[{"article_processing_charge":"No","external_id":{"isi":["000445336600015"]},"publication_status":"published","abstract":[{"lang":"eng","text":"Imaging is a dominant strategy for data collection in neuroscience, yielding stacks of images that often scale to gigabytes of data for a single experiment. Machine learning algorithms from computer vision can serve as a pair of virtual eyes that tirelessly processes these images, automatically detecting and identifying microstructures. Unlike learning methods, our Flexible Learning-free Reconstruction of Imaged Neural volumes (FLoRIN) pipeline exploits structure-specific contextual clues and requires no training. This approach generalizes across different modalities, including serially-sectioned scanning electron microscopy (sSEM) of genetically labeled and contrast enhanced processes, spectral confocal reflectance (SCoRe) microscopy, and high-energy synchrotron X-ray microtomography (μCT) of large tissue volumes. We deploy the FLoRIN pipeline on newly published and novel mouse datasets, demonstrating the high biological fidelity of the pipeline’s reconstructions. FLoRIN reconstructions are of sufficient quality for preliminary biological study, for example examining the distribution and morphology of cells or extracting single axons from functional data. Compared to existing supervised learning methods, FLoRIN is one to two orders of magnitude faster and produces high-quality reconstructions that are tolerant to noise and artifacts, as is shown qualitatively and quantitatively."}],"title":"Flexible learning-free segmentation and reconstruction of neural volumes","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","author":[{"full_name":"Shabazi, Ali","last_name":"Shabazi","first_name":"Ali"},{"first_name":"Jeffery","last_name":"Kinnison","full_name":"Kinnison, Jeffery"},{"full_name":"Vescovi, Rafael","last_name":"Vescovi","first_name":"Rafael"},{"full_name":"Du, Ming","first_name":"Ming","last_name":"Du"},{"last_name":"Hill","first_name":"Robert","full_name":"Hill, Robert"},{"last_name":"Jösch","first_name":"Maximilian A","id":"2BD278E6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-3937-1330","full_name":"Jösch, Maximilian A"},{"first_name":"Marc","last_name":"Takeno","full_name":"Takeno, Marc"},{"full_name":"Zeng, Hongkui","last_name":"Zeng","first_name":"Hongkui"},{"last_name":"Da Costa","first_name":"Nuno","full_name":"Da Costa, Nuno"},{"full_name":"Grutzendler, Jaime","last_name":"Grutzendler","first_name":"Jaime"},{"first_name":"Narayanan","last_name":"Kasthuri","full_name":"Kasthuri, Narayanan"},{"last_name":"Scheirer","first_name":"Walter","full_name":"Scheirer, Walter"}],"volume":8,"related_material":{"link":[{"url":"http://doi.org/10.1038/s41598-018-36220-7","relation":"erratum"}]},"quality_controlled":"1","file":[{"creator":"dernst","date_created":"2018-12-17T12:22:24Z","content_type":"application/pdf","file_name":"2018_ScientificReports_Shahbazi.pdf","checksum":"1a14ae0666b82fbaa04bef110e3f6bf2","relation":"main_file","access_level":"open_access","file_size":4141645,"date_updated":"2020-07-14T12:47:24Z","file_id":"5699"}],"has_accepted_license":"1","ddc":["570"],"date_created":"2018-12-11T11:44:25Z","year":"2018","article_number":"14247","doi":"10.1038/s41598-018-32628-3","issue":"1","publication":"Scientific Reports","isi":1,"file_date_updated":"2020-07-14T12:47:24Z","oa":1,"date_published":"2018-09-24T00:00:00Z","language":[{"iso":"eng"}],"month":"09","date_updated":"2023-09-11T14:02:55Z","publisher":"Nature Publishing Group","department":[{"_id":"MaJö"}],"intvolume":" 8","oa_version":"Published Version","article_type":"original","type":"journal_article","acknowledgement":"Equipment was generously donated by the NVIDIA Corporation, and made available by the National Science Foundation (NSF) through grant #CNS-1629914. This research used resources of the Argonne Leadership Computing Facility, which is a DOE Office of Science User Facility supported under Contract DE-AC02-06CH11357.","publist_id":"7992","scopus_import":"1","_id":"62","citation":{"ama":"Shabazi A, Kinnison J, Vescovi R, et al. Flexible learning-free segmentation and reconstruction of neural volumes. Scientific Reports. 2018;8(1). doi:10.1038/s41598-018-32628-3","ista":"Shabazi A, Kinnison J, Vescovi R, Du M, Hill R, Jösch MA, Takeno M, Zeng H, Da Costa N, Grutzendler J, Kasthuri N, Scheirer W. 2018. Flexible learning-free segmentation and reconstruction of neural volumes. Scientific Reports. 8(1), 14247.","ieee":"A. Shabazi et al., “Flexible learning-free segmentation and reconstruction of neural volumes,” Scientific Reports, vol. 8, no. 1. Nature Publishing Group, 2018.","short":"A. Shabazi, J. Kinnison, R. Vescovi, M. Du, R. Hill, M.A. Jösch, M. Takeno, H. Zeng, N. Da Costa, J. Grutzendler, N. Kasthuri, W. Scheirer, Scientific Reports 8 (2018).","mla":"Shabazi, Ali, et al. “Flexible Learning-Free Segmentation and Reconstruction of Neural Volumes.” Scientific Reports, vol. 8, no. 1, 14247, Nature Publishing Group, 2018, doi:10.1038/s41598-018-32628-3.","chicago":"Shabazi, Ali, Jeffery Kinnison, Rafael Vescovi, Ming Du, Robert Hill, Maximilian A Jösch, Marc Takeno, et al. “Flexible Learning-Free Segmentation and Reconstruction of Neural Volumes.” Scientific Reports. Nature Publishing Group, 2018. https://doi.org/10.1038/s41598-018-32628-3.","apa":"Shabazi, A., Kinnison, J., Vescovi, R., Du, M., Hill, R., Jösch, M. A., … Scheirer, W. (2018). Flexible learning-free segmentation and reconstruction of neural volumes. Scientific Reports. Nature Publishing Group. https://doi.org/10.1038/s41598-018-32628-3"},"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","day":"24"},{"volume":131,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"full_name":"Yamamoto, Wataru","first_name":"Wataru","last_name":"Yamamoto"},{"full_name":"Wada, Suguru","first_name":"Suguru","last_name":"Wada"},{"last_name":"Nagano","first_name":"Makoto","full_name":"Nagano, Makoto"},{"first_name":"Kaito","last_name":"Aoshima","full_name":"Aoshima, Kaito"},{"full_name":"Siekhaus, Daria E","orcid":"0000-0001-8323-8353","id":"3D224B9E-F248-11E8-B48F-1D18A9856A87","first_name":"Daria E","last_name":"Siekhaus"},{"full_name":"Toshima, Junko","first_name":"Junko","last_name":"Toshima"},{"full_name":"Toshima, Jiro","last_name":"Toshima","first_name":"Jiro"}],"pmid":1,"abstract":[{"text":"Clathrin-mediated endocytosis requires the coordinated assembly of various endocytic proteins and lipids at the plasma membrane. Accumulating evidence demonstrates a crucial role for phosphatidylinositol-4,5-bisphosphate (PtdIns(4,5)P2) in endocytosis, but specific roles for PtdIns(4)P other than as the biosynthetic precursor of PtdIns(4,5)P2 have not been clarified. In this study we investigated the role of PtdIns(4)P or PtdIns(4,5)P2 in receptor-mediated endocytosis through the construction of temperature-sensitive (ts) mutants for the PI 4-kinases Stt4p and Pik1p and the PtdIns(4) 5-kinase Mss4p. Quantitative analyses of endocytosis revealed that both the stt4(ts)pik1(ts) and mss4(ts) mutants have a severe defect in endocytic internalization. Live-cell imaging of endocytic protein dynamics in stt4(ts)pik1(ts) and mss4(ts) mutants revealed that PtdIns(4)P is required for the recruitment of the alpha-factor receptor Ste2p to clathrin-coated pits whereas PtdIns(4,5)P2 is required for membrane internalization. We also found that the localization to endocytic sites of the ENTH/ANTH domain-bearing clathrin adaptors, Ent1p/Ent2p and Yap1801p/Yap1802p, is significantly impaired in the stt4(ts)pik1(ts) mutant, but not in the mss4(ts) mutant. These results suggest distinct roles in successive steps for PtdIns(4)P and PtdIns(4,5)P2 during receptor-mediated endocytosis.","lang":"eng"}],"publication_status":"published","external_id":{"pmid":["29192062"],"isi":["000424786900012"]},"article_processing_charge":"No","title":"Distinct roles for plasma membrane PtdIns 4 P and PtdIns 4 5 P2 during yeast receptor mediated endocytosis","article_number":"jcs207696","year":"2018","date_created":"2018-12-11T11:47:32Z","publication":"Journal of Cell Science","issue":"1","doi":"10.1242/jcs.207696","quality_controlled":"1","ddc":["570"],"main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pubmed/29192062"}],"type":"journal_article","intvolume":" 131","oa_version":"Published Version","_id":"620","scopus_import":"1","publist_id":"7184","oa":1,"isi":1,"department":[{"_id":"DaSi"}],"publisher":"Company of Biologists","date_updated":"2026-06-18T19:01:31Z","month":"01","language":[{"iso":"eng"}],"date_published":"2018-01-04T00:00:00Z","status":"public","day":"04","citation":{"chicago":"Yamamoto, Wataru, Suguru Wada, Makoto Nagano, Kaito Aoshima, Daria E Siekhaus, Junko Toshima, and Jiro Toshima. “Distinct Roles for Plasma Membrane PtdIns 4 P and PtdIns 4 5 P2 during Yeast Receptor Mediated Endocytosis.” Journal of Cell Science. Company of Biologists, 2018. https://doi.org/10.1242/jcs.207696.","apa":"Yamamoto, W., Wada, S., Nagano, M., Aoshima, K., Siekhaus, D. E., Toshima, J., & Toshima, J. (2018). Distinct roles for plasma membrane PtdIns 4 P and PtdIns 4 5 P2 during yeast receptor mediated endocytosis. Journal of Cell Science. Company of Biologists. https://doi.org/10.1242/jcs.207696","mla":"Yamamoto, Wataru, et al. “Distinct Roles for Plasma Membrane PtdIns 4 P and PtdIns 4 5 P2 during Yeast Receptor Mediated Endocytosis.” Journal of Cell Science, vol. 131, no. 1, jcs207696, Company of Biologists, 2018, doi:10.1242/jcs.207696.","short":"W. Yamamoto, S. Wada, M. Nagano, K. Aoshima, D.E. Siekhaus, J. Toshima, J. Toshima, Journal of Cell Science 131 (2018).","ieee":"W. Yamamoto et al., “Distinct roles for plasma membrane PtdIns 4 P and PtdIns 4 5 P2 during yeast receptor mediated endocytosis,” Journal of Cell Science, vol. 131, no. 1. Company of Biologists, 2018.","ista":"Yamamoto W, Wada S, Nagano M, Aoshima K, Siekhaus DE, Toshima J, Toshima J. 2018. Distinct roles for plasma membrane PtdIns 4 P and PtdIns 4 5 P2 during yeast receptor mediated endocytosis. Journal of Cell Science. 131(1), jcs207696.","ama":"Yamamoto W, Wada S, Nagano M, et al. Distinct roles for plasma membrane PtdIns 4 P and PtdIns 4 5 P2 during yeast receptor mediated endocytosis. Journal of Cell Science. 2018;131(1). doi:10.1242/jcs.207696"}},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"full_name":"Gammerdinger, William J","orcid":"0000-0001-9638-1220","id":"3A7E01BC-F248-11E8-B48F-1D18A9856A87","first_name":"William J","last_name":"Gammerdinger"},{"last_name":"Kocher","first_name":"Thomas","full_name":"Kocher, Thomas"}],"volume":9,"article_processing_charge":"No","abstract":[{"text":"African cichlids display a remarkable assortment of jaw morphologies, pigmentation patterns, and mating behaviors. In addition to this previously documented diversity, recent studies have documented a rich diversity of sex chromosomes within these fishes. Here we review the known sex-determination network within vertebrates, and the extraordinary number of sex chromosomes systems segregating in African cichlids. We also propose a model for understanding the unusual number of sex chromosome systems within this clade.","lang":"eng"}],"external_id":{"isi":["000448656700018"]},"publication_status":"published","title":"Unusual diversity of sex chromosomes in African cichlid fishes","year":"2018","date_created":"2018-12-11T11:44:26Z","article_number":"480","issue":"10","doi":"10.3390/genes9100480","publication":"Genes","quality_controlled":"1","file":[{"file_size":1415791,"date_updated":"2020-07-14T12:47:27Z","checksum":"bec527692e2c9b56919c0429634ff337","relation":"main_file","access_level":"open_access","file_id":"5743","creator":"dernst","content_type":"application/pdf","file_name":"2018_Genes_Gammerdinger.pdf","date_created":"2018-12-18T09:54:46Z"}],"has_accepted_license":"1","ddc":["570"],"intvolume":" 9","oa_version":"Published Version","type":"journal_article","acknowledgement":"NSF DEB-1830753 and ISTPlus Fellowship","publist_id":"7991","_id":"63","scopus_import":"1","isi":1,"oa":1,"file_date_updated":"2020-07-14T12:47:27Z","language":[{"iso":"eng"}],"month":"10","date_published":"2018-10-04T00:00:00Z","department":[{"_id":"BeVi"}],"publisher":"MDPI","date_updated":"2025-04-15T06:50:01Z","ec_funded":1,"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"day":"04","status":"public","citation":{"short":"W.J. Gammerdinger, T. Kocher, Genes 9 (2018).","ieee":"W. J. Gammerdinger and T. Kocher, “Unusual diversity of sex chromosomes in African cichlid fishes,” Genes, vol. 9, no. 10. MDPI, 2018.","ista":"Gammerdinger WJ, Kocher T. 2018. Unusual diversity of sex chromosomes in African cichlid fishes. Genes. 9(10), 480.","ama":"Gammerdinger WJ, Kocher T. Unusual diversity of sex chromosomes in African cichlid fishes. Genes. 2018;9(10). doi:10.3390/genes9100480","chicago":"Gammerdinger, William J, and Thomas Kocher. “Unusual Diversity of Sex Chromosomes in African Cichlid Fishes.” Genes. MDPI, 2018. https://doi.org/10.3390/genes9100480.","apa":"Gammerdinger, W. J., & Kocher, T. (2018). Unusual diversity of sex chromosomes in African cichlid fishes. Genes. MDPI. https://doi.org/10.3390/genes9100480","mla":"Gammerdinger, William J., and Thomas Kocher. “Unusual Diversity of Sex Chromosomes in African Cichlid Fishes.” Genes, vol. 9, no. 10, 480, MDPI, 2018, doi:10.3390/genes9100480."},"project":[{"name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7","grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425"}]},{"article_number":"165301","year":"2018","date_created":"2019-04-17T10:53:38Z","publication":"Physical Review Letters","issue":"16","doi":"10.1103/physrevlett.121.165301","quality_controlled":"1","main_file_link":[{"url":"https://arxiv.org/abs/1803.07990","open_access":"1"}],"volume":121,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"last_name":"Bighin","first_name":"Giacomo","orcid":"0000-0001-8823-9777","id":"4CA96FD4-F248-11E8-B48F-1D18A9856A87","full_name":"Bighin, Giacomo"},{"last_name":"Tscherbul","first_name":"Timur","full_name":"Tscherbul, Timur"},{"id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6990-7802","full_name":"Lemeshko, Mikhail","last_name":"Lemeshko","first_name":"Mikhail"}],"related_material":{"link":[{"description":"News on IST Homepage","relation":"press_release","url":"https://ist.ac.at/en/news/description-of-rotating-molecules-made-easy/"}]},"abstract":[{"lang":"eng","text":"We introduce a diagrammatic Monte Carlo approach to angular momentum properties of quantum many-particle systems possessing a macroscopic number of degrees of freedom. The treatment is based on a diagrammatic expansion that merges the usual Feynman diagrams with the angular momentum diagrams known from atomic and nuclear structure theory, thereby incorporating the non-Abelian algebra inherent to quantum rotations. Our approach is applicable at arbitrary coupling, is free of systematic errors and of finite-size effects, and naturally provides access to the impurity Green function. We exemplify the technique by obtaining an all-coupling solution of the angulon model; however, the method is quite general and can be applied to a broad variety of systems in which particles exchange quantum angular momentum with their many-body environment."}],"external_id":{"isi":["000447468400008"],"arxiv":["1803.07990"]},"publication_status":"published","article_processing_charge":"No","title":"Diagrammatic Monte Carlo approach to angular momentum in quantum many-particle systems","day":"16","status":"public","project":[{"_id":"26031614-B435-11E9-9278-68D0E5697425","grant_number":"P29902","call_identifier":"FWF","name":"Quantum rotations in the presence of a many-body environment"}],"citation":{"short":"G. Bighin, T. Tscherbul, M. Lemeshko, Physical Review Letters 121 (2018).","ieee":"G. Bighin, T. Tscherbul, and M. Lemeshko, “Diagrammatic Monte Carlo approach to angular momentum in quantum many-particle systems,” Physical Review Letters, vol. 121, no. 16. American Physical Society, 2018.","ama":"Bighin G, Tscherbul T, Lemeshko M. Diagrammatic Monte Carlo approach to angular momentum in quantum many-particle systems. Physical Review Letters. 2018;121(16). doi:10.1103/physrevlett.121.165301","ista":"Bighin G, Tscherbul T, Lemeshko M. 2018. Diagrammatic Monte Carlo approach to angular momentum in quantum many-particle systems. Physical Review Letters. 121(16), 165301.","apa":"Bighin, G., Tscherbul, T., & Lemeshko, M. (2018). Diagrammatic Monte Carlo approach to angular momentum in quantum many-particle systems. Physical Review Letters. American Physical Society. https://doi.org/10.1103/physrevlett.121.165301","chicago":"Bighin, Giacomo, Timur Tscherbul, and Mikhail Lemeshko. “Diagrammatic Monte Carlo Approach to Angular Momentum in Quantum Many-Particle Systems.” Physical Review Letters. American Physical Society, 2018. https://doi.org/10.1103/physrevlett.121.165301.","mla":"Bighin, Giacomo, et al. “Diagrammatic Monte Carlo Approach to Angular Momentum in Quantum Many-Particle Systems.” Physical Review Letters, vol. 121, no. 16, 165301, American Physical Society, 2018, doi:10.1103/physrevlett.121.165301."},"type":"journal_article","intvolume":" 121","oa_version":"Preprint","_id":"6339","scopus_import":"1","oa":1,"isi":1,"publisher":"American Physical Society","arxiv":1,"department":[{"_id":"MiLe"}],"date_updated":"2025-04-15T07:59:29Z","language":[{"iso":"eng"}],"month":"10","date_published":"2018-10-16T00:00:00Z"},{"oa":1,"file_date_updated":"2020-07-14T12:47:28Z","DOAJ_listed":"1","publisher":"Bio-Protocol","department":[{"_id":"MiSi"}],"date_updated":"2025-05-20T07:43:06Z","language":[{"iso":"eng"}],"month":"09","date_published":"2018-09-20T00:00:00Z","acknowledgement":"This protocol was adapted from a previously published study (Gaertner et al., 2017). We thank Michael Lorenz for his excellent assistance in bacteria culture. This work was funded by the DFG SFB 914 (S.M. [B02 and Z01]), the DFG SFB 1123 (S.M. [B06]), the DFG FOR 2033 (S.M. and F.G.), the German Centre for Cardiovascular Research (DZHK) (MHA 1.4VD [S.M.]), FP7 program (project 260309, PRESTIGE [S.M.]), FöFoLe project 947 (F.G.), the Friedrich-Baur-Stiftung project 41/16 (F.G.), Marie Sklodowska Curie Individual Fellowship (EU project 747687, LamelliaActin [F.G.]).","type":"journal_article","article_type":"original","intvolume":" 8","oa_version":"Published Version","_id":"6354","project":[{"name":"Mechanical Adaptation of Lamellipodial Actin Networks in Migrating Cells","call_identifier":"H2020","grant_number":"747687","_id":"260AA4E2-B435-11E9-9278-68D0E5697425"}],"citation":{"ama":"Fan S, Lorenz M, Massberg S, Gärtner FR. Platelet migration and bacterial trapping assay under flow. Bio-Protocol. 2018;8(18). doi:10.21769/bioprotoc.3018","ista":"Fan S, Lorenz M, Massberg S, Gärtner FR. 2018. Platelet migration and bacterial trapping assay under flow. Bio-Protocol. 8(18), e3018.","ieee":"S. Fan, M. Lorenz, S. Massberg, and F. R. Gärtner, “Platelet migration and bacterial trapping assay under flow,” Bio-Protocol, vol. 8, no. 18. Bio-Protocol, 2018.","short":"S. Fan, M. Lorenz, S. Massberg, F.R. Gärtner, Bio-Protocol 8 (2018).","mla":"Fan, Shuxia, et al. “Platelet Migration and Bacterial Trapping Assay under Flow.” Bio-Protocol, vol. 8, no. 18, e3018, Bio-Protocol, 2018, doi:10.21769/bioprotoc.3018.","chicago":"Fan, Shuxia, Michael Lorenz, Steffen Massberg, and Florian R Gärtner. “Platelet Migration and Bacterial Trapping Assay under Flow.” Bio-Protocol. Bio-Protocol, 2018. https://doi.org/10.21769/bioprotoc.3018.","apa":"Fan, S., Lorenz, M., Massberg, S., & Gärtner, F. R. (2018). Platelet migration and bacterial trapping assay under flow. Bio-Protocol. Bio-Protocol. https://doi.org/10.21769/bioprotoc.3018"},"OA_type":"gold","ec_funded":1,"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","day":"20","abstract":[{"lang":"eng","text":"Blood platelets are critical for hemostasis and thrombosis, but also play diverse roles during immune responses. We have recently reported that platelets migrate at sites of infection in vitro and in vivo. Importantly, platelets use their ability to migrate to collect and bundle fibrin (ogen)-bound bacteria accomplishing efficient intravascular bacterial trapping. Here, we describe a method that allows analyzing platelet migration in vitro, focusing on their ability to collect bacteria and trap bacteria under flow."}],"publication_status":"published","external_id":{"pmid":["34395806"]},"article_processing_charge":"Yes","title":"Platelet migration and bacterial trapping assay under flow","keyword":["Platelets","Cell migration","Bacteria","Shear flow","Fibrinogen","E. coli"],"volume":8,"OA_place":"publisher","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"last_name":"Fan","first_name":"Shuxia","full_name":"Fan, Shuxia"},{"first_name":"Michael","last_name":"Lorenz","full_name":"Lorenz, Michael"},{"full_name":"Massberg, Steffen","last_name":"Massberg","first_name":"Steffen"},{"first_name":"Florian R","last_name":"Gärtner","full_name":"Gärtner, Florian R","orcid":"0000-0001-6120-3723","id":"397A88EE-F248-11E8-B48F-1D18A9856A87"}],"pmid":1,"file":[{"file_id":"6360","file_size":2928337,"date_updated":"2020-07-14T12:47:28Z","access_level":"open_access","checksum":"d4588377e789da7f360b553ae02c5119","relation":"main_file","file_name":"2018_BioProtocol_Fan.pdf","content_type":"application/pdf","date_created":"2019-04-30T08:04:33Z","creator":"dernst"}],"quality_controlled":"1","corr_author":"1","ddc":["570"],"has_accepted_license":"1","article_number":"e3018","year":"2018","date_created":"2019-04-29T09:40:33Z","publication":"Bio-Protocol","issue":"18","doi":"10.21769/bioprotoc.3018","publication_identifier":{"issn":["2331-8325"]}},{"corr_author":"1","file":[{"relation":"main_file","checksum":"5a71b24ba712a3eb2e46165a38fbc30a","access_level":"open_access","date_updated":"2020-07-14T12:47:28Z","file_size":249246,"file_id":"6356","creator":"dernst","date_created":"2019-04-30T06:14:58Z","file_name":"2018_ForumMahtematics_Akopyan.pdf","content_type":"application/pdf"}],"quality_controlled":"1","has_accepted_license":"1","ddc":["510"],"date_created":"2019-04-30T06:09:57Z","year":"2018","article_number":"e7","doi":"10.1017/fms.2018.7","publication_identifier":{"issn":["2050-5094"]},"publication":"Forum of Mathematics, Sigma","article_processing_charge":"No","publication_status":"published","external_id":{"arxiv":["1712.10205"],"isi":["000433915500001"]},"abstract":[{"lang":"eng","text":"We prove that any cyclic quadrilateral can be inscribed in any closed convex C1-curve. The smoothness condition is not required if the quadrilateral is a rectangle."}],"title":"Any cyclic quadrilateral can be inscribed in any closed convex smooth curve","author":[{"last_name":"Akopyan","first_name":"Arseniy","id":"430D2C90-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2548-617X","full_name":"Akopyan, Arseniy"},{"first_name":"Sergey","last_name":"Avvakumov","full_name":"Avvakumov, Sergey","id":"3827DAC8-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7840-5062"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","volume":6,"related_material":{"record":[{"status":"public","id":"8156","relation":"dissertation_contains"}]},"citation":{"mla":"Akopyan, Arseniy, and Sergey Avvakumov. “Any Cyclic Quadrilateral Can Be Inscribed in Any Closed Convex Smooth Curve.” Forum of Mathematics, Sigma, vol. 6, e7, Cambridge University Press, 2018, doi:10.1017/fms.2018.7.","chicago":"Akopyan, Arseniy, and Sergey Avvakumov. “Any Cyclic Quadrilateral Can Be Inscribed in Any Closed Convex Smooth Curve.” Forum of Mathematics, Sigma. Cambridge University Press, 2018. https://doi.org/10.1017/fms.2018.7.","apa":"Akopyan, A., & Avvakumov, S. (2018). Any cyclic quadrilateral can be inscribed in any closed convex smooth curve. Forum of Mathematics, Sigma. Cambridge University Press. https://doi.org/10.1017/fms.2018.7","ista":"Akopyan A, Avvakumov S. 2018. Any cyclic quadrilateral can be inscribed in any closed convex smooth curve. Forum of Mathematics, Sigma. 6, e7.","ama":"Akopyan A, Avvakumov S. Any cyclic quadrilateral can be inscribed in any closed convex smooth curve. Forum of Mathematics, Sigma. 2018;6. doi:10.1017/fms.2018.7","ieee":"A. Akopyan and S. Avvakumov, “Any cyclic quadrilateral can be inscribed in any closed convex smooth curve,” Forum of Mathematics, Sigma, vol. 6. Cambridge University Press, 2018.","short":"A. Akopyan, S. Avvakumov, Forum of Mathematics, Sigma 6 (2018)."},"project":[{"grant_number":"716117","_id":"256E75B8-B435-11E9-9278-68D0E5697425","name":"Optimal Transport and Stochastic Dynamics","call_identifier":"H2020"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"ec_funded":1,"day":"31","status":"public","isi":1,"file_date_updated":"2020-07-14T12:47:28Z","oa":1,"date_published":"2018-05-31T00:00:00Z","language":[{"iso":"eng"}],"month":"05","date_updated":"2026-04-08T07:25:54Z","department":[{"_id":"UlWa"},{"_id":"HeEd"},{"_id":"JaMa"}],"publisher":"Cambridge University Press","arxiv":1,"oa_version":"Published Version","intvolume":" 6","type":"journal_article","_id":"6355"},{"publist_id":"7990","_id":"64","scopus_import":"1","article_type":"original","oa_version":"Preprint","intvolume":" 115","type":"journal_article","month":"08","language":[{"iso":"eng"}],"date_published":"2018-08-28T00:00:00Z","publisher":"National Academy of Sciences","arxiv":1,"department":[{"_id":"TaHa"}],"date_updated":"2025-06-03T11:21:16Z","isi":1,"oa":1,"status":"public","day":"28","ec_funded":1,"citation":{"short":"N. Kalinin, A. Guzmán Sáenz, Y. Prieto, M. Shkolnikov, V. Kalinina, E. Lupercio, Proceedings of the National Academy of Sciences of the United States of America 115 (2018) E8135–E8142.","ieee":"N. Kalinin, A. Guzmán Sáenz, Y. Prieto, M. Shkolnikov, V. Kalinina, and E. Lupercio, “Self-organized criticality and pattern emergence through the lens of tropical geometry,” Proceedings of the National Academy of Sciences of the United States of America, vol. 115, no. 35. National Academy of Sciences, pp. E8135–E8142, 2018.","ama":"Kalinin N, Guzmán Sáenz A, Prieto Y, Shkolnikov M, Kalinina V, Lupercio E. Self-organized criticality and pattern emergence through the lens of tropical geometry. Proceedings of the National Academy of Sciences of the United States of America. 2018;115(35):E8135-E8142. doi:10.1073/pnas.1805847115","ista":"Kalinin N, Guzmán Sáenz A, Prieto Y, Shkolnikov M, Kalinina V, Lupercio E. 2018. Self-organized criticality and pattern emergence through the lens of tropical geometry. Proceedings of the National Academy of Sciences of the United States of America. 115(35), E8135–E8142.","apa":"Kalinin, N., Guzmán Sáenz, A., Prieto, Y., Shkolnikov, M., Kalinina, V., & Lupercio, E. (2018). Self-organized criticality and pattern emergence through the lens of tropical geometry. Proceedings of the National Academy of Sciences of the United States of America. National Academy of Sciences. https://doi.org/10.1073/pnas.1805847115","chicago":"Kalinin, Nikita, Aldo Guzmán Sáenz, Y Prieto, Mikhail Shkolnikov, V Kalinina, and Ernesto Lupercio. “Self-Organized Criticality and Pattern Emergence through the Lens of Tropical Geometry.” Proceedings of the National Academy of Sciences of the United States of America. National Academy of Sciences, 2018. https://doi.org/10.1073/pnas.1805847115.","mla":"Kalinin, Nikita, et al. “Self-Organized Criticality and Pattern Emergence through the Lens of Tropical Geometry.” Proceedings of the National Academy of Sciences of the United States of America, vol. 115, no. 35, National Academy of Sciences, 2018, pp. E8135–42, doi:10.1073/pnas.1805847115."},"project":[{"call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme","_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"full_name":"Kalinin, Nikita","first_name":"Nikita","last_name":"Kalinin"},{"full_name":"Guzmán Sáenz, Aldo","last_name":"Guzmán Sáenz","first_name":"Aldo"},{"first_name":"Y","last_name":"Prieto","full_name":"Prieto, Y"},{"full_name":"Shkolnikov, Mikhail","id":"35084A62-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4310-178X","last_name":"Shkolnikov","first_name":"Mikhail"},{"last_name":"Kalinina","first_name":"V","full_name":"Kalinina, V"},{"first_name":"Ernesto","last_name":"Lupercio","full_name":"Lupercio, Ernesto"}],"volume":115,"title":"Self-organized criticality and pattern emergence through the lens of tropical geometry","page":"E8135 - E8142","article_processing_charge":"No","abstract":[{"lang":"eng","text":"Tropical geometry, an established field in pure mathematics, is a place where string theory, mirror symmetry, computational algebra, auction theory, and so forth meet and influence one another. In this paper, we report on our discovery of a tropical model with self-organized criticality (SOC) behavior. Our model is continuous, in contrast to all known models of SOC, and is a certain scaling limit of the sandpile model, the first and archetypical model of SOC. We describe how our model is related to pattern formation and proportional growth phenomena and discuss the dichotomy between continuous and discrete models in several contexts. Our aim in this context is to present an idealized tropical toy model (cf. Turing reaction-diffusion model), requiring further investigation."}],"publication_status":"published","external_id":{"isi":["000442861600009"],"arxiv":["1806.09153"]},"issue":"35","publication_identifier":{"issn":["0027-8424"]},"doi":"10.1073/pnas.1805847115","publication":"Proceedings of the National Academy of Sciences of the United States of America","year":"2018","date_created":"2018-12-11T11:44:26Z","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1806.09153"}],"quality_controlled":"1"},{"citation":{"ama":"Ma W, Veltsos P, Toups MA, et al. Tissue specificity and dynamics of sex biased gene expression in a common frog population with differentiated, yet homomorphic, sex chromosomes. Genes. 2018;9(6). doi:10.3390/genes9060294","ista":"Ma W, Veltsos P, Toups MA, Rodrigues N, Sermier R, Jeffries D, Perrin N. 2018. Tissue specificity and dynamics of sex biased gene expression in a common frog population with differentiated, yet homomorphic, sex chromosomes. Genes. 9(6), 294.","short":"W. Ma, P. Veltsos, M.A. Toups, N. Rodrigues, R. Sermier, D. Jeffries, N. Perrin, Genes 9 (2018).","ieee":"W. Ma et al., “Tissue specificity and dynamics of sex biased gene expression in a common frog population with differentiated, yet homomorphic, sex chromosomes,” Genes, vol. 9, no. 6. MDPI, 2018.","mla":"Ma, Wen, et al. “Tissue Specificity and Dynamics of Sex Biased Gene Expression in a Common Frog Population with Differentiated, yet Homomorphic, Sex Chromosomes.” Genes, vol. 9, no. 6, 294, MDPI, 2018, doi:10.3390/genes9060294.","chicago":"Ma, Wen, Paris Veltsos, Melissa A Toups, Nicolas Rodrigues, Roberto Sermier, Daniel Jeffries, and Nicolas Perrin. “Tissue Specificity and Dynamics of Sex Biased Gene Expression in a Common Frog Population with Differentiated, yet Homomorphic, Sex Chromosomes.” Genes. MDPI, 2018. https://doi.org/10.3390/genes9060294.","apa":"Ma, W., Veltsos, P., Toups, M. A., Rodrigues, N., Sermier, R., Jeffries, D., & Perrin, N. (2018). Tissue specificity and dynamics of sex biased gene expression in a common frog population with differentiated, yet homomorphic, sex chromosomes. Genes. MDPI. https://doi.org/10.3390/genes9060294"},"day":"12","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"date_published":"2018-06-12T00:00:00Z","language":[{"iso":"eng"}],"month":"06","date_updated":"2024-12-11T13:13:35Z","department":[{"_id":"BeVi"}],"publisher":"MDPI","isi":1,"file_date_updated":"2020-07-14T12:45:22Z","oa":1,"publist_id":"7714","scopus_import":"1","_id":"199","oa_version":"Published Version","intvolume":" 9","type":"journal_article","has_accepted_license":"1","ddc":["570"],"quality_controlled":"1","file":[{"relation":"main_file","checksum":"423069beb1cd3cdd25bf3f464b38f1d7","access_level":"open_access","file_size":3985796,"date_updated":"2020-07-14T12:45:22Z","file_id":"5905","creator":"dernst","date_created":"2019-02-01T07:52:28Z","content_type":"application/pdf","file_name":"2018_Genes_Ma.pdf"}],"doi":"10.3390/genes9060294","issue":"6","publication":"Genes","date_created":"2018-12-11T11:45:09Z","year":"2018","article_number":"294","title":"Tissue specificity and dynamics of sex biased gene expression in a common frog population with differentiated, yet homomorphic, sex chromosomes","article_processing_charge":"No","external_id":{"isi":["000436494200026"]},"publication_status":"published","abstract":[{"lang":"eng","text":"Sex-biased genes are central to the study of sexual selection, sexual antagonism, and sex chromosome evolution. We describe a comprehensive de novo assembled transcriptome in the common frog Rana temporaria based on five developmental stages and three adult tissues from both sexes, obtained from a population with karyotypically homomorphic but genetically differentiated sex chromosomes. This allows the study of sex-biased gene expression throughout development, and its effect on the rate of gene evolution while accounting for pleiotropic expression, which is known to negatively correlate with the evolutionary rate. Overall, sex-biased genes had little overlap among developmental stages and adult tissues. Late developmental stages and gonad tissues had the highest numbers of stage-or tissue-specific genes. We find that pleiotropic gene expression is a better predictor than sex bias for the evolutionary rate of genes, though it often interacts with sex bias. Although genetically differentiated, the sex chromosomes were not enriched in sex-biased genes, possibly due to a very recent arrest of XY recombination. These results extend our understanding of the developmental dynamics, tissue specificity, and genomic localization of sex-biased genes."}],"author":[{"last_name":"Ma","first_name":"Wen","full_name":"Ma, Wen"},{"full_name":"Veltsos, Paris","last_name":"Veltsos","first_name":"Paris"},{"id":"4E099E4E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9752-7380","full_name":"Toups, Melissa A","first_name":"Melissa A","last_name":"Toups"},{"first_name":"Nicolas","last_name":"Rodrigues","full_name":"Rodrigues, Nicolas"},{"full_name":"Sermier, Roberto","first_name":"Roberto","last_name":"Sermier"},{"first_name":"Daniel","last_name":"Jeffries","full_name":"Jeffries, Daniel"},{"full_name":"Perrin, Nicolas","first_name":"Nicolas","last_name":"Perrin"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","volume":9},{"related_material":{"record":[{"id":"9807","relation":"research_data","status":"public"},{"id":"9808","relation":"research_data","status":"public"}]},"volume":19,"author":[{"full_name":"Higareda Almaraz, Juan","first_name":"Juan","last_name":"Higareda Almaraz"},{"full_name":"Karbiener, Michael","first_name":"Michael","last_name":"Karbiener"},{"last_name":"Giroud","first_name":"Maude","full_name":"Giroud, Maude"},{"first_name":"Florian","last_name":"Pauler","id":"48EA0138-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7462-0048","full_name":"Pauler, Florian"},{"last_name":"Gerhalter","first_name":"Teresa","full_name":"Gerhalter, Teresa"},{"last_name":"Herzig","first_name":"Stephan","full_name":"Herzig, Stephan"},{"last_name":"Scheideler","first_name":"Marcel","full_name":"Scheideler, Marcel"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","title":"Norepinephrine triggers an immediate-early regulatory network response in primary human white adipocytes","publication_status":"published","external_id":{"isi":["000450976700002"]},"abstract":[{"text":"Background: Norepinephrine (NE) signaling has a key role in white adipose tissue (WAT) functions, including lipolysis, free fatty acid liberation and, under certain conditions, conversion of white into brite (brown-in-white) adipocytes. However, acute effects of NE stimulation have not been described at the transcriptional network level. Results: We used RNA-seq to uncover a broad transcriptional response. The inference of protein-protein and protein-DNA interaction networks allowed us to identify a set of immediate-early genes (IEGs) with high betweenness, validating our approach and suggesting a hierarchical control of transcriptional regulation. In addition, we identified a transcriptional regulatory network with IEGs as master regulators, including HSF1 and NFIL3 as novel NE-induced IEG candidates. Moreover, a functional enrichment analysis and gene clustering into functional modules suggest a crosstalk between metabolic, signaling, and immune responses. Conclusions: Altogether, our network biology approach explores for the first time the immediate-early systems level response of human adipocytes to acute sympathetic activation, thereby providing a first network basis of early cell fate programs and crosstalks between metabolic and transcriptional networks required for proper WAT function.","lang":"eng"}],"article_processing_charge":"No","publication":"BMC Genomics","publication_identifier":{"issn":["1471-2164"]},"doi":"10.1186/s12864-018-5173-0","issue":"1","date_created":"2018-12-11T11:44:12Z","year":"2018","ddc":["570"],"has_accepted_license":"1","file":[{"file_size":4629784,"date_updated":"2020-07-14T12:45:23Z","access_level":"open_access","checksum":"a56516e734dab589dc7f3e1915973b4d","relation":"main_file","file_id":"5712","creator":"dernst","content_type":"application/pdf","file_name":"2018_BMCGenomics_Higareda.pdf","date_created":"2018-12-17T14:52:57Z"}],"quality_controlled":"1","scopus_import":"1","_id":"20","publist_id":"8035","acknowledgement":"This work was funded by the German Centre for Diabetes Research (DZD) and the Austrian Science Fund (FWF, P25729-B19).","type":"journal_article","oa_version":"Published Version","intvolume":" 19","article_type":"original","date_updated":"2023-09-13T09:10:47Z","department":[{"_id":"SiHi"}],"publisher":"BioMed Central","date_published":"2018-11-03T00:00:00Z","language":[{"iso":"eng"}],"month":"11","file_date_updated":"2020-07-14T12:45:23Z","oa":1,"isi":1,"status":"public","day":"03","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"citation":{"chicago":"Higareda Almaraz, Juan, Michael Karbiener, Maude Giroud, Florian Pauler, Teresa Gerhalter, Stephan Herzig, and Marcel Scheideler. “Norepinephrine Triggers an Immediate-Early Regulatory Network Response in Primary Human White Adipocytes.” BMC Genomics. BioMed Central, 2018. https://doi.org/10.1186/s12864-018-5173-0.","apa":"Higareda Almaraz, J., Karbiener, M., Giroud, M., Pauler, F., Gerhalter, T., Herzig, S., & Scheideler, M. (2018). Norepinephrine triggers an immediate-early regulatory network response in primary human white adipocytes. BMC Genomics. BioMed Central. https://doi.org/10.1186/s12864-018-5173-0","mla":"Higareda Almaraz, Juan, et al. “Norepinephrine Triggers an Immediate-Early Regulatory Network Response in Primary Human White Adipocytes.” BMC Genomics, vol. 19, no. 1, BioMed Central, 2018, doi:10.1186/s12864-018-5173-0.","ieee":"J. Higareda Almaraz et al., “Norepinephrine triggers an immediate-early regulatory network response in primary human white adipocytes,” BMC Genomics, vol. 19, no. 1. BioMed Central, 2018.","short":"J. Higareda Almaraz, M. Karbiener, M. Giroud, F. Pauler, T. Gerhalter, S. Herzig, M. Scheideler, BMC Genomics 19 (2018).","ama":"Higareda Almaraz J, Karbiener M, Giroud M, et al. Norepinephrine triggers an immediate-early regulatory network response in primary human white adipocytes. BMC Genomics. 2018;19(1). doi:10.1186/s12864-018-5173-0","ista":"Higareda Almaraz J, Karbiener M, Giroud M, Pauler F, Gerhalter T, Herzig S, Scheideler M. 2018. Norepinephrine triggers an immediate-early regulatory network response in primary human white adipocytes. BMC Genomics. 19(1)."}},{"type":"dissertation","oa_version":"Published Version","_id":"200","publist_id":"7713","oa":1,"file_date_updated":"2020-07-14T12:45:23Z","department":[{"_id":"NiBa"}],"publisher":"Institute of Science and Technology Austria","date_updated":"2026-04-08T14:06:37Z","month":"02","language":[{"iso":"eng"}],"date_published":"2018-02-21T00:00:00Z","tmp":{"short":"CC BY-NC (4.0)","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"},"status":"public","day":"21","pubrep_id":"963","alternative_title":["ISTA Thesis"],"citation":{"ieee":"H. Ringbauer, “Inferring recent demography from spatial genetic structure,” Institute of Science and Technology Austria, 2018.","short":"H. Ringbauer, Inferring Recent Demography from Spatial Genetic Structure, Institute of Science and Technology Austria, 2018.","ista":"Ringbauer H. 2018. Inferring recent demography from spatial genetic structure. Institute of Science and Technology Austria.","ama":"Ringbauer H. Inferring recent demography from spatial genetic structure. 2018. doi:10.15479/AT:ISTA:th_963","chicago":"Ringbauer, Harald. “Inferring Recent Demography from Spatial Genetic Structure.” Institute of Science and Technology Austria, 2018. https://doi.org/10.15479/AT:ISTA:th_963.","apa":"Ringbauer, H. (2018). Inferring recent demography from spatial genetic structure. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:th_963","mla":"Ringbauer, Harald. Inferring Recent Demography from Spatial Genetic Structure. Institute of Science and Technology Austria, 2018, doi:10.15479/AT:ISTA:th_963."},"OA_place":"publisher","author":[{"first_name":"Harald","last_name":"Ringbauer","orcid":"0000-0002-4884-9682","id":"417FCFF4-F248-11E8-B48F-1D18A9856A87","full_name":"Ringbauer, Harald"}],"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","related_material":{"record":[{"relation":"part_of_dissertation","id":"563","status":"public"},{"status":"public","id":"1074","relation":"part_of_dissertation"}]},"abstract":[{"text":"This thesis is concerned with the inference of current population structure based on geo-referenced genetic data. The underlying idea is that population structure affects its spatial genetic structure. Therefore, genotype information can be utilized to estimate important demographic parameters such as migration rates. These indirect estimates of population structure have become very attractive, as genotype data is now widely available. However, there also has been much concern about these approaches. Importantly, genetic structure can be influenced by many complex patterns, which often cannot be disentangled. Moreover, many methods merely fit heuristic patterns of genetic structure, and do not build upon population genetics theory. Here, I describe two novel inference methods that address these shortcomings. In Chapter 2, I introduce an inference scheme based on a new type of signal, identity by descent (IBD) blocks. Recently, it has become feasible to detect such long blocks of genome shared between pairs of samples. These blocks are direct traces of recent coalescence events. As such, they contain ample signal for inferring recent demography. I examine sharing of IBD blocks in two-dimensional populations with local migration. Using a diffusion approximation, I derive formulas for an isolation by distance pattern of long IBD blocks and show that sharing of long IBD blocks approaches rapid exponential decay for growing sample distance. I describe an inference scheme based on these results. It can robustly estimate the dispersal rate and population density, which is demonstrated on simulated data. I also show an application to estimate mean migration and the rate of recent population growth within Eastern Europe. Chapter 3 is about a novel method to estimate barriers to gene flow in a two dimensional population. This inference scheme utilizes geographically localized allele frequency fluctuations - a classical isolation by distance signal. The strength of these local fluctuations increases on average next to a barrier, and there is less correlation across it. I again use a framework of diffusion of ancestral lineages to model this effect, and provide an efficient numerical implementation to fit the results to geo-referenced biallelic SNP data. This inference scheme is able to robustly estimate strong barriers to gene flow, as tests on simulated data confirm.","lang":"eng"}],"publication_status":"published","page":"146","license":"https://creativecommons.org/licenses/by-nc/4.0/","article_processing_charge":"No","title":"Inferring recent demography from spatial genetic structure","degree_awarded":"PhD","supervisor":[{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H","last_name":"Barton","first_name":"Nicholas H"}],"year":"2018","date_created":"2018-12-11T11:45:10Z","publication_identifier":{"issn":["2663-337X"]},"doi":"10.15479/AT:ISTA:th_963","file":[{"file_id":"5111","date_updated":"2020-07-14T12:45:23Z","file_size":5792935,"access_level":"open_access","checksum":"8cc534d2b528ae017acf80874cce48c9","relation":"main_file","content_type":"application/pdf","file_name":"IST-2018-963-v1+1_thesis.pdf","date_created":"2018-12-12T10:14:55Z","creator":"system"},{"date_created":"2019-04-05T09:30:12Z","content_type":"application/zip","file_name":"2018_thesis_ringbauer_source.zip","creator":"dernst","file_id":"6224","relation":"source_file","checksum":"6af18d7e5a7e2728ceda2f41ee24f628","access_level":"closed","file_size":113365,"date_updated":"2020-07-14T12:45:23Z"}],"corr_author":"1","ddc":["576"],"has_accepted_license":"1"},{"oa":1,"isi":1,"department":[{"_id":"JiFr"}],"publisher":"National Academy of Sciences","date_updated":"2026-04-28T08:29:26Z","month":"06","language":[{"iso":"eng"}],"date_published":"2018-06-26T00:00:00Z","type":"journal_article","article_type":"original","intvolume":" 115","oa_version":"Submitted Version","_id":"203","scopus_import":"1","publist_id":"7710","project":[{"call_identifier":"FP7","name":"Polarity and subcellular dynamics in plants","_id":"25716A02-B435-11E9-9278-68D0E5697425","grant_number":"282300"}],"citation":{"ista":"Abbas M, Hernández GJ, Pollmann S, Samodelov SL, Kolb M, Friml J, Hammes UZ, Zurbriggen MD, Blázquez M, Alabadí D. 2018. Auxin methylation is required for differential growth in Arabidopsis. PNAS. 115(26), 6864–6869.","ama":"Abbas M, Hernández GJ, Pollmann S, et al. Auxin methylation is required for differential growth in Arabidopsis. PNAS. 2018;115(26):6864-6869. doi:10.1073/pnas.1806565115","ieee":"M. Abbas et al., “Auxin methylation is required for differential growth in Arabidopsis,” PNAS, vol. 115, no. 26. National Academy of Sciences, pp. 6864–6869, 2018.","short":"M. Abbas, G.J. Hernández, S. Pollmann, S.L. Samodelov, M. Kolb, J. Friml, U.Z. Hammes, M.D. Zurbriggen, M. Blázquez, D. Alabadí, PNAS 115 (2018) 6864–6869.","mla":"Abbas, Mohamad, et al. “Auxin Methylation Is Required for Differential Growth in Arabidopsis.” PNAS, vol. 115, no. 26, National Academy of Sciences, 2018, pp. 6864–69, doi:10.1073/pnas.1806565115.","chicago":"Abbas, Mohamad, García J Hernández, Stephan Pollmann, Sophia L Samodelov, Martina Kolb, Jiří Friml, Ulrich Z Hammes, Matias D Zurbriggen, Miguel Blázquez, and David Alabadí. “Auxin Methylation Is Required for Differential Growth in Arabidopsis.” PNAS. National Academy of Sciences, 2018. https://doi.org/10.1073/pnas.1806565115.","apa":"Abbas, M., Hernández, G. J., Pollmann, S., Samodelov, S. L., Kolb, M., Friml, J., … Alabadí, D. (2018). Auxin methylation is required for differential growth in Arabidopsis. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1806565115"},"OA_type":"green","ec_funded":1,"day":"26","status":"public","abstract":[{"lang":"eng","text":"Asymmetric auxin distribution is instrumental for the differential growth that causes organ bending on tropic stimuli and curvatures during plant development. Local differences in auxin concentrations are achieved mainly by polarized cellular distribution of PIN auxin transporters, but whether other mechanisms involving auxin homeostasis are also relevant for the formation of auxin gradients is not clear. Here we show that auxin methylation is required for asymmetric auxin distribution across the hypocotyl, particularly during its response to gravity. We found that loss-of-function mutants in Arabidopsis IAA CARBOXYL METHYLTRANSFERASE1 (IAMT1) prematurely unfold the apical hook, and that their hypocotyls are impaired in gravitropic reorientation. This defect is linked to an auxin-dependent increase in PIN gene expression, leading to an increased polar auxin transport and lack of asymmetric distribution of PIN3 in the iamt1 mutant. Gravitropic reorientation in the iamt1 mutant could be restored with either endodermis-specific expression of IAMT1 or partial inhibition of polar auxin transport, which also results in normal PIN gene expression levels. We propose that IAA methylation is necessary in gravity-sensing cells to restrict polar auxin transport within the range of auxin levels that allow for differential responses."}],"publication_status":"published","external_id":{"isi":["000436245000096"]},"page":"6864-6869","article_processing_charge":"No","title":"Auxin methylation is required for differential growth in Arabidopsis","volume":115,"OA_place":"repository","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"id":"47E8FC1C-F248-11E8-B48F-1D18A9856A87","full_name":"Abbas, Mohamad","last_name":"Abbas","first_name":"Mohamad"},{"full_name":"Hernández, García J","first_name":"García J","last_name":"Hernández"},{"full_name":"Pollmann, Stephan","first_name":"Stephan","last_name":"Pollmann"},{"full_name":"Samodelov, Sophia L","last_name":"Samodelov","first_name":"Sophia L"},{"full_name":"Kolb, Martina","first_name":"Martina","last_name":"Kolb"},{"last_name":"Friml","first_name":"Jirí","full_name":"Friml, Jirí","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Ulrich Z","last_name":"Hammes","full_name":"Hammes, Ulrich Z"},{"first_name":"Matias D","last_name":"Zurbriggen","full_name":"Zurbriggen, Matias D"},{"first_name":"Miguel","last_name":"Blázquez","full_name":"Blázquez, Miguel"},{"last_name":"Alabadí","first_name":"David","full_name":"Alabadí, David"}],"quality_controlled":"1","main_file_link":[{"open_access":"1","url":"http://eprints.nottingham.ac.uk/52388/"}],"year":"2018","date_created":"2018-12-11T11:45:11Z","publication":"PNAS","issue":"26","doi":"10.1073/pnas.1806565115"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"full_name":"Chalupa, Marek","last_name":"Chalupa","first_name":"Marek"},{"first_name":"Krishnendu","last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"id":"49704004-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8943-0722","full_name":"Pavlogiannis, Andreas","first_name":"Andreas","last_name":"Pavlogiannis"},{"full_name":"Sinha, Nishant","first_name":"Nishant","last_name":"Sinha"},{"last_name":"Vaidya","first_name":"Kapil","full_name":"Vaidya, Kapil"}],"volume":2,"OA_place":"publisher","related_material":{"record":[{"id":"5448","relation":"earlier_version","status":"public"},{"relation":"earlier_version","id":"5456","status":"public"}]},"article_processing_charge":"No","external_id":{"arxiv":["1610.01188"]},"publication_status":"published","abstract":[{"lang":"eng","text":"We present a new dynamic partial-order reduction method for stateless model checking of concurrent programs. A common approach for exploring program behaviors relies on enumerating the traces of the program, without storing the visited states (aka stateless exploration). As the number of distinct traces grows exponentially, dynamic partial-order reduction (DPOR) techniques have been successfully used to partition the space of traces into equivalence classes (Mazurkiewicz partitioning), with the goal of exploring only few representative traces from each class.\r\n\r\nWe introduce a new equivalence on traces under sequential consistency semantics, which we call the observation equivalence. Two traces are observationally equivalent if every read event observes the same write event in both traces. While the traditional Mazurkiewicz equivalence is control-centric, our new definition is data-centric. We show that our observation equivalence is coarser than the Mazurkiewicz equivalence, and in many cases even exponentially coarser. We devise a DPOR exploration of the trace space, called data-centric DPOR, based on the observation equivalence."}],"title":"Data-centric dynamic partial order reduction","date_created":"2021-12-05T23:01:49Z","year":"2018","article_number":"31","doi":"10.1145/3158119","publication_identifier":{"eissn":["2475-1421"]},"issue":"POPL","publication":"Proceedings of the ACM on Programming Languages","quality_controlled":"1","file":[{"success":1,"creator":"dernst","date_created":"2025-05-20T09:44:47Z","file_name":"2018_ACM_Chalupa.pdf","content_type":"application/pdf","access_level":"open_access","relation":"main_file","checksum":"b27ab1745f6dba2387deb785798a657c","file_size":388891,"date_updated":"2025-05-20T09:44:47Z","file_id":"19716"}],"has_accepted_license":"1","conference":{"start_date":"2018-01-07","name":"POPL: Programming Languages","end_date":"2018-01-13","location":"Los Angeles, CA, United States"},"ddc":["000"],"oa_version":"Published Version","intvolume":" 2","article_type":"original","acknowledgement":"The research was partly supported by Austrian Science Fund (FWF) Grant No P23499- N23, FWF\r\nNFN Grant No S11407-N23 (RiSE/SHiNE), ERC Start grant (279307: Graph Games), and Czech\r\nScience Foundation grant GBP202/12/G061.","type":"journal_article","scopus_import":"1","_id":"10417","file_date_updated":"2025-05-20T09:44:47Z","oa":1,"date_published":"2018-01-01T00:00:00Z","language":[{"iso":"eng"}],"month":"01","date_updated":"2025-05-20T09:45:10Z","arxiv":1,"department":[{"_id":"KrCh"}],"publisher":"Association for Computing Machinery","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"OA_type":"hybrid","ec_funded":1,"day":"01","status":"public","citation":{"chicago":"Chalupa, Marek, Krishnendu Chatterjee, Andreas Pavlogiannis, Nishant Sinha, and Kapil Vaidya. “Data-Centric Dynamic Partial Order Reduction.” Proceedings of the ACM on Programming Languages. Association for Computing Machinery, 2018. https://doi.org/10.1145/3158119.","apa":"Chalupa, M., Chatterjee, K., Pavlogiannis, A., Sinha, N., & Vaidya, K. (2018). Data-centric dynamic partial order reduction. Proceedings of the ACM on Programming Languages. Los Angeles, CA, United States: Association for Computing Machinery. https://doi.org/10.1145/3158119","mla":"Chalupa, Marek, et al. “Data-Centric Dynamic Partial Order Reduction.” Proceedings of the ACM on Programming Languages, vol. 2, no. POPL, 31, Association for Computing Machinery, 2018, doi:10.1145/3158119.","ieee":"M. Chalupa, K. Chatterjee, A. Pavlogiannis, N. Sinha, and K. Vaidya, “Data-centric dynamic partial order reduction,” Proceedings of the ACM on Programming Languages, vol. 2, no. POPL. Association for Computing Machinery, 2018.","short":"M. Chalupa, K. Chatterjee, A. Pavlogiannis, N. Sinha, K. Vaidya, Proceedings of the ACM on Programming Languages 2 (2018).","ista":"Chalupa M, Chatterjee K, Pavlogiannis A, Sinha N, Vaidya K. 2018. Data-centric dynamic partial order reduction. Proceedings of the ACM on Programming Languages. 2(POPL), 31.","ama":"Chalupa M, Chatterjee K, Pavlogiannis A, Sinha N, Vaidya K. Data-centric dynamic partial order reduction. Proceedings of the ACM on Programming Languages. 2018;2(POPL). doi:10.1145/3158119"},"project":[{"grant_number":"P 23499-N23","_id":"2584A770-B435-11E9-9278-68D0E5697425","name":"Modern Graph Algorithmic Techniques in Formal Verification","call_identifier":"FWF"},{"name":"Rigorous Systems Engineering","call_identifier":"FWF","grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425"},{"grant_number":"279307","_id":"2581B60A-B435-11E9-9278-68D0E5697425","name":"Quantitative Graph Games: Theory and Applications","call_identifier":"FP7"}]},{"scopus_import":"1","_id":"106","publist_id":"7948","type":"journal_article","oa_version":"Preprint","intvolume":" 40","date_updated":"2023-09-13T08:49:16Z","arxiv":1,"publisher":"Springer","department":[{"_id":"HeEd"}],"date_published":"2018-09-01T00:00:00Z","month":"09","language":[{"iso":"eng"}],"oa":1,"isi":1,"day":"01","status":"public","citation":{"chicago":"Akopyan, Arseniy, and Anton Petrunin. “Long Geodesics on Convex Surfaces.” Mathematical Intelligencer. Springer, 2018. https://doi.org/10.1007/s00283-018-9795-5.","apa":"Akopyan, A., & Petrunin, A. (2018). Long geodesics on convex surfaces. Mathematical Intelligencer. Springer. https://doi.org/10.1007/s00283-018-9795-5","mla":"Akopyan, Arseniy, and Anton Petrunin. “Long Geodesics on Convex Surfaces.” Mathematical Intelligencer, vol. 40, no. 3, Springer, 2018, pp. 26–31, doi:10.1007/s00283-018-9795-5.","short":"A. Akopyan, A. Petrunin, Mathematical Intelligencer 40 (2018) 26–31.","ieee":"A. Akopyan and A. Petrunin, “Long geodesics on convex surfaces,” Mathematical Intelligencer, vol. 40, no. 3. Springer, pp. 26–31, 2018.","ista":"Akopyan A, Petrunin A. 2018. Long geodesics on convex surfaces. Mathematical Intelligencer. 40(3), 26–31.","ama":"Akopyan A, Petrunin A. Long geodesics on convex surfaces. Mathematical Intelligencer. 2018;40(3):26-31. doi:10.1007/s00283-018-9795-5"},"volume":40,"author":[{"first_name":"Arseniy","last_name":"Akopyan","full_name":"Akopyan, Arseniy","orcid":"0000-0002-2548-617X","id":"430D2C90-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Anton","last_name":"Petrunin","full_name":"Petrunin, Anton"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","title":"Long geodesics on convex surfaces","publication_status":"published","external_id":{"isi":["000444141200005"],"arxiv":["1702.05172"]},"abstract":[{"lang":"eng","text":"The goal of this article is to introduce the reader to the theory of intrinsic geometry of convex surfaces. We illustrate the power of the tools by proving a theorem on convex surfaces containing an arbitrarily long closed simple geodesic. Let us remind ourselves that a curve in a surface is called geodesic if every sufficiently short arc of the curve is length minimizing; if, in addition, it has no self-intersections, we call it simple geodesic. A tetrahedron with equal opposite edges is called isosceles. The axiomatic method of Alexandrov geometry allows us to work with the metrics of convex surfaces directly, without approximating it first by a smooth or polyhedral metric. Such approximations destroy the closed geodesics on the surface; therefore it is difficult (if at all possible) to apply approximations in the proof of our theorem. On the other hand, a proof in the smooth or polyhedral case usually admits a translation into Alexandrov’s language; such translation makes the result more general. In fact, our proof resembles a translation of the proof given by Protasov. Note that the main theorem implies in particular that a smooth convex surface does not have arbitrarily long simple closed geodesics. However we do not know a proof of this corollary that is essentially simpler than the one presented below."}],"article_processing_charge":"No","page":"26 - 31","publication":"Mathematical Intelligencer","doi":"10.1007/s00283-018-9795-5","issue":"3","date_created":"2018-12-11T11:44:40Z","year":"2018","main_file_link":[{"url":"https://arxiv.org/abs/1702.05172","open_access":"1"}],"quality_controlled":"1"},{"ddc":["516","000"],"has_accepted_license":"1","file":[{"file_id":"5844","date_updated":"2019-01-18T09:27:36Z","file_size":482518,"access_level":"open_access","relation":"main_file","file_name":"2018_DiscreteComp_Akopyan.pdf","content_type":"application/pdf","date_created":"2019-01-18T09:27:36Z","success":1,"creator":"dernst"}],"quality_controlled":"1","corr_author":"1","publication":"Discrete & Computational Geometry","doi":"10.1007/s00454-017-9883-x","publication_identifier":{"eissn":["1432-0444"],"issn":["0179-5376"]},"issue":"4","date_created":"2018-12-11T11:49:57Z","year":"2018","title":"On the circle covering theorem by A.W. Goodman and R.E. Goodman","publication_status":"published","external_id":{"isi":["000432205500011"]},"abstract":[{"text":"In 1945, A.W. Goodman and R.E. Goodman proved the following conjecture by P. Erdős: Given a family of (round) disks of radii r1, … , rn in the plane, it is always possible to cover them by a disk of radius R= ∑ ri, provided they cannot be separated into two subfamilies by a straight line disjoint from the disks. In this note we show that essentially the same idea may work for different analogues and generalizations of their result. In particular, we prove the following: Given a family of positive homothetic copies of a fixed convex body K⊂ Rd with homothety coefficients τ1, … , τn> 0 , it is always possible to cover them by a translate of d+12(∑τi)K, provided they cannot be separated into two subfamilies by a hyperplane disjoint from the homothets.","lang":"eng"}],"article_processing_charge":"Yes (via OA deal)","page":"1001-1009","volume":59,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"first_name":"Arseniy","last_name":"Akopyan","orcid":"0000-0002-2548-617X","id":"430D2C90-F248-11E8-B48F-1D18A9856A87","full_name":"Akopyan, Arseniy"},{"full_name":"Balitskiy, Alexey","first_name":"Alexey","last_name":"Balitskiy"},{"first_name":"Mikhail","last_name":"Grigorev","full_name":"Grigorev, Mikhail"}],"project":[{"_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734","call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme"}],"citation":{"short":"A. Akopyan, A. Balitskiy, M. Grigorev, Discrete & Computational Geometry 59 (2018) 1001–1009.","ieee":"A. Akopyan, A. Balitskiy, and M. Grigorev, “On the circle covering theorem by A.W. Goodman and R.E. Goodman,” Discrete & Computational Geometry, vol. 59, no. 4. Springer, pp. 1001–1009, 2018.","ista":"Akopyan A, Balitskiy A, Grigorev M. 2018. On the circle covering theorem by A.W. Goodman and R.E. Goodman. Discrete & Computational Geometry. 59(4), 1001–1009.","ama":"Akopyan A, Balitskiy A, Grigorev M. On the circle covering theorem by A.W. Goodman and R.E. Goodman. Discrete & Computational Geometry. 2018;59(4):1001-1009. doi:10.1007/s00454-017-9883-x","chicago":"Akopyan, Arseniy, Alexey Balitskiy, and Mikhail Grigorev. “On the Circle Covering Theorem by A.W. Goodman and R.E. Goodman.” Discrete & Computational Geometry. Springer, 2018. https://doi.org/10.1007/s00454-017-9883-x.","apa":"Akopyan, A., Balitskiy, A., & Grigorev, M. (2018). On the circle covering theorem by A.W. Goodman and R.E. Goodman. Discrete & Computational Geometry. Springer. https://doi.org/10.1007/s00454-017-9883-x","mla":"Akopyan, Arseniy, et al. “On the Circle Covering Theorem by A.W. Goodman and R.E. Goodman.” Discrete & Computational Geometry, vol. 59, no. 4, Springer, 2018, pp. 1001–09, doi:10.1007/s00454-017-9883-x."},"day":"01","status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"ec_funded":1,"date_updated":"2026-05-20T10:19:33Z","department":[{"_id":"HeEd"}],"publisher":"Springer","date_published":"2018-06-01T00:00:00Z","language":[{"iso":"eng"}],"month":"06","file_date_updated":"2019-01-18T09:27:36Z","oa":1,"isi":1,"scopus_import":"1","_id":"1064","publist_id":"6324","type":"journal_article","oa_version":"Published Version","intvolume":" 59","article_type":"original"},{"project":[{"_id":"258AA5B2-B435-11E9-9278-68D0E5697425","grant_number":"682815","call_identifier":"H2020","name":"Teaching Old Crypto New Tricks"},{"_id":"258C570E-B435-11E9-9278-68D0E5697425","grant_number":"259668","call_identifier":"FP7","name":"Provable Security for Physical Cryptography"}],"citation":{"short":"S. Dziembowski, K.Z. Pietrzak, D. Wichs, Journal of the ACM 65 (2018).","ieee":"S. Dziembowski, K. Z. Pietrzak, and D. Wichs, “Non-malleable codes,” Journal of the ACM, vol. 65, no. 4. ACM, 2018.","ama":"Dziembowski S, Pietrzak KZ, Wichs D. Non-malleable codes. Journal of the ACM. 2018;65(4). doi:10.1145/3178432","ista":"Dziembowski S, Pietrzak KZ, Wichs D. 2018. Non-malleable codes. Journal of the ACM. 65(4), 20.","apa":"Dziembowski, S., Pietrzak, K. Z., & Wichs, D. (2018). Non-malleable codes. Journal of the ACM. ACM. https://doi.org/10.1145/3178432","chicago":"Dziembowski, Stefan, Krzysztof Z Pietrzak, and Daniel Wichs. “Non-Malleable Codes.” Journal of the ACM. ACM, 2018. https://doi.org/10.1145/3178432.","mla":"Dziembowski, Stefan, et al. “Non-Malleable Codes.” Journal of the ACM, vol. 65, no. 4, 20, ACM, 2018, doi:10.1145/3178432."},"ec_funded":1,"status":"public","day":"01","oa":1,"isi":1,"date_updated":"2025-04-14T07:22:06Z","publisher":"ACM","department":[{"_id":"KrPi"}],"date_published":"2018-08-01T00:00:00Z","language":[{"iso":"eng"}],"month":"08","type":"journal_article","oa_version":"Preprint","intvolume":" 65","article_type":"original","scopus_import":"1","_id":"107","publist_id":"7947","quality_controlled":"1","main_file_link":[{"url":"https://eprint.iacr.org/2009/608","open_access":"1"}],"article_number":"20","date_created":"2018-12-11T11:44:40Z","year":"2018","publication":"Journal of the ACM","doi":"10.1145/3178432","issue":"4","publication_status":"published","external_id":{"isi":["000442938200004"]},"abstract":[{"lang":"eng","text":"We introduce the notion of “non-malleable codes” which relaxes the notion of error correction and error detection. Informally, a code is non-malleable if the message contained in a modified codeword is either the original message, or a completely unrelated value. In contrast to error correction and error detection, non-malleability can be achieved for very rich classes of modifications. We construct an efficient code that is non-malleable with respect to modifications that affect each bit of the codeword arbitrarily (i.e., leave it untouched, flip it, or set it to either 0 or 1), but independently of the value of the other bits of the codeword. Using the probabilistic method, we also show a very strong and general statement: there exists a non-malleable code for every “small enough” family F of functions via which codewords can be modified. Although this probabilistic method argument does not directly yield efficient constructions, it gives us efficient non-malleable codes in the random-oracle model for very general classes of tampering functions—e.g., functions where every bit in the tampered codeword can depend arbitrarily on any 99% of the bits in the original codeword. As an application of non-malleable codes, we show that they provide an elegant algorithmic solution to the task of protecting functionalities implemented in hardware (e.g., signature cards) against “tampering attacks.” In such attacks, the secret state of a physical system is tampered, in the hopes that future interaction with the modified system will reveal some secret information. This problem was previously studied in the work of Gennaro et al. in 2004 under the name “algorithmic tamper proof security” (ATP). We show that non-malleable codes can be used to achieve important improvements over the prior work. In particular, we show that any functionality can be made secure against a large class of tampering attacks, simply by encoding the secret state with a non-malleable code while it is stored in memory."}],"article_processing_charge":"No","title":"Non-malleable codes","volume":65,"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","author":[{"full_name":"Dziembowski, Stefan","last_name":"Dziembowski","first_name":"Stefan"},{"first_name":"Krzysztof Z","last_name":"Pietrzak","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9139-1654","full_name":"Pietrzak, Krzysztof Z"},{"last_name":"Wichs","first_name":"Daniel","full_name":"Wichs, Daniel"}]},{"volume":2018,"author":[{"last_name":"Obremski","first_name":"Marciej","full_name":"Obremski, Marciej"},{"full_name":"Skorski, Maciej","id":"EC09FA6A-02D0-11E9-8223-86B7C91467DD","first_name":"Maciej","last_name":"Skorski"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","title":"Inverted leftover hash lemma","abstract":[{"lang":"eng","text":"Universal hashing found a lot of applications in computer science. In cryptography the most important fact about universal families is the so called Leftover Hash Lemma, proved by Impagliazzo, Levin and Luby. In the language of modern cryptography it states that almost universal families are good extractors. In this work we provide a somewhat surprising characterization in the opposite direction. Namely, every extractor with sufficiently good parameters yields a universal family on a noticeable fraction of its inputs. Our proof technique is based on tools from extremal graph theory applied to the \\'collision graph\\' induced by the extractor, and may be of independent interest. We discuss possible applications to the theory of randomness extractors and non-malleable codes."}],"publication_status":"published","external_id":{"isi":["000448139300368"]},"article_processing_charge":"No","doi":"10.1109/ISIT.2018.8437654","year":"2018","date_created":"2018-12-11T11:44:40Z","conference":{"start_date":"2018-06-17 ","name":"ISIT: International Symposium on Information Theory","end_date":"2018-06-22","location":"Vail, CO, USA"},"main_file_link":[{"url":"https://eprint.iacr.org/2017/507","open_access":"1"}],"quality_controlled":"1","_id":"108","scopus_import":"1","publist_id":"7946","type":"conference","oa_version":"Submitted Version","intvolume":" 2018","publisher":"IEEE","department":[{"_id":"KrPi"}],"date_updated":"2023-09-13T08:23:18Z","language":[{"iso":"eng"}],"month":"08","date_published":"2018-08-16T00:00:00Z","oa":1,"isi":1,"status":"public","day":"16","alternative_title":["ISIT Proceedings"],"citation":{"ieee":"M. Obremski and M. Skórski, “Inverted leftover hash lemma,” presented at the ISIT: International Symposium on Information Theory, Vail, CO, USA, 2018, vol. 2018.","short":"M. Obremski, M. Skórski, in:, IEEE, 2018.","ama":"Obremski M, Skórski M. Inverted leftover hash lemma. In: Vol 2018. IEEE; 2018. doi:10.1109/ISIT.2018.8437654","ista":"Obremski M, Skórski M. 2018. Inverted leftover hash lemma. ISIT: International Symposium on Information Theory, ISIT Proceedings, vol. 2018.","chicago":"Obremski, Marciej, and Maciej Skórski. “Inverted Leftover Hash Lemma,” Vol. 2018. IEEE, 2018. https://doi.org/10.1109/ISIT.2018.8437654.","apa":"Obremski, M., & Skórski, M. (2018). Inverted leftover hash lemma (Vol. 2018). Presented at the ISIT: International Symposium on Information Theory, Vail, CO, USA: IEEE. https://doi.org/10.1109/ISIT.2018.8437654","mla":"Obremski, Marciej, and Maciej Skórski. Inverted Leftover Hash Lemma. Vol. 2018, IEEE, 2018, doi:10.1109/ISIT.2018.8437654."}},{"date_created":"2018-12-11T11:44:30Z","year":"2018","publication":"Distributed Computing","doi":"10.1007/s00446-018-0342-6","quality_controlled":"1","file":[{"file_id":"5711","file_size":799337,"date_updated":"2020-07-14T12:48:01Z","access_level":"open_access","checksum":"872db70bba9b401500abe3c6ae2f1a61","relation":"main_file","file_name":"2018_DistributedComputing_Lenzen.pdf","content_type":"application/pdf","date_created":"2018-12-17T14:21:22Z","creator":"dernst"}],"corr_author":"1","ddc":["000"],"has_accepted_license":"1","author":[{"last_name":"Lenzen","first_name":"Christoph","full_name":"Lenzen, Christoph"},{"full_name":"Rybicki, Joel","orcid":"0000-0002-6432-6646","id":"334EFD2E-F248-11E8-B48F-1D18A9856A87","last_name":"Rybicki","first_name":"Joel"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publication_status":"published","external_id":{"isi":["000475627800005"]},"abstract":[{"lang":"eng","text":"Consider a fully-connected synchronous distributed system consisting of n nodes, where up to f nodes may be faulty and every node starts in an arbitrary initial state. In the synchronous C-counting problem, all nodes need to eventually agree on a counter that is increased by one modulo C in each round for given C>1. In the self-stabilising firing squad problem, the task is to eventually guarantee that all non-faulty nodes have simultaneous responses to external inputs: if a subset of the correct nodes receive an external “go” signal as input, then all correct nodes should agree on a round (in the not-too-distant future) in which to jointly output a “fire” signal. Moreover, no node should generate a “fire” signal without some correct node having previously received a “go” signal as input. We present a framework reducing both tasks to binary consensus at very small cost. For example, we obtain a deterministic algorithm for self-stabilising Byzantine firing squads with optimal resilience f<n/3, asymptotically optimal stabilisation and response time O(f), and message size O(log f). As our framework does not restrict the type of consensus routines used, we also obtain efficient randomised solutions."}],"article_processing_charge":"Yes (via OA deal)","title":"Near-optimal self-stabilising counting and firing squads","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","day":"12","project":[{"name":"IST Austria Open Access Fund","_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854"}],"citation":{"apa":"Lenzen, C., & Rybicki, J. (2018). Near-optimal self-stabilising counting and firing squads. Distributed Computing. Springer. https://doi.org/10.1007/s00446-018-0342-6","chicago":"Lenzen, Christoph, and Joel Rybicki. “Near-Optimal Self-Stabilising Counting and Firing Squads.” Distributed Computing. Springer, 2018. https://doi.org/10.1007/s00446-018-0342-6.","mla":"Lenzen, Christoph, and Joel Rybicki. “Near-Optimal Self-Stabilising Counting and Firing Squads.” Distributed Computing, Springer, 2018, doi:10.1007/s00446-018-0342-6.","short":"C. Lenzen, J. Rybicki, Distributed Computing (2018).","ieee":"C. Lenzen and J. Rybicki, “Near-optimal self-stabilising counting and firing squads,” Distributed Computing. Springer, 2018.","ama":"Lenzen C, Rybicki J. Near-optimal self-stabilising counting and firing squads. Distributed Computing. 2018. doi:10.1007/s00446-018-0342-6","ista":"Lenzen C, Rybicki J. 2018. Near-optimal self-stabilising counting and firing squads. Distributed Computing."},"type":"journal_article","oa_version":"Published Version","scopus_import":"1","_id":"76","publist_id":"7978","file_date_updated":"2020-07-14T12:48:01Z","oa":1,"isi":1,"date_updated":"2025-04-15T06:53:15Z","publisher":"Springer","department":[{"_id":"DaAl"}],"date_published":"2018-09-12T00:00:00Z","language":[{"iso":"eng"}],"month":"09"},{"title":"A germanium hole spin qubit","article_processing_charge":"Yes","publication_status":"published","external_id":{"isi":["000445560800010"]},"abstract":[{"text":"Holes confined in quantum dots have gained considerable interest in the past few years due to their potential as spin qubits. Here we demonstrate two-axis control of a spin 3/2 qubit in natural Ge. The qubit is formed in a hut wire double quantum dot device. The Pauli spin blockade principle allowed us to demonstrate electric dipole spin resonance by applying a radio frequency electric field to one of the electrodes defining the double quantum dot. Coherent hole spin oscillations with Rabi frequencies reaching 140 MHz are demonstrated and dephasing times of 130 ns are measured. The reported results emphasize the potential of Ge as a platform for fast and electrically tunable hole spin qubit devices.","lang":"eng"}],"acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"NanoFab"}],"related_material":{"record":[{"relation":"popular_science","id":"7977"},{"relation":"dissertation_contains","id":"7996","status":"public"}]},"author":[{"full_name":"Watzinger, Hannes","id":"35DF8E50-F248-11E8-B48F-1D18A9856A87","first_name":"Hannes","last_name":"Watzinger"},{"first_name":"Josip","last_name":"Kukucka","id":"3F5D8856-F248-11E8-B48F-1D18A9856A87","full_name":"Kukucka, Josip"},{"full_name":"Vukusic, Lada","id":"31E9F056-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2424-8636","last_name":"Vukusic","first_name":"Lada"},{"last_name":"Gao","first_name":"Fei","full_name":"Gao, Fei"},{"last_name":"Wang","first_name":"Ting","full_name":"Wang, Ting"},{"first_name":"Friedrich","last_name":"Schäffler","full_name":"Schäffler, Friedrich"},{"last_name":"Zhang","first_name":"Jian","full_name":"Zhang, Jian"},{"first_name":"Georgios","last_name":"Katsaros","orcid":"0000-0001-8342-202X","id":"38DB5788-F248-11E8-B48F-1D18A9856A87","full_name":"Katsaros, Georgios"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","volume":9,"has_accepted_license":"1","ddc":["530"],"file":[{"date_created":"2018-12-17T10:28:30Z","content_type":"application/pdf","file_name":"2018_NatureComm_Watzinger.pdf","creator":"dernst","file_id":"5687","access_level":"open_access","checksum":"e7148c10a64497e279c4de570b6cc544","relation":"main_file","file_size":1063469,"date_updated":"2020-07-14T12:48:02Z"}],"quality_controlled":"1","doi":"10.1038/s41467-018-06418-4","issue":"3902 ","publication":"Nature Communications","date_created":"2018-12-11T11:44:30Z","year":"2018","date_published":"2018-09-25T00:00:00Z","language":[{"iso":"eng"}],"month":"09","date_updated":"2026-04-08T07:27:13Z","publisher":"Nature Publishing Group","department":[{"_id":"GeKa"}],"isi":1,"file_date_updated":"2020-07-14T12:48:02Z","oa":1,"scopus_import":"1","_id":"77","intvolume":" 9","oa_version":"Published Version","article_type":"original","type":"journal_article","citation":{"mla":"Watzinger, Hannes, et al. “A Germanium Hole Spin Qubit.” Nature Communications, vol. 9, no. 3902, Nature Publishing Group, 2018, doi:10.1038/s41467-018-06418-4.","apa":"Watzinger, H., Kukucka, J., Vukušić, L., Gao, F., Wang, T., Schäffler, F., … Katsaros, G. (2018). A germanium hole spin qubit. Nature Communications. Nature Publishing Group. https://doi.org/10.1038/s41467-018-06418-4","chicago":"Watzinger, Hannes, Josip Kukucka, Lada Vukušić, Fei Gao, Ting Wang, Friedrich Schäffler, Jian Zhang, and Georgios Katsaros. “A Germanium Hole Spin Qubit.” Nature Communications. Nature Publishing Group, 2018. https://doi.org/10.1038/s41467-018-06418-4.","ama":"Watzinger H, Kukucka J, Vukušić L, et al. A germanium hole spin qubit. Nature Communications. 2018;9(3902). doi:10.1038/s41467-018-06418-4","ista":"Watzinger H, Kukucka J, Vukušić L, Gao F, Wang T, Schäffler F, Zhang J, Katsaros G. 2018. A germanium hole spin qubit. Nature Communications. 9(3902).","short":"H. Watzinger, J. Kukucka, L. Vukušić, F. Gao, T. Wang, F. Schäffler, J. Zhang, G. Katsaros, Nature Communications 9 (2018).","ieee":"H. Watzinger et al., “A germanium hole spin qubit,” Nature Communications, vol. 9, no. 3902. Nature Publishing Group, 2018."},"project":[{"_id":"25517E86-B435-11E9-9278-68D0E5697425","grant_number":"335497","call_identifier":"FP7","name":"Towards Spin qubits and Majorana fermions in Germanium self assembled hut-wires"},{"grant_number":"Y00715","_id":"2552F888-B435-11E9-9278-68D0E5697425","name":"Loch Spin-Qubits und Majorana-Fermionen in Germanium","call_identifier":"FWF"}],"status":"public","day":"25","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"ec_funded":1},{"oa_version":"Submitted Version","intvolume":" 11022","type":"conference","publist_id":"7976","_id":"78","scopus_import":"1","isi":1,"oa":1,"file_date_updated":"2020-07-14T12:48:03Z","month":"08","language":[{"iso":"eng"}],"date_published":"2018-08-26T00:00:00Z","department":[{"_id":"ToHe"}],"publisher":"Springer","date_updated":"2025-04-15T06:26:03Z","alternative_title":["LNCS"],"day":"26","status":"public","citation":{"mla":"Bakhirkin, Alexey, et al. Online Timed Pattern Matching Using Automata. Vol. 11022, Springer, 2018, pp. 215–32, doi:10.1007/978-3-030-00151-3_13.","apa":"Bakhirkin, A., Ferrere, T., Nickovic, D., Maler, O., & Asarin, E. (2018). Online timed pattern matching using automata (Vol. 11022, pp. 215–232). Presented at the FORMATS: Formal Modeling and Analysis of Timed Systems, Bejing, China: Springer. https://doi.org/10.1007/978-3-030-00151-3_13","chicago":"Bakhirkin, Alexey, Thomas Ferrere, Dejan Nickovic, Oded Maler, and Eugene Asarin. “Online Timed Pattern Matching Using Automata,” 11022:215–32. Springer, 2018. https://doi.org/10.1007/978-3-030-00151-3_13.","ista":"Bakhirkin A, Ferrere T, Nickovic D, Maler O, Asarin E. 2018. Online timed pattern matching using automata. FORMATS: Formal Modeling and Analysis of Timed Systems, LNCS, vol. 11022, 215–232.","ama":"Bakhirkin A, Ferrere T, Nickovic D, Maler O, Asarin E. Online timed pattern matching using automata. In: Vol 11022. Springer; 2018:215-232. doi:10.1007/978-3-030-00151-3_13","ieee":"A. Bakhirkin, T. Ferrere, D. Nickovic, O. Maler, and E. Asarin, “Online timed pattern matching using automata,” presented at the FORMATS: Formal Modeling and Analysis of Timed Systems, Bejing, China, 2018, vol. 11022, pp. 215–232.","short":"A. Bakhirkin, T. Ferrere, D. Nickovic, O. Maler, E. Asarin, in:, Springer, 2018, pp. 215–232."},"project":[{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23","call_identifier":"FWF","name":"Rigorous Systems Engineering"},{"call_identifier":"FWF","name":"Formal methods for the design and analysis of complex systems","_id":"25F42A32-B435-11E9-9278-68D0E5697425","grant_number":"Z211"}],"author":[{"first_name":"Alexey","last_name":"Bakhirkin","full_name":"Bakhirkin, Alexey"},{"first_name":"Thomas","last_name":"Ferrere","id":"40960E6E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5199-3143","full_name":"Ferrere, Thomas"},{"full_name":"Nickovic, Dejan","last_name":"Nickovic","first_name":"Dejan"},{"full_name":"Maler, Oded","first_name":"Oded","last_name":"Maler"},{"full_name":"Asarin, Eugene","first_name":"Eugene","last_name":"Asarin"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","volume":11022,"page":"215 - 232","article_processing_charge":"No","abstract":[{"text":"We provide a procedure for detecting the sub-segments of an incrementally observed Boolean signal ω that match a given temporal pattern ϕ. As a pattern specification language, we use timed regular expressions, a formalism well-suited for expressing properties of concurrent asynchronous behaviors embedded in metric time. We construct a timed automaton accepting the timed language denoted by ϕ and modify it slightly for the purpose of matching. We then apply zone-based reachability computation to this automaton while it reads ω, and retrieve all the matching segments from the results. Since the procedure is automaton based, it can be applied to patterns specified by other formalisms such as timed temporal logics reducible to timed automata or directly encoded as timed automata. The procedure has been implemented and its performance on synthetic examples is demonstrated.","lang":"eng"}],"external_id":{"isi":["000884993200013"]},"publication_status":"published","title":"Online timed pattern matching using automata","year":"2018","date_created":"2018-12-11T11:44:31Z","publication_identifier":{"isbn":["978-3-030-00150-6"]},"doi":"10.1007/978-3-030-00151-3_13","quality_controlled":"1","file":[{"date_updated":"2020-07-14T12:48:03Z","file_size":374851,"access_level":"open_access","relation":"main_file","checksum":"436b7574934324cfa7d1d3986fddc65b","file_id":"7831","creator":"dernst","file_name":"2018_LNCS_Bakhirkin.pdf","content_type":"application/pdf","date_created":"2020-05-14T11:34:34Z"}],"has_accepted_license":"1","conference":{"name":"FORMATS: Formal Modeling and Analysis of Timed Systems","start_date":"2018-09-04","location":"Bejing, China","end_date":"2018-09-06"},"ddc":["000"]},{"year":"2018","date_created":"2020-05-10T22:00:51Z","publication":"6th International Conference on Learning Representations","file":[{"file_id":"7894","checksum":"a4336c167978e81891970e4e4517a8c3","relation":"main_file","access_level":"open_access","date_updated":"2020-07-14T12:48:03Z","file_size":308339,"date_created":"2020-05-26T13:02:00Z","file_name":"2018_ICLR_Polino.pdf","content_type":"application/pdf","creator":"dernst"}],"quality_controlled":"1","ddc":["000"],"conference":{"end_date":"2018-05-03","location":"Vancouver, Canada","name":"ICLR: International Conference on Learning Representations","start_date":"2018-04-30"},"has_accepted_license":"1","author":[{"last_name":"Polino","first_name":"Antonio","full_name":"Polino, Antonio"},{"last_name":"Pascanu","first_name":"Razvan","full_name":"Pascanu, Razvan"},{"orcid":"0000-0003-3650-940X","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","full_name":"Alistarh, Dan-Adrian","first_name":"Dan-Adrian","last_name":"Alistarh"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"lang":"eng","text":"Deep neural networks (DNNs) continue to make significant advances, solving tasks from image classification to translation or reinforcement learning. One aspect of the field receiving considerable attention is efficiently executing deep models in resource-constrained environments, such as mobile or embedded devices. This paper focuses on this problem, and proposes two new compression methods, which jointly leverage weight quantization and distillation of larger teacher networks into smaller student networks. The first method we propose is called quantized distillation and leverages distillation during the training process, by incorporating distillation loss, expressed with respect to the teacher, into the training of a student network whose weights are quantized to a limited set of levels. The second method, differentiable quantization, optimizes the location of quantization points through stochastic gradient descent, to better fit the behavior of the teacher model. We validate both methods through experiments on convolutional and recurrent architectures. We show that quantized shallow students can reach similar accuracy levels to full-precision teacher models, while providing order of magnitude compression, and inference speedup that is linear in the depth reduction. In sum, our results enable DNNs for resource-constrained environments to leverage architecture and accuracy advances developed on more powerful devices."}],"publication_status":"published","external_id":{"arxiv":["1802.05668"]},"article_processing_charge":"No","title":"Model compression via distillation and quantization","day":"01","status":"public","citation":{"ieee":"A. Polino, R. Pascanu, and D.-A. Alistarh, “Model compression via distillation and quantization,” in 6th International Conference on Learning Representations, Vancouver, Canada, 2018.","short":"A. Polino, R. Pascanu, D.-A. Alistarh, in:, 6th International Conference on Learning Representations, 2018.","ista":"Polino A, Pascanu R, Alistarh D-A. 2018. Model compression via distillation and quantization. 6th International Conference on Learning Representations. ICLR: International Conference on Learning Representations.","ama":"Polino A, Pascanu R, Alistarh D-A. Model compression via distillation and quantization. In: 6th International Conference on Learning Representations. ; 2018.","apa":"Polino, A., Pascanu, R., & Alistarh, D.-A. (2018). Model compression via distillation and quantization. In 6th International Conference on Learning Representations. Vancouver, Canada.","chicago":"Polino, Antonio, Razvan Pascanu, and Dan-Adrian Alistarh. “Model Compression via Distillation and Quantization.” In 6th International Conference on Learning Representations, 2018.","mla":"Polino, Antonio, et al. “Model Compression via Distillation and Quantization.” 6th International Conference on Learning Representations, 2018."},"acknowledgement":"We would like to thank Ce Zhang (ETH Zurich), Hantian Zhang (ETH Zurich) and Martin Jaggi ´\r\n(EPFL) for their support with experiments and valuable feedback.\r\n","type":"conference","oa_version":"Published Version","_id":"7812","scopus_import":"1","oa":1,"file_date_updated":"2020-07-14T12:48:03Z","arxiv":1,"department":[{"_id":"DaAl"}],"date_updated":"2025-06-30T10:04:44Z","language":[{"iso":"eng"}],"month":"05","date_published":"2018-05-01T00:00:00Z"}]