[{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_type":"letter_note","intvolume":"       142","year":"2018","_id":"8231","citation":{"apa":"Singer, J., Singer, J., Ilieva, K. M., Matz, M., Herrmann, I., Spillner, E., … Jensen-Jarolim, E. (2018). AllergoOncology: Generating a canine anticancer IgE against the epidermal growth factor receptor. <i>Journal of Allergy and Clinical Immunology</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.jaci.2018.04.021\">https://doi.org/10.1016/j.jaci.2018.04.021</a>","short":"J. Singer, J. Singer, K.M. Ilieva, M. Matz, I. Herrmann, E. Spillner, S.N. Karagiannis, E. Jensen-Jarolim, Journal of Allergy and Clinical Immunology 142 (2018) 973–976.e11.","chicago":"Singer, Judit, Josef Singer, Kristina M. Ilieva, Miroslawa Matz, Ina Herrmann, Edzard Spillner, Sophia N. Karagiannis, and Erika Jensen-Jarolim. “AllergoOncology: Generating a Canine Anticancer IgE against the Epidermal Growth Factor Receptor.” <i>Journal of Allergy and Clinical Immunology</i>. Elsevier, 2018. <a href=\"https://doi.org/10.1016/j.jaci.2018.04.021\">https://doi.org/10.1016/j.jaci.2018.04.021</a>.","ama":"Singer J, Singer J, Ilieva KM, et al. AllergoOncology: Generating a canine anticancer IgE against the epidermal growth factor receptor. <i>Journal of Allergy and Clinical Immunology</i>. 2018;142(3):973-976.e11. doi:<a href=\"https://doi.org/10.1016/j.jaci.2018.04.021\">10.1016/j.jaci.2018.04.021</a>","ieee":"J. Singer <i>et al.</i>, “AllergoOncology: Generating a canine anticancer IgE against the epidermal growth factor receptor,” <i>Journal of Allergy and Clinical Immunology</i>, vol. 142, no. 3. Elsevier, p. 973–976.e11, 2018.","ista":"Singer J, Singer J, Ilieva KM, Matz M, Herrmann I, Spillner E, Karagiannis SN, Jensen-Jarolim E. 2018. AllergoOncology: Generating a canine anticancer IgE against the epidermal growth factor receptor. Journal of Allergy and Clinical Immunology. 142(3), 973–976.e11.","mla":"Singer, Judit, et al. “AllergoOncology: Generating a Canine Anticancer IgE against the Epidermal Growth Factor Receptor.” <i>Journal of Allergy and Clinical Immunology</i>, vol. 142, no. 3, Elsevier, 2018, p. 973–976.e11, doi:<a href=\"https://doi.org/10.1016/j.jaci.2018.04.021\">10.1016/j.jaci.2018.04.021</a>."},"publication_identifier":{"issn":["0091-6749"]},"quality_controlled":"1","article_processing_charge":"No","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1016/j.jaci.2018.04.021"}],"day":"01","volume":142,"author":[{"last_name":"Fazekas-Singer","id":"36432834-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8777-3502","first_name":"Judit","full_name":"Fazekas-Singer, Judit"},{"full_name":"Singer, Josef","first_name":"Josef","last_name":"Singer"},{"first_name":"Kristina M.","full_name":"Ilieva, Kristina M.","last_name":"Ilieva"},{"last_name":"Matz","first_name":"Miroslawa","full_name":"Matz, Miroslawa"},{"last_name":"Herrmann","first_name":"Ina","full_name":"Herrmann, Ina"},{"full_name":"Spillner, Edzard","first_name":"Edzard","last_name":"Spillner"},{"last_name":"Karagiannis","full_name":"Karagiannis, Sophia N.","first_name":"Sophia N."},{"first_name":"Erika","full_name":"Jensen-Jarolim, Erika","last_name":"Jensen-Jarolim"}],"issue":"3","publication_status":"published","extern":"1","date_published":"2018-09-01T00:00:00Z","language":[{"iso":"eng"}],"oa":1,"date_created":"2020-08-10T11:51:36Z","month":"09","publication":"Journal of Allergy and Clinical Immunology","oa_version":"Published Version","doi":"10.1016/j.jaci.2018.04.021","page":"973-976.e11","title":"AllergoOncology: Generating a canine anticancer IgE against the epidermal growth factor receptor","date_updated":"2021-01-12T08:17:37Z","publisher":"Elsevier","status":"public","type":"journal_article"},{"article_type":"original","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":"         9","year":"2018","_id":"8232","citation":{"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. <i>Oncotarget</i>. 2018;9:19026-19038. doi:<a href=\"https://doi.org/10.18632/oncotarget.24876\">10.18632/oncotarget.24876</a>","ieee":"T. Nagaya <i>et al.</i>, “Near infrared photoimmunotherapy targeting bladder cancer with a canine anti-epidermal growth factor receptor (EGFR) antibody,” <i>Oncotarget</i>, vol. 9. Impact Journals, pp. 19026–19038, 2018.","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.","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.” <i>Oncotarget</i>. Impact Journals, 2018. <a href=\"https://doi.org/10.18632/oncotarget.24876\">https://doi.org/10.18632/oncotarget.24876</a>.","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. <i>Oncotarget</i>. Impact Journals. <a href=\"https://doi.org/10.18632/oncotarget.24876\">https://doi.org/10.18632/oncotarget.24876</a>","mla":"Nagaya, Tadanobu, et al. “Near Infrared Photoimmunotherapy Targeting Bladder Cancer with a Canine Anti-Epidermal Growth Factor Receptor (EGFR) Antibody.” <i>Oncotarget</i>, vol. 9, Impact Journals, 2018, pp. 19026–38, doi:<a href=\"https://doi.org/10.18632/oncotarget.24876\">10.18632/oncotarget.24876</a>.","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."},"quality_controlled":"1","publication_identifier":{"eissn":["1949-2553"]},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.18632/oncotarget.24876"}],"article_processing_charge":"No","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."}],"day":"10","volume":9,"author":[{"last_name":"Nagaya","first_name":"Tadanobu","full_name":"Nagaya, Tadanobu"},{"last_name":"Okuyama","full_name":"Okuyama, Shuhei","first_name":"Shuhei"},{"last_name":"Ogata","full_name":"Ogata, Fusa","first_name":"Fusa"},{"first_name":"Yasuhiro","full_name":"Maruoka, Yasuhiro","last_name":"Maruoka"},{"last_name":"Knapp","first_name":"Deborah W.","full_name":"Knapp, Deborah W."},{"last_name":"Karagiannis","first_name":"Sophia N.","full_name":"Karagiannis, Sophia N."},{"first_name":"Judit","orcid":"0000-0002-8777-3502","full_name":"Fazekas-Singer, Judit","last_name":"Fazekas-Singer","id":"36432834-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Choyke, Peter L.","first_name":"Peter L.","last_name":"Choyke"},{"first_name":"Amy K.","full_name":"LeBlanc, Amy K.","last_name":"LeBlanc"},{"last_name":"Jensen-Jarolim","first_name":"Erika","full_name":"Jensen-Jarolim, Erika"},{"first_name":"Hisataka","full_name":"Kobayashi, Hisataka","last_name":"Kobayashi"}],"publication_status":"published","extern":"1","date_published":"2018-04-10T00:00:00Z","publication":"Oncotarget","language":[{"iso":"eng"}],"date_created":"2020-08-10T11:52:54Z","month":"04","oa":1,"oa_version":"Published Version","doi":"10.18632/oncotarget.24876","page":"19026-19038","title":"Near infrared photoimmunotherapy targeting bladder cancer with a canine anti-epidermal growth factor receptor (EGFR) antibody","date_updated":"2021-01-12T08:17:37Z","publisher":"Impact Journals","status":"public","type":"journal_article"},{"month":"05","oa":1,"oa_version":"Published Version","issue":"5","extern":"1","author":[{"full_name":"Herrmann, Ina","first_name":"Ina","last_name":"Herrmann"},{"first_name":"Jelena","full_name":"Gotovina, Jelena","last_name":"Gotovina"},{"last_name":"Fazekas-Singer","id":"36432834-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8777-3502","first_name":"Judit","full_name":"Fazekas-Singer, Judit"},{"last_name":"Fischer","full_name":"Fischer, Michael B.","first_name":"Michael B."},{"last_name":"Hufnagl","first_name":"Karin","full_name":"Hufnagl, Karin"},{"last_name":"Bianchini","full_name":"Bianchini, Rodolfo","first_name":"Rodolfo"},{"last_name":"Jensen-Jarolim","full_name":"Jensen-Jarolim, Erika","first_name":"Erika"}],"type":"journal_article","date_updated":"2021-01-12T08:17:38Z","status":"public","citation":{"ieee":"I. Herrmann <i>et al.</i>, “Canine macrophages can like human macrophages be in vitro activated toward the M2a subtype relevant in allergy,” <i>Developmental &#38; Comparative Immunology</i>, vol. 82, no. 5. Elsevier, pp. 118–127, 2018.","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. <i>Developmental &#38; Comparative Immunology</i>. 2018;82(5):118-127. doi:<a href=\"https://doi.org/10.1016/j.dci.2018.01.005\">10.1016/j.dci.2018.01.005</a>","apa":"Herrmann, I., Gotovina, J., Singer, J., Fischer, M. B., Hufnagl, K., Bianchini, R., &#38; Jensen-Jarolim, E. (2018). Canine macrophages can like human macrophages be in vitro activated toward the M2a subtype relevant in allergy. <i>Developmental &#38; Comparative Immunology</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.dci.2018.01.005\">https://doi.org/10.1016/j.dci.2018.01.005</a>","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.” <i>Developmental &#38; Comparative Immunology</i>. Elsevier, 2018. <a href=\"https://doi.org/10.1016/j.dci.2018.01.005\">https://doi.org/10.1016/j.dci.2018.01.005</a>.","short":"I. Herrmann, J. Gotovina, J. Singer, M.B. Fischer, K. Hufnagl, R. Bianchini, E. Jensen-Jarolim, Developmental &#38; 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.” <i>Developmental &#38; Comparative Immunology</i>, vol. 82, no. 5, Elsevier, 2018, pp. 118–27, doi:<a href=\"https://doi.org/10.1016/j.dci.2018.01.005\">10.1016/j.dci.2018.01.005</a>.","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 &#38; Comparative Immunology. 82(5), 118–127."},"publication_identifier":{"issn":["0145-305X"]},"_id":"8233","year":"2018","article_type":"original","volume":82,"day":"01","article_processing_charge":"No","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1016/j.dci.2018.01.005"}],"language":[{"iso":"eng"}],"publication":"Developmental & Comparative Immunology","date_created":"2020-08-10T11:53:01Z","date_published":"2018-05-01T00:00:00Z","publication_status":"published","publisher":"Elsevier","title":"Canine macrophages can like human macrophages be in vitro activated toward the M2a subtype relevant in allergy","doi":"10.1016/j.dci.2018.01.005","page":"118-127","quality_controlled":"1","intvolume":"        82","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"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.","lang":"eng"}]},{"article_number":"1269830","citation":{"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. <i>Contrast Media &#38; Molecular Imaging</i>. Hindawi. <a href=\"https://doi.org/10.1155/2018/1269830\">https://doi.org/10.1155/2018/1269830</a>","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.” <i>Contrast Media &#38; Molecular Imaging</i>. Hindawi, 2018. <a href=\"https://doi.org/10.1155/2018/1269830\">https://doi.org/10.1155/2018/1269830</a>.","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 &#38; Molecular Imaging 2018 (2018).","ieee":"T. Balber <i>et al.</i>, “Preclinical in vitro and in vivo evaluation of [18F]FE@SUPPY for cancer PET imaging: Limitations of a xenograft model for colorectal cancer,” <i>Contrast Media &#38; Molecular Imaging</i>, vol. 2018. Hindawi, 2018.","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. <i>Contrast Media &#38; Molecular Imaging</i>. 2018;2018. doi:<a href=\"https://doi.org/10.1155/2018/1269830\">10.1155/2018/1269830</a>","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 &#38; Molecular Imaging. 2018, 1269830.","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.” <i>Contrast Media &#38; Molecular Imaging</i>, vol. 2018, 1269830, Hindawi, 2018, doi:<a href=\"https://doi.org/10.1155/2018/1269830\">10.1155/2018/1269830</a>."},"publication_identifier":{"issn":["1555-4309","1555-4317"]},"quality_controlled":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_type":"original","intvolume":"      2018","_id":"8234","year":"2018","volume":2018,"article_processing_charge":"No","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1155/2018/1269830"}],"day":"13","abstract":[{"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.","lang":"eng"}],"date_published":"2018-02-13T00:00:00Z","language":[{"iso":"eng"}],"publication":"Contrast Media & Molecular Imaging","date_created":"2020-08-10T11:53:07Z","oa":1,"month":"02","oa_version":"Published Version","author":[{"last_name":"Balber","full_name":"Balber, T.","first_name":"T."},{"first_name":"Judit","orcid":"0000-0002-8777-3502","full_name":"Singer, Judit","last_name":"Singer","id":"36432834-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Berroterán-Infante, N.","first_name":"N.","last_name":"Berroterán-Infante"},{"full_name":"Dumanic, M.","first_name":"M.","last_name":"Dumanic"},{"last_name":"Fetty","full_name":"Fetty, L.","first_name":"L."},{"last_name":"Fazekas-Singer","orcid":"0000-0002-8777-3502","first_name":"J.","full_name":"Fazekas-Singer, J."},{"first_name":"C.","full_name":"Vraka, C.","last_name":"Vraka"},{"full_name":"Nics, L.","first_name":"L.","last_name":"Nics"},{"full_name":"Bergmann, M.","first_name":"M.","last_name":"Bergmann"},{"last_name":"Pallitsch","first_name":"K.","full_name":"Pallitsch, K."},{"full_name":"Spreitzer, H.","first_name":"H.","last_name":"Spreitzer"},{"last_name":"Wadsak","orcid":"0000-0003-4479-8053","first_name":"W.","full_name":"Wadsak, W."},{"last_name":"Hacker","first_name":"M.","full_name":"Hacker, M."},{"last_name":"Jensen-Jarolim","first_name":"E.","full_name":"Jensen-Jarolim, E."},{"first_name":"H.","full_name":"Viernstein, H.","last_name":"Viernstein"},{"last_name":"Mitterhauser","first_name":"M.","orcid":"0000-0003-3173-5272","full_name":"Mitterhauser, M."}],"publication_status":"published","extern":"1","publisher":"Hindawi","date_updated":"2021-01-12T08:17:38Z","status":"public","type":"journal_article","doi":"10.1155/2018/1269830","title":"Preclinical in vitro and in vivo evaluation of [18F]FE@SUPPY for cancer PET imaging: Limitations of a xenograft model for colorectal cancer"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_type":"original","intvolume":"        19","_id":"8262","year":"2018","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.","mla":"Bochkareva, Olga, et al. “Genome Rearrangements and Selection in Multi-Chromosome Bacteria Burkholderia Spp.” <i>BMC Genomics</i>, vol. 19, 965, Springer Nature, 2018, doi:<a href=\"https://doi.org/10.1186/s12864-018-5245-1\">10.1186/s12864-018-5245-1</a>.","short":"O. Bochkareva, E.V. Moroz, I.I. Davydov, M.S. Gelfand, BMC Genomics 19 (2018).","chicago":"Bochkareva, Olga, Elena V. Moroz, Iakov I. Davydov, and Mikhail S. Gelfand. “Genome Rearrangements and Selection in Multi-Chromosome Bacteria Burkholderia Spp.” <i>BMC Genomics</i>. Springer Nature, 2018. <a href=\"https://doi.org/10.1186/s12864-018-5245-1\">https://doi.org/10.1186/s12864-018-5245-1</a>.","apa":"Bochkareva, O., Moroz, E. V., Davydov, I. I., &#38; Gelfand, M. S. (2018). Genome rearrangements and selection in multi-chromosome bacteria Burkholderia spp. <i>BMC Genomics</i>. Springer Nature. <a href=\"https://doi.org/10.1186/s12864-018-5245-1\">https://doi.org/10.1186/s12864-018-5245-1</a>","ieee":"O. Bochkareva, E. V. Moroz, I. I. Davydov, and M. S. Gelfand, “Genome rearrangements and selection in multi-chromosome bacteria Burkholderia spp.,” <i>BMC Genomics</i>, vol. 19. Springer Nature, 2018.","ama":"Bochkareva O, Moroz EV, Davydov II, Gelfand MS. Genome rearrangements and selection in multi-chromosome bacteria Burkholderia spp. <i>BMC Genomics</i>. 2018;19. doi:<a href=\"https://doi.org/10.1186/s12864-018-5245-1\">10.1186/s12864-018-5245-1</a>"},"article_number":"965","publication_identifier":{"issn":["1471-2164"]},"quality_controlled":"1","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1186/s12864-018-5245-1"}],"article_processing_charge":"No","day":"27","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."}],"volume":19,"author":[{"first_name":"Olga","orcid":"0000-0003-1006-6639","full_name":"Bochkareva, Olga","last_name":"Bochkareva","id":"C4558D3C-6102-11E9-A62E-F418E6697425"},{"last_name":"Moroz","first_name":"Elena V.","full_name":"Moroz, Elena V."},{"last_name":"Davydov","first_name":"Iakov I.","full_name":"Davydov, Iakov I."},{"last_name":"Gelfand","first_name":"Mikhail S.","full_name":"Gelfand, Mikhail S."}],"publication_status":"published","extern":"1","date_published":"2018-12-27T00:00:00Z","oa":1,"publication":"BMC Genomics","language":[{"iso":"eng"}],"date_created":"2020-08-15T11:02:08Z","month":"12","oa_version":"Published Version","doi":"10.1186/s12864-018-5245-1","title":"Genome rearrangements and selection in multi-chromosome bacteria Burkholderia spp.","publisher":"Springer Nature","date_updated":"2023-02-23T13:28:52Z","status":"public","type":"journal_article"},{"quality_controlled":"1","intvolume":"         6","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","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"}],"pmid":1,"date_created":"2020-08-15T11:08:23Z","language":[{"iso":"eng"}],"publication":"PeerJ","date_published":"2018-03-27T00:00:00Z","publication_status":"published","publisher":"PeerJ","title":"Genome rearrangements and phylogeny reconstruction in Yersinia pestis","doi":"10.7717/peerj.4545","publication_identifier":{"issn":["2167-8359"]},"citation":{"ama":"Bochkareva O, Dranenko NO, Ocheredko ES, et al. Genome rearrangements and phylogeny reconstruction in Yersinia pestis. <i>PeerJ</i>. 2018;6. doi:<a href=\"https://doi.org/10.7717/peerj.4545\">10.7717/peerj.4545</a>","ieee":"O. Bochkareva <i>et al.</i>, “Genome rearrangements and phylogeny reconstruction in Yersinia pestis,” <i>PeerJ</i>, vol. 6. PeerJ, 2018.","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).","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.” <i>PeerJ</i>. PeerJ, 2018. <a href=\"https://doi.org/10.7717/peerj.4545\">https://doi.org/10.7717/peerj.4545</a>.","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. <i>PeerJ</i>. PeerJ. <a href=\"https://doi.org/10.7717/peerj.4545\">https://doi.org/10.7717/peerj.4545</a>","mla":"Bochkareva, Olga, et al. “Genome Rearrangements and Phylogeny Reconstruction in Yersinia Pestis.” <i>PeerJ</i>, vol. 6, e4545, PeerJ, 2018, doi:<a href=\"https://doi.org/10.7717/peerj.4545\">10.7717/peerj.4545</a>.","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."},"article_number":"e4545","_id":"8265","year":"2018","article_type":"original","volume":6,"day":"27","main_file_link":[{"open_access":"1","url":"https://doi.org/10.7717/peerj.4545"}],"article_processing_charge":"No","oa_version":"Published Version","oa":1,"month":"03","extern":"1","author":[{"orcid":"0000-0003-1006-6639","first_name":"Olga","full_name":"Bochkareva, Olga","last_name":"Bochkareva","id":"C4558D3C-6102-11E9-A62E-F418E6697425"},{"last_name":"Dranenko","first_name":"Natalia O.","full_name":"Dranenko, Natalia O."},{"last_name":"Ocheredko","full_name":"Ocheredko, Elena S.","first_name":"Elena S."},{"last_name":"Kanevsky","first_name":"German M.","full_name":"Kanevsky, German M."},{"last_name":"Lozinsky","full_name":"Lozinsky, Yaroslav N.","first_name":"Yaroslav N."},{"first_name":"Vera A.","full_name":"Khalaycheva, Vera A.","last_name":"Khalaycheva"},{"full_name":"Artamonova, Irena I.","first_name":"Irena I.","last_name":"Artamonova"},{"last_name":"Gelfand","full_name":"Gelfand, Mikhail S.","first_name":"Mikhail S."}],"type":"journal_article","status":"public","date_updated":"2023-02-23T13:28:57Z","external_id":{"pmid":["29607260"]}},{"author":[{"last_name":"Kokoris Kogias","id":"f5983044-d7ef-11ea-ac6d-fd1430a26d30","first_name":"Eleftherios","full_name":"Kokoris Kogias, Eleftherios"},{"full_name":"Jovanovic, Philipp","first_name":"Philipp","last_name":"Jovanovic"},{"last_name":"Gasser","full_name":"Gasser, Linus","first_name":"Linus"},{"full_name":"Gailly, Nicolas","first_name":"Nicolas","last_name":"Gailly"},{"last_name":"Syta","first_name":"Ewa","full_name":"Syta, Ewa"},{"last_name":"Ford","full_name":"Ford, Bryan","first_name":"Bryan"}],"extern":"1","publication_status":"published","date_published":"2018-07-26T00:00:00Z","oa_version":"Preprint","oa":1,"month":"07","language":[{"iso":"eng"}],"publication":"2018 IEEE Symposium on Security and Privacy","date_created":"2020-08-26T11:46:35Z","page":"583-598","doi":"10.1109/sp.2018.000-5","title":"OmniLedger: A secure, scale-out, decentralized ledger via sharding","status":"public","date_updated":"2021-01-12T08:17:56Z","publisher":"IEEE","type":"conference","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"8297","year":"2018","quality_controlled":"1","publication_identifier":{"isbn":["9781538643532"],"issn":["2375-1207"]},"citation":{"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 <i>2018 IEEE Symposium on Security and Privacy</i>, San Francisco, CA, United States, 2018, pp. 583–598.","ama":"Kokoris Kogias E, Jovanovic P, Gasser L, Gailly N, Syta E, Ford B. OmniLedger: A secure, scale-out, decentralized ledger via sharding. In: <i>2018 IEEE Symposium on Security and Privacy</i>. IEEE; 2018:583-598. doi:<a href=\"https://doi.org/10.1109/sp.2018.000-5\">10.1109/sp.2018.000-5</a>","apa":"Kokoris Kogias, E., Jovanovic, P., Gasser, L., Gailly, N., Syta, E., &#38; Ford, B. (2018). OmniLedger: A secure, scale-out, decentralized ledger via sharding. In <i>2018 IEEE Symposium on Security and Privacy</i> (pp. 583–598). San Francisco, CA, United States: IEEE. <a href=\"https://doi.org/10.1109/sp.2018.000-5\">https://doi.org/10.1109/sp.2018.000-5</a>","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 <i>2018 IEEE Symposium on Security and Privacy</i>, 583–98. IEEE, 2018. <a href=\"https://doi.org/10.1109/sp.2018.000-5\">https://doi.org/10.1109/sp.2018.000-5</a>.","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.” <i>2018 IEEE Symposium on Security and Privacy</i>, IEEE, 2018, pp. 583–98, doi:<a href=\"https://doi.org/10.1109/sp.2018.000-5\">10.1109/sp.2018.000-5</a>.","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."},"article_processing_charge":"No","main_file_link":[{"url":"https://eprint.iacr.org/2017/406","open_access":"1"}],"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"}],"day":"26","conference":{"name":"SP: Symposium on Security and Privacy","start_date":"2018-05-20","location":"San Francisco, CA, United States","end_date":"2018-05-24"}},{"alternative_title":["ISTA Thesis"],"project":[{"call_identifier":"FP7","name":"Provable Security for Physical Cryptography","_id":"258C570E-B435-11E9-9278-68D0E5697425","grant_number":"259668"},{"grant_number":"682815","_id":"258AA5B2-B435-11E9-9278-68D0E5697425","name":"Teaching Old Crypto New Tricks","call_identifier":"H2020"}],"day":"05","ec_funded":1,"article_processing_charge":"No","citation":{"short":"H.M. Abusalah, Proof Systems for Sustainable Decentralized Cryptocurrencies, Institute of Science and Technology Austria, 2018.","chicago":"Abusalah, Hamza M. “Proof Systems for Sustainable Decentralized Cryptocurrencies.” Institute of Science and Technology Austria, 2018. <a href=\"https://doi.org/10.15479/AT:ISTA:TH_1046\">https://doi.org/10.15479/AT:ISTA:TH_1046</a>.","apa":"Abusalah, H. M. (2018). <i>Proof systems for sustainable decentralized cryptocurrencies</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:TH_1046\">https://doi.org/10.15479/AT:ISTA:TH_1046</a>","ama":"Abusalah HM. Proof systems for sustainable decentralized cryptocurrencies. 2018. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:TH_1046\">10.15479/AT:ISTA:TH_1046</a>","ieee":"H. M. Abusalah, “Proof systems for sustainable decentralized cryptocurrencies,” Institute of Science and Technology Austria, 2018.","ista":"Abusalah HM. 2018. Proof systems for sustainable decentralized cryptocurrencies. Institute of Science and Technology Austria.","mla":"Abusalah, Hamza M. <i>Proof Systems for Sustainable Decentralized Cryptocurrencies</i>. Institute of Science and Technology Austria, 2018, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:TH_1046\">10.15479/AT:ISTA:TH_1046</a>."},"publication_identifier":{"issn":["2663-337X"]},"year":"2018","_id":"83","type":"dissertation","date_updated":"2023-09-07T12:30:23Z","status":"public","related_material":{"record":[{"relation":"part_of_dissertation","id":"1229","status":"public"},{"status":"public","id":"1235","relation":"part_of_dissertation"},{"status":"public","relation":"part_of_dissertation","id":"1236"},{"status":"public","relation":"part_of_dissertation","id":"559"}]},"department":[{"_id":"KrPi"}],"month":"09","oa":1,"oa_version":"Published Version","ddc":["004"],"author":[{"last_name":"Abusalah","id":"40297222-F248-11E8-B48F-1D18A9856A87","first_name":"Hamza M","full_name":"Abusalah, Hamza M"}],"file":[{"date_created":"2019-04-09T06:43:41Z","content_type":"application/pdf","creator":"dernst","date_updated":"2020-07-14T12:48:11Z","file_size":876241,"file_id":"6245","relation":"main_file","file_name":"2018_Thesis_Abusalah.pdf","checksum":"c4b5f7d111755d1396787f41886fc674","access_level":"open_access"},{"access_level":"closed","checksum":"0f382ac56b471c48fd907d63eb87dafe","file_name":"2018_Thesis_Abusalah_source.tar.gz","relation":"source_file","file_id":"6246","file_size":2029190,"date_updated":"2020-07-14T12:48:11Z","creator":"dernst","content_type":"application/x-gzip","date_created":"2019-04-09T06:43:41Z"}],"abstract":[{"text":"A proof system is a protocol between a prover and a verifier over a common input in which an honest prover convinces the verifier of the validity of true statements. Motivated by the success of decentralized cryptocurrencies, exemplified by Bitcoin, the focus of this thesis will be on proof systems which found applications in some sustainable alternatives to Bitcoin, such as the Spacemint and Chia cryptocurrencies. In particular, we focus on proofs of space and proofs of sequential work.\r\nProofs of space (PoSpace) were suggested as more ecological, economical, and egalitarian alternative to the energy-wasteful proof-of-work mining of Bitcoin. However, the state-of-the-art constructions of PoSpace are based on sophisticated graph pebbling lower bounds, and are therefore complex. Moreover, when these PoSpace are used in cryptocurrencies like Spacemint, miners can only start mining after ensuring that a commitment to their space is already added in a special transaction to the blockchain. Proofs of sequential work (PoSW) are proof systems in which a prover, upon receiving a statement x and a time parameter T, computes a proof which convinces the verifier that T time units had passed since x was received. Whereas Spacemint assumes synchrony to retain some interesting Bitcoin dynamics, Chia requires PoSW with unique proofs, i.e., PoSW in which it is hard to come up with more than one accepting proof for any true statement. In this thesis we construct simple and practically-efficient PoSpace and PoSW. When using our PoSpace in cryptocurrencies, miners can start mining on the fly, like in Bitcoin, and unlike current constructions of PoSW, which either achieve efficient verification of sequential work, or faster-than-recomputing verification of correctness of proofs, but not both at the same time, ours achieve the best of these two worlds.","lang":"eng"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publisher":"Institute of Science and Technology Austria","publist_id":"7971","title":"Proof systems for sustainable decentralized cryptocurrencies","supervisor":[{"full_name":"Pietrzak, Krzysztof Z","orcid":"0000-0002-9139-1654","first_name":"Krzysztof Z","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","last_name":"Pietrzak"}],"file_date_updated":"2020-07-14T12:48:11Z","page":"59","doi":"10.15479/AT:ISTA:TH_1046","pubrep_id":"1046","date_created":"2018-12-11T11:44:32Z","language":[{"iso":"eng"}],"degree_awarded":"PhD","date_published":"2018-09-05T00:00:00Z","publication_status":"published","has_accepted_license":"1"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":"        31","quality_controlled":"1","abstract":[{"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.","lang":"eng"}],"publication_status":"published","date_published":"2018-10-15T00:00:00Z","publication":"Nonlinearity","date_created":"2020-09-17T10:42:09Z","language":[{"iso":"eng"}],"page":"5214-5234","doi":"10.1088/1361-6544/aadc12","arxiv":1,"title":"Density of convex billiards with rational caustics","publisher":"IOP Publishing","article_type":"original","year":"2018","_id":"8420","publication_identifier":{"issn":["0951-7715","1361-6544"]},"citation":{"apa":"Kaloshin, V., &#38; Zhang, K. (2018). Density of convex billiards with rational caustics. <i>Nonlinearity</i>. IOP Publishing. <a href=\"https://doi.org/10.1088/1361-6544/aadc12\">https://doi.org/10.1088/1361-6544/aadc12</a>","chicago":"Kaloshin, Vadim, and Ke Zhang. “Density of Convex Billiards with Rational Caustics.” <i>Nonlinearity</i>. IOP Publishing, 2018. <a href=\"https://doi.org/10.1088/1361-6544/aadc12\">https://doi.org/10.1088/1361-6544/aadc12</a>.","short":"V. Kaloshin, K. Zhang, Nonlinearity 31 (2018) 5214–5234.","ama":"Kaloshin V, Zhang K. Density of convex billiards with rational caustics. <i>Nonlinearity</i>. 2018;31(11):5214-5234. doi:<a href=\"https://doi.org/10.1088/1361-6544/aadc12\">10.1088/1361-6544/aadc12</a>","ieee":"V. Kaloshin and K. Zhang, “Density of convex billiards with rational caustics,” <i>Nonlinearity</i>, vol. 31, no. 11. IOP Publishing, pp. 5214–5234, 2018.","ista":"Kaloshin V, Zhang K. 2018. Density of convex billiards with rational caustics. Nonlinearity. 31(11), 5214–5234.","mla":"Kaloshin, Vadim, and Ke Zhang. “Density of Convex Billiards with Rational Caustics.” <i>Nonlinearity</i>, vol. 31, no. 11, IOP Publishing, 2018, pp. 5214–34, doi:<a href=\"https://doi.org/10.1088/1361-6544/aadc12\">10.1088/1361-6544/aadc12</a>."},"main_file_link":[{"url":"https://arxiv.org/abs/1706.07968","open_access":"1"}],"article_processing_charge":"No","day":"15","volume":31,"author":[{"id":"FE553552-CDE8-11E9-B324-C0EBE5697425","last_name":"Kaloshin","full_name":"Kaloshin, Vadim","first_name":"Vadim","orcid":"0000-0002-6051-2628"},{"last_name":"Zhang","first_name":"Ke","full_name":"Zhang, Ke"}],"extern":"1","issue":"11","oa_version":"Preprint","month":"10","oa":1,"external_id":{"arxiv":["1706.07968"]},"keyword":["Mathematical Physics","General Physics and Astronomy","Applied Mathematics","Statistical and Nonlinear Physics"],"status":"public","date_updated":"2021-01-12T08:19:10Z","type":"journal_article"},{"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"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":"       188","quality_controlled":"1","arxiv":1,"doi":"10.4007/annals.2018.188.1.6","page":"315-380","title":"On the local Birkhoff conjecture for convex billiards","publisher":"Annals of Mathematics, Princeton U","publication_status":"published","date_published":"2018-07-01T00:00:00Z","language":[{"iso":"eng"}],"date_created":"2020-09-17T10:42:22Z","publication":"Annals of Mathematics","article_processing_charge":"No","main_file_link":[{"url":"https://arxiv.org/abs/1612.09194","open_access":"1"}],"day":"01","volume":188,"article_type":"original","_id":"8421","year":"2018","publication_identifier":{"issn":["0003-486X"]},"citation":{"mla":"Kaloshin, Vadim, and Alfonso Sorrentino. “On the Local Birkhoff Conjecture for Convex Billiards.” <i>Annals of Mathematics</i>, vol. 188, no. 1, Annals of Mathematics, Princeton U, 2018, pp. 315–80, doi:<a href=\"https://doi.org/10.4007/annals.2018.188.1.6\">10.4007/annals.2018.188.1.6</a>.","ista":"Kaloshin V, Sorrentino A. 2018. On the local Birkhoff conjecture for convex billiards. Annals of Mathematics. 188(1), 315–380.","ieee":"V. Kaloshin and A. Sorrentino, “On the local Birkhoff conjecture for convex billiards,” <i>Annals of Mathematics</i>, 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. <i>Annals of Mathematics</i>. 2018;188(1):315-380. doi:<a href=\"https://doi.org/10.4007/annals.2018.188.1.6\">10.4007/annals.2018.188.1.6</a>","apa":"Kaloshin, V., &#38; Sorrentino, A. (2018). On the local Birkhoff conjecture for convex billiards. <i>Annals of Mathematics</i>. Annals of Mathematics, Princeton U. <a href=\"https://doi.org/10.4007/annals.2018.188.1.6\">https://doi.org/10.4007/annals.2018.188.1.6</a>","short":"V. Kaloshin, A. Sorrentino, Annals of Mathematics 188 (2018) 315–380.","chicago":"Kaloshin, Vadim, and Alfonso Sorrentino. “On the Local Birkhoff Conjecture for Convex Billiards.” <i>Annals of Mathematics</i>. Annals of Mathematics, Princeton U, 2018. <a href=\"https://doi.org/10.4007/annals.2018.188.1.6\">https://doi.org/10.4007/annals.2018.188.1.6</a>."},"external_id":{"arxiv":["1612.09194"]},"keyword":["Statistics","Probability and Uncertainty","Statistics and Probability"],"status":"public","date_updated":"2021-01-12T08:19:10Z","type":"journal_article","author":[{"last_name":"Kaloshin","id":"FE553552-CDE8-11E9-B324-C0EBE5697425","orcid":"0000-0002-6051-2628","first_name":"Vadim","full_name":"Kaloshin, Vadim"},{"full_name":"Sorrentino, Alfonso","first_name":"Alfonso","last_name":"Sorrentino"}],"extern":"1","issue":"1","oa_version":"Preprint","month":"07","oa":1},{"keyword":["Geometry and Topology","Analysis"],"external_id":{"arxiv":["1705.10601"]},"type":"journal_article","date_updated":"2021-01-12T08:19:11Z","status":"public","issue":"2","extern":"1","author":[{"last_name":"Huang","full_name":"Huang, Guan","first_name":"Guan"},{"last_name":"Kaloshin","id":"FE553552-CDE8-11E9-B324-C0EBE5697425","orcid":"0000-0002-6051-2628","first_name":"Vadim","full_name":"Kaloshin, Vadim"},{"full_name":"Sorrentino, Alfonso","first_name":"Alfonso","last_name":"Sorrentino"}],"month":"03","oa":1,"oa_version":"Preprint","day":"18","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1705.10601"}],"article_processing_charge":"No","volume":28,"_id":"8422","year":"2018","article_type":"original","citation":{"ama":"Huang G, Kaloshin V, Sorrentino A. Nearly circular domains which are integrable close to the boundary are ellipses. <i>Geometric and Functional Analysis</i>. 2018;28(2):334-392. doi:<a href=\"https://doi.org/10.1007/s00039-018-0440-4\">10.1007/s00039-018-0440-4</a>","ieee":"G. Huang, V. Kaloshin, and A. Sorrentino, “Nearly circular domains which are integrable close to the boundary are ellipses,” <i>Geometric and Functional Analysis</i>, vol. 28, no. 2. Springer Nature, pp. 334–392, 2018.","apa":"Huang, G., Kaloshin, V., &#38; Sorrentino, A. (2018). Nearly circular domains which are integrable close to the boundary are ellipses. <i>Geometric and Functional Analysis</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s00039-018-0440-4\">https://doi.org/10.1007/s00039-018-0440-4</a>","chicago":"Huang, Guan, Vadim Kaloshin, and Alfonso Sorrentino. “Nearly Circular Domains Which Are Integrable Close to the Boundary Are Ellipses.” <i>Geometric and Functional Analysis</i>. Springer Nature, 2018. <a href=\"https://doi.org/10.1007/s00039-018-0440-4\">https://doi.org/10.1007/s00039-018-0440-4</a>.","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.” <i>Geometric and Functional Analysis</i>, vol. 28, no. 2, Springer Nature, 2018, pp. 334–92, doi:<a href=\"https://doi.org/10.1007/s00039-018-0440-4\">10.1007/s00039-018-0440-4</a>.","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."},"publication_identifier":{"issn":["1016-443X","1420-8970"]},"title":"Nearly circular domains which are integrable close to the boundary are ellipses","doi":"10.1007/s00039-018-0440-4","arxiv":1,"page":"334-392","publisher":"Springer Nature","publication_status":"published","publication":"Geometric and Functional Analysis","date_created":"2020-09-17T10:42:30Z","language":[{"iso":"eng"}],"date_published":"2018-03-18T00:00:00Z","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."}],"intvolume":"        28","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","quality_controlled":"1"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":"        23","quality_controlled":"1","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_status":"published","date_published":"2018-02-05T00:00:00Z","publication":"Regular and Chaotic Dynamics","language":[{"iso":"eng"}],"date_created":"2020-09-17T10:43:21Z","doi":"10.1134/s1560354718010057","arxiv":1,"page":"54-59","title":"Nonisometric domains with the same Marvizi-Melrose invariants","publisher":"Springer Nature","article_type":"original","year":"2018","_id":"8426","citation":{"ista":"Buhovsky L, Kaloshin V. 2018. Nonisometric domains with the same Marvizi-Melrose invariants. Regular and Chaotic Dynamics. 23, 54–59.","mla":"Buhovsky, Lev, and Vadim Kaloshin. “Nonisometric Domains with the Same Marvizi-Melrose Invariants.” <i>Regular and Chaotic Dynamics</i>, vol. 23, Springer Nature, 2018, pp. 54–59, doi:<a href=\"https://doi.org/10.1134/s1560354718010057\">10.1134/s1560354718010057</a>.","short":"L. Buhovsky, V. Kaloshin, Regular and Chaotic Dynamics 23 (2018) 54–59.","chicago":"Buhovsky, Lev, and Vadim Kaloshin. “Nonisometric Domains with the Same Marvizi-Melrose Invariants.” <i>Regular and Chaotic Dynamics</i>. Springer Nature, 2018. <a href=\"https://doi.org/10.1134/s1560354718010057\">https://doi.org/10.1134/s1560354718010057</a>.","apa":"Buhovsky, L., &#38; Kaloshin, V. (2018). Nonisometric domains with the same Marvizi-Melrose invariants. <i>Regular and Chaotic Dynamics</i>. Springer Nature. <a href=\"https://doi.org/10.1134/s1560354718010057\">https://doi.org/10.1134/s1560354718010057</a>","ama":"Buhovsky L, Kaloshin V. Nonisometric domains with the same Marvizi-Melrose invariants. <i>Regular and Chaotic Dynamics</i>. 2018;23:54-59. doi:<a href=\"https://doi.org/10.1134/s1560354718010057\">10.1134/s1560354718010057</a>","ieee":"L. Buhovsky and V. Kaloshin, “Nonisometric domains with the same Marvizi-Melrose invariants,” <i>Regular and Chaotic Dynamics</i>, vol. 23. Springer Nature, pp. 54–59, 2018."},"publication_identifier":{"issn":["1560-3547","1468-4845"]},"main_file_link":[{"url":"https://arxiv.org/abs/1801.00952","open_access":"1"}],"article_processing_charge":"No","day":"05","volume":23,"author":[{"first_name":"Lev","full_name":"Buhovsky, Lev","last_name":"Buhovsky"},{"last_name":"Kaloshin","id":"FE553552-CDE8-11E9-B324-C0EBE5697425","orcid":"0000-0002-6051-2628","first_name":"Vadim","full_name":"Kaloshin, Vadim"}],"extern":"1","oa":1,"month":"02","oa_version":"Preprint","external_id":{"arxiv":["1801.00952"]},"date_updated":"2021-01-12T08:19:11Z","status":"public","type":"journal_article"},{"quality_controlled":"1","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","intvolume":"     11014","file":[{"content_type":"application/pdf","date_created":"2019-02-12T07:40:40Z","access_level":"open_access","checksum":"13a3f250be8878405e791b53c19722ad","file_id":"5954","file_size":665372,"relation":"main_file","file_name":"2018_Brown.pdf","date_updated":"2020-07-14T12:48:14Z","creator":"dernst"}],"abstract":[{"lang":"eng","text":"Concurrent accesses to shared data structures must be synchronized to avoid data races. Coarse-grained synchronization, which locks the entire data structure, is easy to implement but does not scale. Fine-grained synchronization can scale well, but can be hard to reason about. Hand-over-hand locking, in which operations are pipelined as they traverse the data structure, combines fine-grained synchronization with ease of use. However, the traditional implementation suffers from inherent overheads. This paper introduces snapshot-based synchronization (SBS), a novel hand-over-hand locking mechanism. SBS decouples the synchronization state from the data, significantly improving cache utilization. Further, it relies on guarantees provided by pipelining to minimize synchronization that requires cross-thread communication. Snapshot-based synchronization thus scales much better than traditional hand-over-hand locking, while maintaining the same ease of use."}],"date_published":"2018-08-01T00:00:00Z","date_created":"2018-12-11T11:44:33Z","language":[{"iso":"eng"}],"has_accepted_license":"1","scopus_import":"1","publication_status":"published","isi":1,"publisher":"Springer","publist_id":"7969","doi":"10.1007/978-3-319-96983-1_33","page":"465 - 479","title":"Snapshot based synchronization: A fast replacement for Hand-over-Hand locking","file_date_updated":"2020-07-14T12:48:14Z","citation":{"ista":"Gilad E, Brown TA, Oskin M, Etsion Y. 2018. Snapshot based synchronization: A fast replacement for Hand-over-Hand locking. Euro-Par: European Conference on Parallel Processing, LNCS, vol. 11014, 465–479.","mla":"Gilad, Eran, et al. <i>Snapshot Based Synchronization: A Fast Replacement for Hand-over-Hand Locking</i>. Vol. 11014, Springer, 2018, pp. 465–79, doi:<a href=\"https://doi.org/10.1007/978-3-319-96983-1_33\">10.1007/978-3-319-96983-1_33</a>.","chicago":"Gilad, Eran, Trevor A Brown, Mark Oskin, and Yoav Etsion. “Snapshot Based Synchronization: A Fast Replacement for Hand-over-Hand Locking,” 11014:465–79. Springer, 2018. <a href=\"https://doi.org/10.1007/978-3-319-96983-1_33\">https://doi.org/10.1007/978-3-319-96983-1_33</a>.","short":"E. Gilad, T.A. Brown, M. Oskin, Y. Etsion, in:, Springer, 2018, pp. 465–479.","apa":"Gilad, E., Brown, T. A., Oskin, M., &#38; Etsion, Y. (2018). Snapshot based synchronization: A fast replacement for Hand-over-Hand locking (Vol. 11014, pp. 465–479). Presented at the Euro-Par: European Conference on Parallel Processing, Turin, Italy: Springer. <a href=\"https://doi.org/10.1007/978-3-319-96983-1_33\">https://doi.org/10.1007/978-3-319-96983-1_33</a>","ama":"Gilad E, Brown TA, Oskin M, Etsion Y. Snapshot based synchronization: A fast replacement for Hand-over-Hand locking. In: Vol 11014. Springer; 2018:465-479. doi:<a href=\"https://doi.org/10.1007/978-3-319-96983-1_33\">10.1007/978-3-319-96983-1_33</a>","ieee":"E. Gilad, T. A. Brown, M. Oskin, and Y. Etsion, “Snapshot based synchronization: A fast replacement for Hand-over-Hand locking,” presented at the Euro-Par: European Conference on Parallel Processing, Turin, Italy, 2018, vol. 11014, pp. 465–479."},"publication_identifier":{"issn":["03029743"]},"year":"2018","_id":"85","alternative_title":["LNCS"],"volume":11014,"conference":{"start_date":"2018-08-27","location":"Turin, Italy","end_date":"2018-08-31","name":"Euro-Par: European Conference on Parallel Processing"},"project":[{"name":"NSERC Postdoctoral fellowship","_id":"26450934-B435-11E9-9278-68D0E5697425"}],"article_processing_charge":"No","day":"01","oa":1,"month":"08","oa_version":"Preprint","ddc":["000"],"author":[{"full_name":"Gilad, Eran","first_name":"Eran","last_name":"Gilad"},{"first_name":"Trevor A","full_name":"Brown, Trevor A","last_name":"Brown","id":"3569F0A0-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Oskin","full_name":"Oskin, Mark","first_name":"Mark"},{"last_name":"Etsion","first_name":"Yoav","full_name":"Etsion, Yoav"}],"acknowledgement":"Trevor Brown was supported in part by the ISF (grants 2005/17 & 1749/14) and by a NSERC post-doctoral fellowship.","date_updated":"2023-09-18T09:32:36Z","status":"public","type":"conference","department":[{"_id":"DaAl"}],"external_id":{"isi":["000851042300031"]}},{"publication_status":"submitted","author":[{"first_name":"Alfredo","full_name":"Llorca, Alfredo","last_name":"Llorca"},{"last_name":"Ciceri","first_name":"Gabriele","full_name":"Ciceri, Gabriele"},{"orcid":"0000-0002-8483-8753","first_name":"Robert J","full_name":"Beattie, Robert J","last_name":"Beattie","id":"2E26DF60-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Wong","full_name":"Wong, Fong K.","first_name":"Fong K."},{"first_name":"Giovanni","full_name":"Diana, Giovanni","last_name":"Diana"},{"first_name":"Eleni","full_name":"Serafeimidou, Eleni","last_name":"Serafeimidou"},{"full_name":"Fernández-Otero, Marian","first_name":"Marian","last_name":"Fernández-Otero"},{"first_name":"Carmen","full_name":"Streicher, Carmen","last_name":"Streicher","id":"36BCB99C-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Sebastian J.","full_name":"Arnold, Sebastian J.","last_name":"Arnold"},{"last_name":"Meyer","full_name":"Meyer, Martin","first_name":"Martin"},{"last_name":"Hippenmeyer","id":"37B36620-F248-11E8-B48F-1D18A9856A87","first_name":"Simon","orcid":"0000-0003-2279-1061","full_name":"Hippenmeyer, Simon"},{"last_name":"Maravall","full_name":"Maravall, Miguel","first_name":"Miguel"},{"full_name":"Marín, Oscar","first_name":"Oscar","last_name":"Marín"}],"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","language":[{"iso":"eng"}],"oa":1,"publication":"bioRxiv","month":"12","date_created":"2020-09-21T12:01:50Z","date_published":"2018-12-13T00:00:00Z","title":"Heterogeneous progenitor cell behaviors underlie the assembly of neocortical cytoarchitecture","department":[{"_id":"SiHi"}],"doi":"10.1101/494088","type":"preprint","status":"public","publisher":"Cold Spring Harbor Laboratory","date_updated":"2021-01-12T08:20:00Z","_id":"8547","year":"2018","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"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.).","chicago":"Llorca, Alfredo, Gabriele Ciceri, Robert J Beattie, Fong K. Wong, Giovanni Diana, Eleni Serafeimidou, Marian Fernández-Otero, et al. “Heterogeneous Progenitor Cell Behaviors Underlie the Assembly of Neocortical Cytoarchitecture.” <i>BioRxiv</i>. Cold Spring Harbor Laboratory, n.d. <a href=\"https://doi.org/10.1101/494088\">https://doi.org/10.1101/494088</a>.","apa":"Llorca, A., Ciceri, G., Beattie, R. J., Wong, F. K., Diana, G., Serafeimidou, E., … Marín, O. (n.d.). Heterogeneous progenitor cell behaviors underlie the assembly of neocortical cytoarchitecture. <i>bioRxiv</i>. Cold Spring Harbor Laboratory. <a href=\"https://doi.org/10.1101/494088\">https://doi.org/10.1101/494088</a>","ama":"Llorca A, Ciceri G, Beattie RJ, et al. Heterogeneous progenitor cell behaviors underlie the assembly of neocortical cytoarchitecture. <i>bioRxiv</i>. doi:<a href=\"https://doi.org/10.1101/494088\">10.1101/494088</a>","ieee":"A. Llorca <i>et al.</i>, “Heterogeneous progenitor cell behaviors underlie the assembly of neocortical cytoarchitecture,” <i>bioRxiv</i>. Cold Spring Harbor Laboratory.","ista":"Llorca A, Ciceri G, Beattie RJ, Wong FK, Diana G, Serafeimidou E, Fernández-Otero M, Streicher C, Arnold SJ, Meyer M, Hippenmeyer S, Maravall M, Marín O. Heterogeneous progenitor cell behaviors underlie the assembly of neocortical cytoarchitecture. bioRxiv, <a href=\"https://doi.org/10.1101/494088\">10.1101/494088</a>.","mla":"Llorca, Alfredo, et al. “Heterogeneous Progenitor Cell Behaviors Underlie the Assembly of Neocortical Cytoarchitecture.” <i>BioRxiv</i>, Cold Spring Harbor Laboratory, doi:<a href=\"https://doi.org/10.1101/494088\">10.1101/494088</a>."},"abstract":[{"text":"The cerebral cortex contains multiple hierarchically organized areas with distinctive cytoarchitectonical patterns, but the cellular mechanisms underlying the emergence of this diversity remain unclear. Here, we have quantitatively investigated the neuronal output of individual progenitor cells in the ventricular zone of the developing mouse neocortex using a combination of methods that together circumvent the biases and limitations of individual approaches. We found that individual cortical progenitor cells show a high degree of stochasticity and generate pyramidal cell lineages that adopt a wide range of laminar configurations. Mathematical modelling these lineage data suggests that a small number of progenitor cell populations, each generating pyramidal cells following different stochastic developmental programs, suffice to generate the heterogenous complement of pyramidal cell lineages that collectively build the complex cytoarchitecture of the neocortex.","lang":"eng"}],"ec_funded":1,"day":"13","article_processing_charge":"No","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1101/494088"}],"project":[{"call_identifier":"H2020","_id":"260018B0-B435-11E9-9278-68D0E5697425","grant_number":"725780","name":"Principles of Neural Stem Cell Lineage Progression in Cerebral Cortex Development"},{"grant_number":"M02416","_id":"264E56E2-B435-11E9-9278-68D0E5697425","name":"Molecular Mechanisms Regulating Gliogenesis in the Cerebral Cortex","call_identifier":"FWF"}]},{"editor":[{"first_name":"Marten","full_name":"Lohstroh, Marten","last_name":"Lohstroh"},{"last_name":"Derler","full_name":"Derler, Patricia","first_name":"Patricia"},{"last_name":"Sirjani","first_name":"Marjan","full_name":"Sirjani, Marjan"}],"abstract":[{"lang":"eng","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."}],"file":[{"checksum":"9995c6ce6957333baf616fc4f20be597","access_level":"open_access","file_name":"2018_PrinciplesModeling_Chatterjee.pdf","file_id":"7053","relation":"main_file","file_size":516307,"date_updated":"2020-07-14T12:48:14Z","creator":"dernst","content_type":"application/pdf","date_created":"2019-11-19T08:22:18Z"}],"quality_controlled":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":"     10760","publist_id":"7968","publisher":"Springer","page":"143 - 161","doi":"10.1007/978-3-319-95246-8_9","file_date_updated":"2020-07-14T12:48:14Z","title":"Computing average response time","date_published":"2018-07-20T00:00:00Z","publication":"Principles of Modeling","date_created":"2018-12-11T11:44:33Z","language":[{"iso":"eng"}],"has_accepted_license":"1","publication_status":"published","scopus_import":1,"alternative_title":["LNCS"],"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","name":"Game Theory","call_identifier":"FWF"},{"call_identifier":"FWF","grant_number":"Z211","_id":"25F42A32-B435-11E9-9278-68D0E5697425","name":"The Wittgenstein Prize"},{"name":"Quantitative Graph Games: Theory and Applications","_id":"2581B60A-B435-11E9-9278-68D0E5697425","grant_number":"279307","call_identifier":"FP7"},{"name":"Efficient Algorithms for Computer Aided Verification","grant_number":"ICT15-003","_id":"25892FC0-B435-11E9-9278-68D0E5697425"}],"volume":10760,"ec_funded":1,"day":"20","citation":{"apa":"Chatterjee, K., Henzinger, T. A., &#38; Otop, J. (2018). Computing average response time. In M. Lohstroh, P. Derler, &#38; M. Sirjani (Eds.), <i>Principles of Modeling</i> (Vol. 10760, pp. 143–161). Springer. <a href=\"https://doi.org/10.1007/978-3-319-95246-8_9\">https://doi.org/10.1007/978-3-319-95246-8_9</a>","chicago":"Chatterjee, Krishnendu, Thomas A Henzinger, and Jan Otop. “Computing Average Response Time.” In <i>Principles of Modeling</i>, edited by Marten Lohstroh, Patricia Derler, and Marjan Sirjani, 10760:143–61. Springer, 2018. <a href=\"https://doi.org/10.1007/978-3-319-95246-8_9\">https://doi.org/10.1007/978-3-319-95246-8_9</a>.","short":"K. Chatterjee, T.A. Henzinger, J. Otop, in:, M. Lohstroh, P. Derler, M. Sirjani (Eds.), Principles of Modeling, Springer, 2018, pp. 143–161.","ieee":"K. Chatterjee, T. A. Henzinger, and J. Otop, “Computing average response time,” in <i>Principles of Modeling</i>, vol. 10760, M. Lohstroh, P. Derler, and M. Sirjani, Eds. Springer, 2018, pp. 143–161.","ama":"Chatterjee K, Henzinger TA, Otop J. Computing average response time. In: Lohstroh M, Derler P, Sirjani M, eds. <i>Principles of Modeling</i>. Vol 10760. Springer; 2018:143-161. doi:<a href=\"https://doi.org/10.1007/978-3-319-95246-8_9\">10.1007/978-3-319-95246-8_9</a>","ista":"Chatterjee K, Henzinger TA, Otop J. 2018.Computing average response time. In: Principles of Modeling. LNCS, vol. 10760, 143–161.","mla":"Chatterjee, Krishnendu, et al. “Computing Average Response Time.” <i>Principles of Modeling</i>, edited by Marten Lohstroh et al., vol. 10760, Springer, 2018, pp. 143–61, doi:<a href=\"https://doi.org/10.1007/978-3-319-95246-8_9\">10.1007/978-3-319-95246-8_9</a>."},"_id":"86","year":"2018","status":"public","date_updated":"2021-01-12T08:20:14Z","type":"book_chapter","department":[{"_id":"KrCh"},{"_id":"ToHe"}],"oa_version":"Submitted Version","month":"07","oa":1,"author":[{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","first_name":"Krishnendu"},{"id":"40876CD8-F248-11E8-B48F-1D18A9856A87","last_name":"Henzinger","full_name":"Henzinger, Thomas A","orcid":"0000−0002−2985−7724","first_name":"Thomas A"},{"full_name":"Otop, Jan","first_name":"Jan","id":"2FC5DA74-F248-11E8-B48F-1D18A9856A87","last_name":"Otop"}],"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.","ddc":["000"]},{"tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"pmid":1,"abstract":[{"lang":"eng","text":"The reversibly switchable fluorescent proteins (RSFPs) commonly used for RESOLFT nanoscopy have been developed from fluorescent proteins of the GFP superfamily. These proteins are bright, but exhibit several drawbacks such as relatively large size, oxygen-dependence, sensitivity to low pH, and limited switching speed. Therefore, RSFPs from other origins with improved properties need to be explored. Here, we report the development of two RSFPs based on the LOV domain of the photoreceptor protein YtvA from Bacillus subtilis. LOV domains obtain their fluorescence by association with the abundant cellular cofactor flavin mononucleotide (FMN). Under illumination with blue and ultraviolet light, they undergo a photocycle, making these proteins inherently photoswitchable. Our first improved variant, rsLOV1, can be used for RESOLFT imaging, whereas rsLOV2 proved useful for STED nanoscopy of living cells with a resolution of down to 50 nm. In addition to their smaller size compared to GFP-related proteins (17 kDa instead of 27 kDa) and their usability at low pH, rsLOV1 and rsLOV2 exhibit faster switching kinetics, switching on and off 3 times faster than rsEGFP2, the fastest-switching RSFP reported to date. Therefore, LOV-domain-based RSFPs have potential for applications where the switching speed of GFP-based proteins is limiting."}],"file":[{"date_updated":"2020-10-06T16:35:16Z","creator":"dernst","access_level":"open_access","checksum":"e642080fcbde9584c63544f587c74f03","file_name":"2018_ScientificReports_Gregor.pdf","file_id":"8619","file_size":2818077,"relation":"main_file","content_type":"application/pdf","date_created":"2020-10-06T16:35:16Z","success":1}],"quality_controlled":"1","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","intvolume":"         8","publisher":"Springer Nature","doi":"10.1038/s41598-018-19947-1","title":"Novel reversibly switchable fluorescent proteins for RESOLFT and STED nanoscopy engineered from the bacterial photoreceptor YtvA","file_date_updated":"2020-10-06T16:35:16Z","date_published":"2018-02-09T00:00:00Z","date_created":"2020-10-06T16:33:37Z","language":[{"iso":"eng"}],"publication":"Scientific Reports","has_accepted_license":"1","isi":1,"publication_status":"published","volume":8,"article_processing_charge":"No","day":"09","publication_identifier":{"issn":["2045-2322"]},"citation":{"ista":"Gregor C, Sidenstein SC, Andresen M, Sahl SJ, Danzl JG, Hell SW. 2018. Novel reversibly switchable fluorescent proteins for RESOLFT and STED nanoscopy engineered from the bacterial photoreceptor YtvA. Scientific Reports. 8, 2724.","mla":"Gregor, Carola, et al. “Novel Reversibly Switchable Fluorescent Proteins for RESOLFT and STED Nanoscopy Engineered from the Bacterial Photoreceptor YtvA.” <i>Scientific Reports</i>, vol. 8, 2724, Springer Nature, 2018, doi:<a href=\"https://doi.org/10.1038/s41598-018-19947-1\">10.1038/s41598-018-19947-1</a>.","apa":"Gregor, C., Sidenstein, S. C., Andresen, M., Sahl, S. J., Danzl, J. G., &#38; Hell, S. W. (2018). Novel reversibly switchable fluorescent proteins for RESOLFT and STED nanoscopy engineered from the bacterial photoreceptor YtvA. <i>Scientific Reports</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41598-018-19947-1\">https://doi.org/10.1038/s41598-018-19947-1</a>","chicago":"Gregor, Carola, Sven C. Sidenstein, Martin Andresen, Steffen J. Sahl, Johann G Danzl, and Stefan W. Hell. “Novel Reversibly Switchable Fluorescent Proteins for RESOLFT and STED Nanoscopy Engineered from the Bacterial Photoreceptor YtvA.” <i>Scientific Reports</i>. Springer Nature, 2018. <a href=\"https://doi.org/10.1038/s41598-018-19947-1\">https://doi.org/10.1038/s41598-018-19947-1</a>.","short":"C. Gregor, S.C. Sidenstein, M. Andresen, S.J. Sahl, J.G. Danzl, S.W. Hell, Scientific Reports 8 (2018).","ieee":"C. Gregor, S. C. Sidenstein, M. Andresen, S. J. Sahl, J. G. Danzl, and S. W. Hell, “Novel reversibly switchable fluorescent proteins for RESOLFT and STED nanoscopy engineered from the bacterial photoreceptor YtvA,” <i>Scientific Reports</i>, vol. 8. Springer Nature, 2018.","ama":"Gregor C, Sidenstein SC, Andresen M, Sahl SJ, Danzl JG, Hell SW. Novel reversibly switchable fluorescent proteins for RESOLFT and STED nanoscopy engineered from the bacterial photoreceptor YtvA. <i>Scientific Reports</i>. 2018;8. doi:<a href=\"https://doi.org/10.1038/s41598-018-19947-1\">10.1038/s41598-018-19947-1</a>"},"article_number":"2724","article_type":"original","_id":"8618","year":"2018","status":"public","date_updated":"2023-09-19T15:04:49Z","type":"journal_article","department":[{"_id":"JoDa"}],"external_id":{"pmid":["29426833"],"isi":["000424630400037"]},"keyword":["Multidisciplinary"],"oa_version":"Published Version","month":"02","oa":1,"author":[{"last_name":"Gregor","full_name":"Gregor, Carola","first_name":"Carola"},{"full_name":"Sidenstein, Sven C.","first_name":"Sven C.","last_name":"Sidenstein"},{"first_name":"Martin","full_name":"Andresen, Martin","last_name":"Andresen"},{"last_name":"Sahl","full_name":"Sahl, Steffen J.","first_name":"Steffen J."},{"first_name":"Johann G","orcid":"0000-0001-8559-3973","full_name":"Danzl, Johann G","last_name":"Danzl","id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Hell, Stefan W.","first_name":"Stefan W.","last_name":"Hell"}],"ddc":["570"]},{"citation":{"ista":"Edelsbrunner H, Nikitenko A. 2018. Random inscribed polytopes have similar radius functions as Poisson-Delaunay mosaics. Annals of Applied Probability. 28(5), 3215–3238.","mla":"Edelsbrunner, Herbert, and Anton Nikitenko. “Random Inscribed Polytopes Have Similar Radius Functions as Poisson-Delaunay Mosaics.” <i>Annals of Applied Probability</i>, vol. 28, no. 5, Institute of Mathematical Statistics, 2018, pp. 3215–38, doi:<a href=\"https://doi.org/10.1214/18-AAP1389\">10.1214/18-AAP1389</a>.","chicago":"Edelsbrunner, Herbert, and Anton Nikitenko. “Random Inscribed Polytopes Have Similar Radius Functions as Poisson-Delaunay Mosaics.” <i>Annals of Applied Probability</i>. Institute of Mathematical Statistics, 2018. <a href=\"https://doi.org/10.1214/18-AAP1389\">https://doi.org/10.1214/18-AAP1389</a>.","short":"H. Edelsbrunner, A. Nikitenko, Annals of Applied Probability 28 (2018) 3215–3238.","apa":"Edelsbrunner, H., &#38; Nikitenko, A. (2018). Random inscribed polytopes have similar radius functions as Poisson-Delaunay mosaics. <i>Annals of Applied Probability</i>. Institute of Mathematical Statistics. <a href=\"https://doi.org/10.1214/18-AAP1389\">https://doi.org/10.1214/18-AAP1389</a>","ieee":"H. Edelsbrunner and A. Nikitenko, “Random inscribed polytopes have similar radius functions as Poisson-Delaunay mosaics,” <i>Annals of Applied Probability</i>, vol. 28, no. 5. Institute of Mathematical Statistics, pp. 3215–3238, 2018.","ama":"Edelsbrunner H, Nikitenko A. Random inscribed polytopes have similar radius functions as Poisson-Delaunay mosaics. <i>Annals of Applied Probability</i>. 2018;28(5):3215-3238. doi:<a href=\"https://doi.org/10.1214/18-AAP1389\">10.1214/18-AAP1389</a>"},"article_type":"original","_id":"87","year":"2018","project":[{"name":"Persistence and stability of geometric complexes","_id":"2561EBF4-B435-11E9-9278-68D0E5697425","grant_number":"I02979-N35","call_identifier":"FWF"}],"volume":28,"article_processing_charge":"No","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1705.02870"}],"day":"01","month":"10","oa":1,"oa_version":"Preprint","author":[{"full_name":"Edelsbrunner, Herbert","orcid":"0000-0002-9823-6833","first_name":"Herbert","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","last_name":"Edelsbrunner"},{"first_name":"Anton","orcid":"0000-0002-0659-3201","full_name":"Nikitenko, Anton","last_name":"Nikitenko","id":"3E4FF1BA-F248-11E8-B48F-1D18A9856A87"}],"issue":"5","date_updated":"2023-09-15T12:10:35Z","status":"public","type":"journal_article","related_material":{"record":[{"id":"6287","relation":"dissertation_contains","status":"public"}]},"department":[{"_id":"HeEd"}],"external_id":{"arxiv":["1705.02870"],"isi":["000442893500018"]},"quality_controlled":"1","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","intvolume":"        28","abstract":[{"text":"Using the geodesic distance on the n-dimensional sphere, we study the expected radius function of the Delaunay mosaic of a random set of points. Specifically, we consider the partition of the mosaic into intervals of the radius function and determine the expected number of intervals whose radii are less than or equal to a given threshold. We find that the expectations are essentially the same as for the Poisson–Delaunay mosaic in n-dimensional Euclidean space. Assuming the points are not contained in a hemisphere, the Delaunay mosaic is isomorphic to the boundary complex of the convex hull in Rn+1, so we also get the expected number of faces of a random inscribed polytope. As proved in Antonelli et al. [Adv. in Appl. Probab. 9–12 (1977–1980)], an orthant section of the n-sphere is isometric to the standard n-simplex equipped with the Fisher information metric. It follows that the latter space has similar stochastic properties as the n-dimensional Euclidean space. Our results are therefore relevant in information geometry and in population genetics.","lang":"eng"}],"date_published":"2018-10-01T00:00:00Z","language":[{"iso":"eng"}],"publication":"Annals of Applied Probability","date_created":"2018-12-11T11:44:33Z","publication_status":"published","scopus_import":"1","isi":1,"publist_id":"7967","publisher":"Institute of Mathematical Statistics","arxiv":1,"page":"3215 - 3238","doi":"10.1214/18-AAP1389","title":"Random inscribed polytopes have similar radius functions as Poisson-Delaunay mosaics"},{"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","abstract":[{"lang":"eng","text":"Immune cells migrating to the sites of infection navigate through diverse tissue architectures and switch their migratory mechanisms upon demand. However, little is known about systemic regulators that could allow the acquisition of these mechanisms. We performed a genetic screen in Drosophila melanogaster to identify regulators of germband invasion by embryonic macrophages into the confined space between the ectoderm and mesoderm. We have found that bZIP circadian transcription factors (TFs) Kayak (dFos) and Vrille (dNFIL3) have opposite effects on macrophage germband infiltration: Kayak facilitated and Vrille inhibited it. These TFs are enriched in the macrophages during migration and genetically interact to control it. Kayak sets a less coordinated mode of migration of the macrophage group and increases the probability and length of Levy walks. Intriguingly, the motility of kayak mutant macrophages was also strongly affected during initial germband invasion but not along another less confined route. Inhibiting Rho1 signaling within the tail ectoderm partially rescued the Kayak mutant phenotype, strongly suggesting that migrating macrophages have to overcome a barrier imposed by the stiffness of the ectoderm. Also, Kayak appeared to be important for the maintenance of the round cell shape and the rear edge translocation of the macrophages invading the germband. Complementary to this, the cortical actin cytoskeleton of Kayak- deficient macrophages was strongly affected. RNA sequencing revealed the filamin Cheerio and tetraspanin TM4SF to be downstream of Kayak. Chromatin immunoprecipitation and immunostaining revealed that the formin Diaphanous is another downstream target of Kayak. Immunostaining revealed that the formin Diaphanous is another downstream target of Kayak. Indeed, Cheerio, TM4SF and Diaphanous are required within macrophages for germband invasion, and expression of constitutively active Diaphanous in macrophages was able to rescue the kayak mutant phenotype. Moreover, Cher and Diaphanous are also reduced in the macrophages overexpressing Vrille. We hypothesize that Kayak, through its targets, increases actin polymerization and cortical tension in macrophages and thus allows extra force generation necessary for macrophage dissemination and migration through confined stiff tissues, while Vrille counterbalances it."}],"file":[{"embargo_to":"open_access","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","date_created":"2019-04-08T14:13:12Z","date_updated":"2020-07-14T12:48:14Z","creator":"dernst","access_level":"closed","checksum":"d27b2465cb70d0c9678a0381b9b6ced1","file_size":102737483,"file_id":"6243","relation":"source_file","file_name":"2018_Thesis_Belyaeva_source.docx"},{"creator":"dernst","date_updated":"2021-02-11T11:17:16Z","embargo":"2019-11-19","file_id":"6244","relation":"main_file","file_size":88077843,"file_name":"2018_Thesis_Belyaeva.pdf","access_level":"open_access","checksum":"a2939b61bde2de7b8ced77bbae0eaaed","date_created":"2019-04-08T14:14:08Z","content_type":"application/pdf"}],"date_published":"2018-07-01T00:00:00Z","degree_awarded":"PhD","date_created":"2018-12-11T11:44:08Z","language":[{"iso":"eng"}],"has_accepted_license":"1","publication_status":"published","publist_id":"8047","publisher":"Institute of Science and Technology Austria","pubrep_id":"1064","page":"96","doi":"10.15479/AT:ISTA:th1064","file_date_updated":"2021-02-11T11:17:16Z","supervisor":[{"full_name":"Siekhaus, Daria E","first_name":"Daria E","orcid":"0000-0001-8323-8353","id":"3D224B9E-F248-11E8-B48F-1D18A9856A87","last_name":"Siekhaus"}],"title":"Transcriptional regulation of macrophage migration in the Drosophila melanogaster embryo ","publication_identifier":{"issn":["2663-337X"]},"citation":{"ista":"Belyaeva V. 2018. Transcriptional regulation of macrophage migration in the Drosophila melanogaster embryo . Institute of Science and Technology Austria.","mla":"Belyaeva, Vera. <i>Transcriptional Regulation of Macrophage Migration in the Drosophila Melanogaster Embryo </i>. Institute of Science and Technology Austria, 2018, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:th1064\">10.15479/AT:ISTA:th1064</a>.","apa":"Belyaeva, V. (2018). <i>Transcriptional regulation of macrophage migration in the Drosophila melanogaster embryo </i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:th1064\">https://doi.org/10.15479/AT:ISTA:th1064</a>","chicago":"Belyaeva, Vera. “Transcriptional Regulation of Macrophage Migration in the Drosophila Melanogaster Embryo .” Institute of Science and Technology Austria, 2018. <a href=\"https://doi.org/10.15479/AT:ISTA:th1064\">https://doi.org/10.15479/AT:ISTA:th1064</a>.","short":"V. Belyaeva, Transcriptional Regulation of Macrophage Migration in the Drosophila Melanogaster Embryo , Institute of Science and Technology Austria, 2018.","ama":"Belyaeva V. Transcriptional regulation of macrophage migration in the Drosophila melanogaster embryo . 2018. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:th1064\">10.15479/AT:ISTA:th1064</a>","ieee":"V. Belyaeva, “Transcriptional regulation of macrophage migration in the Drosophila melanogaster embryo ,” Institute of Science and Technology Austria, 2018."},"_id":"9","year":"2018","alternative_title":["ISTA Thesis"],"article_processing_charge":"No","day":"01","oa_version":"Published Version","oa":1,"month":"07","author":[{"last_name":"Belyaeva","id":"47F080FE-F248-11E8-B48F-1D18A9856A87","first_name":"Vera","full_name":"Belyaeva, Vera"}],"ddc":["570"],"status":"public","date_updated":"2023-09-07T12:43:10Z","type":"dissertation","department":[{"_id":"DaSi"}]},{"scopus_import":"1","publication_status":"published","date_created":"2021-02-01T13:44:41Z","publication":"Soft Matter","language":[{"iso":"eng"}],"date_published":"2018-12-21T00:00:00Z","title":"Diffusiophoretic design of self-spinning microgears from colloidal microswimmers","doi":"10.1039/c8sm01760c","page":"9577-9588","arxiv":1,"publisher":"Royal Society of Chemistry ","intvolume":"        14","user_id":"D865714E-FA4E-11E9-B85B-F5C5E5697425","quality_controlled":"1","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"}],"pmid":1,"issue":"47","extern":"1","author":[{"full_name":"Aubret, Antoine","first_name":"Antoine","last_name":"Aubret"},{"full_name":"Palacci, Jérémie A","orcid":"0000-0002-7253-9465","first_name":"Jérémie A","id":"8fb92548-2b22-11eb-b7c1-a3f0d08d7c7d","last_name":"Palacci"}],"oa":1,"month":"12","oa_version":"Preprint","keyword":["General Chemistry","Condensed Matter Physics"],"external_id":{"arxiv":["1909.11121"],"pmid":["30456407"]},"type":"journal_article","date_updated":"2023-02-23T13:47:43Z","status":"public","year":"2018","_id":"9053","article_type":"original","citation":{"mla":"Aubret, Antoine, and Jérémie A. Palacci. “Diffusiophoretic Design of Self-Spinning Microgears from Colloidal Microswimmers.” <i>Soft Matter</i>, vol. 14, no. 47, Royal Society of Chemistry , 2018, pp. 9577–88, doi:<a href=\"https://doi.org/10.1039/c8sm01760c\">10.1039/c8sm01760c</a>.","ista":"Aubret A, Palacci JA. 2018. Diffusiophoretic design of self-spinning microgears from colloidal microswimmers. Soft Matter. 14(47), 9577–9588.","ieee":"A. Aubret and J. A. Palacci, “Diffusiophoretic design of self-spinning microgears from colloidal microswimmers,” <i>Soft Matter</i>, vol. 14, no. 47. Royal Society of Chemistry , pp. 9577–9588, 2018.","ama":"Aubret A, Palacci JA. Diffusiophoretic design of self-spinning microgears from colloidal microswimmers. <i>Soft Matter</i>. 2018;14(47):9577-9588. doi:<a href=\"https://doi.org/10.1039/c8sm01760c\">10.1039/c8sm01760c</a>","apa":"Aubret, A., &#38; Palacci, J. A. (2018). Diffusiophoretic design of self-spinning microgears from colloidal microswimmers. <i>Soft Matter</i>. Royal Society of Chemistry . <a href=\"https://doi.org/10.1039/c8sm01760c\">https://doi.org/10.1039/c8sm01760c</a>","chicago":"Aubret, Antoine, and Jérémie A Palacci. “Diffusiophoretic Design of Self-Spinning Microgears from Colloidal Microswimmers.” <i>Soft Matter</i>. Royal Society of Chemistry , 2018. <a href=\"https://doi.org/10.1039/c8sm01760c\">https://doi.org/10.1039/c8sm01760c</a>.","short":"A. Aubret, J.A. Palacci, Soft Matter 14 (2018) 9577–9588."},"publication_identifier":{"issn":["1744-683X"],"eissn":["1744-6848"]},"day":"21","article_processing_charge":"No","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1909.11121"}],"volume":14},{"oa_version":"Preprint","oa":1,"month":"11","author":[{"last_name":"Aubret","first_name":"Antoine","full_name":"Aubret, Antoine"},{"last_name":"Youssef","full_name":"Youssef, Mena","first_name":"Mena"},{"full_name":"Sacanna, Stefano","first_name":"Stefano","last_name":"Sacanna"},{"last_name":"Palacci","id":"8fb92548-2b22-11eb-b7c1-a3f0d08d7c7d","orcid":"0000-0002-7253-9465","first_name":"Jérémie A","full_name":"Palacci, Jérémie A"}],"extern":"1","issue":"11","status":"public","date_updated":"2023-02-23T13:48:02Z","type":"journal_article","external_id":{"arxiv":["1810.01033"]},"publication_identifier":{"issn":["1745-2473"],"eissn":["1745-2481"]},"citation":{"ista":"Aubret A, Youssef M, Sacanna S, Palacci JA. 2018. Targeted assembly and synchronization of self-spinning microgears. Nature Physics. 14(11), 1114–1118.","mla":"Aubret, Antoine, et al. “Targeted Assembly and Synchronization of Self-Spinning Microgears.” <i>Nature Physics</i>, vol. 14, no. 11, Springer Nature, 2018, pp. 1114–18, doi:<a href=\"https://doi.org/10.1038/s41567-018-0227-4\">10.1038/s41567-018-0227-4</a>.","apa":"Aubret, A., Youssef, M., Sacanna, S., &#38; Palacci, J. A. (2018). Targeted assembly and synchronization of self-spinning microgears. <i>Nature Physics</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41567-018-0227-4\">https://doi.org/10.1038/s41567-018-0227-4</a>","chicago":"Aubret, Antoine, Mena Youssef, Stefano Sacanna, and Jérémie A Palacci. “Targeted Assembly and Synchronization of Self-Spinning Microgears.” <i>Nature Physics</i>. Springer Nature, 2018. <a href=\"https://doi.org/10.1038/s41567-018-0227-4\">https://doi.org/10.1038/s41567-018-0227-4</a>.","short":"A. Aubret, M. Youssef, S. Sacanna, J.A. Palacci, Nature Physics 14 (2018) 1114–1118.","ieee":"A. Aubret, M. Youssef, S. Sacanna, and J. A. Palacci, “Targeted assembly and synchronization of self-spinning microgears,” <i>Nature Physics</i>, vol. 14, no. 11. Springer Nature, pp. 1114–1118, 2018.","ama":"Aubret A, Youssef M, Sacanna S, Palacci JA. Targeted assembly and synchronization of self-spinning microgears. <i>Nature Physics</i>. 2018;14(11):1114-1118. doi:<a href=\"https://doi.org/10.1038/s41567-018-0227-4\">10.1038/s41567-018-0227-4</a>"},"article_type":"original","_id":"9062","year":"2018","volume":14,"article_processing_charge":"No","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1810.01033"}],"day":"01","date_published":"2018-11-01T00:00:00Z","date_created":"2021-02-02T13:52:49Z","language":[{"iso":"eng"}],"publication":"Nature Physics","scopus_import":"1","publication_status":"published","publisher":"Springer Nature","doi":"10.1038/s41567-018-0227-4","arxiv":1,"page":"1114-1118","title":"Targeted assembly and synchronization of self-spinning microgears","quality_controlled":"1","user_id":"D865714E-FA4E-11E9-B85B-F5C5E5697425","intvolume":"        14","abstract":[{"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.","lang":"eng"}]}]