[{"day":"13","month":"02","publication_identifier":{"issn":["1555-4309","1555-4317"]},"article_processing_charge":"No","publication":"Contrast Media & Molecular Imaging","oa":1,"main_file_link":[{"url":"https://doi.org/10.1155/2018/1269830","open_access":"1"}],"citation":{"mla":"Balber, T., et al. “Preclinical in Vitro and in Vivo Evaluation of [18F]FE@SUPPY for Cancer PET Imaging: Limitations of a Xenograft Model for Colorectal Cancer.” Contrast Media & Molecular Imaging, vol. 2018, 1269830, Hindawi, 2018, doi:10.1155/2018/1269830.","short":"T. Balber, J. Singer, N. Berroterán-Infante, M. Dumanic, L. Fetty, J. Fazekas-Singer, C. Vraka, L. Nics, M. Bergmann, K. Pallitsch, H. Spreitzer, W. Wadsak, M. Hacker, E. Jensen-Jarolim, H. Viernstein, M. Mitterhauser, Contrast Media & Molecular Imaging 2018 (2018).","chicago":"Balber, T., Judit Singer, N. Berroterán-Infante, M. Dumanic, L. Fetty, J. Fazekas-Singer, C. Vraka, et al. “Preclinical in Vitro and in Vivo Evaluation of [18F]FE@SUPPY for Cancer PET Imaging: Limitations of a Xenograft Model for Colorectal Cancer.” Contrast Media & Molecular Imaging. Hindawi, 2018. https://doi.org/10.1155/2018/1269830.","ama":"Balber T, Singer J, Berroterán-Infante N, et al. Preclinical in vitro and in vivo evaluation of [18F]FE@SUPPY for cancer PET imaging: Limitations of a xenograft model for colorectal cancer. Contrast Media & Molecular Imaging. 2018;2018. doi:10.1155/2018/1269830","ista":"Balber T, Singer J, Berroterán-Infante N, Dumanic M, Fetty L, Fazekas-Singer J, Vraka C, Nics L, Bergmann M, Pallitsch K, Spreitzer H, Wadsak W, Hacker M, Jensen-Jarolim E, Viernstein H, Mitterhauser M. 2018. Preclinical in vitro and in vivo evaluation of [18F]FE@SUPPY for cancer PET imaging: Limitations of a xenograft model for colorectal cancer. Contrast Media & Molecular Imaging. 2018, 1269830.","ieee":"T. Balber et al., “Preclinical in vitro and in vivo evaluation of [18F]FE@SUPPY for cancer PET imaging: Limitations of a xenograft model for colorectal cancer,” Contrast Media & Molecular Imaging, vol. 2018. Hindawi, 2018.","apa":"Balber, T., Singer, J., Berroterán-Infante, N., Dumanic, M., Fetty, L., Fazekas-Singer, J., … Mitterhauser, M. (2018). Preclinical in vitro and in vivo evaluation of [18F]FE@SUPPY for cancer PET imaging: Limitations of a xenograft model for colorectal cancer. Contrast Media & Molecular Imaging. Hindawi. https://doi.org/10.1155/2018/1269830"},"quality_controlled":"1","article_type":"original","date_published":"2018-02-13T00:00:00Z","doi":"10.1155/2018/1269830","language":[{"iso":"eng"}],"article_number":"1269830","type":"journal_article","abstract":[{"lang":"eng","text":"Molecular imaging probes such as PET-tracers have the potential to improve the accuracy of tumor characterization by directly visualizing the biochemical situation. Thus, molecular changes can be detected early before morphological manifestation. The A3 adenosine receptor (A3AR) is described to be highly expressed in colon cancer cell lines and human colorectal cancer (CRC), suggesting this receptor as a tumor marker. The aim of this preclinical study was the evaluation of FE@SUPPY as a PET-tracer for CRC using in vitro imaging and in vivo PET imaging. First, affinity and selectivity of FE@SUPPY and its metabolites were determined, proving the favorable binding profile of FE@SUPPY. The human adenocarcinoma cell line HT-29 was characterized regarding its hA3AR expression and was subsequently chosen as tumor graft. Promising results regarding the potential of FE@SUPPY as a PET-tracer for CRC imaging were obtained by autoradiography as ≥2.3-fold higher accumulation of FE@SUPPY was found in CRC tissue compared to adjacent healthy colon tissue from the same patient. Nevertheless, first in vivo studies using HT-29 xenografts showed insufficient tumor uptake due to (1) poor conservation of target expression in xenografts and (2) unfavorable pharmacokinetics of FE@SUPPY in mice. We therefore conclude that HT-29 xenografts are not adequate to visualize hA3ARs using FE@SUPPY."}],"extern":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"8234","year":"2018","title":"Preclinical in vitro and in vivo evaluation of [18F]FE@SUPPY for cancer PET imaging: Limitations of a xenograft model for colorectal cancer","publication_status":"published","status":"public","intvolume":" 2018","publisher":"Hindawi","author":[{"full_name":"Balber, T.","first_name":"T.","last_name":"Balber"},{"first_name":"Judit","last_name":"Singer","id":"36432834-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8777-3502","full_name":"Singer, Judit"},{"first_name":"N.","last_name":"Berroterán-Infante","full_name":"Berroterán-Infante, N."},{"first_name":"M.","last_name":"Dumanic","full_name":"Dumanic, M."},{"last_name":"Fetty","first_name":"L.","full_name":"Fetty, L."},{"full_name":"Fazekas-Singer, J.","orcid":"0000-0002-8777-3502","last_name":"Fazekas-Singer","first_name":"J."},{"first_name":"C.","last_name":"Vraka","full_name":"Vraka, C."},{"full_name":"Nics, L.","last_name":"Nics","first_name":"L."},{"full_name":"Bergmann, M.","first_name":"M.","last_name":"Bergmann"},{"last_name":"Pallitsch","first_name":"K.","full_name":"Pallitsch, K."},{"last_name":"Spreitzer","first_name":"H.","full_name":"Spreitzer, H."},{"full_name":"Wadsak, W.","first_name":"W.","last_name":"Wadsak","orcid":"0000-0003-4479-8053"},{"first_name":"M.","last_name":"Hacker","full_name":"Hacker, M."},{"full_name":"Jensen-Jarolim, E.","first_name":"E.","last_name":"Jensen-Jarolim"},{"full_name":"Viernstein, H.","last_name":"Viernstein","first_name":"H."},{"last_name":"Mitterhauser","first_name":"M.","orcid":"0000-0003-3173-5272","full_name":"Mitterhauser, M."}],"date_created":"2020-08-10T11:53:07Z","date_updated":"2021-01-12T08:17:38Z","oa_version":"Published Version","volume":2018},{"abstract":[{"lang":"eng","text":"Anti-epidermal growth factor receptor (EGFR) antibody therapy is used in EGFR expressing cancers including lung, colon, head and neck, and bladder cancers, however results have been modest. Near infrared photoimmunotherapy (NIR-PIT) is a highly selective tumor treatment that employs an antibody-photo-absorber conjugate which is activated by NIR light. NIR-PIT is in clinical trials in patients with recurrent head and neck cancers using cetuximab-IR700 as the conjugate. However, its use has otherwise been restricted to mouse models. This is an effort to explore larger animal models with NIR-PIT. We describe the use of a recombinant canine anti-EGFR monoclonal antibody (mAb), can225IgG, conjugated to the photo-absorber, IR700DX, in three EGFR expressing canine transitional cell carcinoma (TCC) cell lines as a prelude to possible canine clinical studies. Can225-IR700 conjugate showed specific binding and cell-specific killing after NIR-PIT on EGFR expressing cells in vitro. In the in vivo study, can225-IR700 conjugate demonstrated accumulation of the fluorescent conjugate with high tumor-to-background ratio. Tumor-bearing mice were separated into 4 groups: (1) no treatment; (2) 100 μg of can225-IR700 i.v. only; (3) NIR light exposure only; (4) 100 μg of can225-IR700 i.v., NIR light exposure. Tumor growth was significantly inhibited by NIR-PIT treatment compared with the other groups (p < 0.001), and significantly prolonged survival was achieved (p < 0.001 vs. other groups) in the treatment groups. In conclusion, NIR-PIT with can225-IR700 is a promising treatment for canine EGFR-expressing cancers, including invasive transitional cell carcinoma in pet dogs, that could provide a pathway to translation to humans."}],"extern":"1","type":"journal_article","author":[{"first_name":"Tadanobu","last_name":"Nagaya","full_name":"Nagaya, Tadanobu"},{"first_name":"Shuhei","last_name":"Okuyama","full_name":"Okuyama, Shuhei"},{"full_name":"Ogata, Fusa","last_name":"Ogata","first_name":"Fusa"},{"full_name":"Maruoka, Yasuhiro","last_name":"Maruoka","first_name":"Yasuhiro"},{"first_name":"Deborah W.","last_name":"Knapp","full_name":"Knapp, Deborah W."},{"last_name":"Karagiannis","first_name":"Sophia N.","full_name":"Karagiannis, Sophia N."},{"full_name":"Fazekas-Singer, Judit","first_name":"Judit","last_name":"Fazekas-Singer","id":"36432834-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8777-3502"},{"last_name":"Choyke","first_name":"Peter L.","full_name":"Choyke, Peter L."},{"full_name":"LeBlanc, Amy K.","last_name":"LeBlanc","first_name":"Amy K."},{"full_name":"Jensen-Jarolim, Erika","first_name":"Erika","last_name":"Jensen-Jarolim"},{"full_name":"Kobayashi, Hisataka","first_name":"Hisataka","last_name":"Kobayashi"}],"oa_version":"Published Version","volume":9,"date_created":"2020-08-10T11:52:54Z","date_updated":"2021-01-12T08:17:37Z","_id":"8232","year":"2018","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Impact Journals","intvolume":" 9","publication_status":"published","title":"Near infrared photoimmunotherapy targeting bladder cancer with a canine anti-epidermal growth factor receptor (EGFR) antibody","status":"public","article_processing_charge":"No","publication_identifier":{"eissn":["1949-2553"]},"day":"10","month":"04","date_published":"2018-04-10T00:00:00Z","doi":"10.18632/oncotarget.24876","language":[{"iso":"eng"}],"oa":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.18632/oncotarget.24876"}],"citation":{"short":"T. Nagaya, S. Okuyama, F. Ogata, Y. Maruoka, D.W. Knapp, S.N. Karagiannis, J. Singer, P.L. Choyke, A.K. LeBlanc, E. Jensen-Jarolim, H. Kobayashi, Oncotarget 9 (2018) 19026–19038.","mla":"Nagaya, Tadanobu, et al. “Near Infrared Photoimmunotherapy Targeting Bladder Cancer with a Canine Anti-Epidermal Growth Factor Receptor (EGFR) Antibody.” Oncotarget, vol. 9, Impact Journals, 2018, pp. 19026–38, doi:10.18632/oncotarget.24876.","chicago":"Nagaya, Tadanobu, Shuhei Okuyama, Fusa Ogata, Yasuhiro Maruoka, Deborah W. Knapp, Sophia N. Karagiannis, Judit Singer, et al. “Near Infrared Photoimmunotherapy Targeting Bladder Cancer with a Canine Anti-Epidermal Growth Factor Receptor (EGFR) Antibody.” Oncotarget. Impact Journals, 2018. https://doi.org/10.18632/oncotarget.24876.","ama":"Nagaya T, Okuyama S, Ogata F, et al. Near infrared photoimmunotherapy targeting bladder cancer with a canine anti-epidermal growth factor receptor (EGFR) antibody. Oncotarget. 2018;9:19026-19038. doi:10.18632/oncotarget.24876","apa":"Nagaya, T., Okuyama, S., Ogata, F., Maruoka, Y., Knapp, D. W., Karagiannis, S. N., … Kobayashi, H. (2018). Near infrared photoimmunotherapy targeting bladder cancer with a canine anti-epidermal growth factor receptor (EGFR) antibody. Oncotarget. Impact Journals. https://doi.org/10.18632/oncotarget.24876","ieee":"T. Nagaya et al., “Near infrared photoimmunotherapy targeting bladder cancer with a canine anti-epidermal growth factor receptor (EGFR) antibody,” Oncotarget, vol. 9. Impact Journals, pp. 19026–19038, 2018.","ista":"Nagaya T, Okuyama S, Ogata F, Maruoka Y, Knapp DW, Karagiannis SN, Singer J, Choyke PL, LeBlanc AK, Jensen-Jarolim E, Kobayashi H. 2018. Near infrared photoimmunotherapy targeting bladder cancer with a canine anti-epidermal growth factor receptor (EGFR) antibody. Oncotarget. 9, 19026–19038."},"publication":"Oncotarget","page":"19026-19038","quality_controlled":"1","article_type":"original"},{"status":"public","title":"Canine macrophages can like human macrophages be in vitro activated toward the M2a subtype relevant in allergy","intvolume":" 82","_id":"8233","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Published Version","type":"journal_article","abstract":[{"lang":"eng","text":"The M2a subtype of macrophages plays an important role in human immunoglobulin E (IgE-mediated allergies) and other Th2 type immune reactions. In contrast, very little is known about these cells in the dog. Here we describe an in vitro method to activate canine histiocytic DH82 cells and primary canine monocyte-derived macrophages (MDMs) toward the M2a macrophages using human cytokines. For a side-by-side comparison, we compared the canine cells to human MDMs, and the human monocytic cell line U937 activated towards M1 and M2a cells on the cellular and molecular level. In analogy to activated human M2a cells, canine M2a, differentiated from both DH82 and MDMs, showed an increase in CD206 surface receptor expression compared to M1. Interestingly, canine M2a, but not M1 derived from MDM, upregulated the high-affinity IgE receptor (FcεRI). Transcription levels of M2a-associated genes (IL10, CCL22, TGFβ, CD163) showed a diverse pattern between the human and dog species, whereas M1 genes (IDO1, CXCL11, IL6, TNF-α) were similarly upregulated in canine and human M1 cells (cell lines and MDMs). We suggest that our novel in vitro method will be suitable in comparative allergology studies focussing on macrophages."}],"issue":"5","article_type":"original","page":"118-127","publication":"Developmental & Comparative Immunology","citation":{"ama":"Herrmann I, Gotovina J, Singer J, et al. Canine macrophages can like human macrophages be in vitro activated toward the M2a subtype relevant in allergy. Developmental & Comparative Immunology. 2018;82(5):118-127. doi:10.1016/j.dci.2018.01.005","ieee":"I. Herrmann et al., “Canine macrophages can like human macrophages be in vitro activated toward the M2a subtype relevant in allergy,” Developmental & Comparative Immunology, vol. 82, no. 5. Elsevier, pp. 118–127, 2018.","apa":"Herrmann, I., Gotovina, J., Singer, J., Fischer, M. B., Hufnagl, K., Bianchini, R., & Jensen-Jarolim, E. (2018). Canine macrophages can like human macrophages be in vitro activated toward the M2a subtype relevant in allergy. Developmental & Comparative Immunology. Elsevier. https://doi.org/10.1016/j.dci.2018.01.005","ista":"Herrmann I, Gotovina J, Singer J, Fischer MB, Hufnagl K, Bianchini R, Jensen-Jarolim E. 2018. Canine macrophages can like human macrophages be in vitro activated toward the M2a subtype relevant in allergy. Developmental & Comparative Immunology. 82(5), 118–127.","short":"I. Herrmann, J. Gotovina, J. Singer, M.B. Fischer, K. Hufnagl, R. Bianchini, E. Jensen-Jarolim, Developmental & Comparative Immunology 82 (2018) 118–127.","mla":"Herrmann, Ina, et al. “Canine Macrophages Can like Human Macrophages Be in Vitro Activated toward the M2a Subtype Relevant in Allergy.” Developmental & Comparative Immunology, vol. 82, no. 5, Elsevier, 2018, pp. 118–27, doi:10.1016/j.dci.2018.01.005.","chicago":"Herrmann, Ina, Jelena Gotovina, Judit Singer, Michael B. Fischer, Karin Hufnagl, Rodolfo Bianchini, and Erika Jensen-Jarolim. “Canine Macrophages Can like Human Macrophages Be in Vitro Activated toward the M2a Subtype Relevant in Allergy.” Developmental & Comparative Immunology. Elsevier, 2018. https://doi.org/10.1016/j.dci.2018.01.005."},"date_published":"2018-05-01T00:00:00Z","day":"01","article_processing_charge":"No","publication_status":"published","publisher":"Elsevier","year":"2018","date_created":"2020-08-10T11:53:01Z","date_updated":"2021-01-12T08:17:38Z","volume":82,"author":[{"full_name":"Herrmann, Ina","first_name":"Ina","last_name":"Herrmann"},{"full_name":"Gotovina, Jelena","last_name":"Gotovina","first_name":"Jelena"},{"full_name":"Fazekas-Singer, Judit","first_name":"Judit","last_name":"Fazekas-Singer","id":"36432834-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8777-3502"},{"first_name":"Michael B.","last_name":"Fischer","full_name":"Fischer, Michael B."},{"last_name":"Hufnagl","first_name":"Karin","full_name":"Hufnagl, Karin"},{"full_name":"Bianchini, Rodolfo","first_name":"Rodolfo","last_name":"Bianchini"},{"last_name":"Jensen-Jarolim","first_name":"Erika","full_name":"Jensen-Jarolim, Erika"}],"extern":"1","quality_controlled":"1","oa":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1016/j.dci.2018.01.005"}],"language":[{"iso":"eng"}],"doi":"10.1016/j.dci.2018.01.005","month":"05","publication_identifier":{"issn":["0145-305X"]}},{"type":"journal_article","article_number":"965","abstract":[{"lang":"eng","text":"Background: The genus Burkholderia consists of species that occupy remarkably diverse ecological niches. Its best known members are important pathogens, B. mallei and B. pseudomallei, which cause glanders and melioidosis, respectively. Burkholderia genomes are unusual due to their multichromosomal organization, generally comprised of 2-3 chromosomes.\r\n\r\nResults: We performed integrated genomic analysis of 127 Burkholderia strains. The pan-genome is open with the saturation to be reached between 86,000 and 88,000 genes. The reconstructed rearrangements indicate a strong avoidance of intra-replichore inversions that is likely caused by selection against the transfer of large groups of genes between the leading and the lagging strands. Translocated genes also tend to retain their position in the leading or the lagging strand, and this selection is stronger for large syntenies. Integrated reconstruction of chromosome rearrangements in the context of strains phylogeny reveals parallel rearrangements that may indicate inversion-based phase variation and integration of new genomic islands. In particular, we detected parallel inversions in the second chromosomes of B. pseudomallei with breakpoints formed by genes encoding membrane components of multidrug resistance complex, that may be linked to a phase variation mechanism. Two genomic islands, spreading horizontally between chromosomes, were detected in the B. cepacia group.\r\n\r\nConclusions: This study demonstrates the power of integrated analysis of pan-genomes, chromosome rearrangements, and selection regimes. Non-random inversion patterns indicate selective pressure, inversions are particularly frequent in a recent pathogen B. mallei, and, together with periods of positive selection at other branches, may indicate adaptation to new niches. One such adaptation could be a possible phase variation mechanism in B. pseudomallei."}],"extern":"1","_id":"8262","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2018","publisher":"Springer Nature","intvolume":" 19","publication_status":"published","status":"public","title":"Genome rearrangements and selection in multi-chromosome bacteria Burkholderia spp.","author":[{"first_name":"Olga","last_name":"Bochkareva","id":"C4558D3C-6102-11E9-A62E-F418E6697425","orcid":"0000-0003-1006-6639","full_name":"Bochkareva, Olga"},{"first_name":"Elena V.","last_name":"Moroz","full_name":"Moroz, Elena V."},{"last_name":"Davydov","first_name":"Iakov I.","full_name":"Davydov, Iakov I."},{"first_name":"Mikhail S.","last_name":"Gelfand","full_name":"Gelfand, Mikhail S."}],"oa_version":"Published Version","volume":19,"date_updated":"2023-02-23T13:28:52Z","date_created":"2020-08-15T11:02:08Z","publication_identifier":{"issn":["1471-2164"]},"article_processing_charge":"No","month":"12","day":"27","citation":{"ista":"Bochkareva O, Moroz EV, Davydov II, Gelfand MS. 2018. Genome rearrangements and selection in multi-chromosome bacteria Burkholderia spp. BMC Genomics. 19, 965.","apa":"Bochkareva, O., Moroz, E. V., Davydov, I. I., & Gelfand, M. S. (2018). Genome rearrangements and selection in multi-chromosome bacteria Burkholderia spp. BMC Genomics. Springer Nature. https://doi.org/10.1186/s12864-018-5245-1","ieee":"O. Bochkareva, E. V. Moroz, I. I. Davydov, and M. S. Gelfand, “Genome rearrangements and selection in multi-chromosome bacteria Burkholderia spp.,” BMC Genomics, vol. 19. Springer Nature, 2018.","ama":"Bochkareva O, Moroz EV, Davydov II, Gelfand MS. Genome rearrangements and selection in multi-chromosome bacteria Burkholderia spp. BMC Genomics. 2018;19. doi:10.1186/s12864-018-5245-1","chicago":"Bochkareva, Olga, Elena V. Moroz, Iakov I. Davydov, and Mikhail S. Gelfand. “Genome Rearrangements and Selection in Multi-Chromosome Bacteria Burkholderia Spp.” BMC Genomics. Springer Nature, 2018. https://doi.org/10.1186/s12864-018-5245-1.","mla":"Bochkareva, Olga, et al. “Genome Rearrangements and Selection in Multi-Chromosome Bacteria Burkholderia Spp.” BMC Genomics, vol. 19, 965, Springer Nature, 2018, doi:10.1186/s12864-018-5245-1.","short":"O. Bochkareva, E.V. Moroz, I.I. Davydov, M.S. Gelfand, BMC Genomics 19 (2018)."},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1186/s12864-018-5245-1"}],"oa":1,"publication":"BMC Genomics","article_type":"original","quality_controlled":"1","date_published":"2018-12-27T00:00:00Z","doi":"10.1186/s12864-018-5245-1","language":[{"iso":"eng"}]},{"extern":"1","article_number":"e4545","author":[{"full_name":"Bochkareva, Olga","orcid":"0000-0003-1006-6639","id":"C4558D3C-6102-11E9-A62E-F418E6697425","last_name":"Bochkareva","first_name":"Olga"},{"full_name":"Dranenko, Natalia O.","first_name":"Natalia O.","last_name":"Dranenko"},{"first_name":"Elena S.","last_name":"Ocheredko","full_name":"Ocheredko, Elena S."},{"full_name":"Kanevsky, German M.","first_name":"German M.","last_name":"Kanevsky"},{"full_name":"Lozinsky, Yaroslav N.","first_name":"Yaroslav N.","last_name":"Lozinsky"},{"first_name":"Vera A.","last_name":"Khalaycheva","full_name":"Khalaycheva, Vera A."},{"full_name":"Artamonova, Irena I.","first_name":"Irena I.","last_name":"Artamonova"},{"full_name":"Gelfand, Mikhail S.","first_name":"Mikhail S.","last_name":"Gelfand"}],"date_updated":"2023-02-23T13:28:57Z","date_created":"2020-08-15T11:08:23Z","volume":6,"year":"2018","pmid":1,"publication_status":"published","publisher":"PeerJ","month":"03","publication_identifier":{"issn":["2167-8359"]},"doi":"10.7717/peerj.4545","language":[{"iso":"eng"}],"oa":1,"external_id":{"pmid":["29607260"]},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.7717/peerj.4545"}],"quality_controlled":"1","abstract":[{"text":"Genome rearrangements have played an important role in the evolution of Yersinia pestis from its progenitor Yersinia pseudotuberculosis. Traditional phylogenetic trees for Y. pestis based on sequence comparison have short internal branches and low bootstrap supports as only a small number of nucleotide substitutions have occurred. On the other hand, even a small number of genome rearrangements may resolve topological ambiguities in a phylogenetic tree. We reconstructed phylogenetic trees based on genome rearrangements using several popular approaches such as Maximum likelihood for Gene Order and the Bayesian model of genome rearrangements by inversions. We also reconciled phylogenetic trees for each of the three CRISPR loci to obtain an integrated scenario of the CRISPR cassette evolution. Analysis of contradictions between the obtained evolutionary trees yielded numerous parallel inversions and gain/loss events. Our data indicate that an integrated analysis of sequence-based and inversion-based trees enhances the resolution of phylogenetic reconstruction. In contrast, reconstructions of strain relationships based on solely CRISPR loci may not be reliable, as the history is obscured by large deletions, obliterating the order of spacer gains. Similarly, numerous parallel gene losses preclude reconstruction of phylogeny based on gene content.","lang":"eng"}],"type":"journal_article","oa_version":"Published Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"8265","title":"Genome rearrangements and phylogeny reconstruction in Yersinia pestis","status":"public","intvolume":" 6","day":"27","article_processing_charge":"No","date_published":"2018-03-27T00:00:00Z","publication":"PeerJ","citation":{"ieee":"O. Bochkareva et al., “Genome rearrangements and phylogeny reconstruction in Yersinia pestis,” PeerJ, vol. 6. PeerJ, 2018.","apa":"Bochkareva, O., Dranenko, N. O., Ocheredko, E. S., Kanevsky, G. M., Lozinsky, Y. N., Khalaycheva, V. A., … Gelfand, M. S. (2018). Genome rearrangements and phylogeny reconstruction in Yersinia pestis. PeerJ. PeerJ. https://doi.org/10.7717/peerj.4545","ista":"Bochkareva O, Dranenko NO, Ocheredko ES, Kanevsky GM, Lozinsky YN, Khalaycheva VA, Artamonova II, Gelfand MS. 2018. Genome rearrangements and phylogeny reconstruction in Yersinia pestis. PeerJ. 6, e4545.","ama":"Bochkareva O, Dranenko NO, Ocheredko ES, et al. Genome rearrangements and phylogeny reconstruction in Yersinia pestis. PeerJ. 2018;6. doi:10.7717/peerj.4545","chicago":"Bochkareva, Olga, Natalia O. Dranenko, Elena S. Ocheredko, German M. Kanevsky, Yaroslav N. Lozinsky, Vera A. Khalaycheva, Irena I. Artamonova, and Mikhail S. Gelfand. “Genome Rearrangements and Phylogeny Reconstruction in Yersinia Pestis.” PeerJ. PeerJ, 2018. https://doi.org/10.7717/peerj.4545.","short":"O. Bochkareva, N.O. Dranenko, E.S. Ocheredko, G.M. Kanevsky, Y.N. Lozinsky, V.A. Khalaycheva, I.I. Artamonova, M.S. Gelfand, PeerJ 6 (2018).","mla":"Bochkareva, Olga, et al. “Genome Rearrangements and Phylogeny Reconstruction in Yersinia Pestis.” PeerJ, vol. 6, e4545, PeerJ, 2018, doi:10.7717/peerj.4545."},"article_type":"original"},{"type":"conference","abstract":[{"text":"Designing a secure permissionless distributed ledger (blockchain) that performs on par with centralized payment\r\nprocessors, such as Visa, is a challenging task. Most existing distributed ledgers are unable to scale-out, i.e., to grow their totalprocessing capacity with the number of validators; and those that do, compromise security or decentralization. We present OmniLedger, a novel scale-out distributed ledger that preserves longterm security under permissionless operation. It ensures security and correctness by using a bias-resistant public-randomness protocol for choosing large, statistically representative shards that process transactions, and by introducing an efficient crossshard commit protocol that atomically handles transactions affecting multiple shards. OmniLedger also optimizes performance via parallel intra-shard transaction processing, ledger pruning via collectively-signed state blocks, and low-latency “trust-butverify” \r\nvalidation for low-value transactions. An evaluation ofour experimental prototype shows that OmniLedger’s throughput\r\nscales linearly in the number of active validators, supporting Visa-level workloads and beyond, while confirming typical transactions in under two seconds.","lang":"eng"}],"extern":"1","_id":"8297","year":"2018","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","publication_status":"published","title":"OmniLedger: A secure, scale-out, decentralized ledger via sharding","publisher":"IEEE","author":[{"full_name":"Kokoris Kogias, Eleftherios","id":"f5983044-d7ef-11ea-ac6d-fd1430a26d30","first_name":"Eleftherios","last_name":"Kokoris Kogias"},{"full_name":"Jovanovic, Philipp","last_name":"Jovanovic","first_name":"Philipp"},{"full_name":"Gasser, Linus","first_name":"Linus","last_name":"Gasser"},{"full_name":"Gailly, Nicolas","first_name":"Nicolas","last_name":"Gailly"},{"full_name":"Syta, Ewa","last_name":"Syta","first_name":"Ewa"},{"first_name":"Bryan","last_name":"Ford","full_name":"Ford, Bryan"}],"date_updated":"2021-01-12T08:17:56Z","date_created":"2020-08-26T11:46:35Z","oa_version":"Preprint","month":"07","day":"26","publication_identifier":{"issn":["2375-1207"],"isbn":["9781538643532"]},"article_processing_charge":"No","publication":"2018 IEEE Symposium on Security and Privacy","citation":{"short":"E. Kokoris Kogias, P. Jovanovic, L. Gasser, N. Gailly, E. Syta, B. Ford, in:, 2018 IEEE Symposium on Security and Privacy, IEEE, 2018, pp. 583–598.","mla":"Kokoris Kogias, Eleftherios, et al. “OmniLedger: A Secure, Scale-out, Decentralized Ledger via Sharding.” 2018 IEEE Symposium on Security and Privacy, IEEE, 2018, pp. 583–98, doi:10.1109/sp.2018.000-5.","chicago":"Kokoris Kogias, Eleftherios, Philipp Jovanovic, Linus Gasser, Nicolas Gailly, Ewa Syta, and Bryan Ford. “OmniLedger: A Secure, Scale-out, Decentralized Ledger via Sharding.” In 2018 IEEE Symposium on Security and Privacy, 583–98. IEEE, 2018. https://doi.org/10.1109/sp.2018.000-5.","ama":"Kokoris Kogias E, Jovanovic P, Gasser L, Gailly N, Syta E, Ford B. OmniLedger: A secure, scale-out, decentralized ledger via sharding. In: 2018 IEEE Symposium on Security and Privacy. IEEE; 2018:583-598. doi:10.1109/sp.2018.000-5","apa":"Kokoris Kogias, E., Jovanovic, P., Gasser, L., Gailly, N., Syta, E., & Ford, B. (2018). OmniLedger: A secure, scale-out, decentralized ledger via sharding. In 2018 IEEE Symposium on Security and Privacy (pp. 583–598). San Francisco, CA, United States: IEEE. https://doi.org/10.1109/sp.2018.000-5","ieee":"E. Kokoris Kogias, P. Jovanovic, L. Gasser, N. Gailly, E. Syta, and B. Ford, “OmniLedger: A secure, scale-out, decentralized ledger via sharding,” in 2018 IEEE Symposium on Security and Privacy, San Francisco, CA, United States, 2018, pp. 583–598.","ista":"Kokoris Kogias E, Jovanovic P, Gasser L, Gailly N, Syta E, Ford B. 2018. OmniLedger: A secure, scale-out, decentralized ledger via sharding. 2018 IEEE Symposium on Security and Privacy. SP: Symposium on Security and Privacy, 583–598."},"oa":1,"main_file_link":[{"url":"https://eprint.iacr.org/2017/406","open_access":"1"}],"quality_controlled":"1","page":"583-598","conference":{"name":"SP: Symposium on Security and Privacy","end_date":"2018-05-24","location":"San Francisco, CA, United States","start_date":"2018-05-20"},"date_published":"2018-07-26T00:00:00Z","doi":"10.1109/sp.2018.000-5","language":[{"iso":"eng"}]},{"project":[{"_id":"260018B0-B435-11E9-9278-68D0E5697425","grant_number":"725780","call_identifier":"H2020","name":"Principles of Neural Stem Cell Lineage Progression in Cerebral Cortex Development"},{"grant_number":"M02416","_id":"264E56E2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Molecular Mechanisms Regulating Gliogenesis in the Cerebral Cortex"}],"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1101/494088"}],"oa":1,"citation":{"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, 10.1101/494088.","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. bioRxiv. Cold Spring Harbor Laboratory. https://doi.org/10.1101/494088","ieee":"A. Llorca et al., “Heterogeneous progenitor cell behaviors underlie the assembly of neocortical cytoarchitecture,” bioRxiv. Cold Spring Harbor Laboratory.","ama":"Llorca A, Ciceri G, Beattie RJ, et al. Heterogeneous progenitor cell behaviors underlie the assembly of neocortical cytoarchitecture. bioRxiv. doi:10.1101/494088","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.” BioRxiv. Cold Spring Harbor Laboratory, n.d. https://doi.org/10.1101/494088.","mla":"Llorca, Alfredo, et al. “Heterogeneous Progenitor Cell Behaviors Underlie the Assembly of Neocortical Cytoarchitecture.” BioRxiv, Cold Spring Harbor Laboratory, doi:10.1101/494088.","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.)."},"publication":"bioRxiv","language":[{"iso":"eng"}],"doi":"10.1101/494088","date_published":"2018-12-13T00:00:00Z","article_processing_charge":"No","day":"13","month":"12","publisher":"Cold Spring Harbor Laboratory","department":[{"_id":"SiHi"}],"publication_status":"submitted","status":"public","title":"Heterogeneous progenitor cell behaviors underlie the assembly of neocortical cytoarchitecture","_id":"8547","year":"2018","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","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.","oa_version":"Preprint","date_created":"2020-09-21T12:01:50Z","date_updated":"2021-01-12T08:20:00Z","author":[{"full_name":"Llorca, Alfredo","last_name":"Llorca","first_name":"Alfredo"},{"full_name":"Ciceri, Gabriele","first_name":"Gabriele","last_name":"Ciceri"},{"last_name":"Beattie","first_name":"Robert J","orcid":"0000-0002-8483-8753","id":"2E26DF60-F248-11E8-B48F-1D18A9856A87","full_name":"Beattie, Robert J"},{"full_name":"Wong, Fong K.","last_name":"Wong","first_name":"Fong K."},{"full_name":"Diana, Giovanni","first_name":"Giovanni","last_name":"Diana"},{"last_name":"Serafeimidou","first_name":"Eleni","full_name":"Serafeimidou, Eleni"},{"last_name":"Fernández-Otero","first_name":"Marian","full_name":"Fernández-Otero, Marian"},{"last_name":"Streicher","first_name":"Carmen","id":"36BCB99C-F248-11E8-B48F-1D18A9856A87","full_name":"Streicher, Carmen"},{"first_name":"Sebastian J.","last_name":"Arnold","full_name":"Arnold, Sebastian J."},{"last_name":"Meyer","first_name":"Martin","full_name":"Meyer, Martin"},{"last_name":"Hippenmeyer","first_name":"Simon","orcid":"0000-0003-2279-1061","id":"37B36620-F248-11E8-B48F-1D18A9856A87","full_name":"Hippenmeyer, Simon"},{"full_name":"Maravall, Miguel","last_name":"Maravall","first_name":"Miguel"},{"first_name":"Oscar","last_name":"Marín","full_name":"Marín, Oscar"}],"type":"preprint","ec_funded":1,"abstract":[{"lang":"eng","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."}]},{"publication":"Principles of Modeling","citation":{"short":"K. Chatterjee, T.A. Henzinger, J. Otop, in:, M. Lohstroh, P. Derler, M. Sirjani (Eds.), Principles of Modeling, Springer, 2018, pp. 143–161.","mla":"Chatterjee, Krishnendu, et al. “Computing Average Response Time.” Principles of Modeling, edited by Marten Lohstroh et al., vol. 10760, Springer, 2018, pp. 143–61, doi:10.1007/978-3-319-95246-8_9.","chicago":"Chatterjee, Krishnendu, Thomas A Henzinger, and Jan Otop. “Computing Average Response Time.” In Principles of Modeling, edited by Marten Lohstroh, Patricia Derler, and Marjan Sirjani, 10760:143–61. Springer, 2018. https://doi.org/10.1007/978-3-319-95246-8_9.","ama":"Chatterjee K, Henzinger TA, Otop J. Computing average response time. In: Lohstroh M, Derler P, Sirjani M, eds. Principles of Modeling. Vol 10760. Springer; 2018:143-161. doi:10.1007/978-3-319-95246-8_9","apa":"Chatterjee, K., Henzinger, T. A., & Otop, J. (2018). Computing average response time. In M. Lohstroh, P. Derler, & M. Sirjani (Eds.), Principles of Modeling (Vol. 10760, pp. 143–161). Springer. https://doi.org/10.1007/978-3-319-95246-8_9","ieee":"K. Chatterjee, T. A. Henzinger, and J. Otop, “Computing average response time,” in Principles of Modeling, vol. 10760, M. Lohstroh, P. Derler, and M. Sirjani, Eds. Springer, 2018, pp. 143–161.","ista":"Chatterjee K, Henzinger TA, Otop J. 2018.Computing average response time. In: Principles of Modeling. LNCS, vol. 10760, 143–161."},"page":"143 - 161","date_published":"2018-07-20T00:00:00Z","scopus_import":1,"day":"20","has_accepted_license":"1","_id":"86","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["000"],"status":"public","title":"Computing average response time","intvolume":" 10760","file":[{"file_name":"2018_PrinciplesModeling_Chatterjee.pdf","access_level":"open_access","creator":"dernst","file_size":516307,"content_type":"application/pdf","file_id":"7053","relation":"main_file","date_created":"2019-11-19T08:22:18Z","date_updated":"2020-07-14T12:48:14Z","checksum":"9995c6ce6957333baf616fc4f20be597"}],"oa_version":"Submitted Version","type":"book_chapter","alternative_title":["LNCS"],"abstract":[{"text":"Responsiveness—the requirement that every request to a system be eventually handled—is one of the fundamental liveness properties of a reactive system. Average response time is a quantitative measure for the responsiveness requirement used commonly in performance evaluation. We show how average response time can be computed on state-transition graphs, on Markov chains, and on game graphs. In all three cases, we give polynomial-time algorithms.","lang":"eng"}],"oa":1,"quality_controlled":"1","project":[{"grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425","name":"Rigorous Systems Engineering","call_identifier":"FWF"},{"grant_number":"S11407","_id":"25863FF4-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Game Theory"},{"_id":"25F42A32-B435-11E9-9278-68D0E5697425","grant_number":"Z211","name":"The Wittgenstein Prize","call_identifier":"FWF"},{"_id":"2581B60A-B435-11E9-9278-68D0E5697425","grant_number":"279307","call_identifier":"FP7","name":"Quantitative Graph Games: Theory and Applications"},{"name":"Efficient Algorithms for Computer Aided Verification","_id":"25892FC0-B435-11E9-9278-68D0E5697425","grant_number":"ICT15-003"}],"doi":"10.1007/978-3-319-95246-8_9","language":[{"iso":"eng"}],"month":"07","acknowledgement":"This research was supported in part by the Austrian Science Fund (FWF) under grants S11402-N23, S11407-N23 (RiSE/SHiNE) and Z211-N23 (Wittgenstein Award), ERC Start grant (279307: Graph Games), Vienna Science and Technology Fund (WWTF) through project ICT15-003 and by the National Science Centre (NCN), Poland under grant 2014/15/D/ST6/04543.","year":"2018","publication_status":"published","publisher":"Springer","department":[{"_id":"KrCh"},{"_id":"ToHe"}],"editor":[{"first_name":"Marten","last_name":"Lohstroh","full_name":"Lohstroh, Marten"},{"last_name":"Derler","first_name":"Patricia","full_name":"Derler, Patricia"},{"first_name":"Marjan","last_name":"Sirjani","full_name":"Sirjani, Marjan"}],"author":[{"full_name":"Chatterjee, Krishnendu","first_name":"Krishnendu","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X"},{"first_name":"Thomas A","last_name":"Henzinger","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","orcid":"0000−0002−2985−7724","full_name":"Henzinger, Thomas A"},{"id":"2FC5DA74-F248-11E8-B48F-1D18A9856A87","first_name":"Jan","last_name":"Otop","full_name":"Otop, Jan"}],"date_created":"2018-12-11T11:44:33Z","date_updated":"2021-01-12T08:20:14Z","volume":10760,"file_date_updated":"2020-07-14T12:48:14Z","publist_id":"7968","ec_funded":1},{"scopus_import":"1","article_processing_charge":"No","day":"01","page":"1114-1118","article_type":"original","citation":{"mla":"Aubret, Antoine, et al. “Targeted Assembly and Synchronization of Self-Spinning Microgears.” Nature Physics, vol. 14, no. 11, Springer Nature, 2018, pp. 1114–18, doi:10.1038/s41567-018-0227-4.","short":"A. Aubret, M. Youssef, S. Sacanna, J.A. Palacci, Nature Physics 14 (2018) 1114–1118.","chicago":"Aubret, Antoine, Mena Youssef, Stefano Sacanna, and Jérémie A Palacci. “Targeted Assembly and Synchronization of Self-Spinning Microgears.” Nature Physics. Springer Nature, 2018. https://doi.org/10.1038/s41567-018-0227-4.","ama":"Aubret A, Youssef M, Sacanna S, Palacci JA. Targeted assembly and synchronization of self-spinning microgears. Nature Physics. 2018;14(11):1114-1118. doi:10.1038/s41567-018-0227-4","ista":"Aubret A, Youssef M, Sacanna S, Palacci JA. 2018. Targeted assembly and synchronization of self-spinning microgears. Nature Physics. 14(11), 1114–1118.","apa":"Aubret, A., Youssef, M., Sacanna, S., & Palacci, J. A. (2018). Targeted assembly and synchronization of self-spinning microgears. Nature Physics. Springer Nature. https://doi.org/10.1038/s41567-018-0227-4","ieee":"A. Aubret, M. Youssef, S. Sacanna, and J. A. Palacci, “Targeted assembly and synchronization of self-spinning microgears,” Nature Physics, vol. 14, no. 11. Springer Nature, pp. 1114–1118, 2018."},"publication":"Nature Physics","date_published":"2018-11-01T00:00:00Z","type":"journal_article","issue":"11","abstract":[{"lang":"eng","text":"Self-assembly is the autonomous organization of components into patterns or structures: an essential ingredient of biology and a desired route to complex organization1. At equilibrium, the structure is encoded through specific interactions2,3,4,5,6,7,8, at an unfavourable entropic cost for the system. An alternative approach, widely used by nature, uses energy input to bypass the entropy bottleneck and develop features otherwise impossible at equilibrium9. Dissipative building blocks that inject energy locally were made available by recent advances in colloidal science10,11 but have not been used to control self-assembly. Here we show the targeted formation of self-powered microgears from active particles and their autonomous synchronization into dynamical superstructures. We use a photoactive component that consumes fuel, haematite, to devise phototactic microswimmers that form self-spinning microgears following spatiotemporal light patterns. The gears are coupled via their chemical clouds by diffusiophoresis12 and constitute the elementary bricks of synchronized superstructures, which autonomously regulate their dynamics. The results are quantitatively rationalized on the basis of a stochastic description of diffusio-phoretic oscillators dynamically coupled by chemical gradients. Our findings harness non-equilibrium phoretic phenomena to program interactions and direct self-assembly with fidelity and specificity. It lays the groundwork for the autonomous construction of dynamical architectures and functional micro-machinery."}],"intvolume":" 14","title":"Targeted assembly and synchronization of self-spinning microgears","status":"public","user_id":"D865714E-FA4E-11E9-B85B-F5C5E5697425","_id":"9062","oa_version":"Preprint","publication_identifier":{"issn":["1745-2473"],"eissn":["1745-2481"]},"month":"11","quality_controlled":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1810.01033"}],"oa":1,"external_id":{"arxiv":["1810.01033"]},"language":[{"iso":"eng"}],"doi":"10.1038/s41567-018-0227-4","extern":"1","publisher":"Springer Nature","publication_status":"published","year":"2018","volume":14,"date_created":"2021-02-02T13:52:49Z","date_updated":"2023-02-23T13:48:02Z","author":[{"last_name":"Aubret","first_name":"Antoine","full_name":"Aubret, Antoine"},{"full_name":"Youssef, Mena","first_name":"Mena","last_name":"Youssef"},{"last_name":"Sacanna","first_name":"Stefano","full_name":"Sacanna, Stefano"},{"last_name":"Palacci","first_name":"Jérémie A","orcid":"0000-0002-7253-9465","id":"8fb92548-2b22-11eb-b7c1-a3f0d08d7c7d","full_name":"Palacci, Jérémie A"}]},{"scopus_import":"1","article_processing_charge":"No","day":"30","citation":{"mla":"Danzl, Johann G. “Diffraction-Unlimited Optical Imaging for Synaptic Physiology.” Opera Medica et Physiologica, vol. 4, no. S1, Lobachevsky State University of Nizhny Novgorod, 2018, p. 11, doi:10.20388/omp2018.00s1.001.","short":"J.G. Danzl, Opera Medica et Physiologica 4 (2018) 11.","chicago":"Danzl, Johann G. “Diffraction-Unlimited Optical Imaging for Synaptic Physiology.” Opera Medica et Physiologica. Lobachevsky State University of Nizhny Novgorod, 2018. https://doi.org/10.20388/omp2018.00s1.001.","ama":"Danzl JG. Diffraction-unlimited optical imaging for synaptic physiology. Opera Medica et Physiologica. 2018;4(S1):11. doi:10.20388/omp2018.00s1.001","ista":"Danzl JG. 2018. Diffraction-unlimited optical imaging for synaptic physiology. Opera Medica et Physiologica. 4(S1), 11.","ieee":"J. G. Danzl, “Diffraction-unlimited optical imaging for synaptic physiology,” Opera Medica et Physiologica, vol. 4, no. S1. Lobachevsky State University of Nizhny Novgorod, p. 11, 2018.","apa":"Danzl, J. G. (2018). Diffraction-unlimited optical imaging for synaptic physiology. Opera Medica et Physiologica. Lobachevsky State University of Nizhny Novgorod. https://doi.org/10.20388/omp2018.00s1.001"},"publication":"Opera Medica et Physiologica","page":"11","article_type":"letter_note","date_published":"2018-06-30T00:00:00Z","type":"journal_article","alternative_title":["Molecular and cellular neuroscience"],"issue":"S1","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","_id":"9229","intvolume":" 4","title":"Diffraction-unlimited optical imaging for synaptic physiology","status":"public","oa_version":"Published Version","publication_identifier":{"issn":["2500-2287"],"eissn":["2500-2295"]},"month":"06","main_file_link":[{"url":"http://operamedphys.org/content/molecular-and-cellular-neuroscience","open_access":"1"}],"oa":1,"quality_controlled":"1","doi":"10.20388/omp2018.00s1.001","language":[{"iso":"eng"}],"year":"2018","publisher":"Lobachevsky State University of Nizhny Novgorod","department":[{"_id":"JoDa"}],"publication_status":"published","author":[{"full_name":"Danzl, Johann G","last_name":"Danzl","first_name":"Johann G","orcid":"0000-0001-8559-3973","id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87"}],"volume":4,"date_updated":"2021-12-03T07:31:05Z","date_created":"2021-03-07T23:01:25Z"},{"alternative_title":["LIPIcs"],"type":"conference","abstract":[{"lang":"eng","text":"Network games are widely used as a model for selfish resource-allocation problems. In the classicalmodel, each player selects a path connecting her source and target vertices. The cost of traversingan edge depends on theload; namely, number of players that traverse it. Thus, it abstracts the factthat different users may use a resource at different times and for different durations, which playsan important role in determining the costs of the users in reality. For example, when transmittingpackets in a communication network, routing traffic in a road network, or processing a task in aproduction system, actual sharing and congestion of resources crucially depends on time.In [13], we introducedtimed network games, which add a time component to network games.Each vertexvin the network is associated with a cost function, mapping the load onvto theprice that a player pays for staying invfor one time unit with this load. Each edge in thenetwork is guarded by the time intervals in which it can be traversed, which forces the players tospend time in the vertices. In this work we significantly extend the way time can be referred toin timed network games. In the model we study, the network is equipped withclocks, and, as intimed automata, edges are guarded by constraints on the values of the clocks, and their traversalmay involve a reset of some clocks. We argue that the stronger model captures many realisticnetworks. The addition of clocks breaks the techniques we developed in [13] and we developnew techniques in order to show that positive results on classic network games carry over to thestronger timed setting."}],"ddc":["000"],"status":"public","title":"Timed network games with clocks","intvolume":" 117","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"6005","oa_version":"Published Version","file":[{"date_updated":"2020-07-14T12:47:15Z","date_created":"2019-02-14T14:22:04Z","checksum":"41ab2ae9b63f5eb49fa995250c0ba128","file_id":"6007","relation":"main_file","creator":"dernst","content_type":"application/pdf","file_size":542889,"file_name":"2018_LIPIcs_Avni.pdf","access_level":"open_access"}],"scopus_import":"1","day":"01","article_processing_charge":"No","has_accepted_license":"1","citation":{"ista":"Avni G, Guha S, Kupferman O. 2018. Timed network games with clocks. MFCS: Mathematical Foundations of Computer Science, LIPIcs, vol. 117, 23.","ieee":"G. Avni, S. Guha, and O. Kupferman, “Timed network games with clocks,” presented at the MFCS: Mathematical Foundations of Computer Science, Liverpool, United Kingdom, 2018, vol. 117.","apa":"Avni, G., Guha, S., & Kupferman, O. (2018). Timed network games with clocks (Vol. 117). Presented at the MFCS: Mathematical Foundations of Computer Science, Liverpool, United Kingdom: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPICS.MFCS.2018.23","ama":"Avni G, Guha S, Kupferman O. Timed network games with clocks. In: Vol 117. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2018. doi:10.4230/LIPICS.MFCS.2018.23","chicago":"Avni, Guy, Shibashis Guha, and Orna Kupferman. “Timed Network Games with Clocks,” Vol. 117. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018. https://doi.org/10.4230/LIPICS.MFCS.2018.23.","mla":"Avni, Guy, et al. Timed Network Games with Clocks. Vol. 117, 23, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018, doi:10.4230/LIPICS.MFCS.2018.23.","short":"G. Avni, S. Guha, O. Kupferman, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018."},"date_published":"2018-08-01T00:00:00Z","article_number":"23","license":"https://creativecommons.org/licenses/by/4.0/","file_date_updated":"2020-07-14T12:47:15Z","publication_status":"published","department":[{"_id":"ToHe"}],"publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","year":"2018","date_updated":"2023-02-23T14:02:58Z","date_created":"2019-02-14T14:12:09Z","volume":117,"author":[{"full_name":"Avni, Guy","first_name":"Guy","last_name":"Avni","id":"463C8BC2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5588-8287"},{"full_name":"Guha, Shibashis","first_name":"Shibashis","last_name":"Guha"},{"full_name":"Kupferman, Orna","last_name":"Kupferman","first_name":"Orna"}],"related_material":{"record":[{"status":"public","relation":"earlier_version","id":"963"}]},"month":"08","publication_identifier":{"issn":["1868-8969"]},"quality_controlled":"1","project":[{"name":"Rigorous Systems Engineering","call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23"},{"call_identifier":"FWF","name":"The Wittgenstein Prize","grant_number":"Z211","_id":"25F42A32-B435-11E9-9278-68D0E5697425"},{"grant_number":"M02369","_id":"264B3912-B435-11E9-9278-68D0E5697425","name":"Formal Methods meets Algorithmic Game Theory","call_identifier":"FWF"}],"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"language":[{"iso":"eng"}],"conference":{"end_date":"2018-08-31","start_date":"2018-08-27","location":"Liverpool, United Kingdom","name":"MFCS: Mathematical Foundations of Computer Science"},"doi":"10.4230/LIPICS.MFCS.2018.23"},{"extern":"1","author":[{"first_name":"Bingqing","last_name":"Cheng","id":"cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9","orcid":"0000-0002-3584-9632","full_name":"Cheng, Bingqing"},{"full_name":"Dellago, Christoph","first_name":"Christoph","last_name":"Dellago"},{"full_name":"Ceriotti, Michele","last_name":"Ceriotti","first_name":"Michele"}],"volume":20,"date_updated":"2021-08-09T12:36:47Z","date_created":"2021-07-15T12:51:44Z","pmid":1,"year":"2018","publisher":"Royal Society of Chemistry","publication_status":"published","publication_identifier":{"eissn":["1463-9084"],"issn":["1463-9076"]},"month":"12","doi":"10.1039/c8cp04561e","language":[{"iso":"eng"}],"main_file_link":[{"url":"https://arxiv.org/abs/1807.05551","open_access":"1"}],"external_id":{"pmid":["30412211"],"arxiv":["1807.05551"]},"oa":1,"quality_controlled":"1","issue":"45","abstract":[{"text":"Estimating the homogeneous ice nucleation rate from undercooled liquid water is crucial for understanding many important physical phenomena and technological applications, and challenging for both experiments and theory. From a theoretical point of view, difficulties arise due to the long time scales required, as well as the numerous nucleation pathways involved to form ice nuclei with different stacking disorders. We computed the homogeneous ice nucleation rate at a physically relevant undercooling for a single-site water model, taking into account the diffuse nature of ice–water interfaces, stacking disorders in ice nuclei, and the addition rate of particles to the critical nucleus. We disentangled and investigated the relative importance of all the terms, including interfacial free energy, entropic contributions and the kinetic prefactor, that contribute to the overall nucleation rate. Breaking down the problem into pieces not only provides physical insights into ice nucleation, but also sheds light on the long-standing discrepancy between different theoretical predictions, as well as between theoretical and experimental determinations of the nucleation rate. Moreover, we pinpoint the main shortcomings and suggest strategies to systematically improve the existing simulation methods.","lang":"eng"}],"type":"journal_article","oa_version":"Preprint","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","_id":"9668","intvolume":" 20","title":"Theoretical prediction of the homogeneous ice nucleation rate: Disentangling thermodynamics and kinetics","status":"public","article_processing_charge":"No","day":"07","scopus_import":"1","date_published":"2018-12-07T00:00:00Z","citation":{"ista":"Cheng B, Dellago C, Ceriotti M. 2018. Theoretical prediction of the homogeneous ice nucleation rate: Disentangling thermodynamics and kinetics. Physical Chemistry Chemical Physics. 20(45), 28732–28740.","ieee":"B. Cheng, C. Dellago, and M. Ceriotti, “Theoretical prediction of the homogeneous ice nucleation rate: Disentangling thermodynamics and kinetics,” Physical Chemistry Chemical Physics, vol. 20, no. 45. Royal Society of Chemistry, pp. 28732–28740, 2018.","apa":"Cheng, B., Dellago, C., & Ceriotti, M. (2018). Theoretical prediction of the homogeneous ice nucleation rate: Disentangling thermodynamics and kinetics. Physical Chemistry Chemical Physics. Royal Society of Chemistry. https://doi.org/10.1039/c8cp04561e","ama":"Cheng B, Dellago C, Ceriotti M. Theoretical prediction of the homogeneous ice nucleation rate: Disentangling thermodynamics and kinetics. Physical Chemistry Chemical Physics. 2018;20(45):28732-28740. doi:10.1039/c8cp04561e","chicago":"Cheng, Bingqing, Christoph Dellago, and Michele Ceriotti. “Theoretical Prediction of the Homogeneous Ice Nucleation Rate: Disentangling Thermodynamics and Kinetics.” Physical Chemistry Chemical Physics. Royal Society of Chemistry, 2018. https://doi.org/10.1039/c8cp04561e.","mla":"Cheng, Bingqing, et al. “Theoretical Prediction of the Homogeneous Ice Nucleation Rate: Disentangling Thermodynamics and Kinetics.” Physical Chemistry Chemical Physics, vol. 20, no. 45, Royal Society of Chemistry, 2018, pp. 28732–40, doi:10.1039/c8cp04561e.","short":"B. Cheng, C. Dellago, M. Ceriotti, Physical Chemistry Chemical Physics 20 (2018) 28732–28740."},"publication":"Physical Chemistry Chemical Physics","page":"28732-28740","article_type":"original"},{"article_processing_charge":"No","day":"01","scopus_import":"1","date_published":"2018-02-01T00:00:00Z","citation":{"ama":"Cheng B, Ceriotti M. Computing the absolute Gibbs free energy in atomistic simulations: Applications to defects in solids. Physical Review B. 2018;97(5). doi:10.1103/physrevb.97.054102","ista":"Cheng B, Ceriotti M. 2018. Computing the absolute Gibbs free energy in atomistic simulations: Applications to defects in solids. Physical Review B. 97(5), 054102.","ieee":"B. Cheng and M. Ceriotti, “Computing the absolute Gibbs free energy in atomistic simulations: Applications to defects in solids,” Physical Review B, vol. 97, no. 5. American Physical Society, 2018.","apa":"Cheng, B., & Ceriotti, M. (2018). Computing the absolute Gibbs free energy in atomistic simulations: Applications to defects in solids. Physical Review B. American Physical Society. https://doi.org/10.1103/physrevb.97.054102","mla":"Cheng, Bingqing, and Michele Ceriotti. “Computing the Absolute Gibbs Free Energy in Atomistic Simulations: Applications to Defects in Solids.” Physical Review B, vol. 97, no. 5, 054102, American Physical Society, 2018, doi:10.1103/physrevb.97.054102.","short":"B. Cheng, M. Ceriotti, Physical Review B 97 (2018).","chicago":"Cheng, Bingqing, and Michele Ceriotti. “Computing the Absolute Gibbs Free Energy in Atomistic Simulations: Applications to Defects in Solids.” Physical Review B. American Physical Society, 2018. https://doi.org/10.1103/physrevb.97.054102."},"publication":"Physical Review B","article_type":"original","issue":"5","abstract":[{"text":"The Gibbs free energy is the fundamental thermodynamic potential underlying the relative stability of different states of matter under constant-pressure conditions. However, computing this quantity from atomic-scale simulations is far from trivial, so the potential energy of a system is often used as a proxy. In this paper, we use a combination of thermodynamic integration methods to accurately evaluate the Gibbs free energies associated with defects in crystals, including the vacancy formation energy in bcc iron, and the stacking fault energy in fcc nickel, iron, and cobalt. We quantify the importance of entropic and anharmonic effects in determining the free energies of defects at high temperatures, and show that the potential energy approximation as well as the harmonic approximation may produce inaccurate or even qualitatively wrong results. Our calculations manifest the necessity to employ accurate free energy methods such as thermodynamic integration to estimate the stability of crystallographic defects at high temperatures.","lang":"eng"}],"type":"journal_article","oa_version":"Preprint","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","_id":"9687","intvolume":" 97","status":"public","title":"Computing the absolute Gibbs free energy in atomistic simulations: Applications to defects in solids","publication_identifier":{"eissn":["2469-9969"],"issn":["2469-9950"]},"month":"02","doi":"10.1103/physrevb.97.054102","language":[{"iso":"eng"}],"oa":1,"external_id":{"arxiv":["1710.02815"]},"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1710.02815"}],"quality_controlled":"1","extern":"1","article_number":"054102","author":[{"full_name":"Cheng, Bingqing","id":"cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9","orcid":"0000-0002-3584-9632","first_name":"Bingqing","last_name":"Cheng"},{"full_name":"Ceriotti, Michele","first_name":"Michele","last_name":"Ceriotti"}],"volume":97,"date_updated":"2021-08-09T12:38:26Z","date_created":"2021-07-19T09:39:48Z","year":"2018","publisher":"American Physical Society","publication_status":"published"},{"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"quality_controlled":"1","doi":"10.1371/journal.pbio.2005372","language":[{"iso":"eng"}],"month":"06","publication_identifier":{"issn":["15449173"]},"year":"2018","publication_status":"published","department":[{"_id":"NiBa"}],"publisher":"Public Library of Science","author":[{"first_name":"Jitka","last_name":"Polechova","id":"3BBFB084-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-0951-3112","full_name":"Polechova, Jitka"}],"related_material":{"record":[{"relation":"research_data","status":"public","id":"9839"}]},"date_created":"2018-12-11T11:45:46Z","date_updated":"2023-02-23T14:10:16Z","volume":16,"article_number":"e2005372","file_date_updated":"2020-07-14T12:46:01Z","publist_id":"7550","publication":"PLoS Biology","citation":{"short":"J. Polechova, PLoS Biology 16 (2018).","mla":"Polechova, Jitka. “Is the Sky the Limit? On the Expansion Threshold of a Species’ Range.” PLoS Biology, vol. 16, no. 6, e2005372, Public Library of Science, 2018, doi:10.1371/journal.pbio.2005372.","chicago":"Polechova, Jitka. “Is the Sky the Limit? On the Expansion Threshold of a Species’ Range.” PLoS Biology. Public Library of Science, 2018. https://doi.org/10.1371/journal.pbio.2005372.","ama":"Polechova J. Is the sky the limit? On the expansion threshold of a species’ range. PLoS Biology. 2018;16(6). doi:10.1371/journal.pbio.2005372","ieee":"J. Polechova, “Is the sky the limit? On the expansion threshold of a species’ range,” PLoS Biology, vol. 16, no. 6. Public Library of Science, 2018.","apa":"Polechova, J. (2018). Is the sky the limit? On the expansion threshold of a species’ range. PLoS Biology. Public Library of Science. https://doi.org/10.1371/journal.pbio.2005372","ista":"Polechova J. 2018. Is the sky the limit? On the expansion threshold of a species’ range. PLoS Biology. 16(6), e2005372."},"date_published":"2018-06-15T00:00:00Z","scopus_import":1,"day":"15","has_accepted_license":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"315","status":"public","title":"Is the sky the limit? On the expansion threshold of a species’ range","ddc":["576"],"intvolume":" 16","file":[{"file_size":6968201,"content_type":"application/pdf","creator":"dernst","file_name":"2017_PLOS_Polechova.pdf","access_level":"open_access","date_updated":"2020-07-14T12:46:01Z","date_created":"2019-01-22T08:30:03Z","checksum":"908c52751bba30c55ed36789e5e4c84d","relation":"main_file","file_id":"5870"}],"oa_version":"Published Version","type":"journal_article","abstract":[{"lang":"eng","text":"More than 100 years after Grigg’s influential analysis of species’ borders, the causes of limits to species’ ranges still represent a puzzle that has never been understood with clarity. The topic has become especially important recently as many scientists have become interested in the potential for species’ ranges to shift in response to climate change—and yet nearly all of those studies fail to recognise or incorporate evolutionary genetics in a way that relates to theoretical developments. I show that range margins can be understood based on just two measurable parameters: (i) the fitness cost of dispersal—a measure of environmental heterogeneity—and (ii) the strength of genetic drift, which reduces genetic diversity. Together, these two parameters define an ‘expansion threshold’: adaptation fails when genetic drift reduces genetic diversity below that required for adaptation to a heterogeneous environment. When the key parameters drop below this expansion threshold locally, a sharp range margin forms. When they drop below this threshold throughout the species’ range, adaptation collapses everywhere, resulting in either extinction or formation of a fragmented metapopulation. Because the effects of dispersal differ fundamentally with dimension, the second parameter—the strength of genetic drift—is qualitatively different compared to a linear habitat. In two-dimensional habitats, genetic drift becomes effectively independent of selection. It decreases with ‘neighbourhood size’—the number of individuals accessible by dispersal within one generation. Moreover, in contrast to earlier predictions, which neglected evolution of genetic variance and/or stochasticity in two dimensions, dispersal into small marginal populations aids adaptation. This is because the reduction of both genetic and demographic stochasticity has a stronger effect than the cost of dispersal through increased maladaptation. The expansion threshold thus provides a novel, theoretically justified, and testable prediction for formation of the range margin and collapse of the species’ range."}],"issue":"6"},{"oa_version":"Preprint","title":"Nearly circular domains which are integrable close to the boundary are ellipses","status":"public","intvolume":" 28","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"8422","abstract":[{"lang":"eng","text":"The Birkhoff conjecture says that the boundary of a strictly convex integrable billiard table is necessarily an ellipse. In this article, we consider a stronger notion of integrability, namely integrability close to the boundary, and prove a local version of this conjecture: a small perturbation of an ellipse of small eccentricity which preserves integrability near the boundary, is itself an ellipse. This extends the result in Avila et al. (Ann Math 184:527–558, ADK16), where integrability was assumed on a larger set. In particular, it shows that (local) integrability near the boundary implies global integrability. One of the crucial ideas in the proof consists in analyzing Taylor expansion of the corresponding action-angle coordinates with respect to the eccentricity parameter, deriving and studying higher order conditions for the preservation of integrable rational caustics."}],"issue":"2","type":"journal_article","date_published":"2018-03-18T00:00:00Z","article_type":"original","page":"334-392","publication":"Geometric and Functional Analysis","citation":{"ama":"Huang G, Kaloshin V, Sorrentino A. Nearly circular domains which are integrable close to the boundary are ellipses. Geometric and Functional Analysis. 2018;28(2):334-392. doi:10.1007/s00039-018-0440-4","ieee":"G. Huang, V. Kaloshin, and A. Sorrentino, “Nearly circular domains which are integrable close to the boundary are ellipses,” Geometric and Functional Analysis, vol. 28, no. 2. Springer Nature, pp. 334–392, 2018.","apa":"Huang, G., Kaloshin, V., & Sorrentino, A. (2018). Nearly circular domains which are integrable close to the boundary are ellipses. Geometric and Functional Analysis. Springer Nature. https://doi.org/10.1007/s00039-018-0440-4","ista":"Huang G, Kaloshin V, Sorrentino A. 2018. Nearly circular domains which are integrable close to the boundary are ellipses. Geometric and Functional Analysis. 28(2), 334–392.","short":"G. Huang, V. Kaloshin, A. Sorrentino, Geometric and Functional Analysis 28 (2018) 334–392.","mla":"Huang, Guan, et al. “Nearly Circular Domains Which Are Integrable Close to the Boundary Are Ellipses.” Geometric and Functional Analysis, vol. 28, no. 2, Springer Nature, 2018, pp. 334–92, doi:10.1007/s00039-018-0440-4.","chicago":"Huang, Guan, Vadim Kaloshin, and Alfonso Sorrentino. “Nearly Circular Domains Which Are Integrable Close to the Boundary Are Ellipses.” Geometric and Functional Analysis. Springer Nature, 2018. https://doi.org/10.1007/s00039-018-0440-4."},"day":"18","article_processing_charge":"No","keyword":["Geometry and Topology","Analysis"],"date_updated":"2021-01-12T08:19:11Z","date_created":"2020-09-17T10:42:30Z","volume":28,"author":[{"full_name":"Huang, Guan","last_name":"Huang","first_name":"Guan"},{"first_name":"Vadim","last_name":"Kaloshin","id":"FE553552-CDE8-11E9-B324-C0EBE5697425","orcid":"0000-0002-6051-2628","full_name":"Kaloshin, Vadim"},{"first_name":"Alfonso","last_name":"Sorrentino","full_name":"Sorrentino, Alfonso"}],"publication_status":"published","publisher":"Springer Nature","year":"2018","extern":"1","language":[{"iso":"eng"}],"doi":"10.1007/s00039-018-0440-4","quality_controlled":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1705.10601"}],"oa":1,"external_id":{"arxiv":["1705.10601"]},"month":"03","publication_identifier":{"issn":["1016-443X","1420-8970"]}},{"publication_identifier":{"issn":["0003-486X"]},"month":"07","language":[{"iso":"eng"}],"doi":"10.4007/annals.2018.188.1.6","quality_controlled":"1","oa":1,"external_id":{"arxiv":["1612.09194"]},"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1612.09194"}],"extern":"1","volume":188,"date_updated":"2021-01-12T08:19:10Z","date_created":"2020-09-17T10:42:22Z","author":[{"full_name":"Kaloshin, Vadim","orcid":"0000-0002-6051-2628","id":"FE553552-CDE8-11E9-B324-C0EBE5697425","last_name":"Kaloshin","first_name":"Vadim"},{"first_name":"Alfonso","last_name":"Sorrentino","full_name":"Sorrentino, Alfonso"}],"publisher":"Annals of Mathematics, Princeton U","publication_status":"published","year":"2018","article_processing_charge":"No","day":"01","keyword":["Statistics","Probability and Uncertainty","Statistics and Probability"],"date_published":"2018-07-01T00:00:00Z","page":"315-380","article_type":"original","citation":{"chicago":"Kaloshin, Vadim, and Alfonso Sorrentino. “On the Local Birkhoff Conjecture for Convex Billiards.” Annals of Mathematics. Annals of Mathematics, Princeton U, 2018. https://doi.org/10.4007/annals.2018.188.1.6.","mla":"Kaloshin, Vadim, and Alfonso Sorrentino. “On the Local Birkhoff Conjecture for Convex Billiards.” Annals of Mathematics, vol. 188, no. 1, Annals of Mathematics, Princeton U, 2018, pp. 315–80, doi:10.4007/annals.2018.188.1.6.","short":"V. Kaloshin, A. Sorrentino, Annals of Mathematics 188 (2018) 315–380.","ista":"Kaloshin V, Sorrentino A. 2018. On the local Birkhoff conjecture for convex billiards. Annals of Mathematics. 188(1), 315–380.","apa":"Kaloshin, V., & Sorrentino, A. (2018). On the local Birkhoff conjecture for convex billiards. Annals of Mathematics. Annals of Mathematics, Princeton U. https://doi.org/10.4007/annals.2018.188.1.6","ieee":"V. Kaloshin and A. Sorrentino, “On the local Birkhoff conjecture for convex billiards,” Annals of Mathematics, vol. 188, no. 1. Annals of Mathematics, Princeton U, pp. 315–380, 2018.","ama":"Kaloshin V, Sorrentino A. On the local Birkhoff conjecture for convex billiards. Annals of Mathematics. 2018;188(1):315-380. doi:10.4007/annals.2018.188.1.6"},"publication":"Annals of Mathematics","issue":"1","abstract":[{"text":"The classical Birkhoff conjecture claims that the boundary of a strictly convex integrable billiard table is necessarily an ellipse (or a circle as a special case). In this article we prove a complete local version of this conjecture: a small integrable perturbation of an ellipse must be an ellipse. This extends and completes the result in Avila-De Simoi-Kaloshin, where nearly circular domains were considered. One of the crucial ideas in the proof is to extend action-angle coordinates for elliptic billiards into complex domains (with respect to the angle), and to thoroughly analyze the nature of their complex singularities. As an application, we are able to prove some spectral rigidity results for elliptic domains.","lang":"eng"}],"type":"journal_article","oa_version":"Preprint","intvolume":" 188","status":"public","title":"On the local Birkhoff conjecture for convex billiards","_id":"8421","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"oa_version":"Preprint","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"8420","intvolume":" 31","status":"public","title":"Density of convex billiards with rational caustics","issue":"11","abstract":[{"lang":"eng","text":"We show that in the space of all convex billiard boundaries, the set of boundaries with rational caustics is dense. More precisely, the set of billiard boundaries with caustics of rotation number 1/q is polynomially sense in the smooth case, and exponentially dense in the analytic case."}],"type":"journal_article","date_published":"2018-10-15T00:00:00Z","citation":{"ista":"Kaloshin V, Zhang K. 2018. Density of convex billiards with rational caustics. Nonlinearity. 31(11), 5214–5234.","ieee":"V. Kaloshin and K. Zhang, “Density of convex billiards with rational caustics,” Nonlinearity, vol. 31, no. 11. IOP Publishing, pp. 5214–5234, 2018.","apa":"Kaloshin, V., & Zhang, K. (2018). Density of convex billiards with rational caustics. Nonlinearity. IOP Publishing. https://doi.org/10.1088/1361-6544/aadc12","ama":"Kaloshin V, Zhang K. Density of convex billiards with rational caustics. Nonlinearity. 2018;31(11):5214-5234. doi:10.1088/1361-6544/aadc12","chicago":"Kaloshin, Vadim, and Ke Zhang. “Density of Convex Billiards with Rational Caustics.” Nonlinearity. IOP Publishing, 2018. https://doi.org/10.1088/1361-6544/aadc12.","mla":"Kaloshin, Vadim, and Ke Zhang. “Density of Convex Billiards with Rational Caustics.” Nonlinearity, vol. 31, no. 11, IOP Publishing, 2018, pp. 5214–34, doi:10.1088/1361-6544/aadc12.","short":"V. Kaloshin, K. Zhang, Nonlinearity 31 (2018) 5214–5234."},"publication":"Nonlinearity","page":"5214-5234","article_type":"original","article_processing_charge":"No","day":"15","keyword":["Mathematical Physics","General Physics and Astronomy","Applied Mathematics","Statistical and Nonlinear Physics"],"author":[{"full_name":"Kaloshin, Vadim","id":"FE553552-CDE8-11E9-B324-C0EBE5697425","orcid":"0000-0002-6051-2628","first_name":"Vadim","last_name":"Kaloshin"},{"last_name":"Zhang","first_name":"Ke","full_name":"Zhang, Ke"}],"volume":31,"date_created":"2020-09-17T10:42:09Z","date_updated":"2021-01-12T08:19:10Z","year":"2018","publisher":"IOP Publishing","publication_status":"published","extern":"1","doi":"10.1088/1361-6544/aadc12","language":[{"iso":"eng"}],"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1706.07968"}],"oa":1,"external_id":{"arxiv":["1706.07968"]},"quality_controlled":"1","publication_identifier":{"issn":["0951-7715","1361-6544"]},"month":"10"},{"year":"2018","publication_status":"published","publisher":"Springer Nature","author":[{"first_name":"Lev","last_name":"Buhovsky","full_name":"Buhovsky, Lev"},{"last_name":"Kaloshin","first_name":"Vadim","orcid":"0000-0002-6051-2628","id":"FE553552-CDE8-11E9-B324-C0EBE5697425","full_name":"Kaloshin, Vadim"}],"date_created":"2020-09-17T10:43:21Z","date_updated":"2021-01-12T08:19:11Z","volume":23,"extern":"1","oa":1,"external_id":{"arxiv":["1801.00952"]},"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1801.00952"}],"quality_controlled":"1","doi":"10.1134/s1560354718010057","language":[{"iso":"eng"}],"month":"02","publication_identifier":{"issn":["1560-3547","1468-4845"]},"_id":"8426","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Nonisometric domains with the same Marvizi-Melrose invariants","status":"public","intvolume":" 23","oa_version":"Preprint","type":"journal_article","abstract":[{"text":"For any strictly convex planar domain Ω ⊂ R2 with a C∞ boundary one can associate an infinite sequence of spectral invariants introduced by Marvizi–Merlose [5]. These invariants can generically be determined using the spectrum of the Dirichlet problem of the Laplace operator. A natural question asks if this collection is sufficient to determine Ω up to isometry. In this paper we give a counterexample, namely, we present two nonisometric domains Ω and Ω¯ with the same collection of Marvizi–Melrose invariants. Moreover, each domain has countably many periodic orbits {Sn}n≥1 (resp. {S¯n}n⩾1) of period going to infinity such that Sn and S¯n have the same period and perimeter for each n.","lang":"eng"}],"publication":"Regular and Chaotic Dynamics","citation":{"ama":"Buhovsky L, Kaloshin V. Nonisometric domains with the same Marvizi-Melrose invariants. Regular and Chaotic Dynamics. 2018;23:54-59. doi:10.1134/s1560354718010057","ieee":"L. Buhovsky and V. Kaloshin, “Nonisometric domains with the same Marvizi-Melrose invariants,” Regular and Chaotic Dynamics, vol. 23. Springer Nature, pp. 54–59, 2018.","apa":"Buhovsky, L., & Kaloshin, V. (2018). Nonisometric domains with the same Marvizi-Melrose invariants. Regular and Chaotic Dynamics. Springer Nature. https://doi.org/10.1134/s1560354718010057","ista":"Buhovsky L, Kaloshin V. 2018. Nonisometric domains with the same Marvizi-Melrose invariants. Regular and Chaotic Dynamics. 23, 54–59.","short":"L. Buhovsky, V. Kaloshin, Regular and Chaotic Dynamics 23 (2018) 54–59.","mla":"Buhovsky, Lev, and Vadim Kaloshin. “Nonisometric Domains with the Same Marvizi-Melrose Invariants.” Regular and Chaotic Dynamics, vol. 23, Springer Nature, 2018, pp. 54–59, doi:10.1134/s1560354718010057.","chicago":"Buhovsky, Lev, and Vadim Kaloshin. “Nonisometric Domains with the Same Marvizi-Melrose Invariants.” Regular and Chaotic Dynamics. Springer Nature, 2018. https://doi.org/10.1134/s1560354718010057."},"article_type":"original","page":"54-59","date_published":"2018-02-05T00:00:00Z","day":"05","article_processing_charge":"No"},{"doi":"10.1039/c8sm01760c","language":[{"iso":"eng"}],"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1909.11121"}],"external_id":{"pmid":["30456407"],"arxiv":["1909.11121"]},"oa":1,"quality_controlled":"1","publication_identifier":{"issn":["1744-683X"],"eissn":["1744-6848"]},"month":"12","author":[{"full_name":"Aubret, Antoine","first_name":"Antoine","last_name":"Aubret"},{"full_name":"Palacci, Jérémie A","orcid":"0000-0002-7253-9465","id":"8fb92548-2b22-11eb-b7c1-a3f0d08d7c7d","last_name":"Palacci","first_name":"Jérémie A"}],"volume":14,"date_updated":"2023-02-23T13:47:43Z","date_created":"2021-02-01T13:44:41Z","pmid":1,"year":"2018","publisher":"Royal Society of Chemistry ","publication_status":"published","extern":"1","date_published":"2018-12-21T00:00:00Z","citation":{"ama":"Aubret A, Palacci JA. Diffusiophoretic design of self-spinning microgears from colloidal microswimmers. Soft Matter. 2018;14(47):9577-9588. doi:10.1039/c8sm01760c","ista":"Aubret A, Palacci JA. 2018. Diffusiophoretic design of self-spinning microgears from colloidal microswimmers. Soft Matter. 14(47), 9577–9588.","apa":"Aubret, A., & Palacci, J. A. (2018). Diffusiophoretic design of self-spinning microgears from colloidal microswimmers. Soft Matter. Royal Society of Chemistry . https://doi.org/10.1039/c8sm01760c","ieee":"A. Aubret and J. A. Palacci, “Diffusiophoretic design of self-spinning microgears from colloidal microswimmers,” Soft Matter, vol. 14, no. 47. Royal Society of Chemistry , pp. 9577–9588, 2018.","mla":"Aubret, Antoine, and Jérémie A. Palacci. “Diffusiophoretic Design of Self-Spinning Microgears from Colloidal Microswimmers.” Soft Matter, vol. 14, no. 47, Royal Society of Chemistry , 2018, pp. 9577–88, doi:10.1039/c8sm01760c.","short":"A. Aubret, J.A. Palacci, Soft Matter 14 (2018) 9577–9588.","chicago":"Aubret, Antoine, and Jérémie A Palacci. “Diffusiophoretic Design of Self-Spinning Microgears from Colloidal Microswimmers.” Soft Matter. Royal Society of Chemistry , 2018. https://doi.org/10.1039/c8sm01760c."},"publication":"Soft Matter","page":"9577-9588","article_type":"original","article_processing_charge":"No","day":"21","scopus_import":"1","keyword":["General Chemistry","Condensed Matter Physics"],"oa_version":"Preprint","_id":"9053","user_id":"D865714E-FA4E-11E9-B85B-F5C5E5697425","intvolume":" 14","status":"public","title":"Diffusiophoretic design of self-spinning microgears from colloidal microswimmers","issue":"47","abstract":[{"text":"The development of strategies to assemble microscopic machines from dissipative building blocks are essential on the route to novel active materials. We recently demonstrated the hierarchical self-assembly of phoretic microswimmers into self-spinning microgears and their synchronization by diffusiophoretic interactions [Aubret et al., Nat. Phys., 2018]. In this paper, we adopt a pedagogical approach and expose our strategy to control self-assembly and build machines using phoretic phenomena. We notably introduce Highly Inclined Laminated Optical sheets microscopy (HILO) to image and characterize anisotropic and dynamic diffusiophoretic interactions, which cannot be performed by conventional fluorescence microscopy. The dynamics of a (haematite) photocatalytic material immersed in (hydrogen peroxide) fuel under various illumination patterns is first described and quantitatively rationalized by a model of diffusiophoresis, the migration of a colloidal particle in a concentration gradient. It is further exploited to design phototactic microswimmers that direct towards the high intensity of light, as a result of the reorientation of the haematite in a light gradient. We finally show the assembly of self-spinning microgears from colloidal microswimmers and carefully characterize the interactions using HILO techniques. The results are compared with analytical and numerical predictions and agree quantitatively, stressing the important role played by concentration gradients induced by chemical activity to control and design interactions. Because the approach described hereby is generic, this works paves the way for the rational design of machines by controlling phoretic phenomena.","lang":"eng"}],"type":"journal_article"},{"issue":"3","abstract":[{"lang":"eng","text":"In this study we investigate the scaling of precipitation extremes with temperature in the Mediterranean region by assessing against observations the present day and future regional climate simulations performed in the frame of the HyMeX and MED-CORDEX programs. Over the 1979–2008 period, despite differences in quantitative precipitation simulation across the various models, the change in precipitation extremes with respect to temperature is robust and consistent. The spatial variability of the temperature–precipitation extremes relationship displays a hook shape across the Mediterranean, with negative slope at high temperatures and a slope following Clausius–Clapeyron (CC)-scaling at low temperatures. The temperature at which the slope of the temperature–precipitation extreme relation sharply changes (or temperature break), ranges from about 20 °C in the western Mediterranean to <10 °C in Greece. In addition, this slope is always negative in the arid regions of the Mediterranean. The scaling of the simulated precipitation extremes is insensitive to ocean–atmosphere coupling, while it depends very weakly on the resolution at high temperatures for short precipitation accumulation times. In future climate scenario simulations covering the 2070–2100 period, the temperature break shifts to higher temperatures by a value which is on average the mean regional temperature change due to global warming. The slope of the simulated future temperature–precipitation extremes relationship is close to CC-scaling at temperatures below the temperature break, while at high temperatures, the negative slope is close, but somewhat flatter or steeper, than in the current climate depending on the model. Overall, models predict more intense precipitation extremes in the future. Adjusting the temperature–precipitation extremes relationship in the present climate using the CC law and the temperature shift in the future allows the recovery of the temperature–precipitation extremes relationship in the future climate. This implies negligible regional changes of relative humidity in the future despite the large warming and drying over the Mediterranean. This suggests that the Mediterranean Sea is the primary source of moisture which counteracts the drying and warming impacts on relative humidity in parts of the Mediterranean region."}],"type":"journal_article","oa_version":"Published Version","_id":"9136","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","intvolume":" 51","status":"public","title":"Scaling precipitation extremes with temperature in the Mediterranean: Past climate assessment and projection in anthropogenic scenarios","article_processing_charge":"No","day":"01","keyword":["Atmospheric Science"],"date_published":"2018-08-01T00:00:00Z","citation":{"ama":"Drobinski P, Silva ND, Panthou G, et al. Scaling precipitation extremes with temperature in the Mediterranean: Past climate assessment and projection in anthropogenic scenarios. Climate Dynamics. 2018;51(3):1237-1257. doi:10.1007/s00382-016-3083-x","ista":"Drobinski P, Silva ND, Panthou G, Bastin S, Muller CJ, Ahrens B, Borga M, Conte D, Fosser G, Giorgi F, Güttler I, Kotroni V, Li L, Morin E, Önol B, Quintana-Segui P, Romera R, Torma CZ. 2018. Scaling precipitation extremes with temperature in the Mediterranean: Past climate assessment and projection in anthropogenic scenarios. Climate Dynamics. 51(3), 1237–1257.","ieee":"P. Drobinski et al., “Scaling precipitation extremes with temperature in the Mediterranean: Past climate assessment and projection in anthropogenic scenarios,” Climate Dynamics, vol. 51, no. 3. Springer Nature, pp. 1237–1257, 2018.","apa":"Drobinski, P., Silva, N. D., Panthou, G., Bastin, S., Muller, C. J., Ahrens, B., … Torma, C. Z. (2018). Scaling precipitation extremes with temperature in the Mediterranean: Past climate assessment and projection in anthropogenic scenarios. Climate Dynamics. Springer Nature. https://doi.org/10.1007/s00382-016-3083-x","mla":"Drobinski, Philippe, et al. “Scaling Precipitation Extremes with Temperature in the Mediterranean: Past Climate Assessment and Projection in Anthropogenic Scenarios.” Climate Dynamics, vol. 51, no. 3, Springer Nature, 2018, pp. 1237–57, doi:10.1007/s00382-016-3083-x.","short":"P. Drobinski, N.D. Silva, G. Panthou, S. Bastin, C.J. Muller, B. Ahrens, M. Borga, D. Conte, G. Fosser, F. Giorgi, I. Güttler, V. Kotroni, L. Li, E. Morin, B. Önol, P. Quintana-Segui, R. Romera, C.Z. Torma, Climate Dynamics 51 (2018) 1237–1257.","chicago":"Drobinski, Philippe, Nicolas Da Silva, Gérémy Panthou, Sophie Bastin, Caroline J Muller, Bodo Ahrens, Marco Borga, et al. “Scaling Precipitation Extremes with Temperature in the Mediterranean: Past Climate Assessment and Projection in Anthropogenic Scenarios.” Climate Dynamics. Springer Nature, 2018. https://doi.org/10.1007/s00382-016-3083-x."},"publication":"Climate Dynamics","page":"1237-1257","article_type":"original","extern":"1","author":[{"full_name":"Drobinski, Philippe","last_name":"Drobinski","first_name":"Philippe"},{"first_name":"Nicolas Da","last_name":"Silva","full_name":"Silva, Nicolas Da"},{"full_name":"Panthou, Gérémy","last_name":"Panthou","first_name":"Gérémy"},{"last_name":"Bastin","first_name":"Sophie","full_name":"Bastin, Sophie"},{"orcid":"0000-0001-5836-5350","id":"f978ccb0-3f7f-11eb-b193-b0e2bd13182b","last_name":"Muller","first_name":"Caroline J","full_name":"Muller, Caroline J"},{"last_name":"Ahrens","first_name":"Bodo","full_name":"Ahrens, Bodo"},{"full_name":"Borga, Marco","first_name":"Marco","last_name":"Borga"},{"full_name":"Conte, Dario","last_name":"Conte","first_name":"Dario"},{"first_name":"Giorgia","last_name":"Fosser","full_name":"Fosser, Giorgia"},{"full_name":"Giorgi, Filippo","first_name":"Filippo","last_name":"Giorgi"},{"full_name":"Güttler, Ivan","last_name":"Güttler","first_name":"Ivan"},{"last_name":"Kotroni","first_name":"Vassiliki","full_name":"Kotroni, Vassiliki"},{"full_name":"Li, Laurent","last_name":"Li","first_name":"Laurent"},{"last_name":"Morin","first_name":"Efrat","full_name":"Morin, Efrat"},{"first_name":"Bariş","last_name":"Önol","full_name":"Önol, Bariş"},{"full_name":"Quintana-Segui, Pere","last_name":"Quintana-Segui","first_name":"Pere"},{"full_name":"Romera, Raquel","last_name":"Romera","first_name":"Raquel"},{"first_name":"Csaba Zsolt","last_name":"Torma","full_name":"Torma, Csaba Zsolt"}],"volume":51,"date_created":"2021-02-15T14:18:53Z","date_updated":"2022-01-24T12:40:40Z","year":"2018","publisher":"Springer Nature","publication_status":"published","publication_identifier":{"issn":["0930-7575","1432-0894"]},"month":"08","doi":"10.1007/s00382-016-3083-x","language":[{"iso":"eng"}],"main_file_link":[{"url":"https://doi.org/10.1007/s00382-016-3083-x","open_access":"1"}],"oa":1,"quality_controlled":"1"}]