--- _id: '6920' article_processing_charge: No article_type: original author: - first_name: Christina full_name: Artner, Christina id: 45DF286A-F248-11E8-B48F-1D18A9856A87 last_name: Artner - first_name: Eva full_name: Benková, Eva id: 38F4F166-F248-11E8-B48F-1D18A9856A87 last_name: Benková orcid: 0000-0002-8510-9739 citation: ama: Artner C, Benková E. Ethylene and cytokinin - partners in root growth regulation. Molecular Plant. 2019;12(10):1312-1314. doi:10.1016/j.molp.2019.09.003 apa: Artner, C., & Benková, E. (2019). Ethylene and cytokinin - partners in root growth regulation. Molecular Plant. Cell Press. https://doi.org/10.1016/j.molp.2019.09.003 chicago: Artner, Christina, and Eva Benková. “Ethylene and Cytokinin - Partners in Root Growth Regulation.” Molecular Plant. Cell Press, 2019. https://doi.org/10.1016/j.molp.2019.09.003. ieee: C. Artner and E. Benková, “Ethylene and cytokinin - partners in root growth regulation,” Molecular Plant, vol. 12, no. 10. Cell Press, pp. 1312–1314, 2019. ista: Artner C, Benková E. 2019. Ethylene and cytokinin - partners in root growth regulation. Molecular Plant. 12(10), 1312–1314. mla: Artner, Christina, and Eva Benková. “Ethylene and Cytokinin - Partners in Root Growth Regulation.” Molecular Plant, vol. 12, no. 10, Cell Press, 2019, pp. 1312–14, doi:10.1016/j.molp.2019.09.003. short: C. Artner, E. Benková, Molecular Plant 12 (2019) 1312–1314. date_created: 2019-09-30T10:00:40Z date_published: 2019-10-07T00:00:00Z date_updated: 2023-08-30T06:55:02Z day: '07' department: - _id: EvBe doi: 10.1016/j.molp.2019.09.003 external_id: isi: - '000489132500002' pmid: - '31541740' intvolume: ' 12' isi: 1 issue: '10' language: - iso: eng month: '10' oa_version: None page: 1312-1314 pmid: 1 project: - _id: 2685A872-B435-11E9-9278-68D0E5697425 name: Hormonal regulation of plant adaptive responses to environmental signals publication: Molecular Plant publication_identifier: issn: - 1674-2052 - 1752-9867 publication_status: published publisher: Cell Press quality_controlled: '1' scopus_import: '1' status: public title: Ethylene and cytokinin - partners in root growth regulation type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 12 year: '2019' ... --- _id: '9898' abstract: - lang: eng text: All polyN tracts of length 5 or more nucleotides in sequences of genes from OG1. Sequences were extracted and scanned prior to automatic correction for frameshifts implemented in the RAST pipeline. (CSV 133 kb) article_processing_charge: No author: - first_name: Olga M. full_name: Sigalova, Olga M. last_name: Sigalova - first_name: Andrei V. full_name: Chaplin, Andrei V. last_name: Chaplin - first_name: Olga full_name: Bochkareva, Olga id: C4558D3C-6102-11E9-A62E-F418E6697425 last_name: Bochkareva orcid: 0000-0003-1006-6639 - first_name: Pavel V. full_name: Shelyakin, Pavel V. last_name: Shelyakin - first_name: Vsevolod A. full_name: Filaretov, Vsevolod A. last_name: Filaretov - first_name: Evgeny E. full_name: Akkuratov, Evgeny E. last_name: Akkuratov - first_name: Valentina full_name: Burskaia, Valentina last_name: Burskaia - first_name: Mikhail S. full_name: Gelfand, Mikhail S. last_name: Gelfand citation: ama: Sigalova OM, Chaplin AV, Bochkareva O, et al. Additional file 21 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction. 2019. doi:10.6084/m9.figshare.9808859.v1 apa: Sigalova, O. M., Chaplin, A. V., Bochkareva, O., Shelyakin, P. V., Filaretov, V. A., Akkuratov, E. E., … Gelfand, M. S. (2019). Additional file 21 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction. Springer Nature. https://doi.org/10.6084/m9.figshare.9808859.v1 chicago: Sigalova, Olga M., Andrei V. Chaplin, Olga Bochkareva, Pavel V. Shelyakin, Vsevolod A. Filaretov, Evgeny E. Akkuratov, Valentina Burskaia, and Mikhail S. Gelfand. “Additional File 21 of Chlamydia Pan-Genomic Analysis Reveals Balance between Host Adaptation and Selective Pressure to Genome Reduction.” Springer Nature, 2019. https://doi.org/10.6084/m9.figshare.9808859.v1. ieee: O. M. Sigalova et al., “Additional file 21 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction.” Springer Nature, 2019. ista: Sigalova OM, Chaplin AV, Bochkareva O, Shelyakin PV, Filaretov VA, Akkuratov EE, Burskaia V, Gelfand MS. 2019. Additional file 21 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction, Springer Nature, 10.6084/m9.figshare.9808859.v1. mla: Sigalova, Olga M., et al. Additional File 21 of Chlamydia Pan-Genomic Analysis Reveals Balance between Host Adaptation and Selective Pressure to Genome Reduction. Springer Nature, 2019, doi:10.6084/m9.figshare.9808859.v1. short: O.M. Sigalova, A.V. Chaplin, O. Bochkareva, P.V. Shelyakin, V.A. Filaretov, E.E. Akkuratov, V. Burskaia, M.S. Gelfand, (2019). date_created: 2021-08-12T08:10:23Z date_published: 2019-09-12T00:00:00Z date_updated: 2023-08-30T06:20:22Z day: '12' department: - _id: FyKo doi: 10.6084/m9.figshare.9808859.v1 main_file_link: - open_access: '1' url: https://doi.org/10.6084/m9.figshare.9808859.v1 month: '09' oa: 1 oa_version: Published Version publisher: Springer Nature related_material: record: - id: '6898' relation: used_in_publication status: public status: public title: Additional file 21 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction type: research_data_reference user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf year: '2019' ... --- _id: '9901' abstract: - lang: eng text: Clusters of Orthologous Genes (COGs) and corresponding functional categories assigned to OGs. (CSV 117 kb) article_processing_charge: No author: - first_name: Olga M. full_name: Sigalova, Olga M. last_name: Sigalova - first_name: Andrei V. full_name: Chaplin, Andrei V. last_name: Chaplin - first_name: Olga full_name: Bochkareva, Olga id: C4558D3C-6102-11E9-A62E-F418E6697425 last_name: Bochkareva orcid: 0000-0003-1006-6639 - first_name: Pavel V. full_name: Shelyakin, Pavel V. last_name: Shelyakin - first_name: Vsevolod A. full_name: Filaretov, Vsevolod A. last_name: Filaretov - first_name: Evgeny E. full_name: Akkuratov, Evgeny E. last_name: Akkuratov - first_name: Valentina full_name: Burskaia, Valentina last_name: Burskaia - first_name: Mikhail S. full_name: Gelfand, Mikhail S. last_name: Gelfand citation: ama: Sigalova OM, Chaplin AV, Bochkareva O, et al. Additional file 9 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction. 2019. doi:10.6084/m9.figshare.9808907.v1 apa: Sigalova, O. M., Chaplin, A. V., Bochkareva, O., Shelyakin, P. V., Filaretov, V. A., Akkuratov, E. E., … Gelfand, M. S. (2019). Additional file 9 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction. Springer Nature. https://doi.org/10.6084/m9.figshare.9808907.v1 chicago: Sigalova, Olga M., Andrei V. Chaplin, Olga Bochkareva, Pavel V. Shelyakin, Vsevolod A. Filaretov, Evgeny E. Akkuratov, Valentina Burskaia, and Mikhail S. Gelfand. “Additional File 9 of Chlamydia Pan-Genomic Analysis Reveals Balance between Host Adaptation and Selective Pressure to Genome Reduction.” Springer Nature, 2019. https://doi.org/10.6084/m9.figshare.9808907.v1. ieee: O. M. Sigalova et al., “Additional file 9 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction.” Springer Nature, 2019. ista: Sigalova OM, Chaplin AV, Bochkareva O, Shelyakin PV, Filaretov VA, Akkuratov EE, Burskaia V, Gelfand MS. 2019. Additional file 9 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction, Springer Nature, 10.6084/m9.figshare.9808907.v1. mla: Sigalova, Olga M., et al. Additional File 9 of Chlamydia Pan-Genomic Analysis Reveals Balance between Host Adaptation and Selective Pressure to Genome Reduction. Springer Nature, 2019, doi:10.6084/m9.figshare.9808907.v1. short: O.M. Sigalova, A.V. Chaplin, O. Bochkareva, P.V. Shelyakin, V.A. Filaretov, E.E. Akkuratov, V. Burskaia, M.S. Gelfand, (2019). date_created: 2021-08-12T10:54:03Z date_published: 2019-09-12T00:00:00Z date_updated: 2023-08-30T06:20:22Z day: '12' department: - _id: FyKo doi: 10.6084/m9.figshare.9808907.v1 main_file_link: - open_access: '1' url: https://doi.org/10.6084/m9.figshare.9808907.v1 month: '09' oa: 1 oa_version: Published Version publisher: Springer Nature related_material: record: - id: '6898' relation: used_in_publication status: public status: public title: Additional file 9 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction type: research_data_reference user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf year: '2019' ... --- _id: '9899' abstract: - lang: eng text: Summary of orthologous groups (OGs) for 227 genomes of genus Chlamydia. (CSV 362 kb) article_processing_charge: No author: - first_name: Olga M. full_name: Sigalova, Olga M. last_name: Sigalova - first_name: Andrei V. full_name: Chaplin, Andrei V. last_name: Chaplin - first_name: Olga full_name: Bochkareva, Olga id: C4558D3C-6102-11E9-A62E-F418E6697425 last_name: Bochkareva orcid: 0000-0003-1006-6639 - first_name: Pavel V. full_name: Shelyakin, Pavel V. last_name: Shelyakin - first_name: Vsevolod A. full_name: Filaretov, Vsevolod A. last_name: Filaretov - first_name: Evgeny E. full_name: Akkuratov, Evgeny E. last_name: Akkuratov - first_name: Valentina full_name: Burskaia, Valentina last_name: Burskaia - first_name: Mikhail S. full_name: Gelfand, Mikhail S. last_name: Gelfand citation: ama: Sigalova OM, Chaplin AV, Bochkareva O, et al. Additional file 2 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction. 2019. doi:10.6084/m9.figshare.9808865.v1 apa: Sigalova, O. M., Chaplin, A. V., Bochkareva, O., Shelyakin, P. V., Filaretov, V. A., Akkuratov, E. E., … Gelfand, M. S. (2019). Additional file 2 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction. Springer Nature. https://doi.org/10.6084/m9.figshare.9808865.v1 chicago: Sigalova, Olga M., Andrei V. Chaplin, Olga Bochkareva, Pavel V. Shelyakin, Vsevolod A. Filaretov, Evgeny E. Akkuratov, Valentina Burskaia, and Mikhail S. Gelfand. “Additional File 2 of Chlamydia Pan-Genomic Analysis Reveals Balance between Host Adaptation and Selective Pressure to Genome Reduction.” Springer Nature, 2019. https://doi.org/10.6084/m9.figshare.9808865.v1. ieee: O. M. Sigalova et al., “Additional file 2 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction.” Springer Nature, 2019. ista: Sigalova OM, Chaplin AV, Bochkareva O, Shelyakin PV, Filaretov VA, Akkuratov EE, Burskaia V, Gelfand MS. 2019. Additional file 2 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction, Springer Nature, 10.6084/m9.figshare.9808865.v1. mla: Sigalova, Olga M., et al. Additional File 2 of Chlamydia Pan-Genomic Analysis Reveals Balance between Host Adaptation and Selective Pressure to Genome Reduction. Springer Nature, 2019, doi:10.6084/m9.figshare.9808865.v1. short: O.M. Sigalova, A.V. Chaplin, O. Bochkareva, P.V. Shelyakin, V.A. Filaretov, E.E. Akkuratov, V. Burskaia, M.S. Gelfand, (2019). date_created: 2021-08-12T08:18:09Z date_published: 2019-09-12T00:00:00Z date_updated: 2023-08-30T06:20:22Z day: '12' department: - _id: FyKo doi: 10.6084/m9.figshare.9808865.v1 main_file_link: - open_access: '1' url: https://doi.org/10.6084/m9.figshare.9808865.v1 month: '09' oa: 1 oa_version: Published Version publisher: Springer Nature related_material: record: - id: '6898' relation: used_in_publication status: public status: public title: Additional file 2 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction type: research_data_reference user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf year: '2019' ... --- _id: '9900' abstract: - lang: eng text: Pan-genome statistics by species. (CSV 3 kb) article_processing_charge: No author: - first_name: Olga M. full_name: Sigalova, Olga M. last_name: Sigalova - first_name: Andrei V. full_name: Chaplin, Andrei V. last_name: Chaplin - first_name: Olga full_name: Bochkareva, Olga id: C4558D3C-6102-11E9-A62E-F418E6697425 last_name: Bochkareva orcid: 0000-0003-1006-6639 - first_name: Pavel V. full_name: Shelyakin, Pavel V. last_name: Shelyakin - first_name: Vsevolod A. full_name: Filaretov, Vsevolod A. last_name: Filaretov - first_name: Evgeny E. full_name: Akkuratov, Evgeny E. last_name: Akkuratov - first_name: Valentina full_name: Burskaia, Valentina last_name: Burskaia - first_name: Mikhail S. full_name: Gelfand, Mikhail S. last_name: Gelfand citation: ama: Sigalova OM, Chaplin AV, Bochkareva O, et al. Additional file 5 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction. 2019. doi:10.6084/m9.figshare.9808886.v1 apa: Sigalova, O. M., Chaplin, A. V., Bochkareva, O., Shelyakin, P. V., Filaretov, V. A., Akkuratov, E. E., … Gelfand, M. S. (2019). Additional file 5 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction. Springer Nature. https://doi.org/10.6084/m9.figshare.9808886.v1 chicago: Sigalova, Olga M., Andrei V. Chaplin, Olga Bochkareva, Pavel V. Shelyakin, Vsevolod A. Filaretov, Evgeny E. Akkuratov, Valentina Burskaia, and Mikhail S. Gelfand. “Additional File 5 of Chlamydia Pan-Genomic Analysis Reveals Balance between Host Adaptation and Selective Pressure to Genome Reduction.” Springer Nature, 2019. https://doi.org/10.6084/m9.figshare.9808886.v1. ieee: O. M. Sigalova et al., “Additional file 5 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction.” Springer Nature, 2019. ista: Sigalova OM, Chaplin AV, Bochkareva O, Shelyakin PV, Filaretov VA, Akkuratov EE, Burskaia V, Gelfand MS. 2019. Additional file 5 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction, Springer Nature, 10.6084/m9.figshare.9808886.v1. mla: Sigalova, Olga M., et al. Additional File 5 of Chlamydia Pan-Genomic Analysis Reveals Balance between Host Adaptation and Selective Pressure to Genome Reduction. Springer Nature, 2019, doi:10.6084/m9.figshare.9808886.v1. short: O.M. Sigalova, A.V. Chaplin, O. Bochkareva, P.V. Shelyakin, V.A. Filaretov, E.E. Akkuratov, V. Burskaia, M.S. Gelfand, (2019). date_created: 2021-08-12T08:44:49Z date_published: 2019-09-12T00:00:00Z date_updated: 2023-08-30T06:20:22Z day: '12' department: - _id: FyKo doi: 10.6084/m9.figshare.9808886.v1 main_file_link: - open_access: '1' url: https://doi.org/10.6084/m9.figshare.9808886.v1 month: '09' oa: 1 oa_version: Published Version publisher: Springer Nature related_material: record: - id: '6898' relation: used_in_publication status: public status: public title: Additional file 5 of Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction type: research_data_reference user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf year: '2019' ... --- _id: '6936' abstract: - lang: eng text: "A key challenge for community ecology is to understand to what extent observational data can be used to infer the underlying community assembly processes. As different processes can lead to similar or even identical patterns, statistical analyses of non‐manipulative observational data never yield undisputable causal inference on the underlying processes. Still, most empirical studies in community ecology are based on observational data, and hence understanding under which circumstances such data can shed light on assembly processes is a central concern for community ecologists. We simulated a spatial agent‐based model that generates variation in metacommunity dynamics across multiple axes, including the four classic metacommunity paradigms as special cases. We further simulated a virtual ecologist who analysed snapshot data sampled from the simulations using eighteen output metrics derived from beta‐diversity and habitat variation indices, variation partitioning and joint species distribution modelling. Our results indicated two main axes of variation in the output metrics. The first axis of variation described whether the landscape has patchy or continuous variation, and thus was essentially independent of the properties of the species community. The second axis of variation related to the level of predictability of the metacommunity. The most predictable communities were niche‐based metacommunities inhabiting static landscapes with marked environmental heterogeneity, such as metacommunities following the species sorting paradigm or the mass effects paradigm. The most unpredictable communities were neutral‐based metacommunities inhabiting dynamics landscapes with little spatial heterogeneity, such as metacommunities following the neutral or patch sorting paradigms. The output metrics from joint species distribution modelling yielded generally the highest resolution to disentangle among the simulated scenarios. Yet, the different types of statistical approaches utilized in this study carried complementary information, and thus our results suggest that the most comprehensive evaluation of metacommunity structure can be obtained by combining them.\r\n" article_processing_charge: No article_type: original author: - first_name: Otso full_name: Ovaskainen, Otso last_name: Ovaskainen - first_name: Joel full_name: Rybicki, Joel id: 334EFD2E-F248-11E8-B48F-1D18A9856A87 last_name: Rybicki orcid: 0000-0002-6432-6646 - first_name: Nerea full_name: Abrego, Nerea last_name: Abrego citation: ama: Ovaskainen O, Rybicki J, Abrego N. What can observational data reveal about metacommunity processes? Ecography. 2019;42(11):1877-1886. doi:10.1111/ecog.04444 apa: Ovaskainen, O., Rybicki, J., & Abrego, N. (2019). What can observational data reveal about metacommunity processes? Ecography. Wiley. https://doi.org/10.1111/ecog.04444 chicago: Ovaskainen, Otso, Joel Rybicki, and Nerea Abrego. “What Can Observational Data Reveal about Metacommunity Processes?” Ecography. Wiley, 2019. https://doi.org/10.1111/ecog.04444. ieee: O. Ovaskainen, J. Rybicki, and N. Abrego, “What can observational data reveal about metacommunity processes?,” Ecography, vol. 42, no. 11. Wiley, pp. 1877–1886, 2019. ista: Ovaskainen O, Rybicki J, Abrego N. 2019. What can observational data reveal about metacommunity processes? Ecography. 42(11), 1877–1886. mla: Ovaskainen, Otso, et al. “What Can Observational Data Reveal about Metacommunity Processes?” Ecography, vol. 42, no. 11, Wiley, 2019, pp. 1877–86, doi:10.1111/ecog.04444. short: O. Ovaskainen, J. Rybicki, N. Abrego, Ecography 42 (2019) 1877–1886. date_created: 2019-10-08T13:01:24Z date_published: 2019-11-01T00:00:00Z date_updated: 2023-08-30T06:57:25Z day: '01' ddc: - '577' department: - _id: DaAl doi: 10.1111/ecog.04444 ec_funded: 1 external_id: isi: - '000486348700001' file: - access_level: open_access checksum: 6c9fbbd5ea8ce10ae93e55ad560a7bf9 content_type: application/pdf creator: jrybicki date_created: 2019-10-08T13:07:44Z date_updated: 2020-07-14T12:47:45Z file_id: '6937' file_name: ecog.04444.pdf file_size: 1682718 relation: main_file file_date_updated: 2020-07-14T12:47:45Z has_accepted_license: '1' intvolume: ' 42' isi: 1 issue: '11' language: - iso: eng month: '11' oa: 1 oa_version: Published Version page: 1877-1886 project: - _id: 260C2330-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '754411' name: ISTplus - Postdoctoral Fellowships publication: Ecography publication_identifier: eissn: - 1600-0587 issn: - 0906-7590 publication_status: published publisher: Wiley quality_controlled: '1' scopus_import: '1' status: public title: What can observational data reveal about metacommunity processes? tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 42 year: '2019' ... --- _id: '6857' abstract: - lang: eng text: "Gene Drives are regarded as future tools with a high potential for population control. Due to their inherent ability to overcome the rules of Mendelian inheritance, gene drives (GD) may spread genes rapidly through populations of sexually reproducing organisms. A release of organisms carrying a GD would constitute a paradigm shift in the handling of genetically modified organisms because gene drive organisms (GDO) are designed to drive their transgenes into wild populations and thereby increase the number of GDOs. The rapid development in this field and its focus on wild populations demand a prospective risk assessment with a focus on exposure related aspects. Presently, it is unclear how adequate risk management could be guaranteed to limit the spread of GDs in time and space, in order to avoid potential adverse effects in socio‐ecological systems.\r\n\r\nThe recent workshop on the “Evaluation of Spatial and Temporal Control of Gene Drives” hosted by the Institute of Safety/Security and Risk Sciences (ISR) in Vienna aimed at gaining some insight into the potential population dynamic behavior of GDs and appropriate measures of control. Scientists from France, Germany, England, and the USA discussed both topics in this meeting on April 4–5, 2019. This article summarizes results of the workshop." article_number: '1900151' article_processing_charge: No article_type: original author: - first_name: B full_name: Giese, B last_name: Giese - first_name: J L full_name: Friess, J L last_name: Friess - first_name: 'M F ' full_name: 'Schetelig, M F ' last_name: Schetelig - first_name: Nicholas H full_name: Barton, Nicholas H id: 4880FE40-F248-11E8-B48F-1D18A9856A87 last_name: Barton orcid: 0000-0002-8548-5240 - first_name: Philip full_name: Messer, Philip last_name: Messer - first_name: Florence full_name: Debarre, Florence last_name: Debarre - first_name: H full_name: Meimberg, H last_name: Meimberg - first_name: N full_name: Windbichler, N last_name: Windbichler - first_name: C full_name: Boete, C last_name: Boete citation: ama: 'Giese B, Friess JL, Schetelig MF, et al. Gene Drives: Dynamics and regulatory matters – A report from the workshop “Evaluation of spatial and temporal control of Gene Drives”, 4 – 5 April 2019, Vienna. BioEssays. 2019;41(11). doi:10.1002/bies.201900151' apa: 'Giese, B., Friess, J. L., Schetelig, M. F., Barton, N. H., Messer, P., Debarre, F., … Boete, C. (2019). Gene Drives: Dynamics and regulatory matters – A report from the workshop “Evaluation of spatial and temporal control of Gene Drives”, 4 – 5 April 2019, Vienna. BioEssays. Wiley. https://doi.org/10.1002/bies.201900151' chicago: 'Giese, B, J L Friess, M F Schetelig, Nicholas H Barton, Philip Messer, Florence Debarre, H Meimberg, N Windbichler, and C Boete. “Gene Drives: Dynamics and Regulatory Matters – A Report from the Workshop ‘Evaluation of Spatial and Temporal Control of Gene Drives’, 4 – 5 April 2019, Vienna.” BioEssays. Wiley, 2019. https://doi.org/10.1002/bies.201900151.' ieee: 'B. Giese et al., “Gene Drives: Dynamics and regulatory matters – A report from the workshop ‘Evaluation of spatial and temporal control of Gene Drives’, 4 – 5 April 2019, Vienna,” BioEssays, vol. 41, no. 11. Wiley, 2019.' ista: 'Giese B, Friess JL, Schetelig MF, Barton NH, Messer P, Debarre F, Meimberg H, Windbichler N, Boete C. 2019. Gene Drives: Dynamics and regulatory matters – A report from the workshop “Evaluation of spatial and temporal control of Gene Drives”, 4 – 5 April 2019, Vienna. BioEssays. 41(11), 1900151.' mla: 'Giese, B., et al. “Gene Drives: Dynamics and Regulatory Matters – A Report from the Workshop ‘Evaluation of Spatial and Temporal Control of Gene Drives’, 4 – 5 April 2019, Vienna.” BioEssays, vol. 41, no. 11, 1900151, Wiley, 2019, doi:10.1002/bies.201900151.' short: B. Giese, J.L. Friess, M.F. Schetelig, N.H. Barton, P. Messer, F. Debarre, H. Meimberg, N. Windbichler, C. Boete, BioEssays 41 (2019). date_created: 2019-09-07T14:40:03Z date_published: 2019-11-01T00:00:00Z date_updated: 2023-08-30T06:56:26Z day: '01' ddc: - '570' department: - _id: NiBa doi: 10.1002/bies.201900151 external_id: isi: - '000489502000001' file: - access_level: open_access checksum: 8cc7551bff70b2658f8d5630f228ee12 content_type: application/pdf creator: dernst date_created: 2019-10-11T06:59:26Z date_updated: 2020-07-14T12:47:42Z file_id: '6939' file_name: 2019_BioEssays_Giese.pdf file_size: 193248 relation: main_file file_date_updated: 2020-07-14T12:47:42Z has_accepted_license: '1' intvolume: ' 41' isi: 1 issue: '11' language: - iso: eng month: '11' oa: 1 oa_version: Published Version publication: BioEssays publication_identifier: eissn: - 1521-1878 publication_status: published publisher: Wiley quality_controlled: '1' scopus_import: '1' status: public title: 'Gene Drives: Dynamics and regulatory matters – A report from the workshop “Evaluation of spatial and temporal control of Gene Drives”, 4 – 5 April 2019, Vienna' tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 41 year: '2019' ... --- _id: '6890' abstract: - lang: eng text: Describing the protein interactions that form pleomorphic and asymmetric viruses represents a considerable challenge to most structural biology techniques, including X-ray crystallography and single particle cryo-electron microscopy. Obtaining a detailed understanding of these interactions is nevertheless important, considering the number of relevant human pathogens that do not follow strict icosahedral or helical symmetry. Cryo-electron tomography and subtomogram averaging methods provide structural insights into complex biological environments and are well suited to go beyond structures of perfectly symmetric viruses. This chapter discusses recent developments showing that cryo-ET and subtomogram averaging can provide high-resolution insights into hitherto unknown structural features of pleomorphic and asymmetric virus particles. It also describes how these methods have significantly added to our understanding of retrovirus capsid assemblies in immature and mature viruses. Additional examples of irregular viruses and their associated proteins, whose structures have been studied via cryo-ET and subtomogram averaging, further support the versatility of these methods. article_processing_charge: No author: - first_name: Martin full_name: Obr, Martin id: 4741CA5A-F248-11E8-B48F-1D18A9856A87 last_name: Obr orcid: 0000-0003-1756-6564 - first_name: Florian KM full_name: Schur, Florian KM id: 48AD8942-F248-11E8-B48F-1D18A9856A87 last_name: Schur orcid: 0000-0003-4790-8078 citation: ama: 'Obr M, Schur FK. Structural analysis of pleomorphic and asymmetric viruses using cryo-electron tomography and subtomogram averaging. In: Rey FA, ed. Complementary Strategies to Study Virus Structure and Function. Vol 105. Advances in Virus Research. Elsevier; 2019:117-159. doi:10.1016/bs.aivir.2019.07.008' apa: Obr, M., & Schur, F. K. (2019). Structural analysis of pleomorphic and asymmetric viruses using cryo-electron tomography and subtomogram averaging. In F. A. Rey (Ed.), Complementary Strategies to Study Virus Structure and Function (Vol. 105, pp. 117–159). Elsevier. https://doi.org/10.1016/bs.aivir.2019.07.008 chicago: Obr, Martin, and Florian KM Schur. “Structural Analysis of Pleomorphic and Asymmetric Viruses Using Cryo-Electron Tomography and Subtomogram Averaging.” In Complementary Strategies to Study Virus Structure and Function, edited by Félix A. Rey, 105:117–59. Advances in Virus Research. Elsevier, 2019. https://doi.org/10.1016/bs.aivir.2019.07.008. ieee: M. Obr and F. K. Schur, “Structural analysis of pleomorphic and asymmetric viruses using cryo-electron tomography and subtomogram averaging,” in Complementary Strategies to Study Virus Structure and Function, vol. 105, F. A. Rey, Ed. Elsevier, 2019, pp. 117–159. ista: 'Obr M, Schur FK. 2019.Structural analysis of pleomorphic and asymmetric viruses using cryo-electron tomography and subtomogram averaging. In: Complementary Strategies to Study Virus Structure and Function. vol. 105, 117–159.' mla: Obr, Martin, and Florian KM Schur. “Structural Analysis of Pleomorphic and Asymmetric Viruses Using Cryo-Electron Tomography and Subtomogram Averaging.” Complementary Strategies to Study Virus Structure and Function, edited by Félix A. Rey, vol. 105, Elsevier, 2019, pp. 117–59, doi:10.1016/bs.aivir.2019.07.008. short: M. Obr, F.K. Schur, in:, F.A. Rey (Ed.), Complementary Strategies to Study Virus Structure and Function, Elsevier, 2019, pp. 117–159. date_created: 2019-09-18T08:15:37Z date_published: 2019-08-27T00:00:00Z date_updated: 2023-08-30T06:56:00Z day: '27' department: - _id: FlSc doi: 10.1016/bs.aivir.2019.07.008 editor: - first_name: Félix A. full_name: Rey, Félix A. last_name: Rey external_id: isi: - '000501594500006' pmid: - ' 31522703' intvolume: ' 105' isi: 1 language: - iso: eng month: '08' oa_version: None page: 117-159 pmid: 1 publication: Complementary Strategies to Study Virus Structure and Function publication_identifier: isbn: - '9780128184561' issn: - 0065-3527 publication_status: published publisher: Elsevier quality_controlled: '1' scopus_import: '1' series_title: Advances in Virus Research status: public title: Structural analysis of pleomorphic and asymmetric viruses using cryo-electron tomography and subtomogram averaging type: book_chapter user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 105 year: '2019' ... --- _id: '6940' abstract: - lang: eng text: "We study the effect of a linear tunneling coupling between two-dimensional systems, each separately\r\nexhibiting the topological Berezinskii-Kosterlitz-Thouless (BKT) transition. In the uncoupled limit, there\r\nare two phases: one where the one-body correlation functions are algebraically decaying and the other with\r\nexponential decay. When the linear coupling is turned on, a third BKT-paired phase emerges, in which one-body correlations are exponentially decaying, while two-body correlation functions exhibit power-law\r\ndecay. We perform numerical simulations in the paradigmatic case of two coupled XY models at finite\r\ntemperature, finding evidences that for any finite value of the interlayer coupling, the BKT-paired phase is\r\npresent. We provide a picture of the phase diagram using a renormalization group approach." acknowledgement: "We thank S. Chiacchiera, G. Delfino, N. Dupuis, T. Enss, M. Fabrizio and G. Gori for many stimulating discussions.\r\nG.B. acknowledges support from the Austrian Science Fund (FWF), under project No. M2461-N27. N.D. acknowledges\r\nsupport from Deutsche Forschungsgemeinschaft (DFG) under Germany’s Excellence Strategy EXC-2181/1 - 390900948 (the Heidelberg STRUCTURES Excellence Cluster) and from the DFG Collaborative Research Centre “SFB 1225 ISOQUANT”. Support from the CNR/MTA Italy-Hungary 2019-2021 Joint Project “Strongly interacting systems in confined geometries” is gratefully acknowledged." article_number: '100601' article_processing_charge: No article_type: original author: - first_name: Giacomo full_name: Bighin, Giacomo id: 4CA96FD4-F248-11E8-B48F-1D18A9856A87 last_name: Bighin orcid: 0000-0001-8823-9777 - first_name: Nicolò full_name: Defenu, Nicolò last_name: Defenu - first_name: István full_name: Nándori, István last_name: Nándori - first_name: Luca full_name: Salasnich, Luca last_name: Salasnich - first_name: Andrea full_name: Trombettoni, Andrea last_name: Trombettoni citation: ama: Bighin G, Defenu N, Nándori I, Salasnich L, Trombettoni A. Berezinskii-Kosterlitz-Thouless paired phase in coupled XY models. Physical Review Letters. 2019;123(10). doi:10.1103/physrevlett.123.100601 apa: Bighin, G., Defenu, N., Nándori, I., Salasnich, L., & Trombettoni, A. (2019). Berezinskii-Kosterlitz-Thouless paired phase in coupled XY models. Physical Review Letters. American Physical Society. https://doi.org/10.1103/physrevlett.123.100601 chicago: Bighin, Giacomo, Nicolò Defenu, István Nándori, Luca Salasnich, and Andrea Trombettoni. “Berezinskii-Kosterlitz-Thouless Paired Phase in Coupled XY Models.” Physical Review Letters. American Physical Society, 2019. https://doi.org/10.1103/physrevlett.123.100601. ieee: G. Bighin, N. Defenu, I. Nándori, L. Salasnich, and A. Trombettoni, “Berezinskii-Kosterlitz-Thouless paired phase in coupled XY models,” Physical Review Letters, vol. 123, no. 10. American Physical Society, 2019. ista: Bighin G, Defenu N, Nándori I, Salasnich L, Trombettoni A. 2019. Berezinskii-Kosterlitz-Thouless paired phase in coupled XY models. Physical Review Letters. 123(10), 100601. mla: Bighin, Giacomo, et al. “Berezinskii-Kosterlitz-Thouless Paired Phase in Coupled XY Models.” Physical Review Letters, vol. 123, no. 10, 100601, American Physical Society, 2019, doi:10.1103/physrevlett.123.100601. short: G. Bighin, N. Defenu, I. Nándori, L. Salasnich, A. Trombettoni, Physical Review Letters 123 (2019). date_created: 2019-10-14T06:31:13Z date_published: 2019-09-06T00:00:00Z date_updated: 2023-08-30T06:57:53Z day: '06' department: - _id: MiLe doi: 10.1103/physrevlett.123.100601 external_id: arxiv: - '1907.06253' isi: - '000483587200004' intvolume: ' 123' isi: 1 issue: '10' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1907.06253 month: '09' oa: 1 oa_version: Preprint project: - _id: 26986C82-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: M02641 name: A path-integral approach to composite impurities publication: Physical Review Letters publication_identifier: eissn: - 1079-7114 issn: - 0031-9007 publication_status: published publisher: American Physical Society quality_controlled: '1' related_material: link: - description: News auf IST Website relation: press_release url: https://ist.ac.at/en/news/new-form-of-magnetism-found/ scopus_import: '1' status: public title: Berezinskii-Kosterlitz-Thouless paired phase in coupled XY models type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 123 year: '2019' ... --- _id: '6919' article_number: eaaw6490 article_processing_charge: No author: - first_name: Chao full_name: Qi, Chao last_name: Qi - first_name: Giulio Di full_name: Minin, Giulio Di last_name: Minin - first_name: Irene full_name: Vercellino, Irene id: 3ED6AF16-F248-11E8-B48F-1D18A9856A87 last_name: Vercellino orcid: 0000-0001-5618-3449 - first_name: Anton full_name: Wutz, Anton last_name: Wutz - first_name: Volodymyr M. full_name: Korkhov, Volodymyr M. last_name: Korkhov citation: ama: Qi C, Minin GD, Vercellino I, Wutz A, Korkhov VM. Structural basis of sterol recognition by human hedgehog receptor PTCH1. Science Advances. 2019;5(9). doi:10.1126/sciadv.aaw6490 apa: Qi, C., Minin, G. D., Vercellino, I., Wutz, A., & Korkhov, V. M. (2019). Structural basis of sterol recognition by human hedgehog receptor PTCH1. Science Advances. American Association for the Advancement of Science. https://doi.org/10.1126/sciadv.aaw6490 chicago: Qi, Chao, Giulio Di Minin, Irene Vercellino, Anton Wutz, and Volodymyr M. Korkhov. “Structural Basis of Sterol Recognition by Human Hedgehog Receptor PTCH1.” Science Advances. American Association for the Advancement of Science, 2019. https://doi.org/10.1126/sciadv.aaw6490. ieee: C. Qi, G. D. Minin, I. Vercellino, A. Wutz, and V. M. Korkhov, “Structural basis of sterol recognition by human hedgehog receptor PTCH1,” Science Advances, vol. 5, no. 9. American Association for the Advancement of Science, 2019. ista: Qi C, Minin GD, Vercellino I, Wutz A, Korkhov VM. 2019. Structural basis of sterol recognition by human hedgehog receptor PTCH1. Science Advances. 5(9), eaaw6490. mla: Qi, Chao, et al. “Structural Basis of Sterol Recognition by Human Hedgehog Receptor PTCH1.” Science Advances, vol. 5, no. 9, eaaw6490, American Association for the Advancement of Science, 2019, doi:10.1126/sciadv.aaw6490. short: C. Qi, G.D. Minin, I. Vercellino, A. Wutz, V.M. Korkhov, Science Advances 5 (2019). date_created: 2019-09-29T22:00:45Z date_published: 2019-09-18T00:00:00Z date_updated: 2023-08-30T06:55:31Z day: '18' ddc: - '570' department: - _id: LeSa doi: 10.1126/sciadv.aaw6490 external_id: isi: - '000491128800062' file: - access_level: open_access checksum: b2256c9117655bc15f621ba0babf219f content_type: application/pdf creator: kschuh date_created: 2019-10-02T11:13:54Z date_updated: 2020-07-14T12:47:44Z file_id: '6928' file_name: 2019_AAAS_Qi.pdf file_size: 1236101 relation: main_file file_date_updated: 2020-07-14T12:47:44Z has_accepted_license: '1' intvolume: ' 5' isi: 1 issue: '9' language: - iso: eng license: https://creativecommons.org/licenses/by-nc/4.0/ month: '09' oa: 1 oa_version: Published Version publication: Science Advances publication_identifier: eissn: - '23752548' publication_status: published publisher: American Association for the Advancement of Science quality_controlled: '1' scopus_import: '1' status: public title: Structural basis of sterol recognition by human hedgehog receptor PTCH1 tmp: image: /images/cc_by_nc.png legal_code_url: https://creativecommons.org/licenses/by-nc/4.0/legalcode name: Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0) short: CC BY-NC (4.0) type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 5 year: '2019' ... --- _id: '6983' abstract: - lang: eng text: Malaria, a disease caused by parasites of the Plasmodium genus, begins when Plasmodium-infected mosquitoes inject malaria sporozoites while searching for blood. Sporozoites migrate from the skin via blood to the liver, infect hepatocytes, and form liver stages which in mice 48 h later escape into blood and cause clinical malaria. Vaccine-induced activated or memory CD8 T cells are capable of locating and eliminating all liver stages in 48 h, thus preventing the blood-stage disease. However, the rules of how CD8 T cells are able to locate all liver stages within a relatively short time period remains poorly understood. We recently reported formation of clusters consisting of variable numbers of activated CD8 T cells around Plasmodium yoelii (Py)-infected hepatocytes. Using a combination of experimental data and mathematical models we now provide additional insights into mechanisms of formation of these clusters. First, we show that a model in which cluster formation is driven exclusively by T-cell-extrinsic factors, such as variability in “attractiveness” of different liver stages, cannot explain distribution of cluster sizes in different experimental conditions. In contrast, the model in which cluster formation is driven by the positive feedback loop (i.e., larger clusters attract more CD8 T cells) can accurately explain the available data. Second, while both Py-specific CD8 T cells and T cells of irrelevant specificity (non-specific CD8 T cells) are attracted to the clusters, we found no evidence that non-specific CD8 T cells play a role in cluster formation. Third and finally, mathematical modeling suggested that formation of clusters occurs rapidly, within few hours after adoptive transfer of CD8 T cells, thus illustrating high efficiency of CD8 T cells in locating their targets in complex peripheral organs, such as the liver. Taken together, our analysis provides novel insights into and attempts to discriminate between alternative mechanisms driving the formation of clusters of antigen-specific CD8 T cells in the liver. article_number: '2153' article_processing_charge: No article_type: original author: - first_name: Réka K full_name: Kelemen, Réka K id: 48D3F8DE-F248-11E8-B48F-1D18A9856A87 last_name: Kelemen orcid: 0000-0002-8489-9281 - first_name: H full_name: Rajakaruna, H last_name: Rajakaruna - first_name: IA full_name: Cockburn, IA last_name: Cockburn - first_name: VV full_name: Ganusov, VV last_name: Ganusov citation: ama: Kelemen RK, Rajakaruna H, Cockburn I, Ganusov V. Clustering of activated CD8 T cells around Malaria-infected hepatocytes is rapid and is driven by antigen-specific cells. Frontiers in Immunology. 2019;10. doi:10.3389/fimmu.2019.02153 apa: Kelemen, R. K., Rajakaruna, H., Cockburn, I., & Ganusov, V. (2019). Clustering of activated CD8 T cells around Malaria-infected hepatocytes is rapid and is driven by antigen-specific cells. Frontiers in Immunology. Frontiers. https://doi.org/10.3389/fimmu.2019.02153 chicago: Kelemen, Réka K, H Rajakaruna, IA Cockburn, and VV Ganusov. “Clustering of Activated CD8 T Cells around Malaria-Infected Hepatocytes Is Rapid and Is Driven by Antigen-Specific Cells.” Frontiers in Immunology. Frontiers, 2019. https://doi.org/10.3389/fimmu.2019.02153. ieee: R. K. Kelemen, H. Rajakaruna, I. Cockburn, and V. Ganusov, “Clustering of activated CD8 T cells around Malaria-infected hepatocytes is rapid and is driven by antigen-specific cells,” Frontiers in Immunology, vol. 10. Frontiers, 2019. ista: Kelemen RK, Rajakaruna H, Cockburn I, Ganusov V. 2019. Clustering of activated CD8 T cells around Malaria-infected hepatocytes is rapid and is driven by antigen-specific cells. Frontiers in Immunology. 10, 2153. mla: Kelemen, Réka K., et al. “Clustering of Activated CD8 T Cells around Malaria-Infected Hepatocytes Is Rapid and Is Driven by Antigen-Specific Cells.” Frontiers in Immunology, vol. 10, 2153, Frontiers, 2019, doi:10.3389/fimmu.2019.02153. short: R.K. Kelemen, H. Rajakaruna, I. Cockburn, V. Ganusov, Frontiers in Immunology 10 (2019). date_created: 2019-11-04T15:50:06Z date_published: 2019-09-20T00:00:00Z date_updated: 2023-08-30T07:18:23Z day: '20' ddc: - '570' department: - _id: BeVi doi: 10.3389/fimmu.2019.02153 external_id: isi: - '000487187000001' pmid: - '31616407' file: - access_level: open_access checksum: 68d1708f7aa412544159b498ef17a6b9 content_type: application/pdf creator: dernst date_created: 2019-11-04T15:54:00Z date_updated: 2020-07-14T12:47:46Z file_id: '6984' file_name: 2019_FrontiersImmonology_Kelemen.pdf file_size: 2083061 relation: main_file file_date_updated: 2020-07-14T12:47:46Z has_accepted_license: '1' intvolume: ' 10' isi: 1 language: - iso: eng month: '09' oa: 1 oa_version: Published Version pmid: 1 publication: Frontiers in Immunology publication_identifier: issn: - 1664-3224 publication_status: published publisher: Frontiers quality_controlled: '1' scopus_import: '1' status: public title: Clustering of activated CD8 T cells around Malaria-infected hepatocytes is rapid and is driven by antigen-specific cells tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 10 year: '2019' ... --- _id: '6972' abstract: - lang: eng text: 'We give fault-tolerant algorithms for establishing synchrony in distributed systems in which each of thennodes has its own clock. Our algorithms operate in a very strong fault model: we require self-stabilisation, i.e.,the initial state of the system may be arbitrary, and there can be up to fJournal of the ACM. 2019;66(5). doi:10.1145/3339471 apa: Lenzen, C., & Rybicki, J. (2019). Self-stabilising Byzantine clock synchronisation is almost as easy as consensus. Journal of the ACM. ACM. https://doi.org/10.1145/3339471 chicago: Lenzen, Christoph, and Joel Rybicki. “Self-Stabilising Byzantine Clock Synchronisation Is Almost as Easy as Consensus.” Journal of the ACM. ACM, 2019. https://doi.org/10.1145/3339471. ieee: C. Lenzen and J. Rybicki, “Self-stabilising Byzantine clock synchronisation is almost as easy as consensus,” Journal of the ACM, vol. 66, no. 5. ACM, 2019. ista: Lenzen C, Rybicki J. 2019. Self-stabilising Byzantine clock synchronisation is almost as easy as consensus. Journal of the ACM. 66(5), 32. mla: Lenzen, Christoph, and Joel Rybicki. “Self-Stabilising Byzantine Clock Synchronisation Is Almost as Easy as Consensus.” Journal of the ACM, vol. 66, no. 5, 32, ACM, 2019, doi:10.1145/3339471. short: C. Lenzen, J. Rybicki, Journal of the ACM 66 (2019). date_created: 2019-10-24T17:12:48Z date_published: 2019-09-01T00:00:00Z date_updated: 2023-08-30T07:07:23Z day: '01' ddc: - '000' department: - _id: DaAl doi: 10.1145/3339471 ec_funded: 1 external_id: arxiv: - '1705.06173' isi: - '000496514100001' file: - access_level: open_access checksum: 7e5d95c478e0e393f4927fcf7e48194e content_type: application/pdf creator: dernst date_created: 2019-10-25T12:58:38Z date_updated: 2020-07-14T12:47:46Z file_id: '6975' file_name: 2019_JACM_Lenzen.pdf file_size: 2183085 relation: main_file file_date_updated: 2020-07-14T12:47:46Z has_accepted_license: '1' intvolume: ' 66' isi: 1 issue: '5' language: - iso: eng month: '09' oa: 1 oa_version: Published Version project: - _id: 260C2330-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '754411' name: ISTplus - Postdoctoral Fellowships publication: Journal of the ACM publication_identifier: issn: - 0004-5411 publication_status: published publisher: ACM quality_controlled: '1' scopus_import: '1' status: public title: Self-stabilising Byzantine clock synchronisation is almost as easy as consensus tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 66 year: '2019' ... --- _id: '6942' abstract: - lang: eng text: "Graph games and Markov decision processes (MDPs) are standard models in reactive synthesis and verification of probabilistic systems with nondeterminism. The class of \U0001D714 -regular winning conditions; e.g., safety, reachability, liveness, parity conditions; provides a robust and expressive specification formalism for properties that arise in analysis of reactive systems. The resolutions of nondeterminism in games and MDPs are represented as strategies, and we consider succinct representation of such strategies. The decision-tree data structure from machine learning retains the flavor of decisions of strategies and allows entropy-based minimization to obtain succinct trees. However, in contrast to traditional machine-learning problems where small errors are allowed, for winning strategies in graph games and MDPs no error is allowed, and the decision tree must represent the entire strategy. In this work we propose decision trees with linear classifiers for representation of strategies in graph games and MDPs. We have implemented strategy representation using this data structure and we present experimental results for problems on graph games and MDPs, which show that this new data structure presents a much more efficient strategy representation as compared to standard decision trees." alternative_title: - LNCS article_processing_charge: No author: - first_name: Pranav full_name: Ashok, Pranav last_name: Ashok - first_name: Tomáš full_name: Brázdil, Tomáš last_name: Brázdil - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Jan full_name: Křetínský, Jan last_name: Křetínský - first_name: Christoph full_name: Lampert, Christoph id: 40C20FD2-F248-11E8-B48F-1D18A9856A87 last_name: Lampert orcid: 0000-0001-8622-7887 - first_name: Viktor full_name: Toman, Viktor id: 3AF3DA7C-F248-11E8-B48F-1D18A9856A87 last_name: Toman orcid: 0000-0001-9036-063X citation: ama: 'Ashok P, Brázdil T, Chatterjee K, Křetínský J, Lampert C, Toman V. Strategy representation by decision trees with linear classifiers. In: 16th International Conference on Quantitative Evaluation of Systems. Vol 11785. Springer Nature; 2019:109-128. doi:10.1007/978-3-030-30281-8_7' apa: 'Ashok, P., Brázdil, T., Chatterjee, K., Křetínský, J., Lampert, C., & Toman, V. (2019). Strategy representation by decision trees with linear classifiers. In 16th International Conference on Quantitative Evaluation of Systems (Vol. 11785, pp. 109–128). Glasgow, United Kingdom: Springer Nature. https://doi.org/10.1007/978-3-030-30281-8_7' chicago: Ashok, Pranav, Tomáš Brázdil, Krishnendu Chatterjee, Jan Křetínský, Christoph Lampert, and Viktor Toman. “Strategy Representation by Decision Trees with Linear Classifiers.” In 16th International Conference on Quantitative Evaluation of Systems, 11785:109–28. Springer Nature, 2019. https://doi.org/10.1007/978-3-030-30281-8_7. ieee: P. Ashok, T. Brázdil, K. Chatterjee, J. Křetínský, C. Lampert, and V. Toman, “Strategy representation by decision trees with linear classifiers,” in 16th International Conference on Quantitative Evaluation of Systems, Glasgow, United Kingdom, 2019, vol. 11785, pp. 109–128. ista: 'Ashok P, Brázdil T, Chatterjee K, Křetínský J, Lampert C, Toman V. 2019. Strategy representation by decision trees with linear classifiers. 16th International Conference on Quantitative Evaluation of Systems. QEST: Quantitative Evaluation of Systems, LNCS, vol. 11785, 109–128.' mla: Ashok, Pranav, et al. “Strategy Representation by Decision Trees with Linear Classifiers.” 16th International Conference on Quantitative Evaluation of Systems, vol. 11785, Springer Nature, 2019, pp. 109–28, doi:10.1007/978-3-030-30281-8_7. short: P. Ashok, T. Brázdil, K. Chatterjee, J. Křetínský, C. Lampert, V. Toman, in:, 16th International Conference on Quantitative Evaluation of Systems, Springer Nature, 2019, pp. 109–128. conference: end_date: 2019-09-12 location: Glasgow, United Kingdom name: 'QEST: Quantitative Evaluation of Systems' start_date: 2019-09-10 date_created: 2019-10-14T06:57:49Z date_published: 2019-09-04T00:00:00Z date_updated: 2023-08-30T06:59:36Z day: '04' department: - _id: KrCh - _id: ChLa doi: 10.1007/978-3-030-30281-8_7 external_id: arxiv: - '1906.08178' isi: - '000679281300007' intvolume: ' 11785' isi: 1 language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1906.08178 month: '09' oa: 1 oa_version: Preprint page: 109-128 project: - _id: 25863FF4-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S11407 name: Game Theory - _id: 25F2ACDE-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S11402-N23 name: Rigorous Systems Engineering - _id: 25892FC0-B435-11E9-9278-68D0E5697425 grant_number: ICT15-003 name: Efficient Algorithms for Computer Aided Verification publication: 16th International Conference on Quantitative Evaluation of Systems publication_identifier: eisbn: - '9783030302818' isbn: - '9783030302801' issn: - 0302-9743 publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: Strategy representation by decision trees with linear classifiers type: conference user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 11785 year: '2019' ... --- _id: '6955' abstract: - lang: eng text: We study few-body bound states of charged particles subject to attractive zero-range/short-range plus repulsive Coulomb interparticle forces. The characteristic length scales of the system at zero energy are set by the Coulomb length scale D and the Coulomb-modified effective range r eff. We study shallow bound states of charged particles with D >> r eff and show that these systems obey universal scaling laws different from neutral particles. An accurate description of these states requires both the Coulomb-modified scattering length and the effective range unless the Coulomb interaction is very weak (D -> ). Our findings are relevant for bound states whose spatial extent is significantly larger than the range of the attractive potential. These states enjoy universality – their character is independent of the shape of the short-range potential. article_number: '135016' article_processing_charge: No article_type: original author: - first_name: C.H. full_name: Schmickler, C.H. last_name: Schmickler - first_name: H.-W. full_name: Hammer, H.-W. last_name: Hammer - first_name: Artem full_name: Volosniev, Artem id: 37D278BC-F248-11E8-B48F-1D18A9856A87 last_name: Volosniev orcid: 0000-0003-0393-5525 citation: ama: Schmickler CH, Hammer H-W, Volosniev A. Universal physics of bound states of a few charged particles. Physics Letters B. 2019;798. doi:10.1016/j.physletb.2019.135016 apa: Schmickler, C. H., Hammer, H.-W., & Volosniev, A. (2019). Universal physics of bound states of a few charged particles. Physics Letters B. Elsevier. https://doi.org/10.1016/j.physletb.2019.135016 chicago: Schmickler, C.H., H.-W. Hammer, and Artem Volosniev. “Universal Physics of Bound States of a Few Charged Particles.” Physics Letters B. Elsevier, 2019. https://doi.org/10.1016/j.physletb.2019.135016. ieee: C. H. Schmickler, H.-W. Hammer, and A. Volosniev, “Universal physics of bound states of a few charged particles,” Physics Letters B, vol. 798. Elsevier, 2019. ista: Schmickler CH, Hammer H-W, Volosniev A. 2019. Universal physics of bound states of a few charged particles. Physics Letters B. 798, 135016. mla: Schmickler, C. H., et al. “Universal Physics of Bound States of a Few Charged Particles.” Physics Letters B, vol. 798, 135016, Elsevier, 2019, doi:10.1016/j.physletb.2019.135016. short: C.H. Schmickler, H.-W. Hammer, A. Volosniev, Physics Letters B 798 (2019). date_created: 2019-10-18T18:33:32Z date_published: 2019-11-10T00:00:00Z date_updated: 2023-08-30T07:06:42Z day: '10' ddc: - '530' department: - _id: MiLe doi: 10.1016/j.physletb.2019.135016 external_id: arxiv: - '1904.00913' isi: - '000494939000086' file: - access_level: open_access checksum: d27f983b34ea7dafdf356afbf9472fbf content_type: application/pdf creator: dernst date_created: 2019-10-25T12:47:04Z date_updated: 2020-07-14T12:47:46Z file_id: '6974' file_name: 2019_PhysicsLettersB_Schmickler.pdf file_size: 528362 relation: main_file file_date_updated: 2020-07-14T12:47:46Z has_accepted_license: '1' intvolume: ' 798' isi: 1 language: - iso: eng month: '11' oa: 1 oa_version: Published Version publication: Physics Letters B publication_identifier: issn: - 0370-2693 publication_status: published publisher: Elsevier quality_controlled: '1' scopus_import: '1' status: public title: Universal physics of bound states of a few charged particles tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 798 year: '2019' ... --- _id: '7005' abstract: - lang: eng text: Activity-dependent bulk endocytosis generates synaptic vesicles (SVs) during intense neuronal activity via a two-step process. First, bulk endosomes are formed direct from the plasma membrane from which SVs are then generated. SV generation from bulk endosomes requires the efflux of previously accumulated calcium and activation of the protein phosphatase calcineurin. However, it is still unknown how calcineurin mediates SV generation. We addressed this question using a series of acute interventions that decoupled the generation of SVs from bulk endosomes in rat primary neuronal culture. This was achieved by either disruption of protein–protein interactions via delivery of competitive peptides, or inhibition of enzyme activity by known inhibitors. SV generation was monitored using either a morphological horseradish peroxidase assay or an optical assay that monitors the replenishment of the reserve SV pool. We found that SV generation was inhibited by, (i) peptides that disrupt calcineurin interactions, (ii) an inhibitor of dynamin I GTPase activity and (iii) peptides that disrupt the phosphorylation-dependent dynamin I–syndapin I interaction. Peptides that disrupted syndapin I interactions with eps15 homology domain-containing proteins had no effect. This revealed that (i) calcineurin must be localized at bulk endosomes to mediate its effect, (ii) dynamin I GTPase activity is essential for SV fission and (iii) the calcineurin-dependent interaction between dynamin I and syndapin I is essential for SV generation. We therefore propose that a calcineurin-dependent dephosphorylation cascade that requires both dynamin I GTPase and syndapin I lipid-deforming activity is essential for SV generation from bulk endosomes. article_processing_charge: No article_type: original author: - first_name: Giselle T full_name: Cheung, Giselle T id: 471195F6-F248-11E8-B48F-1D18A9856A87 last_name: Cheung orcid: 0000-0001-8457-2572 - first_name: Michael A. full_name: Cousin, Michael A. last_name: Cousin citation: ama: Cheung GT, Cousin MA. Synaptic vesicle generation from activity‐dependent bulk endosomes requires a dephosphorylation‐dependent dynamin–syndapin interaction. Journal of Neurochemistry. 2019;151(5):570-583. doi:10.1111/jnc.14862 apa: Cheung, G. T., & Cousin, M. A. (2019). Synaptic vesicle generation from activity‐dependent bulk endosomes requires a dephosphorylation‐dependent dynamin–syndapin interaction. Journal of Neurochemistry. Wiley. https://doi.org/10.1111/jnc.14862 chicago: Cheung, Giselle T, and Michael A. Cousin. “Synaptic Vesicle Generation from Activity‐dependent Bulk Endosomes Requires a Dephosphorylation‐dependent Dynamin–Syndapin Interaction.” Journal of Neurochemistry. Wiley, 2019. https://doi.org/10.1111/jnc.14862. ieee: G. T. Cheung and M. A. Cousin, “Synaptic vesicle generation from activity‐dependent bulk endosomes requires a dephosphorylation‐dependent dynamin–syndapin interaction,” Journal of Neurochemistry, vol. 151, no. 5. Wiley, pp. 570–583, 2019. ista: Cheung GT, Cousin MA. 2019. Synaptic vesicle generation from activity‐dependent bulk endosomes requires a dephosphorylation‐dependent dynamin–syndapin interaction. Journal of Neurochemistry. 151(5), 570–583. mla: Cheung, Giselle T., and Michael A. Cousin. “Synaptic Vesicle Generation from Activity‐dependent Bulk Endosomes Requires a Dephosphorylation‐dependent Dynamin–Syndapin Interaction.” Journal of Neurochemistry, vol. 151, no. 5, Wiley, 2019, pp. 570–83, doi:10.1111/jnc.14862. short: G.T. Cheung, M.A. Cousin, Journal of Neurochemistry 151 (2019) 570–583. date_created: 2019-11-12T14:37:08Z date_published: 2019-12-01T00:00:00Z date_updated: 2023-08-30T07:21:50Z day: '01' ddc: - '570' department: - _id: SiHi doi: 10.1111/jnc.14862 external_id: isi: - '000490703100001' pmid: - '31479508' file: - access_level: open_access checksum: ec1fb2aebb874009bc309adaada6e1d7 content_type: application/pdf creator: dernst date_created: 2020-02-05T10:30:02Z date_updated: 2020-07-14T12:47:47Z file_id: '7452' file_name: 2019_JournNeurochemistry_Cheung.pdf file_size: 4334962 relation: main_file file_date_updated: 2020-07-14T12:47:47Z has_accepted_license: '1' intvolume: ' 151' isi: 1 issue: '5' language: - iso: eng month: '12' oa: 1 oa_version: Published Version page: 570-583 pmid: 1 publication: Journal of Neurochemistry publication_identifier: eissn: - 1471-4159 issn: - 0022-3042 publication_status: published publisher: Wiley quality_controlled: '1' scopus_import: '1' status: public title: Synaptic vesicle generation from activity‐dependent bulk endosomes requires a dephosphorylation‐dependent dynamin–syndapin interaction tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 151 year: '2019' ... --- _id: '7000' abstract: - lang: eng text: The main contributions of this paper are the proposition and the convergence analysis of a class of inertial projection-type algorithm for solving variational inequality problems in real Hilbert spaces where the underline operator is monotone and uniformly continuous. We carry out a unified analysis of the proposed method under very mild assumptions. In particular, weak convergence of the generated sequence is established and nonasymptotic O(1 / n) rate of convergence is established, where n denotes the iteration counter. We also present some experimental results to illustrate the profits gained by introducing the inertial extrapolation steps. article_number: '161' article_processing_charge: No article_type: original author: - first_name: Yekini full_name: Shehu, Yekini id: 3FC7CB58-F248-11E8-B48F-1D18A9856A87 last_name: Shehu orcid: 0000-0001-9224-7139 - first_name: Olaniyi S. full_name: Iyiola, Olaniyi S. last_name: Iyiola - first_name: Xiao-Huan full_name: Li, Xiao-Huan last_name: Li - first_name: Qiao-Li full_name: Dong, Qiao-Li last_name: Dong citation: ama: Shehu Y, Iyiola OS, Li X-H, Dong Q-L. Convergence analysis of projection method for variational inequalities. Computational and Applied Mathematics. 2019;38(4). doi:10.1007/s40314-019-0955-9 apa: Shehu, Y., Iyiola, O. S., Li, X.-H., & Dong, Q.-L. (2019). Convergence analysis of projection method for variational inequalities. Computational and Applied Mathematics. Springer Nature. https://doi.org/10.1007/s40314-019-0955-9 chicago: Shehu, Yekini, Olaniyi S. Iyiola, Xiao-Huan Li, and Qiao-Li Dong. “Convergence Analysis of Projection Method for Variational Inequalities.” Computational and Applied Mathematics. Springer Nature, 2019. https://doi.org/10.1007/s40314-019-0955-9. ieee: Y. Shehu, O. S. Iyiola, X.-H. Li, and Q.-L. Dong, “Convergence analysis of projection method for variational inequalities,” Computational and Applied Mathematics, vol. 38, no. 4. Springer Nature, 2019. ista: Shehu Y, Iyiola OS, Li X-H, Dong Q-L. 2019. Convergence analysis of projection method for variational inequalities. Computational and Applied Mathematics. 38(4), 161. mla: Shehu, Yekini, et al. “Convergence Analysis of Projection Method for Variational Inequalities.” Computational and Applied Mathematics, vol. 38, no. 4, 161, Springer Nature, 2019, doi:10.1007/s40314-019-0955-9. short: Y. Shehu, O.S. Iyiola, X.-H. Li, Q.-L. Dong, Computational and Applied Mathematics 38 (2019). date_created: 2019-11-12T12:41:44Z date_published: 2019-12-01T00:00:00Z date_updated: 2023-08-30T07:20:32Z day: '01' ddc: - '510' - '515' - '518' department: - _id: VlKo doi: 10.1007/s40314-019-0955-9 ec_funded: 1 external_id: arxiv: - '2101.09081' isi: - '000488973100005' has_accepted_license: '1' intvolume: ' 38' isi: 1 issue: '4' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1007/s40314-019-0955-9 month: '12' oa: 1 oa_version: Published Version project: - _id: 25FBA906-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '616160' name: 'Discrete Optimization in Computer Vision: Theory and Practice' publication: Computational and Applied Mathematics publication_identifier: eissn: - 1807-0302 issn: - 2238-3603 publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: Convergence analysis of projection method for variational inequalities type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 38 year: '2019' ... --- _id: '7009' abstract: - lang: eng text: Cell migration is essential for physiological processes as diverse as development, immune defence and wound healing. It is also a hallmark of cancer malignancy. Thousands of publications have elucidated detailed molecular and biophysical mechanisms of cultured cells migrating on flat, 2D substrates of glass and plastic. However, much less is known about how cells successfully navigate the complex 3D environments of living tissues. In these more complex, native environments, cells use multiple modes of migration, including mesenchymal, amoeboid, lobopodial and collective, and these are governed by the local extracellular microenvironment, specific modalities of Rho GTPase signalling and non- muscle myosin contractility. Migration through 3D environments is challenging because it requires the cell to squeeze through complex or dense extracellular structures. Doing so requires specific cellular adaptations to mechanical features of the extracellular matrix (ECM) or its remodelling. In addition, besides navigating through diverse ECM environments and overcoming extracellular barriers, cells often interact with neighbouring cells and tissues through physical and signalling interactions. Accordingly, cells need to call on an impressively wide diversity of mechanisms to meet these challenges. This Review examines how cells use both classical and novel mechanisms of locomotion as they traverse challenging 3D matrices and cellular environments. It focuses on principles rather than details of migratory mechanisms and draws comparisons between 1D, 2D and 3D migration. article_processing_charge: No article_type: review author: - first_name: KM full_name: Yamada, KM last_name: Yamada - first_name: Michael K full_name: Sixt, Michael K id: 41E9FBEA-F248-11E8-B48F-1D18A9856A87 last_name: Sixt orcid: 0000-0002-6620-9179 citation: ama: Yamada K, Sixt MK. Mechanisms of 3D cell migration. Nature Reviews Molecular Cell Biology. 2019;20(12):738–752. doi:10.1038/s41580-019-0172-9 apa: Yamada, K., & Sixt, M. K. (2019). Mechanisms of 3D cell migration. Nature Reviews Molecular Cell Biology. Springer Nature. https://doi.org/10.1038/s41580-019-0172-9 chicago: Yamada, KM, and Michael K Sixt. “Mechanisms of 3D Cell Migration.” Nature Reviews Molecular Cell Biology. Springer Nature, 2019. https://doi.org/10.1038/s41580-019-0172-9. ieee: K. Yamada and M. K. Sixt, “Mechanisms of 3D cell migration,” Nature Reviews Molecular Cell Biology, vol. 20, no. 12. Springer Nature, pp. 738–752, 2019. ista: Yamada K, Sixt MK. 2019. Mechanisms of 3D cell migration. Nature Reviews Molecular Cell Biology. 20(12), 738–752. mla: Yamada, KM, and Michael K. Sixt. “Mechanisms of 3D Cell Migration.” Nature Reviews Molecular Cell Biology, vol. 20, no. 12, Springer Nature, 2019, pp. 738–752, doi:10.1038/s41580-019-0172-9. short: K. Yamada, M.K. Sixt, Nature Reviews Molecular Cell Biology 20 (2019) 738–752. date_created: 2019-11-12T14:54:42Z date_published: 2019-12-01T00:00:00Z date_updated: 2023-08-30T07:22:20Z day: '01' department: - _id: MiSi doi: 10.1038/s41580-019-0172-9 external_id: isi: - '000497966900007' pmid: - '31582855' intvolume: ' 20' isi: 1 issue: '12' language: - iso: eng month: '12' oa_version: None page: 738–752 pmid: 1 publication: Nature Reviews Molecular Cell Biology publication_identifier: eissn: - 1471-0080 issn: - 1471-0072 publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: Mechanisms of 3D cell migration type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 20 year: '2019' ... --- _id: '6988' abstract: - lang: eng text: 'Platelets are central players in thrombosis and hemostasis but are increasingly recognized as key components of the immune system. They shape ensuing immune responses by recruiting leukocytes, and support the development of adaptive immunity. Recent data shed new light on the complex role of platelets in immunity. Here, we summarize experimental and clinical data on the role of platelets in host defense against bacteria. Platelets bind, contain, and kill bacteria directly; however, platelet proinflammatory effector functions and cross-talk with the coagulation system, can also result in damage to the host (e.g., acute lung injury and sepsis). Novel clinical insights support this dichotomy: platelet inhibition/thrombocytopenia can be either harmful or protective, depending on pathophysiological context. Clinical studies are currently addressing this aspect in greater depth.' article_processing_charge: No article_type: review author: - first_name: Leo full_name: Nicolai, Leo last_name: Nicolai - first_name: Florian R full_name: Gärtner, Florian R id: 397A88EE-F248-11E8-B48F-1D18A9856A87 last_name: Gärtner orcid: 0000-0001-6120-3723 - first_name: Steffen full_name: Massberg, Steffen last_name: Massberg citation: ama: 'Nicolai L, Gärtner FR, Massberg S. Platelets in host defense: Experimental and clinical insights. Trends in Immunology. 2019;40(10):922-938. doi:10.1016/j.it.2019.08.004' apa: 'Nicolai, L., Gärtner, F. R., & Massberg, S. (2019). Platelets in host defense: Experimental and clinical insights. Trends in Immunology. Cell Press. https://doi.org/10.1016/j.it.2019.08.004' chicago: 'Nicolai, Leo, Florian R Gärtner, and Steffen Massberg. “Platelets in Host Defense: Experimental and Clinical Insights.” Trends in Immunology. Cell Press, 2019. https://doi.org/10.1016/j.it.2019.08.004.' ieee: 'L. Nicolai, F. R. Gärtner, and S. Massberg, “Platelets in host defense: Experimental and clinical insights,” Trends in Immunology, vol. 40, no. 10. Cell Press, pp. 922–938, 2019.' ista: 'Nicolai L, Gärtner FR, Massberg S. 2019. Platelets in host defense: Experimental and clinical insights. Trends in Immunology. 40(10), 922–938.' mla: 'Nicolai, Leo, et al. “Platelets in Host Defense: Experimental and Clinical Insights.” Trends in Immunology, vol. 40, no. 10, Cell Press, 2019, pp. 922–38, doi:10.1016/j.it.2019.08.004.' short: L. Nicolai, F.R. Gärtner, S. Massberg, Trends in Immunology 40 (2019) 922–938. date_created: 2019-11-04T16:27:36Z date_published: 2019-10-01T00:00:00Z date_updated: 2023-08-30T07:19:23Z day: '01' department: - _id: MiSi doi: 10.1016/j.it.2019.08.004 ec_funded: 1 external_id: isi: - '000493292100005' pmid: - '31601520' intvolume: ' 40' isi: 1 issue: '10' language: - iso: eng month: '10' oa_version: None page: 922-938 pmid: 1 project: - _id: 260AA4E2-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '747687' name: Mechanical Adaptation of Lamellipodial Actin Networks in Migrating Cells publication: Trends in Immunology publication_identifier: issn: - 1471-4906 publication_status: published publisher: Cell Press quality_controlled: '1' scopus_import: '1' status: public title: 'Platelets in host defense: Experimental and clinical insights' type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 40 year: '2019' ... --- _id: '7002' abstract: - lang: eng text: Multiple Importance Sampling (MIS) is a key technique for achieving robustness of Monte Carlo estimators in computer graphics and other fields. We derive optimal weighting functions for MIS that provably minimize the variance of an MIS estimator, given a set of sampling techniques. We show that the resulting variance reduction over the balance heuristic can be higher than predicted by the variance bounds derived by Veach and Guibas, who assumed only non-negative weights in their proof. We theoretically analyze the variance of the optimal MIS weights and show the relation to the variance of the balance heuristic. Furthermore, we establish a connection between the new weighting functions and control variates as previously applied to mixture sampling. We apply the new optimal weights to integration problems in light transport and show that they allow for new design considerations when choosing the appropriate sampling techniques for a given integration problem. article_number: '37' article_processing_charge: No article_type: original author: - first_name: Ivo full_name: Kondapaneni, Ivo last_name: Kondapaneni - first_name: Petr full_name: Vevoda, Petr last_name: Vevoda - first_name: Pascal full_name: Grittmann, Pascal last_name: Grittmann - first_name: Tomas full_name: Skrivan, Tomas id: 486A5A46-F248-11E8-B48F-1D18A9856A87 last_name: Skrivan - first_name: Philipp full_name: Slusallek, Philipp last_name: Slusallek - first_name: Jaroslav full_name: Křivánek, Jaroslav last_name: Křivánek citation: ama: Kondapaneni I, Vevoda P, Grittmann P, Skrivan T, Slusallek P, Křivánek J. Optimal multiple importance sampling. ACM Transactions on Graphics. 2019;38(4). doi:10.1145/3306346.3323009 apa: Kondapaneni, I., Vevoda, P., Grittmann, P., Skrivan, T., Slusallek, P., & Křivánek, J. (2019). Optimal multiple importance sampling. ACM Transactions on Graphics. ACM. https://doi.org/10.1145/3306346.3323009 chicago: Kondapaneni, Ivo, Petr Vevoda, Pascal Grittmann, Tomas Skrivan, Philipp Slusallek, and Jaroslav Křivánek. “Optimal Multiple Importance Sampling.” ACM Transactions on Graphics. ACM, 2019. https://doi.org/10.1145/3306346.3323009. ieee: I. Kondapaneni, P. Vevoda, P. Grittmann, T. Skrivan, P. Slusallek, and J. Křivánek, “Optimal multiple importance sampling,” ACM Transactions on Graphics, vol. 38, no. 4. ACM, 2019. ista: Kondapaneni I, Vevoda P, Grittmann P, Skrivan T, Slusallek P, Křivánek J. 2019. Optimal multiple importance sampling. ACM Transactions on Graphics. 38(4), 37. mla: Kondapaneni, Ivo, et al. “Optimal Multiple Importance Sampling.” ACM Transactions on Graphics, vol. 38, no. 4, 37, ACM, 2019, doi:10.1145/3306346.3323009. short: I. Kondapaneni, P. Vevoda, P. Grittmann, T. Skrivan, P. Slusallek, J. Křivánek, ACM Transactions on Graphics 38 (2019). date_created: 2019-11-12T13:05:40Z date_published: 2019-07-01T00:00:00Z date_updated: 2023-08-30T07:21:25Z day: '01' department: - _id: ChWo doi: 10.1145/3306346.3323009 ec_funded: 1 external_id: isi: - '000475740600011' intvolume: ' 38' isi: 1 issue: '4' language: - iso: eng month: '07' oa_version: None project: - _id: 2508E324-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '642841' name: Distributed 3D Object Design publication: ACM Transactions on Graphics publication_identifier: issn: - 0730-0301 publication_status: published publisher: ACM quality_controlled: '1' scopus_import: '1' status: public title: Optimal multiple importance sampling type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 38 year: '2019' ... --- _id: '6978' abstract: - lang: eng text: In pipes and channels, the onset of turbulence is initially dominated by localizedtransients, which lead to sustained turbulence through their collective dynamics. In thepresent work, we study numerically the localized turbulence in pipe flow and elucidate astate space structure that gives rise to transient chaos. Starting from the basin boundaryseparating laminar and turbulent flow, we identify transverse homoclinic orbits, thepresence of which necessitates a homoclinic tangle and chaos. A direct consequence ofthe homoclinic tangle is the fractal nature of the laminar-turbulent boundary, which wasconjectured in various earlier studies. By mapping the transverse intersections between thestable and unstable manifold of a periodic orbit, we identify the gateways that promote anescape from turbulence. acknowledged_ssus: - _id: ScienComp article_processing_charge: No article_type: original author: - first_name: Nazmi B full_name: Budanur, Nazmi B id: 3EA1010E-F248-11E8-B48F-1D18A9856A87 last_name: Budanur orcid: 0000-0003-0423-5010 - first_name: Akshunna full_name: Dogra, Akshunna last_name: Dogra - first_name: Björn full_name: Hof, Björn id: 3A374330-F248-11E8-B48F-1D18A9856A87 last_name: Hof orcid: 0000-0003-2057-2754 citation: ama: Budanur NB, Dogra A, Hof B. Geometry of transient chaos in streamwise-localized pipe flow turbulence. Physical Review Fluids. 2019;4(10):102401. doi:10.1103/PhysRevFluids.4.102401 apa: Budanur, N. B., Dogra, A., & Hof, B. (2019). Geometry of transient chaos in streamwise-localized pipe flow turbulence. Physical Review Fluids. American Physical Society. https://doi.org/10.1103/PhysRevFluids.4.102401 chicago: Budanur, Nazmi B, Akshunna Dogra, and Björn Hof. “Geometry of Transient Chaos in Streamwise-Localized Pipe Flow Turbulence.” Physical Review Fluids. American Physical Society, 2019. https://doi.org/10.1103/PhysRevFluids.4.102401. ieee: N. B. Budanur, A. Dogra, and B. Hof, “Geometry of transient chaos in streamwise-localized pipe flow turbulence,” Physical Review Fluids, vol. 4, no. 10. American Physical Society, p. 102401, 2019. ista: Budanur NB, Dogra A, Hof B. 2019. Geometry of transient chaos in streamwise-localized pipe flow turbulence. Physical Review Fluids. 4(10), 102401. mla: Budanur, Nazmi B., et al. “Geometry of Transient Chaos in Streamwise-Localized Pipe Flow Turbulence.” Physical Review Fluids, vol. 4, no. 10, American Physical Society, 2019, p. 102401, doi:10.1103/PhysRevFluids.4.102401. short: N.B. Budanur, A. Dogra, B. Hof, Physical Review Fluids 4 (2019) 102401. date_created: 2019-11-04T10:04:01Z date_published: 2019-10-01T00:00:00Z date_updated: 2023-08-30T07:20:03Z day: '01' department: - _id: BjHo doi: 10.1103/PhysRevFluids.4.102401 external_id: arxiv: - '1810.02211' isi: - '000493510400001' intvolume: ' 4' isi: 1 issue: '10' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1810.02211 month: '10' oa: 1 oa_version: Preprint page: '102401' publication: Physical Review Fluids publication_status: published publisher: American Physical Society quality_controlled: '1' scopus_import: '1' status: public title: Geometry of transient chaos in streamwise-localized pipe flow turbulence type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 4 year: '2019' ...