for c hanges in allele frequencies. By aggregating small signal s of change across many such loci, directional natural selection is now in principle detect- able using genetic data, even for highly polygenic traits. This is an exciting arena of progress – with these methods, tests can be made for selection associated with traits, and we can now study selection in what may be its most prevalent mode. The continuing fast pace of GWAS publications suggest there will be many more polygenic tests of selection in the near future, as every new GWAS is an opportunity for an accom- panying test of polygenic selection. However, it is important to be aware of complications th at arise in interpretation, especially given that these studies may easily be misinter- preted both in and outside the evolutionary genetics commu- nity. Here, we provide context for understanding polygenic tests and urge caution regarding how these results are inter- preted and reported upon more broadly."}],"title":"Tread lightly interpreting polygenic tests of selection","status":"public","publication_status":"published","has_accepted_license":"1","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"file":[{"file_size":500129,"date_updated":"2020-07-14T12:46:26Z","access_level":"open_access","date_created":"2018-12-12T10:12:40Z","creator":"system","content_type":"application/pdf","relation":"main_file","checksum":"3d838dc285df394376555b794b6a5ad1","file_id":"4958","file_name":"IST-2018-1012-v1+1_2018_Barton_Tread.pdf"}],"_id":"430","citation":{"ieee":"J. Novembre and N. H. Barton, “Tread lightly interpreting polygenic tests of selection,” <i>Genetics</i>, vol. 208, no. 4. Genetics Society of America, pp. 1351–1355, 2018.","ama":"Novembre J, Barton NH. Tread lightly interpreting polygenic tests of selection. <i>Genetics</i>. 2018;208(4):1351-1355. doi:<a href=\"https://doi.org/10.1534/genetics.118.300786\">10.1534/genetics.118.300786</a>","apa":"Novembre, J., &#38; Barton, N. H. (2018). Tread lightly interpreting polygenic tests of selection. <i>Genetics</i>. Genetics Society of America. <a href=\"https://doi.org/10.1534/genetics.118.300786\">https://doi.org/10.1534/genetics.118.300786</a>","chicago":"Novembre, John, and Nicholas H Barton. “Tread Lightly Interpreting Polygenic Tests of Selection.” <i>Genetics</i>. Genetics Society of America, 2018. <a href=\"https://doi.org/10.1534/genetics.118.300786\">https://doi.org/10.1534/genetics.118.300786</a>.","mla":"Novembre, John, and Nicholas H. Barton. “Tread Lightly Interpreting Polygenic Tests of Selection.” <i>Genetics</i>, vol. 208, no. 4, Genetics Society of America, 2018, pp. 1351–55, doi:<a href=\"https://doi.org/10.1534/genetics.118.300786\">10.1534/genetics.118.300786</a>.","short":"J. Novembre, N.H. Barton, Genetics 208 (2018) 1351–1355.","ista":"Novembre J, Barton NH. 2018. Tread lightly interpreting polygenic tests of selection. Genetics. 208(4), 1351–1355."},"day":"01","quality_controlled":"1","publication":"Genetics","external_id":{"isi":["000429094400005"]},"doi":"10.1534/genetics.118.300786","date_published":"2018-04-01T00:00:00Z","isi":1,"publist_id":"7393","month":"04","type":"journal_article","page":"1351 - 1355","date_updated":"2023-09-19T10:17:30Z","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","date_created":"2018-12-11T11:46:26Z","oa_version":"Published Version","publisher":"Genetics Society of America","file_date_updated":"2020-07-14T12:46:26Z","ddc":["576"],"volume":208,"oa":1,"scopus_import":"1","author":[{"full_name":"Novembre, John","last_name":"Novembre","first_name":"John"},{"first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H","last_name":"Barton"}],"department":[{"_id":"NiBa"}],"article_processing_charge":"No","language":[{"iso":"eng"}],"issue":"4","intvolume":"       208","fulldoi":"https://doi.org/10.1534/genetics.118.300786","pubrep_id":"1012"},{"corr_author":"1","title":"Thrackles: An improved upper bound","status":"public","year":"2018","abstract":[{"lang":"eng","text":"A thrackle is a graph drawn in the plane so that every pair of its edges meet exactly once: either at a common end vertex or in a proper crossing. We prove that any thrackle of n vertices has at most 1.3984n edges. Quasi-thrackles are defined similarly, except that every pair of edges that do not share a vertex are allowed to cross an odd number of times. It is also shown that the maximum number of edges of a quasi-thrackle on n vertices is 3/2(n-1), and that this bound is best possible for infinitely many values of n."}],"conference":{"start_date":"201-09-25","location":"Boston, MA, United States","name":"GD: Graph Drawing and Network Visualization","end_date":"2017-09-27"},"quality_controlled":"1","day":"21","alternative_title":["LNCS"],"citation":{"ista":"Fulek R, Pach J. 2018. Thrackles: An improved upper bound. GD: Graph Drawing and Network Visualization, LNCS, vol. 10692, 160–166.","short":"R. Fulek, J. Pach, in:, Springer, 2018, pp. 160–166.","mla":"Fulek, Radoslav, and János Pach. <i>Thrackles: An Improved Upper Bound</i>. Vol. 10692, Springer, 2018, pp. 160–66, doi:<a href=\"https://doi.org/10.1007/978-3-319-73915-1_14\">10.1007/978-3-319-73915-1_14</a>.","chicago":"Fulek, Radoslav, and János Pach. “Thrackles: An Improved Upper Bound,” 10692:160–66. Springer, 2018. <a href=\"https://doi.org/10.1007/978-3-319-73915-1_14\">https://doi.org/10.1007/978-3-319-73915-1_14</a>.","apa":"Fulek, R., &#38; Pach, J. (2018). Thrackles: An improved upper bound (Vol. 10692, pp. 160–166). Presented at the GD: Graph Drawing and Network Visualization, Boston, MA, United States: Springer. <a href=\"https://doi.org/10.1007/978-3-319-73915-1_14\">https://doi.org/10.1007/978-3-319-73915-1_14</a>","ama":"Fulek R, Pach J. Thrackles: An improved upper bound. In: Vol 10692. Springer; 2018:160-166. doi:<a href=\"https://doi.org/10.1007/978-3-319-73915-1_14\">10.1007/978-3-319-73915-1_14</a>","ieee":"R. Fulek and J. Pach, “Thrackles: An improved upper bound,” presented at the GD: Graph Drawing and Network Visualization, Boston, MA, United States, 2018, vol. 10692, pp. 160–166."},"_id":"433","publication_status":"published","arxiv":1,"doi":"10.1007/978-3-319-73915-1_14","date_published":"2018-01-21T00:00:00Z","external_id":{"arxiv":["1708.08037"]},"page":"160 - 166","type":"conference","main_file_link":[{"url":"https://arxiv.org/abs/1708.08037","open_access":"1"}],"month":"01","publist_id":"7390","date_created":"2018-12-11T11:46:27Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2026-04-16T09:48:11Z","related_material":{"record":[{"relation":"later_version","id":"5857","status":"public"}]},"volume":10692,"publisher":"Springer","oa_version":"Submitted Version","author":[{"orcid":"0000-0001-8485-1774","first_name":"Radoslav","id":"39F3FFE4-F248-11E8-B48F-1D18A9856A87","full_name":"Fulek, Radoslav","last_name":"Fulek"},{"full_name":"Pach, János","last_name":"Pach","first_name":"János"}],"department":[{"_id":"UlWa"}],"article_processing_charge":"No","oa":1,"scopus_import":"1","fulldoi":"https://doi.org/10.1007/978-3-319-73915-1_14","intvolume":"     10692","language":[{"iso":"eng"}]},{"date_created":"2018-12-11T11:46:27Z","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","date_updated":"2025-09-22T09:39:54Z","related_material":{"record":[{"status":"public","relation":"earlier_version","id":"1205"}]},"volume":19,"publisher":"IEEE","oa_version":"None","article_processing_charge":"No","author":[{"last_name":"Jiang","full_name":"Jiang, Yu","first_name":"Yu"},{"last_name":"Liu","full_name":"Liu, Han","first_name":"Han"},{"first_name":"Huobing","last_name":"Song","full_name":"Song, Huobing"},{"first_name":"Hui","id":"3BDE25AA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-3066-6941","full_name":"Kong, Hui","last_name":"Kong"},{"first_name":"Rui","full_name":"Wang, Rui","last_name":"Wang"},{"last_name":"Guan","full_name":"Guan, Yong","first_name":"Yong"},{"first_name":"Lui","last_name":"Sha","full_name":"Sha, Lui"}],"department":[{"_id":"ToHe"}],"scopus_import":"1","fulldoi":"https://doi.org/10.1109/TITS.2017.2778077","intvolume":"        19","issue":"10","language":[{"iso":"eng"}],"title":"Safety-assured model-driven design of the multifunction vehicle bus controller","status":"public","abstract":[{"text":"In this paper, we present a formal model-driven design approach to establish a safety-assured implementation of multifunction vehicle bus controller (MVBC), which controls the data transmission among the devices of the vehicle. First, the generic models and safety requirements described in International Electrotechnical Commission Standard 61375 are formalized as time automata and timed computation tree logic formulas, respectively. With model checking tool Uppaal, we verify whether or not the constructed timed automata satisfy the formulas and several logic inconsistencies in the original standard are detected and corrected. Then, we apply the code generation tool Times to generate C code from the verified model, which is later synthesized into a real MVBC chip, with some handwriting glue code. Furthermore, the runtime verification tool RMOR is applied on the integrated code, to verify some safety requirements that cannot be formalized on the timed automata. For evaluation, we compare the proposed approach with existing MVBC design methods, such as BeagleBone, Galsblock, and Simulink. Experiments show that more ambiguousness or bugs in the standard are detected during Uppaal verification, and the generated code of Times outperforms the C code generated by others in terms of the synthesized binary code size. The errors in the standard have been confirmed and the resulting MVBC has been deployed in the real train communication network.","lang":"eng"}],"year":"2018","publication":"IEEE Transactions on Intelligent Transportation Systems","quality_controlled":"1","day":"01","citation":{"apa":"Jiang, Y., Liu, H., Song, H., Kong, H., Wang, R., Guan, Y., &#38; Sha, L. (2018). Safety-assured model-driven design of the multifunction vehicle bus controller. <i>IEEE Transactions on Intelligent Transportation Systems</i>. IEEE. <a href=\"https://doi.org/10.1109/TITS.2017.2778077\">https://doi.org/10.1109/TITS.2017.2778077</a>","ieee":"Y. Jiang <i>et al.</i>, “Safety-assured model-driven design of the multifunction vehicle bus controller,” <i>IEEE Transactions on Intelligent Transportation Systems</i>, vol. 19, no. 10. IEEE, pp. 3320–3333, 2018.","ama":"Jiang Y, Liu H, Song H, et al. Safety-assured model-driven design of the multifunction vehicle bus controller. <i>IEEE Transactions on Intelligent Transportation Systems</i>. 2018;19(10):3320-3333. doi:<a href=\"https://doi.org/10.1109/TITS.2017.2778077\">10.1109/TITS.2017.2778077</a>","ista":"Jiang Y, Liu H, Song H, Kong H, Wang R, Guan Y, Sha L. 2018. Safety-assured model-driven design of the multifunction vehicle bus controller. IEEE Transactions on Intelligent Transportation Systems. 19(10), 3320–3333.","short":"Y. Jiang, H. Liu, H. Song, H. Kong, R. Wang, Y. Guan, L. Sha, IEEE Transactions on Intelligent Transportation Systems 19 (2018) 3320–3333.","mla":"Jiang, Yu, et al. “Safety-Assured Model-Driven Design of the Multifunction Vehicle Bus Controller.” <i>IEEE Transactions on Intelligent Transportation Systems</i>, vol. 19, no. 10, IEEE, 2018, pp. 3320–33, doi:<a href=\"https://doi.org/10.1109/TITS.2017.2778077\">10.1109/TITS.2017.2778077</a>.","chicago":"Jiang, Yu, Han Liu, Huobing Song, Hui Kong, Rui Wang, Yong Guan, and Lui Sha. “Safety-Assured Model-Driven Design of the Multifunction Vehicle Bus Controller.” <i>IEEE Transactions on Intelligent Transportation Systems</i>. IEEE, 2018. <a href=\"https://doi.org/10.1109/TITS.2017.2778077\">https://doi.org/10.1109/TITS.2017.2778077</a>."},"_id":"434","publication_status":"published","doi":"10.1109/TITS.2017.2778077","date_published":"2018-01-01T00:00:00Z","external_id":{"isi":["000446651100020"]},"page":"3320 - 3333","type":"journal_article","month":"01","publist_id":"7389","isi":1},{"day":"01","citation":{"apa":"Kolmogorov, V., &#38; Rolinek, M. (2018). Superconcentrators of density 25.3. <i>Ars Combinatoria</i>. Charles Babbage Research Centre.","ieee":"V. Kolmogorov and M. Rolinek, “Superconcentrators of density 25.3,” <i>Ars Combinatoria</i>, vol. 141, no. 10. Charles Babbage Research Centre, pp. 269–304, 2018.","ama":"Kolmogorov V, Rolinek M. Superconcentrators of density 25.3. <i>Ars Combinatoria</i>. 2018;141(10):269-304.","ista":"Kolmogorov V, Rolinek M. 2018. Superconcentrators of density 25.3. Ars Combinatoria. 141(10), 269–304.","short":"V. Kolmogorov, M. Rolinek, Ars Combinatoria 141 (2018) 269–304.","chicago":"Kolmogorov, Vladimir, and Michal Rolinek. “Superconcentrators of Density 25.3.” <i>Ars Combinatoria</i>. Charles Babbage Research Centre, 2018.","mla":"Kolmogorov, Vladimir, and Michal Rolinek. “Superconcentrators of Density 25.3.” <i>Ars Combinatoria</i>, vol. 141, no. 10, Charles Babbage Research Centre, 2018, pp. 269–304."},"quality_controlled":"1","publication":"Ars Combinatoria","_id":"18","publication_status":"published","status":"public","title":"Superconcentrators of density 25.3","year":"2018","abstract":[{"lang":"eng","text":"An N-superconcentrator is a directed, acyclic graph with N input nodes and N output nodes such that every subset of the inputs and every subset of the outputs of same cardinality can be connected by node-disjoint paths. It is known that linear-size and bounded-degree superconcentrators exist. We prove the existence of such superconcentrators with asymptotic density 25.3 (where the density is the number of edges divided by N). The previously best known densities were 28 [12] and 27.4136 [17]."}],"page":"269 - 304","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1405.7828"}],"type":"journal_article","isi":1,"publist_id":"8037","month":"10","arxiv":1,"date_published":"2018-10-01T00:00:00Z","publication_identifier":{"issn":["0381-7032"]},"external_id":{"arxiv":["1405.7828"],"isi":["000446809500022"]},"volume":141,"publisher":"Charles Babbage Research Centre","oa_version":"Preprint","date_created":"2018-12-11T11:44:11Z","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","date_updated":"2023-09-19T14:46:18Z","issue":"10","intvolume":"       141","language":[{"iso":"eng"}],"article_processing_charge":"No","department":[{"_id":"VlKo"}],"author":[{"last_name":"Kolmogorov","full_name":"Kolmogorov, Vladimir","id":"3D50B0BA-F248-11E8-B48F-1D18A9856A87","first_name":"Vladimir"},{"full_name":"Rolinek, Michal","last_name":"Rolinek","first_name":"Michal","id":"3CB3BC06-F248-11E8-B48F-1D18A9856A87"}],"oa":1,"scopus_import":"1"},{"language":[{"iso":"eng"}],"intvolume":"         5","project":[{"grant_number":"694227","call_identifier":"H2020","_id":"25C6DC12-B435-11E9-9278-68D0E5697425","name":"Analysis of quantum many-body systems"},{"call_identifier":"FWF","_id":"25C878CE-B435-11E9-9278-68D0E5697425","name":"Structure of the Excitation Spectrum for Many-Body Quantum Systems","grant_number":"P27533_N27"}],"fulldoi":"https://doi.org/10.5802/jep.64","scopus_import":"1","oa":1,"article_processing_charge":"No","author":[{"full_name":"Lewi, Mathieu","last_name":"Lewi","first_name":"Mathieu"},{"first_name":"Élliott","last_name":"Lieb","full_name":"Lieb, Élliott"},{"id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","first_name":"Robert","orcid":"0000-0002-6781-0521","last_name":"Seiringer","full_name":"Seiringer, Robert"}],"department":[{"_id":"RoSe"}],"oa_version":"Published Version","article_type":"original","publisher":"Ecole Polytechnique","ddc":["510"],"file_date_updated":"2020-07-14T12:45:16Z","volume":5,"date_updated":"2025-04-14T07:26:59Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2018-12-11T11:45:03Z","publist_id":"7741","month":"07","type":"journal_article","ec_funded":1,"page":"79 - 116","external_id":{"arxiv":["1705.10676"]},"publication_identifier":{"issn":["2429-7100"],"eissn":["2270-518X"]},"date_published":"2018-07-01T00:00:00Z","doi":"10.5802/jep.64","arxiv":1,"publication_status":"published","has_accepted_license":"1","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nd/4.0/legalcode","short":"CC BY-ND (4.0)","name":"Creative Commons Attribution-NoDerivatives 4.0 International (CC BY-ND 4.0)","image":"/image/cc_by_nd.png"},"file":[{"file_id":"5726","file_name":"2018_JournaldeLecoleMath_Lewi.pdf","relation":"main_file","checksum":"1ba7cccdf3900f42c4f715ae75d6813c","access_level":"open_access","date_created":"2018-12-17T16:38:18Z","content_type":"application/pdf","creator":"dernst","file_size":843938,"date_updated":"2020-07-14T12:45:16Z"}],"_id":"180","day":"01","citation":{"ista":"Lewi M, Lieb É, Seiringer R. 2018. Statistical mechanics of the uniform electron gas. Journal de l’Ecole Polytechnique - Mathematiques. 5, 79–116.","short":"M. Lewi, É. Lieb, R. Seiringer, Journal de l’Ecole Polytechnique - Mathematiques 5 (2018) 79–116.","mla":"Lewi, Mathieu, et al. “Statistical Mechanics of the Uniform Electron Gas.” <i>Journal de l’Ecole Polytechnique - Mathematiques</i>, vol. 5, Ecole Polytechnique, 2018, pp. 79–116, doi:<a href=\"https://doi.org/10.5802/jep.64\">10.5802/jep.64</a>.","chicago":"Lewi, Mathieu, Élliott Lieb, and Robert Seiringer. “Statistical Mechanics of the Uniform Electron Gas.” <i>Journal de l’Ecole Polytechnique - Mathematiques</i>. Ecole Polytechnique, 2018. <a href=\"https://doi.org/10.5802/jep.64\">https://doi.org/10.5802/jep.64</a>.","apa":"Lewi, M., Lieb, É., &#38; Seiringer, R. (2018). Statistical mechanics of the uniform electron gas. <i>Journal de l’Ecole Polytechnique - Mathematiques</i>. Ecole Polytechnique. <a href=\"https://doi.org/10.5802/jep.64\">https://doi.org/10.5802/jep.64</a>","ieee":"M. Lewi, É. Lieb, and R. Seiringer, “Statistical mechanics of the uniform electron gas,” <i>Journal de l’Ecole Polytechnique - Mathematiques</i>, vol. 5. Ecole Polytechnique, pp. 79–116, 2018.","ama":"Lewi M, Lieb É, Seiringer R. Statistical mechanics of the uniform electron gas. <i>Journal de l’Ecole Polytechnique - Mathematiques</i>. 2018;5:79-116. doi:<a href=\"https://doi.org/10.5802/jep.64\">10.5802/jep.64</a>"},"publication":"Journal de l'Ecole Polytechnique - Mathematiques","quality_controlled":"1","acknowledgement":"This project has received funding from the European Research Council (ERC) under the European\r\nUnion’s Horizon 2020 research and innovation programme (grant agreement 694227 for R.S. and MDFT 725528 for M.L.). Financial support by the Austrian Science Fund (FWF), project No P 27533-N27 (R.S.) and by the US National Science Foundation, grant No PHY12-1265118 (E.H.L.) are gratefully acknowledged.","year":"2018","license":"https://creativecommons.org/licenses/by-nd/4.0/","abstract":[{"lang":"eng","text":"In this paper we define and study the classical Uniform Electron Gas (UEG), a system of infinitely many electrons whose density is constant everywhere in space. The UEG is defined differently from Jellium, which has a positive constant background but no constraint on the density. We prove that the UEG arises in Density Functional Theory in the limit of a slowly varying density, minimizing the indirect Coulomb energy. We also construct the quantum UEG and compare it to the classical UEG at low density."}],"title":"Statistical mechanics of the uniform electron gas","status":"public"},{"conference":{"name":"HSCC: Hybrid Systems - Computation and Control","end_date":"2018-04-13","location":"Porto, Portugal","start_date":"2018-04-11"},"abstract":[{"lang":"eng","text":"We describe a new algorithm for the parametric identification problem for signal temporal logic (STL), stated as follows. Given a densetime real-valued signal w and a parameterized temporal logic formula φ, compute the subset of the parameter space that renders the formula satisfied by the signal. Unlike previous solutions, which were based on search in the parameter space or quantifier elimination, our procedure works recursively on φ and computes the evolution over time of the set of valid parameter assignments. This procedure is similar to that of monitoring or computing the robustness of φ relative to w. Our implementation and experiments demonstrate that this approach can work well in practice."}],"year":"2018","status":"public","title":"Efficient parametric identification for STL","has_accepted_license":"1","publication_status":"published","file":[{"date_created":"2020-05-14T12:18:29Z","access_level":"open_access","creator":"dernst","content_type":"application/pdf","date_updated":"2020-07-14T12:45:17Z","file_size":5900421,"file_id":"7833","file_name":"2018_HSCC_Bakhirkin.pdf","checksum":"81eabc96430e84336ea88310ac0a1ad0","relation":"main_file"}],"_id":"182","publication":"Proceedings of the 21st International Conference on Hybrid Systems","quality_controlled":"1","citation":{"ieee":"A. Bakhirkin, T. Ferrere, and O. Maler, “Efficient parametric identification for STL,” in <i>Proceedings of the 21st International Conference on Hybrid Systems</i>, Porto, Portugal, 2018, pp. 177–186.","ama":"Bakhirkin A, Ferrere T, Maler O. Efficient parametric identification for STL. In: <i>Proceedings of the 21st International Conference on Hybrid Systems</i>. ACM; 2018:177-186. doi:<a href=\"https://doi.org/10.1145/3178126.3178132\">10.1145/3178126.3178132</a>","apa":"Bakhirkin, A., Ferrere, T., &#38; Maler, O. (2018). Efficient parametric identification for STL. In <i>Proceedings of the 21st International Conference on Hybrid Systems</i> (pp. 177–186). Porto, Portugal: ACM. <a href=\"https://doi.org/10.1145/3178126.3178132\">https://doi.org/10.1145/3178126.3178132</a>","mla":"Bakhirkin, Alexey, et al. “Efficient Parametric Identification for STL.” <i>Proceedings of the 21st International Conference on Hybrid Systems</i>, ACM, 2018, pp. 177–86, doi:<a href=\"https://doi.org/10.1145/3178126.3178132\">10.1145/3178126.3178132</a>.","chicago":"Bakhirkin, Alexey, Thomas Ferrere, and Oded Maler. “Efficient Parametric Identification for STL.” In <i>Proceedings of the 21st International Conference on Hybrid Systems</i>, 177–86. ACM, 2018. <a href=\"https://doi.org/10.1145/3178126.3178132\">https://doi.org/10.1145/3178126.3178132</a>.","ista":"Bakhirkin A, Ferrere T, Maler O. 2018. Efficient parametric identification for STL. Proceedings of the 21st International Conference on Hybrid Systems. HSCC: Hybrid Systems - Computation and Control, HSCC Proceedings, , 177–186.","short":"A. Bakhirkin, T. Ferrere, O. Maler, in:, Proceedings of the 21st International Conference on Hybrid Systems, ACM, 2018, pp. 177–186."},"alternative_title":["HSCC Proceedings"],"day":"11","external_id":{"isi":["000474781600020"]},"publication_identifier":{"isbn":["978-1-4503-5642-8 "]},"doi":"10.1145/3178126.3178132","date_published":"2018-04-11T00:00:00Z","publist_id":"7739","month":"04","isi":1,"type":"conference","page":"177 - 186","date_updated":"2025-07-10T11:51:21Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2018-12-11T11:45:04Z","oa_version":"Submitted Version","publisher":"ACM","ddc":["000"],"file_date_updated":"2020-07-14T12:45:17Z","oa":1,"scopus_import":"1","author":[{"first_name":"Alexey","full_name":"Bakhirkin, Alexey","last_name":"Bakhirkin"},{"orcid":"0000-0001-5199-3143","id":"40960E6E-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas","last_name":"Ferrere","full_name":"Ferrere, Thomas"},{"first_name":"Oded","last_name":"Maler","full_name":"Maler, Oded"}],"article_processing_charge":"No","department":[{"_id":"ToHe"}],"language":[{"iso":"eng"}],"fulldoi":"https://doi.org/10.1145/3178126.3178132","project":[{"grant_number":"S 11407_N23","call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425","name":"Rigorous Systems Engineering"}]},{"conference":{"end_date":"2018-04-13","name":"HSCC: Hybrid Systems - Computation and Control","start_date":"2018-04-11","location":"Porto, Portugal"},"acknowledgement":"This work was partially supported by the Austrian Science Fund (FWF) under grants S11402-N23 and S11405-N23 (RiSE/SHiNE), the CPS/IoT project (HRSM), the EU ICT COST Action IC1402 on Run-time Verification beyond Monitoring (ARVI), the AMASS project (ECSEL 692474), and the ENABLE-S3 project (ECSEL 692455). The CPS/IoT project receives support from the Austrian government through the Federal Ministry of Science, Research and Economy (BMWFW) in the funding program Hochschulraum-Strukturmittel (HRSM) 2016. The ECSEL Joint Undertaking receives support from the European Union’s Horizon 2020 research and innovation programme and Austria, Denmark, Germany, Finland, Czech Republic, Italy, Spain, Portugal, Poland, Ireland, Belgium, France, Netherlands, United Kingdom, Slovakia, Norway.","title":"Localizing faults in simulink/stateflow models with STL","status":"public","abstract":[{"text":"Fault-localization is considered to be a very tedious and time-consuming activity in the design of complex Cyber-Physical Systems (CPS). This laborious task essentially requires expert knowledge of the system in order to discover the cause of the fault. In this context, we propose a new procedure that AIDS designers in debugging Simulink/Stateflow hybrid system models, guided by Signal Temporal Logic (STL) specifications. The proposed method relies on three main ingredients: (1) a monitoring and a trace diagnostics procedure that checks whether a tested behavior satisfies or violates an STL specification, localizes time segments and interfaces variables contributing to the property violations; (2) a slicing procedure that maps these observable behavior segments to the internal states and transitions of the Simulink model; and (3) a spectrum-based fault-localization method that combines the previous analysis from multiple tests to identify the internal states and/or transitions that are the most likely to explain the fault. We demonstrate the applicability of our approach on two Simulink models from the automotive and the avionics domain.","lang":"eng"}],"year":"2018","publication_status":"published","alternative_title":["HSCC Proceedings"],"citation":{"ama":"Bartocci E, Ferrere T, Manjunath N, Nickovic D. Localizing faults in simulink/stateflow models with STL. In: Association for Computing Machinery; 2018:197-206. doi:<a href=\"https://doi.org/10.1145/3178126.3178131\">10.1145/3178126.3178131</a>","ieee":"E. Bartocci, T. Ferrere, N. Manjunath, and D. Nickovic, “Localizing faults in simulink/stateflow models with STL,” presented at the HSCC: Hybrid Systems - Computation and Control, Porto, Portugal, 2018, pp. 197–206.","apa":"Bartocci, E., Ferrere, T., Manjunath, N., &#38; Nickovic, D. (2018). Localizing faults in simulink/stateflow models with STL (pp. 197–206). Presented at the HSCC: Hybrid Systems - Computation and Control, Porto, Portugal: Association for Computing Machinery. <a href=\"https://doi.org/10.1145/3178126.3178131\">https://doi.org/10.1145/3178126.3178131</a>","mla":"Bartocci, Ezio, et al. <i>Localizing Faults in Simulink/Stateflow Models with STL</i>. Association for Computing Machinery, 2018, pp. 197–206, doi:<a href=\"https://doi.org/10.1145/3178126.3178131\">10.1145/3178126.3178131</a>.","chicago":"Bartocci, Ezio, Thomas Ferrere, Niveditha Manjunath, and Dejan Nickovic. “Localizing Faults in Simulink/Stateflow Models with STL,” 197–206. Association for Computing Machinery, 2018. <a href=\"https://doi.org/10.1145/3178126.3178131\">https://doi.org/10.1145/3178126.3178131</a>.","ista":"Bartocci E, Ferrere T, Manjunath N, Nickovic D. 2018. Localizing faults in simulink/stateflow models with STL. HSCC: Hybrid Systems - Computation and Control, HSCC Proceedings, , 197–206.","short":"E. Bartocci, T. Ferrere, N. Manjunath, D. Nickovic, in:, Association for Computing Machinery, 2018, pp. 197–206."},"day":"11","quality_controlled":"1","_id":"183","external_id":{"isi":["000474781600022"]},"date_published":"2018-04-11T00:00:00Z","doi":"10.1145/3178126.3178131","isi":1,"month":"04","publist_id":"7738","page":"197 - 206","type":"conference","date_updated":"2025-07-10T11:51:22Z","date_created":"2018-12-11T11:45:04Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Association for Computing Machinery","oa_version":"None","author":[{"first_name":"Ezio","full_name":"Bartocci, Ezio","last_name":"Bartocci"},{"orcid":"0000-0001-5199-3143","id":"40960E6E-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas","last_name":"Ferrere","full_name":"Ferrere, Thomas"},{"full_name":"Manjunath, Niveditha","last_name":"Manjunath","first_name":"Niveditha"},{"first_name":"Dejan","full_name":"Nickovic, Dejan","last_name":"Nickovic"}],"department":[{"_id":"ToHe"}],"article_processing_charge":"No","scopus_import":"1","language":[{"iso":"eng"}],"project":[{"name":"Rigorous Systems Engineering","_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"S 11407_N23"}],"fulldoi":"https://doi.org/10.1145/3178126.3178131"},{"fulldoi":"https://doi.org/10.4230/LIPIcs.SoCG.2018.41","intvolume":"        99","language":[{"iso":"eng"}],"department":[{"_id":"UlWa"}],"author":[{"last_name":"Goaoc","full_name":"Goaoc, Xavier","first_name":"Xavier"},{"last_name":"Paták","full_name":"Paták, Pavel","first_name":"Pavel"},{"last_name":"Patakova","full_name":"Patakova, Zuzana","id":"48B57058-F248-11E8-B48F-1D18A9856A87","first_name":"Zuzana","orcid":"0000-0002-3975-1683"},{"id":"38AC689C-F248-11E8-B48F-1D18A9856A87","first_name":"Martin","orcid":"0000-0002-1191-6714","last_name":"Tancer","full_name":"Tancer, Martin"},{"last_name":"Wagner","full_name":"Wagner, Uli","id":"36690CA2-F248-11E8-B48F-1D18A9856A87","first_name":"Uli","orcid":"0000-0002-1494-0568"}],"oa":1,"scopus_import":1,"volume":99,"file_date_updated":"2020-07-14T12:45:18Z","ddc":["516","000"],"publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","oa_version":"Published Version","date_created":"2018-12-11T11:45:04Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2025-06-04T07:49:02Z","related_material":{"record":[{"status":"public","relation":"later_version","id":"7108"}]},"page":"41:1 - 41:16","type":"conference","month":"06","publist_id":"7736","doi":"10.4230/LIPIcs.SoCG.2018.41","date_published":"2018-06-11T00:00:00Z","alternative_title":["Leibniz International Proceedings in Information, LIPIcs"],"citation":{"apa":"Goaoc, X., Paták, P., Patakova, Z., Tancer, M., &#38; Wagner, U. (2018). Shellability is NP-complete (Vol. 99, p. 41:1-41:16). Presented at the SoCG: Symposium on Computational Geometry, Budapest, Hungary: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. <a href=\"https://doi.org/10.4230/LIPIcs.SoCG.2018.41\">https://doi.org/10.4230/LIPIcs.SoCG.2018.41</a>","ieee":"X. Goaoc, P. Paták, Z. Patakova, M. Tancer, and U. Wagner, “Shellability is NP-complete,” presented at the SoCG: Symposium on Computational Geometry, Budapest, Hungary, 2018, vol. 99, p. 41:1-41:16.","ama":"Goaoc X, Paták P, Patakova Z, Tancer M, Wagner U. Shellability is NP-complete. In: Vol 99. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2018:41:1-41:16. doi:<a href=\"https://doi.org/10.4230/LIPIcs.SoCG.2018.41\">10.4230/LIPIcs.SoCG.2018.41</a>","short":"X. Goaoc, P. Paták, Z. Patakova, M. Tancer, U. Wagner, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018, p. 41:1-41:16.","ista":"Goaoc X, Paták P, Patakova Z, Tancer M, Wagner U. 2018. Shellability is NP-complete. SoCG: Symposium on Computational Geometry, Leibniz International Proceedings in Information, LIPIcs, vol. 99, 41:1-41:16.","mla":"Goaoc, Xavier, et al. <i>Shellability Is NP-Complete</i>. Vol. 99, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018, p. 41:1-41:16, doi:<a href=\"https://doi.org/10.4230/LIPIcs.SoCG.2018.41\">10.4230/LIPIcs.SoCG.2018.41</a>.","chicago":"Goaoc, Xavier, Pavel Paták, Zuzana Patakova, Martin Tancer, and Uli Wagner. “Shellability Is NP-Complete,” 99:41:1-41:16. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018. <a href=\"https://doi.org/10.4230/LIPIcs.SoCG.2018.41\">https://doi.org/10.4230/LIPIcs.SoCG.2018.41</a>."},"day":"11","quality_controlled":"1","_id":"184","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"file":[{"relation":"main_file","checksum":"d12bdd60f04a57307867704b5f930afd","file_id":"5725","file_name":"2018_LIPIcs_Goaoc.pdf","file_size":718414,"date_updated":"2020-07-14T12:45:18Z","access_level":"open_access","date_created":"2018-12-17T16:35:02Z","creator":"dernst","content_type":"application/pdf"}],"has_accepted_license":"1","publication_status":"published","status":"public","title":"Shellability is NP-complete","abstract":[{"text":"We prove that for every d ≥ 2, deciding if a pure, d-dimensional, simplicial complex is shellable is NP-hard, hence NP-complete. This resolves a question raised, e.g., by Danaraj and Klee in 1978. Our reduction also yields that for every d ≥ 2 and k ≥ 0, deciding if a pure, d-dimensional, simplicial complex is k-decomposable is NP-hard. For d ≥ 3, both problems remain NP-hard when restricted to contractible pure d-dimensional complexes.","lang":"eng"}],"year":"2018","conference":{"start_date":"2018-06-11","location":"Budapest, Hungary","end_date":"2018-06-14","name":"SoCG: Symposium on Computational Geometry"},"acknowledgement":"Partially supported by the project EMBEDS II (CZ: 7AMB17FR029, FR: 38087RM) of Czech-French collaboration."},{"intvolume":"        29","issue":"22","fulldoi":"https://doi.org/10.1091/mbc.e18-02-0082","language":[{"iso":"eng"}],"oa":1,"scopus_import":"1","author":[{"full_name":"Dolati, Setareh","last_name":"Dolati","first_name":"Setareh"},{"first_name":"Frieda","last_name":"Kage","full_name":"Kage, Frieda"},{"last_name":"Mueller","full_name":"Mueller, Jan","first_name":"Jan"},{"full_name":"Müsken, Mathias","last_name":"Müsken","first_name":"Mathias"},{"full_name":"Kirchner, Marieluise","last_name":"Kirchner","first_name":"Marieluise"},{"first_name":"Gunnar","full_name":"Dittmar, Gunnar","last_name":"Dittmar"},{"id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","first_name":"Michael K","orcid":"0000-0002-6620-9179","last_name":"Sixt","full_name":"Sixt, Michael K"},{"full_name":"Rottner, Klemens","last_name":"Rottner","first_name":"Klemens"},{"first_name":"Martin","full_name":"Falcke, Martin","last_name":"Falcke"}],"department":[{"_id":"MiSi"}],"article_processing_charge":"No","ddc":["570"],"file_date_updated":"2020-07-14T12:47:15Z","volume":29,"oa_version":"Published Version","pmid":1,"publisher":"American Society for Cell Biology","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2019-02-14T12:25:47Z","date_updated":"2026-07-06T12:25:34Z","type":"journal_article","page":"2674-2686","month":"11","isi":1,"date_published":"2018-11-01T00:00:00Z","doi":"10.1091/mbc.e18-02-0082","external_id":{"isi":["000455641000011"],"pmid":["30156465"]},"publication_identifier":{"eissn":["1939-4586"]},"_id":"5992","quality_controlled":"1","das_tickbox":"1","publication":"Molecular Biology of the Cell","day":"01","citation":{"apa":"Dolati, S., Kage, F., Mueller, J., Müsken, M., Kirchner, M., Dittmar, G., … Falcke, M. (2018). On the relation between filament density, force generation, and protrusion rate in mesenchymal cell motility. <i>Molecular Biology of the Cell</i>. American Society for Cell Biology. <a href=\"https://doi.org/10.1091/mbc.e18-02-0082\">https://doi.org/10.1091/mbc.e18-02-0082</a>","ieee":"S. Dolati <i>et al.</i>, “On the relation between filament density, force generation, and protrusion rate in mesenchymal cell motility,” <i>Molecular Biology of the Cell</i>, vol. 29, no. 22. American Society for Cell Biology, pp. 2674–2686, 2018.","ama":"Dolati S, Kage F, Mueller J, et al. On the relation between filament density, force generation, and protrusion rate in mesenchymal cell motility. <i>Molecular Biology of the Cell</i>. 2018;29(22):2674-2686. doi:<a href=\"https://doi.org/10.1091/mbc.e18-02-0082\">10.1091/mbc.e18-02-0082</a>","short":"S. Dolati, F. Kage, J. Mueller, M. Müsken, M. Kirchner, G. Dittmar, M.K. Sixt, K. Rottner, M. Falcke, Molecular Biology of the Cell 29 (2018) 2674–2686.","ista":"Dolati S, Kage F, Mueller J, Müsken M, Kirchner M, Dittmar G, Sixt MK, Rottner K, Falcke M. 2018. On the relation between filament density, force generation, and protrusion rate in mesenchymal cell motility. Molecular Biology of the Cell. 29(22), 2674–2686.","chicago":"Dolati, Setareh, Frieda Kage, Jan Mueller, Mathias Müsken, Marieluise Kirchner, Gunnar Dittmar, Michael K Sixt, Klemens Rottner, and Martin Falcke. “On the Relation between Filament Density, Force Generation, and Protrusion Rate in Mesenchymal Cell Motility.” <i>Molecular Biology of the Cell</i>. American Society for Cell Biology, 2018. <a href=\"https://doi.org/10.1091/mbc.e18-02-0082\">https://doi.org/10.1091/mbc.e18-02-0082</a>.","mla":"Dolati, Setareh, et al. “On the Relation between Filament Density, Force Generation, and Protrusion Rate in Mesenchymal Cell Motility.” <i>Molecular Biology of the Cell</i>, vol. 29, no. 22, American Society for Cell Biology, 2018, pp. 2674–86, doi:<a href=\"https://doi.org/10.1091/mbc.e18-02-0082\">10.1091/mbc.e18-02-0082</a>."},"has_accepted_license":"1","publication_status":"published","file":[{"access_level":"open_access","date_created":"2019-02-14T12:34:29Z","creator":"kschuh","content_type":"application/pdf","file_size":6668971,"date_updated":"2020-07-14T12:47:15Z","file_id":"5994","file_name":"2018_ASCB_Dolati.pdf","relation":"main_file","checksum":"e98465b4416b3e804c47f40086932af2"}],"tmp":{"name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","image":"/images/cc_by_nc_sa.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","short":"CC BY-NC-SA (4.0)"},"year":"2018","license":"https://creativecommons.org/licenses/by-nc-sa/4.0/","abstract":[{"lang":"eng","text":"Lamellipodia are flat membrane protrusions formed during mesenchymal motion. Polymerization at the leading edge assembles the actin filament network and generates protrusion force. How this force is supported by the network and how the assembly rate is shared between protrusion and network retrograde flow determines the protrusion rate. We use mathematical modeling to understand experiments changing the F-actin density in lamellipodia of B16-F1 melanoma cells by modulation of Arp2/3 complex activity or knockout of the formins FMNL2 and FMNL3. Cells respond to a reduction of density with a decrease of protrusion velocity, an increase in the ratio of force to filament number, but constant network assembly rate. The relation between protrusion force and tension gradient in the F-actin network and the density dependency of friction, elasticity, and viscosity of the network explain the experimental observations. The formins act as filament nucleators and elongators with differential rates. Modulation of their activity suggests an effect on network assembly rate. Contrary to these expectations, the effect of changes in elongator composition is much weaker than the consequences of the density change. We conclude that the force acting on the leading edge membrane is the force required to drive F-actin network retrograde flow."}],"title":"On the relation between filament density, force generation, and protrusion rate in mesenchymal cell motility","status":"public"},{"oa":1,"doi":"10.1101/494088","date_published":"2018-12-13T00:00:00Z","department":[{"_id":"SiHi"}],"article_processing_charge":"No","author":[{"first_name":"Alfredo","full_name":"Llorca, Alfredo","last_name":"Llorca"},{"first_name":"Gabriele","last_name":"Ciceri","full_name":"Ciceri, Gabriele"},{"last_name":"Beattie","full_name":"Beattie, Robert J","id":"2E26DF60-F248-11E8-B48F-1D18A9856A87","first_name":"Robert J","orcid":"0000-0002-8483-8753"},{"last_name":"Wong","full_name":"Wong, Fong K.","first_name":"Fong K."},{"last_name":"Diana","full_name":"Diana, Giovanni","first_name":"Giovanni"},{"first_name":"Eleni","full_name":"Serafeimidou, Eleni","last_name":"Serafeimidou"},{"first_name":"Marian","full_name":"Fernández-Otero, Marian","last_name":"Fernández-Otero"},{"last_name":"Streicher","full_name":"Streicher, Carmen","id":"36BCB99C-F248-11E8-B48F-1D18A9856A87","first_name":"Carmen"},{"first_name":"Sebastian J.","last_name":"Arnold","full_name":"Arnold, Sebastian J."},{"full_name":"Meyer, Martin","last_name":"Meyer","first_name":"Martin"},{"full_name":"Hippenmeyer, Simon","last_name":"Hippenmeyer","first_name":"Simon","id":"37B36620-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2279-1061"},{"first_name":"Miguel","last_name":"Maravall","full_name":"Maravall, Miguel"},{"first_name":"Oscar","full_name":"Marín, Oscar","last_name":"Marín"}],"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1101/494088"}],"type":"preprint","ec_funded":1,"fulldoi":"https://doi.org/10.1101/494088","project":[{"name":"Principles of Neural Stem Cell Lineage Progression in Cerebral Cortex Development","_id":"260018B0-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"725780"},{"_id":"264E56E2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Molecular Mechanisms Regulating Gliogenesis in the Neocortex","grant_number":"M02416"}],"language":[{"iso":"eng"}],"month":"12","abstract":[{"text":"The cerebral cortex contains multiple hierarchically organized areas with distinctive cytoarchitectonical patterns, but the cellular mechanisms underlying the emergence of this diversity remain unclear. Here, we have quantitatively investigated the neuronal output of individual progenitor cells in the ventricular zone of the developing mouse neocortex using a combination of methods that together circumvent the biases and limitations of individual approaches. We found that individual cortical progenitor cells show a high degree of stochasticity and generate pyramidal cell lineages that adopt a wide range of laminar configurations. Mathematical modelling these lineage data suggests that a small number of progenitor cell populations, each generating pyramidal cells following different stochastic developmental programs, suffice to generate the heterogenous complement of pyramidal cell lineages that collectively build the complex cytoarchitecture of the neocortex.","lang":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2018","status":"public","title":"Heterogeneous progenitor cell behaviors underlie the assembly of neocortical cytoarchitecture","date_created":"2020-09-21T12:01:50Z","acknowledgement":"We thank I. Andrew and S.E. Bae for excellent technical assistance, F. Gage for plasmids, and K. Nave (Nex-Cre) for mouse colonies. We thank members of the Marín and Rico laboratories for stimulating discussions and ideas. Our research on this topic is supported by grants from the European Research Council (ERC-2017-AdG 787355 to O.M and ERC2016-CoG 725780 to S.H.) and Wellcome Trust (103714MA) to O.M. L.L. was the recipient of an EMBO long-term postdoctoral fellowship, R.B. received support from FWF Lise-Meitner program (M 2416) and F.K.W. was supported by an EMBO postdoctoral fellowship and is currently a Marie Skłodowska-Curie Fellow from the European Commission under the H2020 Programme.","date_updated":"2026-07-06T12:52:50Z","_id":"8547","citation":{"mla":"Llorca, Alfredo, et al. “Heterogeneous Progenitor Cell Behaviors Underlie the Assembly of Neocortical Cytoarchitecture.” <i>BioRxiv</i>, doi:<a href=\"https://doi.org/10.1101/494088\">10.1101/494088</a>.","chicago":"Llorca, Alfredo, Gabriele Ciceri, Robert J Beattie, Fong K. Wong, Giovanni Diana, Eleni Serafeimidou, Marian Fernández-Otero, et al. “Heterogeneous Progenitor Cell Behaviors Underlie the Assembly of Neocortical Cytoarchitecture.” <i>BioRxiv</i>, n.d. <a href=\"https://doi.org/10.1101/494088\">https://doi.org/10.1101/494088</a>.","ista":"Llorca A, Ciceri G, Beattie RJ, Wong FK, Diana G, Serafeimidou E, Fernández-Otero M, Streicher C, Arnold SJ, Meyer M, Hippenmeyer S, Maravall M, Marín O. Heterogeneous progenitor cell behaviors underlie the assembly of neocortical cytoarchitecture. bioRxiv, <a href=\"https://doi.org/10.1101/494088\">10.1101/494088</a>.","short":"A. Llorca, G. Ciceri, R.J. Beattie, F.K. Wong, G. Diana, E. Serafeimidou, M. Fernández-Otero, C. Streicher, S.J. Arnold, M. Meyer, S. Hippenmeyer, M. Maravall, O. Marín, BioRxiv (n.d.).","ieee":"A. Llorca <i>et al.</i>, “Heterogeneous progenitor cell behaviors underlie the assembly of neocortical cytoarchitecture,” <i>bioRxiv</i>. .","ama":"Llorca A, Ciceri G, Beattie RJ, et al. Heterogeneous progenitor cell behaviors underlie the assembly of neocortical cytoarchitecture. <i>bioRxiv</i>. doi:<a href=\"https://doi.org/10.1101/494088\">10.1101/494088</a>","apa":"Llorca, A., Ciceri, G., Beattie, R. J., Wong, F. K., Diana, G., Serafeimidou, E., … Marín, O. (n.d.). Heterogeneous progenitor cell behaviors underlie the assembly of neocortical cytoarchitecture. <i>bioRxiv</i>. <a href=\"https://doi.org/10.1101/494088\">https://doi.org/10.1101/494088</a>"},"day":"13","das_tickbox":"1","publication":"bioRxiv","oa_version":"Preprint","publication_status":"submitted"},{"scopus_import":"1","oa":1,"department":[{"_id":"KrPi"}],"OA_type":"diamond","author":[{"first_name":"Elie Noumon","last_name":"Allini","full_name":"Allini, Elie Noumon"},{"last_name":"Skórski","full_name":"Skórski, Maciej","id":"EC09FA6A-02D0-11E9-8223-86B7C91467DD","first_name":"Maciej"},{"full_name":"Petura, Oto","last_name":"Petura","first_name":"Oto"},{"first_name":"Florent","last_name":"Bernard","full_name":"Bernard, Florent"},{"first_name":"Marek","full_name":"Laban, Marek","last_name":"Laban"},{"full_name":"Fischer, Viktor","last_name":"Fischer","first_name":"Viktor"}],"article_processing_charge":"No","intvolume":"      2018","issue":"3","fulldoi":"https://doi.org/10.13154/tches.v2018.i3.214-242","language":[{"iso":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2021-11-14T23:01:25Z","date_updated":"2026-07-06T13:16:35Z","ddc":["000"],"file_date_updated":"2021-11-15T10:27:29Z","volume":2018,"article_type":"original","oa_version":"Published Version","publisher":"International Association for Cryptologic Research","date_published":"2018-01-01T00:00:00Z","doi":"10.13154/tches.v2018.i3.214-242","publication_identifier":{"eissn":["2569-2925"]},"type":"journal_article","page":"214-242","month":"01","year":"2018","abstract":[{"lang":"eng","text":"In this paper, we evaluate clock signals generated in ring oscillators and self-timed rings and the way their jitter can be transformed into random numbers. We show that counting the periods of the jittery clock signal produces random numbers of significantly better quality than the methods in which the jittery signal is simply sampled (the case in almost all current methods). Moreover, we use the counter values to characterize and continuously monitor the source of randomness. However, instead of using the widely used statistical variance, we propose to use Allan variance to do so. There are two main advantages: Allan variance is insensitive to low frequency noises such as flicker noise that are known to be autocorrelated and significantly less circuitry is required for its computation than that used to compute commonly used variance. We also show that it is essential to use a differential principle of randomness extraction from the jitter based on the use of two identical oscillators to avoid autocorrelations originating from external and internal global jitter sources and that this fact is valid for both kinds of rings. Last but not least, we propose a method of statistical testing based on high order Markov model to show the reduced dependencies when the proposed randomness extraction is applied."}],"corr_author":"1","status":"public","title":"Evaluation and monitoring of free running oscillators serving as source of randomness","OA_place":"publisher","_id":"10286","das_tickbox":"1","quality_controlled":"1","publication":"IACR Transactions on Cryptographic Hardware and Embedded Systems","day":"01","citation":{"apa":"Allini, E. N., Skórski, M., Petura, O., Bernard, F., Laban, M., &#38; Fischer, V. (2018). Evaluation and monitoring of free running oscillators serving as source of randomness. <i>IACR Transactions on Cryptographic Hardware and Embedded Systems</i>. International Association for Cryptologic Research. <a href=\"https://doi.org/10.13154/tches.v2018.i3.214-242\">https://doi.org/10.13154/tches.v2018.i3.214-242</a>","ama":"Allini EN, Skórski M, Petura O, Bernard F, Laban M, Fischer V. Evaluation and monitoring of free running oscillators serving as source of randomness. <i>IACR Transactions on Cryptographic Hardware and Embedded Systems</i>. 2018;2018(3):214-242. doi:<a href=\"https://doi.org/10.13154/tches.v2018.i3.214-242\">10.13154/tches.v2018.i3.214-242</a>","ieee":"E. N. Allini, M. Skórski, O. Petura, F. Bernard, M. Laban, and V. Fischer, “Evaluation and monitoring of free running oscillators serving as source of randomness,” <i>IACR Transactions on Cryptographic Hardware and Embedded Systems</i>, vol. 2018, no. 3. International Association for Cryptologic Research, pp. 214–242, 2018.","short":"E.N. Allini, M. Skórski, O. Petura, F. Bernard, M. Laban, V. Fischer, IACR Transactions on Cryptographic Hardware and Embedded Systems 2018 (2018) 214–242.","ista":"Allini EN, Skórski M, Petura O, Bernard F, Laban M, Fischer V. 2018. Evaluation and monitoring of free running oscillators serving as source of randomness. IACR Transactions on Cryptographic Hardware and Embedded Systems. 2018(3), 214–242.","mla":"Allini, Elie Noumon, et al. “Evaluation and Monitoring of Free Running Oscillators Serving as Source of Randomness.” <i>IACR Transactions on Cryptographic Hardware and Embedded Systems</i>, vol. 2018, no. 3, International Association for Cryptologic Research, 2018, pp. 214–42, doi:<a href=\"https://doi.org/10.13154/tches.v2018.i3.214-242\">10.13154/tches.v2018.i3.214-242</a>.","chicago":"Allini, Elie Noumon, Maciej Skórski, Oto Petura, Florent Bernard, Marek Laban, and Viktor Fischer. “Evaluation and Monitoring of Free Running Oscillators Serving as Source of Randomness.” <i>IACR Transactions on Cryptographic Hardware and Embedded Systems</i>. International Association for Cryptologic Research, 2018. <a href=\"https://doi.org/10.13154/tches.v2018.i3.214-242\">https://doi.org/10.13154/tches.v2018.i3.214-242</a>."},"has_accepted_license":"1","publication_status":"published","file":[{"access_level":"open_access","date_created":"2021-11-15T10:27:29Z","content_type":"application/pdf","creator":"cchlebak","file_size":955755,"date_updated":"2021-11-15T10:27:29Z","success":1,"file_id":"10289","file_name":"2018_IACR_Allini.pdf","relation":"main_file","checksum":"b816b848f046c48a8357700d9305dce5"}],"tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"}},{"volume":34,"ddc":["570"],"file_date_updated":"2020-07-14T12:47:15Z","publisher":"Oxford University Press","pmid":1,"oa_version":"Published Version","date_created":"2019-02-14T12:48:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2026-07-06T13:48:02Z","project":[{"call_identifier":"FP7","_id":"26120F5C-B435-11E9-9278-68D0E5697425","name":"Systematic investigation of epistasis in molecular evolution","grant_number":"335980"}],"fulldoi":"https://doi.org/10.1093/bioinformatics/bty340","intvolume":"        34","issue":"21","language":[{"iso":"eng"}],"article_processing_charge":"No","author":[{"first_name":"Dinara R","last_name":"Usmanova","full_name":"Usmanova, Dinara R"},{"last_name":"Bogatyreva","full_name":"Bogatyreva, Natalya S","first_name":"Natalya S"},{"first_name":"Joan","full_name":"Ariño Bernad, Joan","last_name":"Ariño Bernad"},{"full_name":"Eremina, Aleksandra A","last_name":"Eremina","first_name":"Aleksandra A"},{"full_name":"Gorshkova, Anastasiya A","last_name":"Gorshkova","first_name":"Anastasiya A"},{"last_name":"Kanevskiy","full_name":"Kanevskiy, German M","first_name":"German M"},{"full_name":"Lonishin, Lyubov R","last_name":"Lonishin","first_name":"Lyubov R"},{"last_name":"Meister","full_name":"Meister, Alexander V","first_name":"Alexander V"},{"first_name":"Alisa G","full_name":"Yakupova, Alisa G","last_name":"Yakupova"},{"orcid":"0000-0001-8243-4694","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","first_name":"Fyodor","last_name":"Kondrashov","full_name":"Kondrashov, Fyodor"},{"first_name":"Dmitry","id":"49FF1036-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8224-4118","full_name":"Ivankov, Dmitry","last_name":"Ivankov"}],"department":[{"_id":"FyKo"}],"oa":1,"scopus_import":"1","citation":{"chicago":"Usmanova, Dinara R, Natalya S Bogatyreva, Joan Ariño Bernad, Aleksandra A Eremina, Anastasiya A Gorshkova, German M Kanevskiy, Lyubov R Lonishin, et al. “Self-Consistency Test Reveals Systematic Bias in Programs for Prediction Change of Stability upon Mutation.” <i>Bioinformatics</i>. Oxford University Press, 2018. <a href=\"https://doi.org/10.1093/bioinformatics/bty340\">https://doi.org/10.1093/bioinformatics/bty340</a>.","mla":"Usmanova, Dinara R., et al. “Self-Consistency Test Reveals Systematic Bias in Programs for Prediction Change of Stability upon Mutation.” <i>Bioinformatics</i>, vol. 34, no. 21, Oxford University Press, 2018, pp. 3653–58, doi:<a href=\"https://doi.org/10.1093/bioinformatics/bty340\">10.1093/bioinformatics/bty340</a>.","ista":"Usmanova DR, Bogatyreva NS, Ariño Bernad J, Eremina AA, Gorshkova AA, Kanevskiy GM, Lonishin LR, Meister AV, Yakupova AG, Kondrashov F, Ivankov D. 2018. Self-consistency test reveals systematic bias in programs for prediction change of stability upon mutation. Bioinformatics. 34(21), 3653–3658.","short":"D.R. Usmanova, N.S. Bogatyreva, J. Ariño Bernad, A.A. Eremina, A.A. Gorshkova, G.M. Kanevskiy, L.R. Lonishin, A.V. Meister, A.G. Yakupova, F. Kondrashov, D. Ivankov, Bioinformatics 34 (2018) 3653–3658.","ama":"Usmanova DR, Bogatyreva NS, Ariño Bernad J, et al. Self-consistency test reveals systematic bias in programs for prediction change of stability upon mutation. <i>Bioinformatics</i>. 2018;34(21):3653-3658. doi:<a href=\"https://doi.org/10.1093/bioinformatics/bty340\">10.1093/bioinformatics/bty340</a>","ieee":"D. R. Usmanova <i>et al.</i>, “Self-consistency test reveals systematic bias in programs for prediction change of stability upon mutation,” <i>Bioinformatics</i>, vol. 34, no. 21. Oxford University Press, pp. 3653–3658, 2018.","apa":"Usmanova, D. R., Bogatyreva, N. S., Ariño Bernad, J., Eremina, A. A., Gorshkova, A. A., Kanevskiy, G. M., … Ivankov, D. (2018). Self-consistency test reveals systematic bias in programs for prediction change of stability upon mutation. <i>Bioinformatics</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/bioinformatics/bty340\">https://doi.org/10.1093/bioinformatics/bty340</a>"},"day":"01","das_tickbox":"1","quality_controlled":"1","publication":"Bioinformatics","_id":"5995","tmp":{"name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","image":"/images/cc_by_nc.png","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","short":"CC BY-NC (4.0)"},"file":[{"relation":"main_file","checksum":"7e0495153f44211479674601d7f6ee03","file_name":"2018_Oxford_Usmanova.pdf","file_id":"5997","file_size":291969,"date_updated":"2020-07-14T12:47:15Z","creator":"kschuh","content_type":"application/pdf","access_level":"open_access","date_created":"2019-02-14T13:00:55Z"}],"has_accepted_license":"1","publication_status":"published","title":"Self-consistency test reveals systematic bias in programs for prediction change of stability upon mutation","status":"public","year":"2018","license":"https://creativecommons.org/licenses/by-nc/4.0/","abstract":[{"lang":"eng","text":"Motivation\r\nComputational prediction of the effect of mutations on protein stability is used by researchers in many fields. The utility of the prediction methods is affected by their accuracy and bias. Bias, a systematic shift of the predicted change of stability, has been noted as an issue for several methods, but has not been investigated systematically. Presence of the bias may lead to misleading results especially when exploring the effects of combination of different mutations.\r\n\r\nResults\r\nHere we use a protocol to measure the bias as a function of the number of introduced mutations. It is based on a self-consistency test of the reciprocity the effect of a mutation. An advantage of the used approach is that it relies solely on crystal structures without experimentally measured stability values. We applied the protocol to four popular algorithms predicting change of protein stability upon mutation, FoldX, Eris, Rosetta and I-Mutant, and found an inherent bias. For one program, FoldX, we manage to substantially reduce the bias using additional relaxation by Modeller. Authors using algorithms for predicting effects of mutations should be aware of the bias described here."}],"ec_funded":1,"page":"3653-3658","type":"journal_article","isi":1,"month":"11","doi":"10.1093/bioinformatics/bty340","date_published":"2018-11-01T00:00:00Z","publication_identifier":{"eissn":["1367-4811"]},"external_id":{"pmid":["29722803"],"isi":["000450038900008"]}},{"isi":1,"publist_id":"7425","month":"01","type":"journal_article","page":"411 - 455","external_id":{"isi":["000426630900015"]},"doi":"10.1137/16M1098796","date_published":"2018-01-30T00:00:00Z","publication_status":"published","has_accepted_license":"1","file":[{"file_id":"6992","file_name":"2018_SIAM_Fischer.pdf","relation":"main_file","checksum":"89a8eae7c52bb356c04f52b44bff4b5a","access_level":"open_access","date_created":"2019-11-07T12:20:25Z","content_type":"application/pdf","creator":"dernst","file_size":557338,"date_updated":"2020-07-14T12:46:22Z"}],"_id":"404","day":"30","citation":{"ieee":"J. L. Fischer and G. Grün, “Existence of positive solutions to stochastic thin-film equations,” <i>SIAM Journal on Mathematical Analysis</i>, vol. 50, no. 1. Society for Industrial and Applied Mathematics, pp. 411–455, 2018.","ama":"Fischer JL, Grün G. Existence of positive solutions to stochastic thin-film equations. <i>SIAM Journal on Mathematical Analysis</i>. 2018;50(1):411-455. doi:<a href=\"https://doi.org/10.1137/16M1098796\">10.1137/16M1098796</a>","apa":"Fischer, J. L., &#38; Grün, G. (2018). Existence of positive solutions to stochastic thin-film equations. <i>SIAM Journal on Mathematical Analysis</i>. Society for Industrial and Applied Mathematics. <a href=\"https://doi.org/10.1137/16M1098796\">https://doi.org/10.1137/16M1098796</a>","chicago":"Fischer, Julian L, and Günther Grün. “Existence of Positive Solutions to Stochastic Thin-Film Equations.” <i>SIAM Journal on Mathematical Analysis</i>. Society for Industrial and Applied Mathematics, 2018. <a href=\"https://doi.org/10.1137/16M1098796\">https://doi.org/10.1137/16M1098796</a>.","mla":"Fischer, Julian L., and Günther Grün. “Existence of Positive Solutions to Stochastic Thin-Film Equations.” <i>SIAM Journal on Mathematical Analysis</i>, vol. 50, no. 1, Society for Industrial and Applied Mathematics, 2018, pp. 411–55, doi:<a href=\"https://doi.org/10.1137/16M1098796\">10.1137/16M1098796</a>.","short":"J.L. Fischer, G. Grün, SIAM Journal on Mathematical Analysis 50 (2018) 411–455.","ista":"Fischer JL, Grün G. 2018. Existence of positive solutions to stochastic thin-film equations. SIAM Journal on Mathematical Analysis. 50(1), 411–455."},"das_tickbox":"1","publication":"SIAM Journal on Mathematical Analysis","quality_controlled":"1","abstract":[{"text":"We construct martingale solutions to stochastic thin-film equations by introducing a (spatial) semidiscretization and establishing convergence. The discrete scheme allows for variants of the energy and entropy estimates in the continuous setting as long as the discrete energy does not exceed certain threshold values depending on the spatial grid size $h$. Using a stopping time argument to prolongate high-energy paths constant in time, arbitrary moments of coupled energy/entropy functionals can be controlled. Having established Hölder regularity of approximate solutions, the convergence proof is then based on compactness arguments---in particular on Jakubowski's generalization of Skorokhod's theorem---weak convergence methods, and recent tools on martingale convergence.\r\n\r\n","lang":"eng"}],"year":"2018","title":"Existence of positive solutions to stochastic thin-film equations","status":"public","corr_author":"1","language":[{"iso":"eng"}],"intvolume":"        50","issue":"1","fulldoi":"https://doi.org/10.1137/16M1098796","scopus_import":"1","oa":1,"author":[{"full_name":"Fischer, Julian L","last_name":"Fischer","orcid":"0000-0002-0479-558X","first_name":"Julian L","id":"2C12A0B0-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Günther","last_name":"Grün","full_name":"Grün, Günther"}],"article_processing_charge":"No","department":[{"_id":"JuFi"}],"oa_version":"Published Version","article_type":"original","publisher":"Society for Industrial and Applied Mathematics","ddc":["510"],"file_date_updated":"2020-07-14T12:46:22Z","volume":50,"date_updated":"2026-07-06T14:01:18Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2018-12-11T11:46:17Z"}]