--- _id: '7711' abstract: - lang: eng text: The nature and extent of mitochondrial DNA variation in a population and how it affects traits is poorly understood. Here we resequence the mitochondrial genomes of 169 Drosophila Genetic Reference Panel lines, identifying 231 variants that stratify along 12 mitochondrial haplotypes. We identify 1,845 cases of mitonuclear allelic imbalances, thus implying that mitochondrial haplotypes are reflected in the nuclear genome. However, no major fitness effects are associated with mitonuclear imbalance, suggesting that such imbalances reflect population structure at the mitochondrial level rather than genomic incompatibilities. Although mitochondrial haplotypes have no direct impact on mitochondrial respiration, some haplotypes are associated with stress- and metabolism-related phenotypes, including food intake in males. Finally, through reciprocal swapping of mitochondrial genomes, we demonstrate that a mitochondrial haplotype associated with high food intake can rescue a low food intake phenotype. Together, our findings provide new insight into population structure at the mitochondrial level and point to the importance of incorporating mitochondrial haplotypes in genotype–phenotype relationship studies. article_processing_charge: No article_type: original author: - first_name: Roel P. J. full_name: Bevers, Roel P. J. last_name: Bevers - first_name: Maria full_name: Litovchenko, Maria last_name: Litovchenko - first_name: Adamandia full_name: Kapopoulou, Adamandia last_name: Kapopoulou - first_name: Virginie S. full_name: Braman, Virginie S. last_name: Braman - first_name: Matthew Richard full_name: Robinson, Matthew Richard id: E5D42276-F5DA-11E9-8E24-6303E6697425 last_name: Robinson orcid: 0000-0001-8982-8813 - first_name: Johan full_name: Auwerx, Johan last_name: Auwerx - first_name: Brian full_name: Hollis, Brian last_name: Hollis - first_name: Bart full_name: Deplancke, Bart last_name: Deplancke citation: ama: Bevers RPJ, Litovchenko M, Kapopoulou A, et al. Mitochondrial haplotypes affect metabolic phenotypes in the Drosophila Genetic Reference Panel. Nature Metabolism. 2019;1(12):1226-1242. doi:10.1038/s42255-019-0147-3 apa: Bevers, R. P. J., Litovchenko, M., Kapopoulou, A., Braman, V. S., Robinson, M. R., Auwerx, J., … Deplancke, B. (2019). Mitochondrial haplotypes affect metabolic phenotypes in the Drosophila Genetic Reference Panel. Nature Metabolism. Springer Nature. https://doi.org/10.1038/s42255-019-0147-3 chicago: Bevers, Roel P. J., Maria Litovchenko, Adamandia Kapopoulou, Virginie S. Braman, Matthew Richard Robinson, Johan Auwerx, Brian Hollis, and Bart Deplancke. “Mitochondrial Haplotypes Affect Metabolic Phenotypes in the Drosophila Genetic Reference Panel.” Nature Metabolism. Springer Nature, 2019. https://doi.org/10.1038/s42255-019-0147-3. ieee: R. P. J. Bevers et al., “Mitochondrial haplotypes affect metabolic phenotypes in the Drosophila Genetic Reference Panel,” Nature Metabolism, vol. 1, no. 12. Springer Nature, pp. 1226–1242, 2019. ista: Bevers RPJ, Litovchenko M, Kapopoulou A, Braman VS, Robinson MR, Auwerx J, Hollis B, Deplancke B. 2019. Mitochondrial haplotypes affect metabolic phenotypes in the Drosophila Genetic Reference Panel. Nature Metabolism. 1(12), 1226–1242. mla: Bevers, Roel P. J., et al. “Mitochondrial Haplotypes Affect Metabolic Phenotypes in the Drosophila Genetic Reference Panel.” Nature Metabolism, vol. 1, no. 12, Springer Nature, 2019, pp. 1226–42, doi:10.1038/s42255-019-0147-3. short: R.P.J. Bevers, M. Litovchenko, A. Kapopoulou, V.S. Braman, M.R. Robinson, J. Auwerx, B. Hollis, B. Deplancke, Nature Metabolism 1 (2019) 1226–1242. date_created: 2020-04-30T10:40:56Z date_published: 2019-12-09T00:00:00Z date_updated: 2021-01-12T08:15:01Z day: '09' doi: 10.1038/s42255-019-0147-3 extern: '1' intvolume: ' 1' issue: '12' language: - iso: eng month: '12' oa_version: None page: 1226-1242 publication: Nature Metabolism publication_identifier: issn: - 2522-5812 publication_status: published publisher: Springer Nature quality_controlled: '1' related_material: link: - relation: erratum url: https://doi.org/10.1038/s42255-020-0202-0 status: public title: Mitochondrial haplotypes affect metabolic phenotypes in the Drosophila Genetic Reference Panel type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 1 year: '2019' ... --- _id: '7782' abstract: - lang: eng text: As genome-wide association studies (GWAS) increased in size, numerous gene-environment interactions (GxE) have been discovered, many of which however explore only one environment at a time and may suffer from statistical artefacts leading to biased interaction estimates. Here we propose a maximum likelihood method to estimate the contribution of GxE to complex traits taking into account all interacting environmental variables at the same time, without the need to measure any. This is possible because GxE induces fluctuations in the conditional trait variance, the extent of which depends on the strength of GxE. The approach can be applied to continuous outcomes and for single SNPs or genetic risk scores (GRS). Extensive simulations demonstrated that our method yields unbiased interaction estimates and excellent confidence interval coverage. We also offer a strategy to distinguish specific GxE from general heteroscedasticity (scale effects). Applying our method to 32 complex traits in the UK Biobank reveals that for body mass index (BMI) the GRSxE explains an additional 1.9% variance on top of the 5.2% GRS contribution. However, this interaction is not specific to the GRS and holds for any variable similarly correlated with BMI. On the contrary, the GRSxE interaction effect for leg impedance Embedded Image is significantly (P < 10−56) larger than it would be expected for a similarly correlated variable Embedded Image. We showed that our method could robustly detect the global contribution of GxE to complex traits, which turned out to be substantial for certain obesity measures. article_processing_charge: No author: - first_name: Jonathan full_name: Sulc, Jonathan last_name: Sulc - first_name: Ninon full_name: Mounier, Ninon last_name: Mounier - first_name: Felix full_name: Günther, Felix last_name: Günther - first_name: Thomas full_name: Winkler, Thomas last_name: Winkler - first_name: Andrew R. full_name: Wood, Andrew R. last_name: Wood - first_name: Timothy M. full_name: Frayling, Timothy M. last_name: Frayling - first_name: Iris M. full_name: Heid, Iris M. last_name: Heid - first_name: Matthew Richard full_name: Robinson, Matthew Richard id: E5D42276-F5DA-11E9-8E24-6303E6697425 last_name: Robinson orcid: 0000-0001-8982-8813 - first_name: Zoltán full_name: Kutalik, Zoltán last_name: Kutalik citation: ama: 'Sulc J, Mounier N, Günther F, et al. Maximum likelihood method quantifies the overall contribution of gene-environment interaction to continuous traits: An application to complex traits in the UK Biobank. bioRxiv. 2019.' apa: 'Sulc, J., Mounier, N., Günther, F., Winkler, T., Wood, A. R., Frayling, T. M., … Kutalik, Z. (2019). Maximum likelihood method quantifies the overall contribution of gene-environment interaction to continuous traits: An application to complex traits in the UK Biobank. bioRxiv. Cold Spring Harbor Laboratory.' chicago: 'Sulc, Jonathan, Ninon Mounier, Felix Günther, Thomas Winkler, Andrew R. Wood, Timothy M. Frayling, Iris M. Heid, Matthew Richard Robinson, and Zoltán Kutalik. “Maximum Likelihood Method Quantifies the Overall Contribution of Gene-Environment Interaction to Continuous Traits: An Application to Complex Traits in the UK Biobank.” BioRxiv. Cold Spring Harbor Laboratory, 2019.' ieee: 'J. Sulc et al., “Maximum likelihood method quantifies the overall contribution of gene-environment interaction to continuous traits: An application to complex traits in the UK Biobank,” bioRxiv. Cold Spring Harbor Laboratory, 2019.' ista: 'Sulc J, Mounier N, Günther F, Winkler T, Wood AR, Frayling TM, Heid IM, Robinson MR, Kutalik Z. 2019. Maximum likelihood method quantifies the overall contribution of gene-environment interaction to continuous traits: An application to complex traits in the UK Biobank. bioRxiv, .' mla: 'Sulc, Jonathan, et al. “Maximum Likelihood Method Quantifies the Overall Contribution of Gene-Environment Interaction to Continuous Traits: An Application to Complex Traits in the UK Biobank.” BioRxiv, Cold Spring Harbor Laboratory, 2019.' short: J. Sulc, N. Mounier, F. Günther, T. Winkler, A.R. Wood, T.M. Frayling, I.M. Heid, M.R. Robinson, Z. Kutalik, BioRxiv (2019). date_created: 2020-04-30T13:04:26Z date_published: 2019-06-14T00:00:00Z date_updated: 2021-01-12T08:15:30Z day: '14' extern: '1' language: - iso: eng main_file_link: - open_access: '1' url: 'https://doi.org/10.1101/632380 ' month: '06' oa: 1 oa_version: Preprint page: '20' publication: bioRxiv publication_status: published publisher: Cold Spring Harbor Laboratory status: public title: 'Maximum likelihood method quantifies the overall contribution of gene-environment interaction to continuous traits: An application to complex traits in the UK Biobank' type: preprint user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2019' ... --- _id: '8013' article_number: e1007049 article_processing_charge: No article_type: original author: - first_name: Christopher B. full_name: Currin, Christopher B. last_name: Currin - first_name: Phumlani N. full_name: Khoza, Phumlani N. last_name: Khoza - first_name: Alexander D. full_name: Antrobus, Alexander D. last_name: Antrobus - first_name: Peter E. full_name: Latham, Peter E. last_name: Latham - first_name: Tim P full_name: Vogels, Tim P id: CB6FF8D2-008F-11EA-8E08-2637E6697425 last_name: Vogels orcid: 0000-0003-3295-6181 - first_name: Joseph V. full_name: Raimondo, Joseph V. last_name: Raimondo citation: ama: 'Currin CB, Khoza PN, Antrobus AD, Latham PE, Vogels TP, Raimondo JV. Think: Theory for Africa. PLOS Computational Biology. 2019;15(7). doi:10.1371/journal.pcbi.1007049' apa: 'Currin, C. B., Khoza, P. N., Antrobus, A. D., Latham, P. E., Vogels, T. P., & Raimondo, J. V. (2019). Think: Theory for Africa. PLOS Computational Biology. Public Library of Science. https://doi.org/10.1371/journal.pcbi.1007049' chicago: 'Currin, Christopher B., Phumlani N. Khoza, Alexander D. Antrobus, Peter E. Latham, Tim P Vogels, and Joseph V. Raimondo. “Think: Theory for Africa.” PLOS Computational Biology. Public Library of Science, 2019. https://doi.org/10.1371/journal.pcbi.1007049.' ieee: 'C. B. Currin, P. N. Khoza, A. D. Antrobus, P. E. Latham, T. P. Vogels, and J. V. Raimondo, “Think: Theory for Africa,” PLOS Computational Biology, vol. 15, no. 7. Public Library of Science, 2019.' ista: 'Currin CB, Khoza PN, Antrobus AD, Latham PE, Vogels TP, Raimondo JV. 2019. Think: Theory for Africa. PLOS Computational Biology. 15(7), e1007049.' mla: 'Currin, Christopher B., et al. “Think: Theory for Africa.” PLOS Computational Biology, vol. 15, no. 7, e1007049, Public Library of Science, 2019, doi:10.1371/journal.pcbi.1007049.' short: C.B. Currin, P.N. Khoza, A.D. Antrobus, P.E. Latham, T.P. Vogels, J.V. Raimondo, PLOS Computational Biology 15 (2019). date_created: 2020-06-25T12:50:39Z date_published: 2019-07-11T00:00:00Z date_updated: 2021-01-12T08:16:31Z day: '11' ddc: - '570' doi: 10.1371/journal.pcbi.1007049 extern: '1' external_id: pmid: - '31295253' file: - access_level: open_access checksum: 723bdfb6ee5c747cbbb32baf01d17fad content_type: application/pdf creator: cziletti date_created: 2020-07-02T12:22:57Z date_updated: 2020-07-14T12:48:08Z file_id: '8079' file_name: 2019_PlosCompBio_Currin.pdf file_size: 773969 relation: main_file file_date_updated: 2020-07-14T12:48:08Z has_accepted_license: '1' intvolume: ' 15' issue: '7' language: - iso: eng month: '07' oa: 1 oa_version: Published Version pmid: 1 publication: PLOS Computational Biology publication_identifier: issn: - 1553-7358 publication_status: published publisher: Public Library of Science quality_controlled: '1' status: public title: 'Think: Theory for Africa' 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: D865714E-FA4E-11E9-B85B-F5C5E5697425 volume: 15 year: '2019' ... --- _id: '8014' abstract: - lang: eng text: 'Working memory, the ability to keep recently accessed information available for immediate manipulation, has been proposed to rely on two mechanisms that appear difficult to reconcile: self-sustained neural firing, or the opposite—activity-silent synaptic traces. Here we review and contrast models of these two mechanisms, and then show that both phenomena can co-exist within a unified system in which neurons hold information in both activity and synapses. Rapid plasticity in flexibly-coding neurons allows features to be bound together into objects, with an important emergent property being the focus of attention. One memory item is held by persistent activity in an attended or “focused” state, and is thus remembered better than other items. Other, previously attended items can remain in memory but in the background, encoded in activity-silent synaptic traces. This dual functional architecture provides a unified common mechanism accounting for a diversity of perplexing attention and memory effects that have been hitherto difficult to explain in a single theoretical framework.' article_processing_charge: No article_type: original author: - first_name: Sanjay G. full_name: Manohar, Sanjay G. last_name: Manohar - first_name: Nahid full_name: Zokaei, Nahid last_name: Zokaei - first_name: Sean J. full_name: Fallon, Sean J. last_name: Fallon - first_name: Tim P full_name: Vogels, Tim P id: CB6FF8D2-008F-11EA-8E08-2637E6697425 last_name: Vogels orcid: 0000-0003-3295-6181 - first_name: Masud full_name: Husain, Masud last_name: Husain citation: ama: Manohar SG, Zokaei N, Fallon SJ, Vogels TP, Husain M. Neural mechanisms of attending to items in working memory. Neuroscience and Biobehavioral Reviews. 2019;101:1-12. doi:10.1016/j.neubiorev.2019.03.017 apa: Manohar, S. G., Zokaei, N., Fallon, S. J., Vogels, T. P., & Husain, M. (2019). Neural mechanisms of attending to items in working memory. Neuroscience and Biobehavioral Reviews. Elsevier . https://doi.org/10.1016/j.neubiorev.2019.03.017 chicago: Manohar, Sanjay G., Nahid Zokaei, Sean J. Fallon, Tim P Vogels, and Masud Husain. “Neural Mechanisms of Attending to Items in Working Memory.” Neuroscience and Biobehavioral Reviews. Elsevier , 2019. https://doi.org/10.1016/j.neubiorev.2019.03.017. ieee: S. G. Manohar, N. Zokaei, S. J. Fallon, T. P. Vogels, and M. Husain, “Neural mechanisms of attending to items in working memory,” Neuroscience and Biobehavioral Reviews, vol. 101. Elsevier , pp. 1–12, 2019. ista: Manohar SG, Zokaei N, Fallon SJ, Vogels TP, Husain M. 2019. Neural mechanisms of attending to items in working memory. Neuroscience and Biobehavioral Reviews. 101, 1–12. mla: Manohar, Sanjay G., et al. “Neural Mechanisms of Attending to Items in Working Memory.” Neuroscience and Biobehavioral Reviews, vol. 101, Elsevier , 2019, pp. 1–12, doi:10.1016/j.neubiorev.2019.03.017. short: S.G. Manohar, N. Zokaei, S.J. Fallon, T.P. Vogels, M. Husain, Neuroscience and Biobehavioral Reviews 101 (2019) 1–12. date_created: 2020-06-25T12:52:13Z date_published: 2019-06-01T00:00:00Z date_updated: 2021-01-12T08:16:31Z day: '01' ddc: - '570' doi: 10.1016/j.neubiorev.2019.03.017 extern: '1' external_id: pmid: - '30922977' file: - access_level: open_access checksum: 7b972e3d6f7bb3122c8c5648f44e60ca content_type: application/pdf creator: cziletti date_created: 2020-07-02T13:17:52Z date_updated: 2020-07-14T12:48:08Z file_id: '8080' file_name: 2019_NeurosBiobehavRev_Manohar.pdf file_size: 1754418 relation: main_file file_date_updated: 2020-07-14T12:48:08Z has_accepted_license: '1' intvolume: ' 101' language: - iso: eng main_file_link: - open_access: '1' url: 'https://doi.org/10.1101/233007 ' month: '06' oa: 1 oa_version: Published Version page: 1-12 pmid: 1 publication: Neuroscience and Biobehavioral Reviews publication_identifier: issn: - 0149-7634 publication_status: published publisher: 'Elsevier ' quality_controlled: '1' status: public title: Neural mechanisms of attending to items in working memory 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: D865714E-FA4E-11E9-B85B-F5C5E5697425 volume: 101 year: '2019' ... --- _id: '8175' abstract: - lang: eng text: We study edge asymptotics of poissonized Plancherel-type measures on skew Young diagrams (integer partitions). These measures can be seen as generalizations of those studied by Baik--Deift--Johansson and Baik--Rains in resolving Ulam's problem on longest increasing subsequences of random permutations and the last passage percolation (corner growth) discrete versions thereof. Moreover they interpolate between said measures and the uniform measure on partitions. In the new KPZ-like 1/3 exponent edge scaling limit with logarithmic corrections, we find new probability distributions generalizing the classical Tracy--Widom GUE, GOE and GSE distributions from the theory of random matrices. acknowledgement: "D.B. is especially grateful to Patrik Ferrari for suggesting simplifications in Section 3 and\r\nto Alessandra Occelli for suggesting the name for the models of Section 2.\r\n" article_number: '34' article_processing_charge: No author: - first_name: Dan full_name: Betea, Dan last_name: Betea - first_name: Jérémie full_name: Bouttier, Jérémie last_name: Bouttier - first_name: Peter full_name: Nejjar, Peter id: 4BF426E2-F248-11E8-B48F-1D18A9856A87 last_name: Nejjar - first_name: Mirjana full_name: Vuletíc, Mirjana last_name: Vuletíc citation: ama: 'Betea D, Bouttier J, Nejjar P, Vuletíc M. New edge asymptotics of skew Young diagrams via free boundaries. In: Proceedings on the 31st International Conference on Formal Power Series and Algebraic Combinatorics. Formal Power Series and Algebraic Combinatorics; 2019.' apa: 'Betea, D., Bouttier, J., Nejjar, P., & Vuletíc, M. (2019). New edge asymptotics of skew Young diagrams via free boundaries. In Proceedings on the 31st International Conference on Formal Power Series and Algebraic Combinatorics. Ljubljana, Slovenia: Formal Power Series and Algebraic Combinatorics.' chicago: Betea, Dan, Jérémie Bouttier, Peter Nejjar, and Mirjana Vuletíc. “New Edge Asymptotics of Skew Young Diagrams via Free Boundaries.” In Proceedings on the 31st International Conference on Formal Power Series and Algebraic Combinatorics. Formal Power Series and Algebraic Combinatorics, 2019. ieee: D. Betea, J. Bouttier, P. Nejjar, and M. Vuletíc, “New edge asymptotics of skew Young diagrams via free boundaries,” in Proceedings on the 31st International Conference on Formal Power Series and Algebraic Combinatorics, Ljubljana, Slovenia, 2019. ista: 'Betea D, Bouttier J, Nejjar P, Vuletíc M. 2019. New edge asymptotics of skew Young diagrams via free boundaries. Proceedings on the 31st International Conference on Formal Power Series and Algebraic Combinatorics. FPSAC: International Conference on Formal Power Series and Algebraic Combinatorics, 34.' mla: Betea, Dan, et al. “New Edge Asymptotics of Skew Young Diagrams via Free Boundaries.” Proceedings on the 31st International Conference on Formal Power Series and Algebraic Combinatorics, 34, Formal Power Series and Algebraic Combinatorics, 2019. short: D. Betea, J. Bouttier, P. Nejjar, M. Vuletíc, in:, Proceedings on the 31st International Conference on Formal Power Series and Algebraic Combinatorics, Formal Power Series and Algebraic Combinatorics, 2019. conference: end_date: 2019-07-05 location: Ljubljana, Slovenia name: 'FPSAC: International Conference on Formal Power Series and Algebraic Combinatorics' start_date: 2019-07-01 date_created: 2020-07-26T22:01:04Z date_published: 2019-07-01T00:00:00Z date_updated: 2021-01-12T08:17:18Z day: '01' department: - _id: LaEr ec_funded: 1 external_id: arxiv: - '1902.08750' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1902.08750 month: '07' oa: 1 oa_version: Preprint project: - _id: 258DCDE6-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '338804' name: Random matrices, universality and disordered quantum systems - _id: 256E75B8-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '716117' name: Optimal Transport and Stochastic Dynamics publication: Proceedings on the 31st International Conference on Formal Power Series and Algebraic Combinatorics publication_status: published publisher: Formal Power Series and Algebraic Combinatorics quality_controlled: '1' scopus_import: '1' status: public title: New edge asymptotics of skew Young diagrams via free boundaries type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2019' ... --- _id: '8228' abstract: - lang: eng text: "Background: Atopics have a lower risk for malignancies, and IgE targeted to tumors is superior to IgG in fighting cancer. Whether IgE-mediated innate or adaptive immune surveillance can confer protection against tumors remains unclear.\r\nObjective: We aimed to investigate the effects of active and passive immunotherapy to the tumor-associated antigen HER-2 in three murine models differing in Epsilon-B-cell-receptor expression affecting the levels of expressed IgE.\r\nMethods: We compared the levels of several serum specific anti-HER-2 antibodies (IgE, IgG1, IgG2a, IgG2b, IgA) and the survival rates in low-IgE ΔM1M2 mice lacking the transmembrane/cytoplasmic domain of Epsilon-B-cell-receptors expressing reduced IgE levels, high-IgE KN1 mice expressing chimeric Epsilon-Gamma1-B-cell receptors with 4-6-fold elevated serum IgE levels, and wild type (WT) BALB/c. Prior engrafting mice with D2F2/E2 mammary tumors overexpressing HER-2, mice were vaccinated with HER-2 or vehicle control PBS using the Th2-adjuvant Al(OH)3 (active immunotherapy), or treated with the murine anti-HER-2 IgG1 antibody 4D5 (passive immunotherapy).\r\nResults: Overall, among the three strains of mice, HER-2 vaccination induced significantly higher levels of HER-2 specific IgE and IgG1 in high-IgE KN1, while low-IgE ΔM1M2 mice had higher IgG2a levels. HER-2 vaccination and passive immunotherapy prolonged the survival in tumor-grafted WT and low-IgE ΔM1M2 strains compared with treatment controls; active vaccination provided the highest benefit. Notably, untreated high-IgE KN1 mice displayed the longest survival of all strains, which could not be further extended by active or passive immunotherapy.\r\nConclusion: Active and passive immunotherapies prolong survival in wild type and low-IgE ΔM1M2 mice engrafted with mammary tumors. High-IgE KN1 mice have an innate survival benefit following tumor challenge." article_number: '100044' article_processing_charge: No article_type: original author: - first_name: Josef full_name: Singer, Josef last_name: Singer orcid: 0000-0002-8701-2412 - first_name: Gertrude full_name: Achatz-Straussberger, Gertrude last_name: Achatz-Straussberger - first_name: Anna full_name: Bentley-Lukschal, Anna last_name: Bentley-Lukschal - first_name: Judit full_name: Fazekas-Singer, Judit id: 36432834-F248-11E8-B48F-1D18A9856A87 last_name: Fazekas-Singer orcid: 0000-0002-8777-3502 - first_name: Gernot full_name: Achatz, Gernot last_name: Achatz - first_name: Sophia N. full_name: Karagiannis, Sophia N. last_name: Karagiannis - first_name: Erika full_name: Jensen-Jarolim, Erika last_name: Jensen-Jarolim citation: ama: 'Singer J, Achatz-Straussberger G, Bentley-Lukschal A, et al. AllergoOncology: High innate IgE levels are decisive for the survival of cancer-bearing mice. World Allergy Organization Journal. 2019;12(7). doi:10.1016/j.waojou.2019.100044' apa: 'Singer, J., Achatz-Straussberger, G., Bentley-Lukschal, A., Singer, J., Achatz, G., Karagiannis, S. N., & Jensen-Jarolim, E. (2019). AllergoOncology: High innate IgE levels are decisive for the survival of cancer-bearing mice. World Allergy Organization Journal. Elsevier. https://doi.org/10.1016/j.waojou.2019.100044' chicago: 'Singer, Josef, Gertrude Achatz-Straussberger, Anna Bentley-Lukschal, Judit Singer, Gernot Achatz, Sophia N. Karagiannis, and Erika Jensen-Jarolim. “AllergoOncology: High Innate IgE Levels Are Decisive for the Survival of Cancer-Bearing Mice.” World Allergy Organization Journal. Elsevier, 2019. https://doi.org/10.1016/j.waojou.2019.100044.' ieee: 'J. Singer et al., “AllergoOncology: High innate IgE levels are decisive for the survival of cancer-bearing mice,” World Allergy Organization Journal, vol. 12, no. 7. Elsevier, 2019.' ista: 'Singer J, Achatz-Straussberger G, Bentley-Lukschal A, Singer J, Achatz G, Karagiannis SN, Jensen-Jarolim E. 2019. AllergoOncology: High innate IgE levels are decisive for the survival of cancer-bearing mice. World Allergy Organization Journal. 12(7), 100044.' mla: 'Singer, Josef, et al. “AllergoOncology: High Innate IgE Levels Are Decisive for the Survival of Cancer-Bearing Mice.” World Allergy Organization Journal, vol. 12, no. 7, 100044, Elsevier, 2019, doi:10.1016/j.waojou.2019.100044.' short: J. Singer, G. Achatz-Straussberger, A. Bentley-Lukschal, J. Singer, G. Achatz, S.N. Karagiannis, E. Jensen-Jarolim, World Allergy Organization Journal 12 (2019). date_created: 2020-08-10T11:50:54Z date_published: 2019-07-29T00:00:00Z date_updated: 2021-01-12T08:17:36Z day: '29' doi: 10.1016/j.waojou.2019.100044 extern: '1' intvolume: ' 12' issue: '7' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1016/j.waojou.2019.100044 month: '07' oa: 1 oa_version: Published Version publication: World Allergy Organization Journal publication_identifier: issn: - 1939-4551 publication_status: published publisher: Elsevier quality_controlled: '1' status: public title: 'AllergoOncology: High innate IgE levels are decisive for the survival of cancer-bearing mice' type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 12 year: '2019' ... --- _id: '8229' abstract: - lang: eng text: Food proteins may get nitrated by various exogenous or endogenous mechanisms. As individuals might get recurrently exposed to nitrated proteins via daily diet, we aimed to investigate the effect of repeatedly ingested nitrated food proteins on the subsequent immune response in non-allergic and allergic mice using the milk allergen beta-lactoglobulin (BLG) as model food protein in a mouse model. Evaluating the presence of nitrated proteins in food, we could detect 3-nitrotyrosine (3-NT) in extracts of different foods and in stomach content extracts of non-allergic mice under physiological conditions. Chemically nitrated BLG (BLGn) exhibited enhanced susceptibility to degradation in simulated gastric fluid experiments compared to untreated BLG (BLGu). Gavage of BLGn to non-allergic animals increased interferon-γ and interleukin-10 release of stimulated spleen cells and led to the formation of BLG-specific serum IgA. Allergic mice receiving three oral gavages of BLGn had higher levels of mouse mast cell protease-1 (mMCP-1) compared to allergic mice receiving BLGu. Regardless of the preceding immune status, non-allergic or allergic, repeatedly ingested nitrated food proteins seem to considerably influence the subsequent immune response. article_number: '2463' article_processing_charge: No article_type: original author: - first_name: Anna S. full_name: Ondracek, Anna S. last_name: Ondracek orcid: 0000-0001-7625-3651 - first_name: Denise full_name: Heiden, Denise last_name: Heiden - first_name: Gertie J. full_name: Oostingh, Gertie J. last_name: Oostingh - first_name: Elisabeth full_name: Fuerst, Elisabeth last_name: Fuerst - first_name: Judit full_name: Fazekas-Singer, Judit id: 36432834-F248-11E8-B48F-1D18A9856A87 last_name: Fazekas-Singer orcid: 0000-0002-8777-3502 - first_name: Cornelia full_name: Bergmayr, Cornelia last_name: Bergmayr - first_name: Johanna full_name: Rohrhofer, Johanna last_name: Rohrhofer orcid: 0000-0002-2783-2099 - first_name: Erika full_name: Jensen-Jarolim, Erika last_name: Jensen-Jarolim orcid: 0000-0003-4019-5765 - first_name: Albert full_name: Duschl, Albert last_name: Duschl orcid: 0000-0002-7034-9860 - first_name: Eva full_name: Untersmayr, Eva last_name: Untersmayr orcid: 0000-0002-1963-499X citation: ama: Ondracek AS, Heiden D, Oostingh GJ, et al. Immune effects of the nitrated food allergen beta-lactoglobulin in an experimental food allergy model. Nutrients. 2019;11(10). doi:10.3390/nu11102463 apa: Ondracek, A. S., Heiden, D., Oostingh, G. J., Fuerst, E., Singer, J., Bergmayr, C., … Untersmayr, E. (2019). Immune effects of the nitrated food allergen beta-lactoglobulin in an experimental food allergy model. Nutrients. MDPI. https://doi.org/10.3390/nu11102463 chicago: Ondracek, Anna S., Denise Heiden, Gertie J. Oostingh, Elisabeth Fuerst, Judit Singer, Cornelia Bergmayr, Johanna Rohrhofer, Erika Jensen-Jarolim, Albert Duschl, and Eva Untersmayr. “Immune Effects of the Nitrated Food Allergen Beta-Lactoglobulin in an Experimental Food Allergy Model.” Nutrients. MDPI, 2019. https://doi.org/10.3390/nu11102463. ieee: A. S. Ondracek et al., “Immune effects of the nitrated food allergen beta-lactoglobulin in an experimental food allergy model,” Nutrients, vol. 11, no. 10. MDPI, 2019. ista: Ondracek AS, Heiden D, Oostingh GJ, Fuerst E, Singer J, Bergmayr C, Rohrhofer J, Jensen-Jarolim E, Duschl A, Untersmayr E. 2019. Immune effects of the nitrated food allergen beta-lactoglobulin in an experimental food allergy model. Nutrients. 11(10), 2463. mla: Ondracek, Anna S., et al. “Immune Effects of the Nitrated Food Allergen Beta-Lactoglobulin in an Experimental Food Allergy Model.” Nutrients, vol. 11, no. 10, 2463, MDPI, 2019, doi:10.3390/nu11102463. short: A.S. Ondracek, D. Heiden, G.J. Oostingh, E. Fuerst, J. Singer, C. Bergmayr, J. Rohrhofer, E. Jensen-Jarolim, A. Duschl, E. Untersmayr, Nutrients 11 (2019). date_created: 2020-08-10T11:51:04Z date_published: 2019-10-15T00:00:00Z date_updated: 2021-01-12T08:17:36Z day: '15' doi: 10.3390/nu11102463 extern: '1' intvolume: ' 11' issue: '10' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.3390/nu11102463 month: '10' oa: 1 oa_version: Published Version publication: Nutrients publication_identifier: issn: - 2072-6643 publication_status: published publisher: MDPI quality_controlled: '1' status: public title: Immune effects of the nitrated food allergen beta-lactoglobulin in an experimental food allergy model type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 11 year: '2019' ... --- _id: '8227' article_processing_charge: No article_type: letter_note author: - first_name: Kristina M. full_name: Ilieva, Kristina M. last_name: Ilieva - first_name: Judit full_name: Fazekas-Singer, Judit id: 36432834-F248-11E8-B48F-1D18A9856A87 last_name: Fazekas-Singer orcid: 0000-0002-8777-3502 - first_name: Heather J. full_name: Bax, Heather J. last_name: Bax - first_name: Silvia full_name: Crescioli, Silvia last_name: Crescioli - first_name: Laura full_name: Montero‐Morales, Laura last_name: Montero‐Morales - first_name: Silvia full_name: Mele, Silvia last_name: Mele - first_name: Heng Sheng full_name: Sow, Heng Sheng last_name: Sow - first_name: Chara full_name: Stavraka, Chara last_name: Stavraka - first_name: Debra H. full_name: Josephs, Debra H. last_name: Josephs - first_name: James F. full_name: Spicer, James F. last_name: Spicer - first_name: Herta full_name: Steinkellner, Herta last_name: Steinkellner orcid: 0000-0003-4823-1505 - first_name: Erika full_name: Jensen‐Jarolim, Erika last_name: Jensen‐Jarolim orcid: 0000-0003-4019-5765 - first_name: Andrew N. J. full_name: Tutt, Andrew N. J. last_name: Tutt orcid: 0000-0001-8715-2901 - first_name: Sophia N. full_name: Karagiannis, Sophia N. last_name: Karagiannis orcid: 0000-0002-4100-7810 citation: ama: 'Ilieva KM, Singer J, Bax HJ, et al. AllergoOncology: Expression platform development and functional profiling of an anti‐HER2 IgE antibody. Allergy. 2019;74(10):1985-1989. doi:10.1111/all.13818' apa: 'Ilieva, K. M., Singer, J., Bax, H. J., Crescioli, S., Montero‐Morales, L., Mele, S., … Karagiannis, S. N. (2019). AllergoOncology: Expression platform development and functional profiling of an anti‐HER2 IgE antibody. Allergy. Wiley. https://doi.org/10.1111/all.13818' chicago: 'Ilieva, Kristina M., Judit Singer, Heather J. Bax, Silvia Crescioli, Laura Montero‐Morales, Silvia Mele, Heng Sheng Sow, et al. “AllergoOncology: Expression Platform Development and Functional Profiling of an Anti‐HER2 IgE Antibody.” Allergy. Wiley, 2019. https://doi.org/10.1111/all.13818.' ieee: 'K. M. Ilieva et al., “AllergoOncology: Expression platform development and functional profiling of an anti‐HER2 IgE antibody,” Allergy, vol. 74, no. 10. Wiley, pp. 1985–1989, 2019.' ista: 'Ilieva KM, Singer J, Bax HJ, Crescioli S, Montero‐Morales L, Mele S, Sow HS, Stavraka C, Josephs DH, Spicer JF, Steinkellner H, Jensen‐Jarolim E, Tutt ANJ, Karagiannis SN. 2019. AllergoOncology: Expression platform development and functional profiling of an anti‐HER2 IgE antibody. Allergy. 74(10), 1985–1989.' mla: 'Ilieva, Kristina M., et al. “AllergoOncology: Expression Platform Development and Functional Profiling of an Anti‐HER2 IgE Antibody.” Allergy, vol. 74, no. 10, Wiley, 2019, pp. 1985–89, doi:10.1111/all.13818.' short: K.M. Ilieva, J. Singer, H.J. Bax, S. Crescioli, L. Montero‐Morales, S. Mele, H.S. Sow, C. Stavraka, D.H. Josephs, J.F. Spicer, H. Steinkellner, E. Jensen‐Jarolim, A.N.J. Tutt, S.N. Karagiannis, Allergy 74 (2019) 1985–1989. date_created: 2020-08-10T11:50:42Z date_published: 2019-10-01T00:00:00Z date_updated: 2021-01-12T08:17:35Z day: '01' doi: 10.1111/all.13818 extern: '1' intvolume: ' 74' issue: '10' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1111/all.13818 month: '10' oa: 1 oa_version: Published Version page: 1985-1989 publication: Allergy publication_identifier: issn: - 0105-4538 - 1398-9995 publication_status: published publisher: Wiley quality_controlled: '1' status: public title: 'AllergoOncology: Expression platform development and functional profiling of an anti‐HER2 IgE antibody' type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 74 year: '2019' ... --- _id: '8263' abstract: - lang: eng text: "Background: The genus Streptococcus comprises pathogens that strongly influence the health of humans and animals. Genome sequencing of multiple Streptococcus strains demonstrated high variability in gene content and order even in closely related strains of the same species and created a newly emerged object for genomic analysis, the pan-genome. Here we analysed the genome evolution of 25 strains of Streptococcus suis, 50 strains of Streptococcus pyogenes and 28 strains of Streptococcus pneumoniae.\r\n\r\nResults: Fractions of the pan-genome, unique, periphery, and universal genes differ in size, functional composition, the level of nucleotide substitutions, and predisposition to horizontal gene transfer and genomic rearrangements. The density of substitutions in intergenic regions appears to be correlated with selection acting on adjacent genes, implying that more conserved genes tend to have more conserved regulatory regions.\r\nThe total pan-genome of the genus is open, but only due to strain-specific genes, whereas other pan-genome fractions reach saturation. We have identified the set of genes with phylogenies inconsistent with species and non-conserved location in the chromosome; these genes are rare in at least one species and have likely experienced recent horizontal transfer between species. The strain-specific fraction is enriched with mobile elements and hypothetical proteins, but also contains a number of candidate virulence-related genes, so it may have a strong impact on adaptability and pathogenicity.\r\nMapping the rearrangements to the phylogenetic tree revealed large parallel inversions in all species. A parallel inversion of length 15 kB with breakpoints formed by genes encoding surface antigen proteins PhtD and PhtB in S. pneumoniae leads to replacement of gene fragments that likely indicates the action of an antigen variation mechanism.\r\n\r\nConclusions: Members of genus Streptococcus have a highly dynamic, open pan-genome, that potentially confers them with the ability to adapt to changing environmental conditions, i.e. antibiotic resistance or transmission between different hosts. Hence, integrated analysis of all aspects of genome evolution is important for the identification of potential pathogens and design of drugs and vaccines." article_number: '83' article_processing_charge: No article_type: original author: - first_name: Pavel V. full_name: Shelyakin, Pavel V. last_name: Shelyakin orcid: 0000-0003-0120-9319 - first_name: Olga full_name: Bochkareva, Olga id: C4558D3C-6102-11E9-A62E-F418E6697425 last_name: Bochkareva orcid: 0000-0003-1006-6639 - first_name: Anna A. full_name: Karan, Anna A. last_name: Karan - first_name: Mikhail S. full_name: Gelfand, Mikhail S. last_name: Gelfand citation: ama: 'Shelyakin PV, Bochkareva O, Karan AA, Gelfand MS. Micro-evolution of three Streptococcus species: Selection, antigenic variation, and horizontal gene inflow. BMC Evolutionary Biology. 2019;19. doi:10.1186/s12862-019-1403-6' apa: 'Shelyakin, P. V., Bochkareva, O., Karan, A. A., & Gelfand, M. S. (2019). Micro-evolution of three Streptococcus species: Selection, antigenic variation, and horizontal gene inflow. BMC Evolutionary Biology. Springer Nature. https://doi.org/10.1186/s12862-019-1403-6' chicago: 'Shelyakin, Pavel V., Olga Bochkareva, Anna A. Karan, and Mikhail S. Gelfand. “Micro-Evolution of Three Streptococcus Species: Selection, Antigenic Variation, and Horizontal Gene Inflow.” BMC Evolutionary Biology. Springer Nature, 2019. https://doi.org/10.1186/s12862-019-1403-6.' ieee: 'P. V. Shelyakin, O. Bochkareva, A. A. Karan, and M. S. Gelfand, “Micro-evolution of three Streptococcus species: Selection, antigenic variation, and horizontal gene inflow,” BMC Evolutionary Biology, vol. 19. Springer Nature, 2019.' ista: 'Shelyakin PV, Bochkareva O, Karan AA, Gelfand MS. 2019. Micro-evolution of three Streptococcus species: Selection, antigenic variation, and horizontal gene inflow. BMC Evolutionary Biology. 19, 83.' mla: 'Shelyakin, Pavel V., et al. “Micro-Evolution of Three Streptococcus Species: Selection, Antigenic Variation, and Horizontal Gene Inflow.” BMC Evolutionary Biology, vol. 19, 83, Springer Nature, 2019, doi:10.1186/s12862-019-1403-6.' short: P.V. Shelyakin, O. Bochkareva, A.A. Karan, M.S. Gelfand, BMC Evolutionary Biology 19 (2019). date_created: 2020-08-15T11:04:07Z date_published: 2019-03-27T00:00:00Z date_updated: 2023-02-23T13:28:54Z day: '27' doi: 10.1186/s12862-019-1403-6 extern: '1' intvolume: ' 19' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1186/s12862-019-1403-6 month: '03' oa: 1 oa_version: Published Version publication: BMC Evolutionary Biology publication_identifier: issn: - 1471-2148 publication_status: published publisher: Springer Nature quality_controlled: '1' status: public title: 'Micro-evolution of three Streptococcus species: Selection, antigenic variation, and horizontal gene inflow' type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 19 year: '2019' ... --- _id: '8296' abstract: - lang: eng text: While showing great promise, smart contracts are difficult to program correctly, as they need a deep understanding of cryptography and distributed algorithms, and offer limited functionality, as they have to be deterministic and cannot operate on secret data. In this paper we present Protean, a general-purpose decentralized computing platform that addresses these limitations by moving from a monolithic execution model, where all participating nodes store all the state and execute every computation, to a modular execution-model. Protean employs secure specialized modules, called functional units, for building decentralized applications that are currently insecure or impossible to implement with smart contracts. Each functional unit is a distributed system that provides a special-purpose functionality by exposing atomic transactions to the smart-contract developer. Combining these transactions into arbitrarily-defined workflows, developers can build a larger class of decentralized applications, such as provably-secure and fair lotteries or e-voting. article_processing_charge: No author: - first_name: Enis Ceyhun full_name: Alp, Enis Ceyhun last_name: Alp - first_name: Eleftherios full_name: Kokoris Kogias, Eleftherios id: f5983044-d7ef-11ea-ac6d-fd1430a26d30 last_name: Kokoris Kogias - first_name: Georgia full_name: Fragkouli, Georgia last_name: Fragkouli - first_name: Bryan full_name: Ford, Bryan last_name: Ford citation: ama: 'Alp EC, Kokoris Kogias E, Fragkouli G, Ford B. Rethinking general-purpose decentralized computing. In: Proceedings of the Workshop on Hot Topics in Operating Systems. ACM; 2019:105-112. doi:10.1145/3317550.3321448' apa: 'Alp, E. C., Kokoris Kogias, E., Fragkouli, G., & Ford, B. (2019). Rethinking general-purpose decentralized computing. In Proceedings of the Workshop on Hot Topics in Operating Systems (pp. 105–112). Bertinoro, Italy: ACM. https://doi.org/10.1145/3317550.3321448' chicago: Alp, Enis Ceyhun, Eleftherios Kokoris Kogias, Georgia Fragkouli, and Bryan Ford. “Rethinking General-Purpose Decentralized Computing.” In Proceedings of the Workshop on Hot Topics in Operating Systems, 105–12. ACM, 2019. https://doi.org/10.1145/3317550.3321448. ieee: E. C. Alp, E. Kokoris Kogias, G. Fragkouli, and B. Ford, “Rethinking general-purpose decentralized computing,” in Proceedings of the Workshop on Hot Topics in Operating Systems, Bertinoro, Italy, 2019, pp. 105–112. ista: 'Alp EC, Kokoris Kogias E, Fragkouli G, Ford B. 2019. Rethinking general-purpose decentralized computing. Proceedings of the Workshop on Hot Topics in Operating Systems. HotOS: Workshop on Hot Topics in Operating Systems, 105–112.' mla: Alp, Enis Ceyhun, et al. “Rethinking General-Purpose Decentralized Computing.” Proceedings of the Workshop on Hot Topics in Operating Systems, ACM, 2019, pp. 105–12, doi:10.1145/3317550.3321448. short: E.C. Alp, E. Kokoris Kogias, G. Fragkouli, B. Ford, in:, Proceedings of the Workshop on Hot Topics in Operating Systems, ACM, 2019, pp. 105–112. conference: end_date: 2019-05-15 location: Bertinoro, Italy name: 'HotOS: Workshop on Hot Topics in Operating Systems' start_date: 2019-05-13 date_created: 2020-08-26T11:45:45Z date_published: 2019-05-01T00:00:00Z date_updated: 2021-01-12T08:17:56Z day: '01' doi: 10.1145/3317550.3321448 extern: '1' language: - iso: eng month: '05' oa_version: None page: 105-112 publication: Proceedings of the Workshop on Hot Topics in Operating Systems publication_identifier: isbn: - '9781450367271' publication_status: published publisher: ACM quality_controlled: '1' scopus_import: '1' status: public title: Rethinking general-purpose decentralized computing type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2019' ... --- _id: '8304' abstract: - lang: eng text: "Enabling secure communication across distributed systems is usually studied under the assumption of trust between the different systems and an external adversary trying to compromise the messages. With the appearance of distributed ledgers or blockchains, numerous protocols have emerged, which attempt to achieve trustless communication between distrusting ledgers and participants. Cross-chain communication (CCC) thereby plays a fundamental role in cryptocurrency exchanges, sharding, bootstrapping of new and feature-extension of existing distributed ledgers. Unfortunately, existing proposals are designed ad-hoc for specific use-cases, making it hard to gain confidence on their correctness and composability.\r\nWe provide the first systematic exposition of protocols for CCC. First, we formalize the underlying research problem and show that CCC is impossible without a trusted third party, contrary to common beliefs in the blockchain community. We then develop a framework to evaluate existing and to design new cross-chain protocols. The framework is based on the use case, the trust model, and the security assumptions of interlinked blockchains. Finally, we identify security and privacy challenges faced by protocols in the cross-chain setting.\r\nThis Systematization of Knowledge (SoK) offers a comprehensive guide for designing protocols bridging the numerous distributed ledgers available today. It aims to facilitate clearer communication between academia and industry in the field." article_number: 2019/1128 article_processing_charge: No author: - first_name: Alexei full_name: Zamyatin, Alexei last_name: Zamyatin - first_name: Mustafa full_name: Al-Bassam, Mustafa last_name: Al-Bassam - first_name: Dionysis full_name: Zindros, Dionysis last_name: Zindros - first_name: Eleftherios full_name: Kokoris Kogias, Eleftherios id: f5983044-d7ef-11ea-ac6d-fd1430a26d30 last_name: Kokoris Kogias - first_name: Pedro full_name: Moreno-Sanchez, Pedro last_name: Moreno-Sanchez - first_name: Aggelos full_name: Kiayias, Aggelos last_name: Kiayias - first_name: William J. full_name: Knottenbelt, William J. last_name: Knottenbelt citation: ama: 'Zamyatin A, Al-Bassam M, Zindros D, et al. SoK: Communication across distributed ledgers. Cryptology ePrint Archive.' apa: 'Zamyatin, A., Al-Bassam, M., Zindros, D., Kokoris Kogias, E., Moreno-Sanchez, P., Kiayias, A., & Knottenbelt, W. J. (n.d.). SoK: Communication across distributed ledgers. Cryptology ePrint Archive.' chicago: 'Zamyatin, Alexei, Mustafa Al-Bassam, Dionysis Zindros, Eleftherios Kokoris Kogias, Pedro Moreno-Sanchez, Aggelos Kiayias, and William J. Knottenbelt. “SoK: Communication across Distributed Ledgers.” Cryptology EPrint Archive, n.d.' ieee: 'A. Zamyatin et al., “SoK: Communication across distributed ledgers,” Cryptology ePrint Archive. .' ista: 'Zamyatin A, Al-Bassam M, Zindros D, Kokoris Kogias E, Moreno-Sanchez P, Kiayias A, Knottenbelt WJ. SoK: Communication across distributed ledgers. Cryptology ePrint Archive, 2019/1128.' mla: 'Zamyatin, Alexei, et al. “SoK: Communication across Distributed Ledgers.” Cryptology EPrint Archive, 2019/1128.' short: A. Zamyatin, M. Al-Bassam, D. Zindros, E. Kokoris Kogias, P. Moreno-Sanchez, A. Kiayias, W.J. Knottenbelt, Cryptology EPrint Archive (n.d.). date_created: 2020-08-26T12:16:38Z date_published: 2019-10-01T00:00:00Z date_updated: 2021-09-24T12:08:14Z day: '01' extern: '1' language: - iso: eng main_file_link: - open_access: '1' url: 'https://eprint.iacr.org/2019/1128 ' month: '10' oa: 1 oa_version: Preprint publication: Cryptology ePrint Archive publication_status: submitted status: public title: 'SoK: Communication across distributed ledgers' type: preprint user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 year: '2019' ... --- _id: '8303' abstract: - lang: eng text: 'ByzCoin, a promising alternative of Bitcoin, is a scalable consensus protocol used as a building block of many research and enterprise-level decentralized systems. In this paper, we show that ByzCoin is unsuitable for deployment in an anopen, adversarial network and instead introduceMOTOR. MOTORis designed as a secure, robust, and scalable consensus suitable for permissionless sharded blockchains. MOTORachieves these properties by making four key design choices: (a) it prioritizes robustness in adversarial environments while maintaining adequate scalability, (b) it employees provably correct cryptography that resists DoS attacks from individual nodes, (c) it deploys unpredictable rotating leaders to defend against mildly-adaptive adversaries and prevents censorship, and (d) it creates an incentive compatible reward mechanism. These choices are materialized as (a) a “rotating subleader” communication pattern that balances the scalability needs with the robustness requirements under failures, (b) deployment of provable secure BLS multi-signatures, (c) use of deterministic thresh-old signatures as a source of randomness and (d) careful design of the reward allocation mechanism. We have implemented MOTORand compare it withByzCoin. We show that MOTORcan scale similar to ByzCoin with an at most2xoverhead whereas it maintains good performance even under high-percentage of faults, unlike ByzCoin.' article_number: 2019/676 article_processing_charge: No author: - first_name: Eleftherios full_name: Kokoris Kogias, Eleftherios id: f5983044-d7ef-11ea-ac6d-fd1430a26d30 last_name: Kokoris Kogias citation: ama: Kokoris Kogias E. Robust and scalable consensus for sharded distributed ledgers. Cryptology ePrint Archive. apa: Kokoris Kogias, E. (n.d.). Robust and scalable consensus for sharded distributed ledgers. Cryptology ePrint Archive. chicago: Kokoris Kogias, Eleftherios. “Robust and Scalable Consensus for Sharded Distributed Ledgers.” Cryptology EPrint Archive, n.d. ieee: E. Kokoris Kogias, “Robust and scalable consensus for sharded distributed ledgers,” Cryptology ePrint Archive. . ista: Kokoris Kogias E. Robust and scalable consensus for sharded distributed ledgers. Cryptology ePrint Archive, 2019/676. mla: Kokoris Kogias, Eleftherios. “Robust and Scalable Consensus for Sharded Distributed Ledgers.” Cryptology EPrint Archive, 2019/676. short: E. Kokoris Kogias, Cryptology EPrint Archive (n.d.). date_created: 2020-08-26T12:13:56Z date_published: 2019-06-06T00:00:00Z date_updated: 2021-09-24T12:07:11Z day: '06' extern: '1' language: - iso: eng main_file_link: - open_access: '1' url: https://eprint.iacr.org/2019/676 month: '06' oa: 1 oa_version: Preprint publication: Cryptology ePrint Archive publication_status: submitted status: public title: Robust and scalable consensus for sharded distributed ledgers type: preprint user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 year: '2019' ... --- _id: '8311' abstract: - lang: eng text: 'One of the core promises of blockchain technology is that of enabling trustworthy data dissemination in a trustless environment. What current blockchain systems deliver, however, is slow dissemination of public data, rendering blockchain technology unusable in settings where latency, transaction capacity, or data confidentiality are important. In this thesis we focus on providing solutions on two of the most pressing problems blockchain technology currently faces: scalability and data confidentiality. To address the scalability issue, we present OMNILEDGER, a novel scale-out distributed ledger that preserves long-term 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 cross-shard commit protocol that atomically handles transactions affecting multiple shards. To enable secure sharing of confidential data we present CALYPSO, the first fully decentralized, auditable access-control framework for secure blockchain-based data sharing which builds upon two abstractions. First, on-chain secrets enable collective management of (verifiably shared) secrets under a Byzantine adversary where an access-control blockchain enforces user-specific access rules and a secret-management cothority administers encrypted data. Second, skipchain-based identity and access management enables efficient administration of dynamic, sovereign identities and access policies and, in particular, permits clients to maintain long-term relationships with respect to evolving user identities thanks to the trust-delegating forward links of skipchains. In order to build OMNILEDGER and CALYPSO, we first build a set of tools for efficient decentralization, which are presented in Part II of this dissertation. These tools can be used in decentralized and distributed systems to achieve (1) scalable consensus (BYZCOIN), (2) bias- resistant distributed randomness creations (RANDHOUND), and (3) relationship-keeping between independently updating communication endpoints (SKIPCHAINIAC). Although we use this tools in the scope off this thesis, they can be (and already have been) used in a far wider scope.' article_processing_charge: No author: - first_name: Eleftherios full_name: Kokoris Kogias, Eleftherios id: f5983044-d7ef-11ea-ac6d-fd1430a26d30 last_name: Kokoris Kogias citation: ama: Kokoris Kogias E. Secure, confidential blockchains providing high throughput and low latency. 2019. doi:10.5075/epfl-thesis-7101 apa: Kokoris Kogias, E. (2019). Secure, confidential blockchains providing high throughput and low latency. École Polytechnique Fédérale de Lausanne. https://doi.org/10.5075/epfl-thesis-7101 chicago: Kokoris Kogias, Eleftherios. “Secure, Confidential Blockchains Providing High Throughput and Low Latency.” École Polytechnique Fédérale de Lausanne, 2019. https://doi.org/10.5075/epfl-thesis-7101. ieee: E. Kokoris Kogias, “Secure, confidential blockchains providing high throughput and low latency,” École Polytechnique Fédérale de Lausanne, 2019. ista: Kokoris Kogias E. 2019. Secure, confidential blockchains providing high throughput and low latency. École Polytechnique Fédérale de Lausanne. mla: Kokoris Kogias, Eleftherios. Secure, Confidential Blockchains Providing High Throughput and Low Latency. École Polytechnique Fédérale de Lausanne, 2019, doi:10.5075/epfl-thesis-7101. short: E. Kokoris Kogias, Secure, Confidential Blockchains Providing High Throughput and Low Latency, École Polytechnique Fédérale de Lausanne, 2019. date_created: 2020-08-27T11:22:24Z date_published: 2019-09-27T00:00:00Z date_updated: 2021-12-20T15:30:47Z day: '27' degree_awarded: PhD doi: 10.5075/epfl-thesis-7101 extern: '1' language: - iso: eng main_file_link: - open_access: '1' url: https://www.doi.org/10.5075/epfl-thesis-7101 month: '09' oa: 1 oa_version: Published Version page: '244' publication_status: published publisher: École Polytechnique Fédérale de Lausanne status: public supervisor: - first_name: Bryan Alexander full_name: Ford, Bryan Alexander last_name: Ford title: Secure, confidential blockchains providing high throughput and low latency type: dissertation user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 year: '2019' ... --- _id: '8314' abstract: - lang: eng text: "Off-chain protocols (channels) are a promising solution to the scalability and privacy challenges of blockchain payments. Current proposals, however, require synchrony assumptions to preserve the safety of a channel, leaking to an adversary the exact amount of time needed to control the network for a successful attack. In this paper, we introduce Brick, the first payment channel that remains secure under network asynchrony and concurrently provides correct incentives. The core idea is to incorporate the conflict resolution process within the channel by introducing a rational committee of external parties, called Wardens. Hence, if a party wants to close a channel unilaterally, it can only get the committee's approval for the last valid state. Brick provides sub-second latency because it does not employ heavy-weight consensus. Instead,\r\nBrick uses consistent broadcast to announce updates and close the channel, a light-weight abstraction that is powerful enough to preserve safety and liveness to any rational parties. Furthermore, we consider permissioned blockchains, where the additional property of auditability might be desired for regulatory purposes. We introduce Brick+, an off-chain construction that provides auditability on top of Brick without conflicting with its privacy guarantees. We formally define the properties our payment channel construction should fulfill, and prove that both Brick and Brick+ satisfy them. We also design incentives for Brick such that honest and rational behavior aligns. Finally, we provide a reference implementation of the smart contracts in Solidity." article_number: '1905.11360' article_processing_charge: No author: - first_name: Georgia full_name: Avarikioti, Georgia last_name: Avarikioti - first_name: Eleftherios full_name: Kokoris Kogias, Eleftherios id: f5983044-d7ef-11ea-ac6d-fd1430a26d30 last_name: Kokoris Kogias - first_name: Roger full_name: Wattenhofer, Roger last_name: Wattenhofer - first_name: Dionysis full_name: Zindros, Dionysis last_name: Zindros citation: ama: 'Avarikioti G, Kokoris Kogias E, Wattenhofer R, Zindros D. Brick: Asynchronous payment channels. arXiv.' apa: 'Avarikioti, G., Kokoris Kogias, E., Wattenhofer, R., & Zindros, D. (n.d.). Brick: Asynchronous payment channels. arXiv.' chicago: 'Avarikioti, Georgia, Eleftherios Kokoris Kogias, Roger Wattenhofer, and Dionysis Zindros. “Brick: Asynchronous Payment Channels.” ArXiv, n.d.' ieee: 'G. Avarikioti, E. Kokoris Kogias, R. Wattenhofer, and D. Zindros, “Brick: Asynchronous payment channels,” arXiv. .' ista: 'Avarikioti G, Kokoris Kogias E, Wattenhofer R, Zindros D. Brick: Asynchronous payment channels. arXiv, 1905.11360.' mla: 'Avarikioti, Georgia, et al. “Brick: Asynchronous Payment Channels.” ArXiv, 1905.11360.' short: G. Avarikioti, E. Kokoris Kogias, R. Wattenhofer, D. Zindros, ArXiv (n.d.). date_created: 2020-08-27T11:36:54Z date_published: 2019-05-27T00:00:00Z date_updated: 2021-01-12T08:18:04Z day: '27' extern: '1' external_id: arxiv: - '1905.11360' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1905.11360 month: '05' oa: 1 oa_version: Preprint publication: arXiv publication_status: submitted status: public title: 'Brick: Asynchronous payment channels' type: preprint user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2019' ... --- _id: '8315' abstract: - lang: eng text: "Sharding distributed ledgers is the most promising on-chain solution for scaling blockchain technology. In this work, we define and analyze the properties a sharded distributed ledger should fulfill. More specifically, we show that a sharded blockchain cannot be scalable under a fully adaptive adversary, but it can scale up to $O(n/\\log n)$ under an epoch-adaptive adversary. This is possible only if the distributed ledger creates succinct proofs of the valid state updates at the end of each epoch. Our model builds upon and extends the Bitcoin backbone protocol by defining consistency and\r\nscalability. Consistency encompasses the need for atomic execution of cross-shard transactions to preserve safety, whereas scalability encapsulates the speedup a sharded system can gain in comparison to a non-sharded system. In\r\norder to show the power of our framework, we analyze the most prominent sharded blockchains and either prove their correctness (OmniLedger, RapidChain) under our model or pinpoint where they fail to balance the consistency and\r\nscalability requirements (Elastico, Monoxide). " article_number: '1910.10434' article_processing_charge: No author: - first_name: Georgia full_name: Avarikioti, Georgia last_name: Avarikioti - first_name: Eleftherios full_name: Kokoris Kogias, Eleftherios id: f5983044-d7ef-11ea-ac6d-fd1430a26d30 last_name: Kokoris Kogias - first_name: Roger full_name: Wattenhofer, Roger last_name: Wattenhofer citation: ama: 'Avarikioti G, Kokoris Kogias E, Wattenhofer R. Divide and scale: Formalization of distributed ledger sharding protocols. arXiv.' apa: 'Avarikioti, G., Kokoris Kogias, E., & Wattenhofer, R. (n.d.). Divide and scale: Formalization of distributed ledger sharding protocols. arXiv.' chicago: 'Avarikioti, Georgia, Eleftherios Kokoris Kogias, and Roger Wattenhofer. “Divide and Scale: Formalization of Distributed Ledger Sharding Protocols.” ArXiv, n.d.' ieee: 'G. Avarikioti, E. Kokoris Kogias, and R. Wattenhofer, “Divide and scale: Formalization of distributed ledger sharding protocols,” arXiv. .' ista: 'Avarikioti G, Kokoris Kogias E, Wattenhofer R. Divide and scale: Formalization of distributed ledger sharding protocols. arXiv, 1910.10434.' mla: 'Avarikioti, Georgia, et al. “Divide and Scale: Formalization of Distributed Ledger Sharding Protocols.” ArXiv, 1910.10434.' short: G. Avarikioti, E. Kokoris Kogias, R. Wattenhofer, ArXiv (n.d.). date_created: 2020-08-27T11:37:43Z date_published: 2019-10-23T00:00:00Z date_updated: 2021-01-12T08:18:05Z day: '23' extern: '1' external_id: arxiv: - '1910.10434' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1910.10434 month: '10' oa: 1 oa_version: Preprint publication: arXiv publication_status: submitted status: public title: 'Divide and scale: Formalization of distributed ledger sharding protocols' type: preprint user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2019' ... --- _id: '8313' abstract: - lang: eng text: The present invention concerns a computer-implemented method for secure data exchange between a sender (A) and a recipient (B), wherein the method is performed by the sender (A) and comprises encrypting data using a symmetric key k, creating a write transaction T W , wherein the write transaction T W comprises information usable to derive the symmetric key k and an access policy identifying the recipient (B) as being allowed to decrypt the encrypted data, providing the recipient (B) access to the encrypted data, and sending the write transaction T W to a first group of servers (AC) for being stored in a blockchain data structure maintained by the first group of servers (AC). applicant: - 'École Polytechnique Fédérale De Lausanne ' article_processing_charge: No author: - first_name: Bryan full_name: Ford, Bryan last_name: Ford - first_name: Linus full_name: Gasser, Linus last_name: Gasser - first_name: Eleftherios full_name: Kokoris Kogias, Eleftherios id: f5983044-d7ef-11ea-ac6d-fd1430a26d30 last_name: Kokoris Kogias - first_name: Philipp full_name: Janovic, Philipp last_name: Janovic citation: ama: Ford B, Gasser L, Kokoris Kogias E, Janovic P. Methods and systems for secure data exchange. 2019. apa: Ford, B., Gasser, L., Kokoris Kogias, E., & Janovic, P. (2019). Methods and systems for secure data exchange. chicago: Ford, Bryan, Linus Gasser, Eleftherios Kokoris Kogias, and Philipp Janovic. “Methods and Systems for Secure Data Exchange,” 2019. ieee: B. Ford, L. Gasser, E. Kokoris Kogias, and P. Janovic, “Methods and systems for secure data exchange.” 2019. ista: Ford B, Gasser L, Kokoris Kogias E, Janovic P. 2019. Methods and systems for secure data exchange. mla: Ford, Bryan, et al. Methods and Systems for Secure Data Exchange. 2019. short: B. Ford, L. Gasser, E. Kokoris Kogias, P. Janovic, (2019). date_created: 2020-08-27T11:24:44Z date_published: 2019-08-22T00:00:00Z date_updated: 2022-01-05T14:00:32Z day: '22' extern: '1' ipc: G06F21/62 ; H04L9/08 ; H04L9/32 ipn: WO2019158209 (A1) main_file_link: - open_access: '1' url: https://patents.google.com/patent/WO2019158209A1 month: '08' oa: 1 oa_version: Published Version publication_date: 2019-08-22 status: public title: Methods and systems for secure data exchange type: patent user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 year: '2019' ... --- _id: '8405' abstract: - lang: eng text: Atomic-resolution structure determination is crucial for understanding protein function. Cryo-EM and NMR spectroscopy both provide structural information, but currently cryo-EM does not routinely give access to atomic-level structural data, and, generally, NMR structure determination is restricted to small (<30 kDa) proteins. We introduce an integrated structure determination approach that simultaneously uses NMR and EM data to overcome the limits of each of these methods. The approach enables structure determination of the 468 kDa large dodecameric aminopeptidase TET2 to a precision and accuracy below 1 Å by combining secondary-structure information obtained from near-complete magic-angle-spinning NMR assignments of the 39 kDa-large subunits, distance restraints from backbone amides and ILV methyl groups, and a 4.1 Å resolution EM map. The resulting structure exceeds current standards of NMR and EM structure determination in terms of molecular weight and precision. Importantly, the approach is successful even in cases where only medium-resolution cryo-EM data are available. article_number: '2697' article_processing_charge: No article_type: original author: - first_name: Diego F. full_name: Gauto, Diego F. last_name: Gauto - first_name: Leandro F. full_name: Estrozi, Leandro F. last_name: Estrozi - first_name: Charles D. full_name: Schwieters, Charles D. last_name: Schwieters - first_name: Gregory full_name: Effantin, Gregory last_name: Effantin - first_name: Pavel full_name: Macek, Pavel last_name: Macek - first_name: Remy full_name: Sounier, Remy last_name: Sounier - first_name: Astrid C. full_name: Sivertsen, Astrid C. last_name: Sivertsen - first_name: Elena full_name: Schmidt, Elena last_name: Schmidt - first_name: Rime full_name: Kerfah, Rime last_name: Kerfah - first_name: Guillaume full_name: Mas, Guillaume last_name: Mas - first_name: Jacques-Philippe full_name: Colletier, Jacques-Philippe last_name: Colletier - first_name: Peter full_name: Güntert, Peter last_name: Güntert - first_name: Adrien full_name: Favier, Adrien last_name: Favier - first_name: Guy full_name: Schoehn, Guy last_name: Schoehn - first_name: Paul full_name: Schanda, Paul id: 7B541462-FAF6-11E9-A490-E8DFE5697425 last_name: Schanda orcid: 0000-0002-9350-7606 - first_name: Jerome full_name: Boisbouvier, Jerome last_name: Boisbouvier citation: ama: Gauto DF, Estrozi LF, Schwieters CD, et al. Integrated NMR and cryo-EM atomic-resolution structure determination of a half-megadalton enzyme complex. Nature Communications. 2019;10. doi:10.1038/s41467-019-10490-9 apa: Gauto, D. F., Estrozi, L. F., Schwieters, C. D., Effantin, G., Macek, P., Sounier, R., … Boisbouvier, J. (2019). Integrated NMR and cryo-EM atomic-resolution structure determination of a half-megadalton enzyme complex. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-019-10490-9 chicago: Gauto, Diego F., Leandro F. Estrozi, Charles D. Schwieters, Gregory Effantin, Pavel Macek, Remy Sounier, Astrid C. Sivertsen, et al. “Integrated NMR and Cryo-EM Atomic-Resolution Structure Determination of a Half-Megadalton Enzyme Complex.” Nature Communications. Springer Nature, 2019. https://doi.org/10.1038/s41467-019-10490-9. ieee: D. F. Gauto et al., “Integrated NMR and cryo-EM atomic-resolution structure determination of a half-megadalton enzyme complex,” Nature Communications, vol. 10. Springer Nature, 2019. ista: Gauto DF, Estrozi LF, Schwieters CD, Effantin G, Macek P, Sounier R, Sivertsen AC, Schmidt E, Kerfah R, Mas G, Colletier J-P, Güntert P, Favier A, Schoehn G, Schanda P, Boisbouvier J. 2019. Integrated NMR and cryo-EM atomic-resolution structure determination of a half-megadalton enzyme complex. Nature Communications. 10, 2697. mla: Gauto, Diego F., et al. “Integrated NMR and Cryo-EM Atomic-Resolution Structure Determination of a Half-Megadalton Enzyme Complex.” Nature Communications, vol. 10, 2697, Springer Nature, 2019, doi:10.1038/s41467-019-10490-9. short: D.F. Gauto, L.F. Estrozi, C.D. Schwieters, G. Effantin, P. Macek, R. Sounier, A.C. Sivertsen, E. Schmidt, R. Kerfah, G. Mas, J.-P. Colletier, P. Güntert, A. Favier, G. Schoehn, P. Schanda, J. Boisbouvier, Nature Communications 10 (2019). date_created: 2020-09-17T10:28:25Z date_published: 2019-06-19T00:00:00Z date_updated: 2021-01-12T08:19:03Z day: '19' doi: 10.1038/s41467-019-10490-9 extern: '1' external_id: pmid: - '31217444' intvolume: ' 10' keyword: - General Biochemistry - Genetics and Molecular Biology - General Physics and Astronomy - General Chemistry language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1038/s41467-019-10490-9 month: '06' oa: 1 oa_version: Published Version pmid: 1 publication: Nature Communications publication_identifier: issn: - 2041-1723 publication_status: published publisher: Springer Nature quality_controlled: '1' status: public title: Integrated NMR and cryo-EM atomic-resolution structure determination of a half-megadalton enzyme complex type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 10 year: '2019' ... --- _id: '8406' abstract: - lang: eng text: Coordinated conformational transitions in oligomeric enzymatic complexes modulate function in response to substrates and play a crucial role in enzyme inhibition and activation. Caseinolytic protease (ClpP) is a tetradecameric complex, which has emerged as a drug target against multiple pathogenic bacteria. Activation of different ClpPs by inhibitors has been independently reported from drug development efforts, but no rationale for inhibitor-induced activation has been hitherto proposed. Using an integrated approach that includes x-ray crystallography, solid- and solution-state nuclear magnetic resonance, molecular dynamics simulations, and isothermal titration calorimetry, we show that the proteasome inhibitor bortezomib binds to the ClpP active-site serine, mimicking a peptide substrate, and induces a concerted allosteric activation of the complex. The bortezomib-activated conformation also exhibits a higher affinity for its cognate unfoldase ClpX. We propose a universal allosteric mechanism, where substrate binding to a single subunit locks ClpP into an active conformation optimized for chaperone association and protein processive degradation. article_number: eaaw3818 article_processing_charge: No article_type: original author: - first_name: Jan full_name: Felix, Jan last_name: Felix - first_name: Katharina full_name: Weinhäupl, Katharina last_name: Weinhäupl - first_name: Christophe full_name: Chipot, Christophe last_name: Chipot - first_name: François full_name: Dehez, François last_name: Dehez - first_name: Audrey full_name: Hessel, Audrey last_name: Hessel - first_name: Diego F. full_name: Gauto, Diego F. last_name: Gauto - first_name: Cecile full_name: Morlot, Cecile last_name: Morlot - first_name: Olga full_name: Abian, Olga last_name: Abian - first_name: Irina full_name: Gutsche, Irina last_name: Gutsche - first_name: Adrian full_name: Velazquez-Campoy, Adrian last_name: Velazquez-Campoy - first_name: Paul full_name: Schanda, Paul id: 7B541462-FAF6-11E9-A490-E8DFE5697425 last_name: Schanda orcid: 0000-0002-9350-7606 - first_name: Hugo full_name: Fraga, Hugo last_name: Fraga citation: ama: Felix J, Weinhäupl K, Chipot C, et al. Mechanism of the allosteric activation of the ClpP protease machinery by substrates and active-site inhibitors. Science Advances. 2019;5(9). doi:10.1126/sciadv.aaw3818 apa: Felix, J., Weinhäupl, K., Chipot, C., Dehez, F., Hessel, A., Gauto, D. F., … Fraga, H. (2019). Mechanism of the allosteric activation of the ClpP protease machinery by substrates and active-site inhibitors. Science Advances. American Association for the Advancement of Science. https://doi.org/10.1126/sciadv.aaw3818 chicago: Felix, Jan, Katharina Weinhäupl, Christophe Chipot, François Dehez, Audrey Hessel, Diego F. Gauto, Cecile Morlot, et al. “Mechanism of the Allosteric Activation of the ClpP Protease Machinery by Substrates and Active-Site Inhibitors.” Science Advances. American Association for the Advancement of Science, 2019. https://doi.org/10.1126/sciadv.aaw3818. ieee: J. Felix et al., “Mechanism of the allosteric activation of the ClpP protease machinery by substrates and active-site inhibitors,” Science Advances, vol. 5, no. 9. American Association for the Advancement of Science, 2019. ista: Felix J, Weinhäupl K, Chipot C, Dehez F, Hessel A, Gauto DF, Morlot C, Abian O, Gutsche I, Velazquez-Campoy A, Schanda P, Fraga H. 2019. Mechanism of the allosteric activation of the ClpP protease machinery by substrates and active-site inhibitors. Science Advances. 5(9), eaaw3818. mla: Felix, Jan, et al. “Mechanism of the Allosteric Activation of the ClpP Protease Machinery by Substrates and Active-Site Inhibitors.” Science Advances, vol. 5, no. 9, eaaw3818, American Association for the Advancement of Science, 2019, doi:10.1126/sciadv.aaw3818. short: J. Felix, K. Weinhäupl, C. Chipot, F. Dehez, A. Hessel, D.F. Gauto, C. Morlot, O. Abian, I. Gutsche, A. Velazquez-Campoy, P. Schanda, H. Fraga, Science Advances 5 (2019). date_created: 2020-09-17T10:28:36Z date_published: 2019-09-04T00:00:00Z date_updated: 2021-01-12T08:19:03Z day: '04' doi: 10.1126/sciadv.aaw3818 extern: '1' intvolume: ' 5' issue: '9' language: - iso: eng main_file_link: - open_access: '1' url: ' https://doi.org/10.1126/sciadv.aaw3818' month: '09' oa: 1 oa_version: Published Version publication: Science Advances publication_identifier: issn: - 2375-2548 publication_status: published publisher: American Association for the Advancement of Science quality_controlled: '1' status: public title: Mechanism of the allosteric activation of the ClpP protease machinery by substrates and active-site inhibitors type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 5 year: '2019' ... --- _id: '8413' abstract: - lang: eng text: NMR relaxation dispersion methods provide a holistic way to observe microsecond time-scale protein backbone motion both in solution and in the solid state. Different nuclei (1H and 15N) and different relaxation dispersion techniques (Bloch–McConnell and near-rotary-resonance) give complementary information about the amplitudes and time scales of the conformational dynamics and provide comprehensive insights into the mechanistic details of the structural rearrangements. In this paper, we exemplify the benefits of the combination of various solution- and solid-state relaxation dispersion methods on a microcrystalline protein (α-spectrin SH3 domain), for which we are able to identify and model the functionally relevant conformational rearrangements around the ligand recognition loop occurring on multiple microsecond time scales. The observed loop motions suggest that the SH3 domain exists in a binding-competent conformation in dynamic equilibrium with a sterically impaired ground-state conformation both in solution and in crystalline form. This inherent plasticity between the interconverting macrostates is compatible with a conformational-preselection model and provides new insights into the recognition mechanisms of SH3 domains. article_processing_charge: No article_type: original author: - first_name: Petra full_name: Rovó, Petra last_name: Rovó - first_name: Colin A. full_name: Smith, Colin A. last_name: Smith - first_name: Diego full_name: Gauto, Diego last_name: Gauto - first_name: Bert L. full_name: de Groot, Bert L. last_name: de Groot - first_name: Paul full_name: Schanda, Paul id: 7B541462-FAF6-11E9-A490-E8DFE5697425 last_name: Schanda orcid: 0000-0002-9350-7606 - first_name: Rasmus full_name: Linser, Rasmus last_name: Linser citation: ama: Rovó P, Smith CA, Gauto D, de Groot BL, Schanda P, Linser R. Mechanistic insights into microsecond time-scale motion of solid proteins using complementary 15N and 1H relaxation dispersion techniques. Journal of the American Chemical Society. 2019;141(2):858-869. doi:10.1021/jacs.8b09258 apa: Rovó, P., Smith, C. A., Gauto, D., de Groot, B. L., Schanda, P., & Linser, R. (2019). Mechanistic insights into microsecond time-scale motion of solid proteins using complementary 15N and 1H relaxation dispersion techniques. Journal of the American Chemical Society. American Chemical Society. https://doi.org/10.1021/jacs.8b09258 chicago: Rovó, Petra, Colin A. Smith, Diego Gauto, Bert L. de Groot, Paul Schanda, and Rasmus Linser. “Mechanistic Insights into Microsecond Time-Scale Motion of Solid Proteins Using Complementary 15N and 1H Relaxation Dispersion Techniques.” Journal of the American Chemical Society. American Chemical Society, 2019. https://doi.org/10.1021/jacs.8b09258. ieee: P. Rovó, C. A. Smith, D. Gauto, B. L. de Groot, P. Schanda, and R. Linser, “Mechanistic insights into microsecond time-scale motion of solid proteins using complementary 15N and 1H relaxation dispersion techniques,” Journal of the American Chemical Society, vol. 141, no. 2. American Chemical Society, pp. 858–869, 2019. ista: Rovó P, Smith CA, Gauto D, de Groot BL, Schanda P, Linser R. 2019. Mechanistic insights into microsecond time-scale motion of solid proteins using complementary 15N and 1H relaxation dispersion techniques. Journal of the American Chemical Society. 141(2), 858–869. mla: Rovó, Petra, et al. “Mechanistic Insights into Microsecond Time-Scale Motion of Solid Proteins Using Complementary 15N and 1H Relaxation Dispersion Techniques.” Journal of the American Chemical Society, vol. 141, no. 2, American Chemical Society, 2019, pp. 858–69, doi:10.1021/jacs.8b09258. short: P. Rovó, C.A. Smith, D. Gauto, B.L. de Groot, P. Schanda, R. Linser, Journal of the American Chemical Society 141 (2019) 858–869. date_created: 2020-09-17T10:29:50Z date_published: 2019-01-08T00:00:00Z date_updated: 2021-01-12T08:19:07Z day: '08' doi: 10.1021/jacs.8b09258 extern: '1' external_id: pmid: - '30620186' intvolume: ' 141' issue: '2' keyword: - Colloid and Surface Chemistry - Biochemistry - General Chemistry - Catalysis language: - iso: eng month: '01' oa_version: Submitted Version page: 858-869 pmid: 1 publication: Journal of the American Chemical Society publication_identifier: issn: - 0002-7863 - 1520-5126 publication_status: published publisher: American Chemical Society quality_controlled: '1' status: public title: Mechanistic insights into microsecond time-scale motion of solid proteins using complementary 15N and 1H relaxation dispersion techniques type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 141 year: '2019' ... --- _id: '8412' abstract: - lang: eng text: Microsecond to millisecond timescale backbone dynamics of the amyloid core residues in Y145Stop human prion protein (PrP) fibrils were investigated by using 15N rotating frame (R1ρ) relaxation dispersion solid‐state nuclear magnetic resonance spectroscopy over a wide range of spin‐lock fields. Numerical simulations enabled the experimental relaxation dispersion profiles for most of the fibril core residues to be modelled by using a two‐state exchange process with a common exchange rate of 1000 s−1, corresponding to protein backbone motion on the timescale of 1 ms, and an excited‐state population of 2 %. We also found that the relaxation dispersion profiles for several amino acids positioned near the edges of the most structured regions of the amyloid core were better modelled by assuming somewhat higher excited‐state populations (∼5–15 %) and faster exchange rate constants, corresponding to protein backbone motions on the timescale of ∼100–300 μs. The slow backbone dynamics of the core residues were evaluated in the context of the structural model of human Y145Stop PrP amyloid. article_processing_charge: No article_type: original author: - first_name: Matthew D. full_name: Shannon, Matthew D. last_name: Shannon - first_name: Theint full_name: Theint, Theint last_name: Theint - first_name: Dwaipayan full_name: Mukhopadhyay, Dwaipayan last_name: Mukhopadhyay - first_name: Krystyna full_name: Surewicz, Krystyna last_name: Surewicz - first_name: Witold K. full_name: Surewicz, Witold K. last_name: Surewicz - first_name: Dominique full_name: Marion, Dominique last_name: Marion - first_name: Paul full_name: Schanda, Paul id: 7B541462-FAF6-11E9-A490-E8DFE5697425 last_name: Schanda orcid: 0000-0002-9350-7606 - first_name: Christopher P. full_name: Jaroniec, Christopher P. last_name: Jaroniec citation: ama: Shannon MD, Theint T, Mukhopadhyay D, et al. Conformational dynamics in the core of human Y145Stop prion protein amyloid probed by relaxation dispersion NMR. ChemPhysChem. 2019;20(2):311-317. doi:10.1002/cphc.201800779 apa: Shannon, M. D., Theint, T., Mukhopadhyay, D., Surewicz, K., Surewicz, W. K., Marion, D., … Jaroniec, C. P. (2019). Conformational dynamics in the core of human Y145Stop prion protein amyloid probed by relaxation dispersion NMR. ChemPhysChem. Wiley. https://doi.org/10.1002/cphc.201800779 chicago: Shannon, Matthew D., Theint Theint, Dwaipayan Mukhopadhyay, Krystyna Surewicz, Witold K. Surewicz, Dominique Marion, Paul Schanda, and Christopher P. Jaroniec. “Conformational Dynamics in the Core of Human Y145Stop Prion Protein Amyloid Probed by Relaxation Dispersion NMR.” ChemPhysChem. Wiley, 2019. https://doi.org/10.1002/cphc.201800779. ieee: M. D. Shannon et al., “Conformational dynamics in the core of human Y145Stop prion protein amyloid probed by relaxation dispersion NMR,” ChemPhysChem, vol. 20, no. 2. Wiley, pp. 311–317, 2019. ista: Shannon MD, Theint T, Mukhopadhyay D, Surewicz K, Surewicz WK, Marion D, Schanda P, Jaroniec CP. 2019. Conformational dynamics in the core of human Y145Stop prion protein amyloid probed by relaxation dispersion NMR. ChemPhysChem. 20(2), 311–317. mla: Shannon, Matthew D., et al. “Conformational Dynamics in the Core of Human Y145Stop Prion Protein Amyloid Probed by Relaxation Dispersion NMR.” ChemPhysChem, vol. 20, no. 2, Wiley, 2019, pp. 311–17, doi:10.1002/cphc.201800779. short: M.D. Shannon, T. Theint, D. Mukhopadhyay, K. Surewicz, W.K. Surewicz, D. Marion, P. Schanda, C.P. Jaroniec, ChemPhysChem 20 (2019) 311–317. date_created: 2020-09-17T10:29:43Z date_published: 2019-01-21T00:00:00Z date_updated: 2021-01-12T08:19:06Z day: '21' doi: 10.1002/cphc.201800779 extern: '1' external_id: pmid: - '30276945' intvolume: ' 20' issue: '2' keyword: - Physical and Theoretical Chemistry - Atomic and Molecular Physics - and Optics language: - iso: eng month: '01' oa_version: Submitted Version page: 311-317 pmid: 1 publication: ChemPhysChem publication_identifier: issn: - 1439-4235 publication_status: published publisher: Wiley quality_controlled: '1' status: public title: Conformational dynamics in the core of human Y145Stop prion protein amyloid probed by relaxation dispersion NMR type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 20 year: '2019' ... --- _id: '8411' abstract: - lang: eng text: 'Studying protein dynamics on microsecond‐to‐millisecond (μs‐ms) time scales can provide important insight into protein function. In magic‐angle‐spinning (MAS) NMR, μs dynamics can be visualized by R1p rotating‐frame relaxation dispersion experiments in different regimes of radio‐frequency field strengths: at low RF field strength, isotropic‐chemical‐shift fluctuation leads to “Bloch‐McConnell‐type” relaxation dispersion, while when the RF field approaches rotary resonance conditions bond angle fluctuations manifest as increased R1p rate constants (“Near‐Rotary‐Resonance Relaxation Dispersion”, NERRD). Here we explore the joint analysis of both regimes to gain comprehensive insight into motion in terms of geometric amplitudes, chemical‐shift changes, populations and exchange kinetics. We use a numerical simulation procedure to illustrate these effects and the potential of extracting exchange parameters, and apply the methodology to the study of a previously described conformational exchange process in microcrystalline ubiquitin.' article_processing_charge: No article_type: original author: - first_name: Dominique full_name: Marion, Dominique last_name: Marion - first_name: Diego F. full_name: Gauto, Diego F. last_name: Gauto - first_name: Isabel full_name: Ayala, Isabel last_name: Ayala - first_name: Karine full_name: Giandoreggio-Barranco, Karine last_name: Giandoreggio-Barranco - first_name: Paul full_name: Schanda, Paul id: 7B541462-FAF6-11E9-A490-E8DFE5697425 last_name: Schanda orcid: 0000-0002-9350-7606 citation: ama: Marion D, Gauto DF, Ayala I, Giandoreggio-Barranco K, Schanda P. Microsecond protein dynamics from combined Bloch-McConnell and Near-Rotary-Resonance R1p relaxation-dispersion MAS NMR. ChemPhysChem. 2019;20(2):276-284. doi:10.1002/cphc.201800935 apa: Marion, D., Gauto, D. F., Ayala, I., Giandoreggio-Barranco, K., & Schanda, P. (2019). Microsecond protein dynamics from combined Bloch-McConnell and Near-Rotary-Resonance R1p relaxation-dispersion MAS NMR. ChemPhysChem. Wiley. https://doi.org/10.1002/cphc.201800935 chicago: Marion, Dominique, Diego F. Gauto, Isabel Ayala, Karine Giandoreggio-Barranco, and Paul Schanda. “Microsecond Protein Dynamics from Combined Bloch-McConnell and Near-Rotary-Resonance R1p Relaxation-Dispersion MAS NMR.” ChemPhysChem. Wiley, 2019. https://doi.org/10.1002/cphc.201800935. ieee: D. Marion, D. F. Gauto, I. Ayala, K. Giandoreggio-Barranco, and P. Schanda, “Microsecond protein dynamics from combined Bloch-McConnell and Near-Rotary-Resonance R1p relaxation-dispersion MAS NMR,” ChemPhysChem, vol. 20, no. 2. Wiley, pp. 276–284, 2019. ista: Marion D, Gauto DF, Ayala I, Giandoreggio-Barranco K, Schanda P. 2019. Microsecond protein dynamics from combined Bloch-McConnell and Near-Rotary-Resonance R1p relaxation-dispersion MAS NMR. ChemPhysChem. 20(2), 276–284. mla: Marion, Dominique, et al. “Microsecond Protein Dynamics from Combined Bloch-McConnell and Near-Rotary-Resonance R1p Relaxation-Dispersion MAS NMR.” ChemPhysChem, vol. 20, no. 2, Wiley, 2019, pp. 276–84, doi:10.1002/cphc.201800935. short: D. Marion, D.F. Gauto, I. Ayala, K. Giandoreggio-Barranco, P. Schanda, ChemPhysChem 20 (2019) 276–284. date_created: 2020-09-17T10:29:36Z date_published: 2019-01-21T00:00:00Z date_updated: 2021-01-12T08:19:06Z day: '21' doi: 10.1002/cphc.201800935 extern: '1' external_id: pmid: - '30444575' intvolume: ' 20' issue: '2' keyword: - Physical and Theoretical Chemistry - Atomic and Molecular Physics - and Optics language: - iso: eng month: '01' oa_version: Submitted Version page: 276-284 pmid: 1 publication: ChemPhysChem publication_identifier: issn: - 1439-4235 publication_status: published publisher: Wiley quality_controlled: '1' status: public title: Microsecond protein dynamics from combined Bloch-McConnell and Near-Rotary-Resonance R1p relaxation-dispersion MAS NMR type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 20 year: '2019' ... --- _id: '8415' abstract: - lang: eng text: 'We consider billiards obtained by removing three strictly convex obstacles satisfying the non-eclipse condition on the plane. The restriction of the dynamics to the set of non-escaping orbits is conjugated to a subshift on three symbols that provides a natural labeling of all periodic orbits. We study the following inverse problem: does the Marked Length Spectrum (i.e., the set of lengths of periodic orbits together with their labeling), determine the geometry of the billiard table? We show that from the Marked Length Spectrum it is possible to recover the curvature at periodic points of period two, as well as the Lyapunov exponent of each periodic orbit.' article_processing_charge: No article_type: original author: - first_name: Péter full_name: Bálint, Péter last_name: Bálint - first_name: Jacopo full_name: De Simoi, Jacopo last_name: De Simoi - first_name: Vadim full_name: Kaloshin, Vadim id: FE553552-CDE8-11E9-B324-C0EBE5697425 last_name: Kaloshin orcid: 0000-0002-6051-2628 - first_name: Martin full_name: Leguil, Martin last_name: Leguil citation: ama: Bálint P, De Simoi J, Kaloshin V, Leguil M. Marked length spectrum, homoclinic orbits and the geometry of open dispersing billiards. Communications in Mathematical Physics. 2019;374(3):1531-1575. doi:10.1007/s00220-019-03448-x apa: Bálint, P., De Simoi, J., Kaloshin, V., & Leguil, M. (2019). Marked length spectrum, homoclinic orbits and the geometry of open dispersing billiards. Communications in Mathematical Physics. Springer Nature. https://doi.org/10.1007/s00220-019-03448-x chicago: Bálint, Péter, Jacopo De Simoi, Vadim Kaloshin, and Martin Leguil. “Marked Length Spectrum, Homoclinic Orbits and the Geometry of Open Dispersing Billiards.” Communications in Mathematical Physics. Springer Nature, 2019. https://doi.org/10.1007/s00220-019-03448-x. ieee: P. Bálint, J. De Simoi, V. Kaloshin, and M. Leguil, “Marked length spectrum, homoclinic orbits and the geometry of open dispersing billiards,” Communications in Mathematical Physics, vol. 374, no. 3. Springer Nature, pp. 1531–1575, 2019. ista: Bálint P, De Simoi J, Kaloshin V, Leguil M. 2019. Marked length spectrum, homoclinic orbits and the geometry of open dispersing billiards. Communications in Mathematical Physics. 374(3), 1531–1575. mla: Bálint, Péter, et al. “Marked Length Spectrum, Homoclinic Orbits and the Geometry of Open Dispersing Billiards.” Communications in Mathematical Physics, vol. 374, no. 3, Springer Nature, 2019, pp. 1531–75, doi:10.1007/s00220-019-03448-x. short: P. Bálint, J. De Simoi, V. Kaloshin, M. Leguil, Communications in Mathematical Physics 374 (2019) 1531–1575. date_created: 2020-09-17T10:41:27Z date_published: 2019-05-09T00:00:00Z date_updated: 2021-01-12T08:19:08Z day: '09' doi: 10.1007/s00220-019-03448-x extern: '1' external_id: arxiv: - '1809.08947' intvolume: ' 374' issue: '3' keyword: - Mathematical Physics - Statistical and Nonlinear Physics language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1809.08947 month: '05' oa: 1 oa_version: Preprint page: 1531-1575 publication: Communications in Mathematical Physics publication_identifier: issn: - 0010-3616 - 1432-0916 publication_status: published publisher: Springer Nature quality_controlled: '1' status: public title: Marked length spectrum, homoclinic orbits and the geometry of open dispersing billiards type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 374 year: '2019' ... --- _id: '8409' abstract: - lang: eng text: The bacterial cell wall is composed of the peptidoglycan (PG), a large polymer that maintains the integrity of the bacterial cell. Due to its multi-gigadalton size, heterogeneity, and dynamics, atomic-resolution studies are inherently complex. Solid-state NMR is an important technique to gain insight into its structure, dynamics and interactions. Here, we explore the possibilities to study the PG with ultra-fast (100 kHz) magic-angle spinning NMR. We demonstrate that highly resolved spectra can be obtained, and show strategies to obtain site-specific resonance assignments and distance information. We also explore the use of proton-proton correlation experiments, thus opening the way for NMR studies of intact cell walls without the need for isotope labeling. article_processing_charge: No article_type: original author: - first_name: Catherine full_name: Bougault, Catherine last_name: Bougault - first_name: Isabel full_name: Ayala, Isabel last_name: Ayala - first_name: Waldemar full_name: Vollmer, Waldemar last_name: Vollmer - first_name: Jean-Pierre full_name: Simorre, Jean-Pierre last_name: Simorre - first_name: Paul full_name: Schanda, Paul id: 7B541462-FAF6-11E9-A490-E8DFE5697425 last_name: Schanda orcid: 0000-0002-9350-7606 citation: ama: Bougault C, Ayala I, Vollmer W, Simorre J-P, Schanda P. Studying intact bacterial peptidoglycan by proton-detected NMR spectroscopy at 100 kHz MAS frequency. Journal of Structural Biology. 2019;206(1):66-72. doi:10.1016/j.jsb.2018.07.009 apa: Bougault, C., Ayala, I., Vollmer, W., Simorre, J.-P., & Schanda, P. (2019). Studying intact bacterial peptidoglycan by proton-detected NMR spectroscopy at 100 kHz MAS frequency. Journal of Structural Biology. Elsevier. https://doi.org/10.1016/j.jsb.2018.07.009 chicago: Bougault, Catherine, Isabel Ayala, Waldemar Vollmer, Jean-Pierre Simorre, and Paul Schanda. “Studying Intact Bacterial Peptidoglycan by Proton-Detected NMR Spectroscopy at 100 kHz MAS Frequency.” Journal of Structural Biology. Elsevier, 2019. https://doi.org/10.1016/j.jsb.2018.07.009. ieee: C. Bougault, I. Ayala, W. Vollmer, J.-P. Simorre, and P. Schanda, “Studying intact bacterial peptidoglycan by proton-detected NMR spectroscopy at 100 kHz MAS frequency,” Journal of Structural Biology, vol. 206, no. 1. Elsevier, pp. 66–72, 2019. ista: Bougault C, Ayala I, Vollmer W, Simorre J-P, Schanda P. 2019. Studying intact bacterial peptidoglycan by proton-detected NMR spectroscopy at 100 kHz MAS frequency. Journal of Structural Biology. 206(1), 66–72. mla: Bougault, Catherine, et al. “Studying Intact Bacterial Peptidoglycan by Proton-Detected NMR Spectroscopy at 100 kHz MAS Frequency.” Journal of Structural Biology, vol. 206, no. 1, Elsevier, 2019, pp. 66–72, doi:10.1016/j.jsb.2018.07.009. short: C. Bougault, I. Ayala, W. Vollmer, J.-P. Simorre, P. Schanda, Journal of Structural Biology 206 (2019) 66–72. date_created: 2020-09-17T10:29:10Z date_published: 2019-04-01T00:00:00Z date_updated: 2021-01-12T08:19:05Z day: '01' doi: 10.1016/j.jsb.2018.07.009 extern: '1' external_id: pmid: - '30031884' intvolume: ' 206' issue: '1' keyword: - Structural Biology language: - iso: eng month: '04' oa_version: Submitted Version page: 66-72 pmid: 1 publication: Journal of Structural Biology publication_identifier: issn: - 1047-8477 publication_status: published publisher: Elsevier quality_controlled: '1' status: public title: Studying intact bacterial peptidoglycan by proton-detected NMR spectroscopy at 100 kHz MAS frequency type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 206 year: '2019' ... --- _id: '8407' article_processing_charge: No article_type: original author: - first_name: Paul full_name: Schanda, Paul id: 7B541462-FAF6-11E9-A490-E8DFE5697425 last_name: Schanda orcid: 0000-0002-9350-7606 citation: ama: Schanda P. Relaxing with liquids and solids – A perspective on biomolecular dynamics. Journal of Magnetic Resonance. 2019;306:180-186. doi:10.1016/j.jmr.2019.07.025 apa: Schanda, P. (2019). Relaxing with liquids and solids – A perspective on biomolecular dynamics. Journal of Magnetic Resonance. Elsevier. https://doi.org/10.1016/j.jmr.2019.07.025 chicago: Schanda, Paul. “Relaxing with Liquids and Solids – A Perspective on Biomolecular Dynamics.” Journal of Magnetic Resonance. Elsevier, 2019. https://doi.org/10.1016/j.jmr.2019.07.025. ieee: P. Schanda, “Relaxing with liquids and solids – A perspective on biomolecular dynamics,” Journal of Magnetic Resonance, vol. 306. Elsevier, pp. 180–186, 2019. ista: Schanda P. 2019. Relaxing with liquids and solids – A perspective on biomolecular dynamics. Journal of Magnetic Resonance. 306, 180–186. mla: Schanda, Paul. “Relaxing with Liquids and Solids – A Perspective on Biomolecular Dynamics.” Journal of Magnetic Resonance, vol. 306, Elsevier, 2019, pp. 180–86, doi:10.1016/j.jmr.2019.07.025. short: P. Schanda, Journal of Magnetic Resonance 306 (2019) 180–186. date_created: 2020-09-17T10:28:47Z date_published: 2019-09-01T00:00:00Z date_updated: 2021-01-12T08:19:04Z day: '01' doi: 10.1016/j.jmr.2019.07.025 extern: '1' external_id: pmid: - '31350165' intvolume: ' 306' keyword: - Nuclear and High Energy Physics - Biophysics - Biochemistry - Condensed Matter Physics language: - iso: eng month: '09' oa_version: Submitted Version page: 180-186 pmid: 1 publication: Journal of Magnetic Resonance publication_identifier: issn: - 1090-7807 publication_status: published publisher: Elsevier quality_controlled: '1' status: public title: Relaxing with liquids and solids – A perspective on biomolecular dynamics type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 306 year: '2019' ... --- _id: '8410' article_processing_charge: No article_type: letter_note author: - first_name: Paul full_name: Schanda, Paul id: 7B541462-FAF6-11E9-A490-E8DFE5697425 last_name: Schanda orcid: 0000-0002-9350-7606 - first_name: Eduard Y. full_name: Chekmenev, Eduard Y. last_name: Chekmenev citation: ama: Schanda P, Chekmenev EY. NMR for Biological Systems. ChemPhysChem. 2019;20(2):177-177. doi:10.1002/cphc.201801100 apa: Schanda, P., & Chekmenev, E. Y. (2019). NMR for Biological Systems. ChemPhysChem. Wiley. https://doi.org/10.1002/cphc.201801100 chicago: Schanda, Paul, and Eduard Y. Chekmenev. “NMR for Biological Systems.” ChemPhysChem. Wiley, 2019. https://doi.org/10.1002/cphc.201801100. ieee: P. Schanda and E. Y. Chekmenev, “NMR for Biological Systems,” ChemPhysChem, vol. 20, no. 2. Wiley, pp. 177–177, 2019. ista: Schanda P, Chekmenev EY. 2019. NMR for Biological Systems. ChemPhysChem. 20(2), 177–177. mla: Schanda, Paul, and Eduard Y. Chekmenev. “NMR for Biological Systems.” ChemPhysChem, vol. 20, no. 2, Wiley, 2019, pp. 177–177, doi:10.1002/cphc.201801100. short: P. Schanda, E.Y. Chekmenev, ChemPhysChem 20 (2019) 177–177. date_created: 2020-09-17T10:29:26Z date_published: 2019-01-21T00:00:00Z date_updated: 2021-01-12T08:19:05Z day: '21' doi: 10.1002/cphc.201801100 extern: '1' external_id: pmid: - '30556633' intvolume: ' 20' issue: '2' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1002/cphc.201801100 month: '01' oa: 1 oa_version: Published Version page: 177-177 pmid: 1 publication: ChemPhysChem publication_identifier: issn: - 1439-4235 publication_status: published publisher: Wiley quality_controlled: '1' status: public title: NMR for Biological Systems type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 20 year: '2019' ... --- _id: '8570' abstract: - lang: eng text: 'This report presents the results of a friendly competition for formal verification of continuous and hybrid systems with linear continuous dynamics. The friendly competition took place as part of the workshop Applied Verification for Continuous and Hybrid Systems (ARCH) in 2019. In its third edition, seven tools have been applied to solve six different benchmark problems in the category for linear continuous dynamics (in alphabetical order): CORA, CORA/SX, HyDRA, Hylaa, JuliaReach, SpaceEx, and XSpeed. This report is a snapshot of the current landscape of tools and the types of benchmarks they are particularly suited for. Due to the diversity of problems, we are not ranking tools, yet the presented results provide one of the most complete assessments of tools for the safety verification of continuous and hybrid systems with linear continuous dynamics up to this date.' article_processing_charge: No author: - first_name: Matthias full_name: Althoff, Matthias last_name: Althoff - first_name: Stanley full_name: Bak, Stanley last_name: Bak - first_name: Marcelo full_name: Forets, Marcelo last_name: Forets - first_name: Goran full_name: Frehse, Goran last_name: Frehse - first_name: Niklas full_name: Kochdumper, Niklas last_name: Kochdumper - first_name: Rajarshi full_name: Ray, Rajarshi last_name: Ray - first_name: Christian full_name: Schilling, Christian id: 3A2F4DCE-F248-11E8-B48F-1D18A9856A87 last_name: Schilling orcid: 0000-0003-3658-1065 - first_name: Stefan full_name: Schupp, Stefan last_name: Schupp citation: ama: 'Althoff M, Bak S, Forets M, et al. ARCH-COMP19 Category Report: Continuous and hybrid systems with linear continuous dynamics. In: EPiC Series in Computing. Vol 61. EasyChair; 2019:14-40. doi:10.29007/bj1w' apa: 'Althoff, M., Bak, S., Forets, M., Frehse, G., Kochdumper, N., Ray, R., … Schupp, S. (2019). ARCH-COMP19 Category Report: Continuous and hybrid systems with linear continuous dynamics. In EPiC Series in Computing (Vol. 61, pp. 14–40). Montreal, Canada: EasyChair. https://doi.org/10.29007/bj1w' chicago: 'Althoff, Matthias, Stanley Bak, Marcelo Forets, Goran Frehse, Niklas Kochdumper, Rajarshi Ray, Christian Schilling, and Stefan Schupp. “ARCH-COMP19 Category Report: Continuous and Hybrid Systems with Linear Continuous Dynamics.” In EPiC Series in Computing, 61:14–40. EasyChair, 2019. https://doi.org/10.29007/bj1w.' ieee: 'M. Althoff et al., “ARCH-COMP19 Category Report: Continuous and hybrid systems with linear continuous dynamics,” in EPiC Series in Computing, Montreal, Canada, 2019, vol. 61, pp. 14–40.' ista: 'Althoff M, Bak S, Forets M, Frehse G, Kochdumper N, Ray R, Schilling C, Schupp S. 2019. ARCH-COMP19 Category Report: Continuous and hybrid systems with linear continuous dynamics. EPiC Series in Computing. ARCH: International Workshop on Applied Verification on Continuous and Hybrid Systems vol. 61, 14–40.' mla: 'Althoff, Matthias, et al. “ARCH-COMP19 Category Report: Continuous and Hybrid Systems with Linear Continuous Dynamics.” EPiC Series in Computing, vol. 61, EasyChair, 2019, pp. 14–40, doi:10.29007/bj1w.' short: M. Althoff, S. Bak, M. Forets, G. Frehse, N. Kochdumper, R. Ray, C. Schilling, S. Schupp, in:, EPiC Series in Computing, EasyChair, 2019, pp. 14–40. conference: end_date: 2019-04-15 location: Montreal, Canada name: 'ARCH: International Workshop on Applied Verification on Continuous and Hybrid Systems' start_date: 2019-04-15 date_created: 2020-09-26T14:23:54Z date_published: 2019-05-25T00:00:00Z date_updated: 2021-01-12T08:20:05Z day: '25' department: - _id: ToHe doi: 10.29007/bj1w intvolume: ' 61' language: - iso: eng main_file_link: - open_access: '1' url: https://easychair.org/publications/open/1gbP month: '05' oa: 1 oa_version: Published Version page: 14-40 publication: EPiC Series in Computing publication_identifier: eissn: - '23987340' publication_status: published publisher: EasyChair quality_controlled: '1' status: public title: 'ARCH-COMP19 Category Report: Continuous and hybrid systems with linear continuous dynamics' type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 61 year: '2019' ... --- _id: '9016' abstract: - lang: eng text: Inhibiting the histone H3–ASF1 (anti‐silencing function 1) protein–protein interaction (PPI) represents a potential approach for treating numerous cancers. As an α‐helix‐mediated PPI, constraining the key histone H3 helix (residues 118–135) is a strategy through which chemical probes might be elaborated to test this hypothesis. In this work, variant H3118–135 peptides bearing pentenylglycine residues at the i and i+4 positions were constrained by olefin metathesis. Biophysical analyses revealed that promotion of a bioactive helical conformation depends on the position at which the constraint is introduced, but that the potency of binding towards ASF1 is unaffected by the constraint and instead that enthalpy–entropy compensation occurs. article_processing_charge: No article_type: original author: - first_name: May M full_name: Bakail, May M id: FB3C3F8E-522F-11EA-B186-22963DDC885E last_name: Bakail orcid: 0000-0002-9592-1587 - first_name: Silvia full_name: Rodriguez‐Marin, Silvia last_name: Rodriguez‐Marin - first_name: Zsófia full_name: Hegedüs, Zsófia last_name: Hegedüs - first_name: Marie E. full_name: Perrin, Marie E. last_name: Perrin - first_name: Françoise full_name: Ochsenbein, Françoise last_name: Ochsenbein - first_name: Andrew J. full_name: Wilson, Andrew J. last_name: Wilson citation: ama: Bakail MM, Rodriguez‐Marin S, Hegedüs Z, Perrin ME, Ochsenbein F, Wilson AJ. Recognition of ASF1 by using hydrocarbon‐constrained peptides. ChemBioChem. 2019;20(7):891-895. doi:10.1002/cbic.201800633 apa: Bakail, M. M., Rodriguez‐Marin, S., Hegedüs, Z., Perrin, M. E., Ochsenbein, F., & Wilson, A. J. (2019). Recognition of ASF1 by using hydrocarbon‐constrained peptides. ChemBioChem. Wiley. https://doi.org/10.1002/cbic.201800633 chicago: Bakail, May M, Silvia Rodriguez‐Marin, Zsófia Hegedüs, Marie E. Perrin, Françoise Ochsenbein, and Andrew J. Wilson. “Recognition of ASF1 by Using Hydrocarbon‐constrained Peptides.” ChemBioChem. Wiley, 2019. https://doi.org/10.1002/cbic.201800633. ieee: M. M. Bakail, S. Rodriguez‐Marin, Z. Hegedüs, M. E. Perrin, F. Ochsenbein, and A. J. Wilson, “Recognition of ASF1 by using hydrocarbon‐constrained peptides,” ChemBioChem, vol. 20, no. 7. Wiley, pp. 891–895, 2019. ista: Bakail MM, Rodriguez‐Marin S, Hegedüs Z, Perrin ME, Ochsenbein F, Wilson AJ. 2019. Recognition of ASF1 by using hydrocarbon‐constrained peptides. ChemBioChem. 20(7), 891–895. mla: Bakail, May M., et al. “Recognition of ASF1 by Using Hydrocarbon‐constrained Peptides.” ChemBioChem, vol. 20, no. 7, Wiley, 2019, pp. 891–95, doi:10.1002/cbic.201800633. short: M.M. Bakail, S. Rodriguez‐Marin, Z. Hegedüs, M.E. Perrin, F. Ochsenbein, A.J. Wilson, ChemBioChem 20 (2019) 891–895. date_created: 2021-01-19T10:59:14Z date_published: 2019-04-01T00:00:00Z date_updated: 2023-02-23T13:46:48Z day: '01' doi: 10.1002/cbic.201800633 extern: '1' intvolume: ' 20' issue: '7' language: - iso: eng main_file_link: - open_access: '1' url: ' https://doi.org/10.1002/cbic.201800633' month: '04' oa: 1 oa_version: Published Version page: 891-895 publication: ChemBioChem publication_identifier: issn: - 1439-4227 - 1439-7633 publication_status: published publisher: Wiley quality_controlled: '1' status: public title: Recognition of ASF1 by using hydrocarbon‐constrained peptides type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 20 year: '2019' ... --- _id: '9060' abstract: - lang: eng text: Molecular motors are essential to the living, generating fluctuations that boost transport and assist assembly. Active colloids, that consume energy to move, hold similar potential for man-made materials controlled by forces generated from within. Yet, their use as a powerhouse in materials science lacks. Here we show a massive acceleration of the annealing of a monolayer of passive beads by moderate addition of self-propelled microparticles. We rationalize our observations with a model of collisions that drive active fluctuations and activate the annealing. The experiment is quantitatively compared with Brownian dynamic simulations that further unveil a dynamical transition in the mechanism of annealing. Active dopants travel uniformly in the system or co-localize at the grain boundaries as a result of the persistence of their motion. Our findings uncover the potential of internal activity to control materials and lay the groundwork for the rise of materials science beyond equilibrium. article_number: '3380' article_processing_charge: No article_type: original author: - first_name: Sophie full_name: Ramananarivo, Sophie last_name: Ramananarivo - first_name: Etienne full_name: Ducrot, Etienne last_name: Ducrot - first_name: Jérémie A full_name: Palacci, Jérémie A id: 8fb92548-2b22-11eb-b7c1-a3f0d08d7c7d last_name: Palacci orcid: 0000-0002-7253-9465 citation: ama: Ramananarivo S, Ducrot E, Palacci JA. Activity-controlled annealing of colloidal monolayers. Nature Communications. 2019;10(1). doi:10.1038/s41467-019-11362-y apa: Ramananarivo, S., Ducrot, E., & Palacci, J. A. (2019). Activity-controlled annealing of colloidal monolayers. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-019-11362-y chicago: Ramananarivo, Sophie, Etienne Ducrot, and Jérémie A Palacci. “Activity-Controlled Annealing of Colloidal Monolayers.” Nature Communications. Springer Nature, 2019. https://doi.org/10.1038/s41467-019-11362-y. ieee: S. Ramananarivo, E. Ducrot, and J. A. Palacci, “Activity-controlled annealing of colloidal monolayers,” Nature Communications, vol. 10, no. 1. Springer Nature, 2019. ista: Ramananarivo S, Ducrot E, Palacci JA. 2019. Activity-controlled annealing of colloidal monolayers. Nature Communications. 10(1), 3380. mla: Ramananarivo, Sophie, et al. “Activity-Controlled Annealing of Colloidal Monolayers.” Nature Communications, vol. 10, no. 1, 3380, Springer Nature, 2019, doi:10.1038/s41467-019-11362-y. short: S. Ramananarivo, E. Ducrot, J.A. Palacci, Nature Communications 10 (2019). date_created: 2021-02-02T13:43:36Z date_published: 2019-07-29T00:00:00Z date_updated: 2023-02-23T13:47:59Z day: '29' ddc: - '530' doi: 10.1038/s41467-019-11362-y extern: '1' external_id: arxiv: - '1909.07382' pmid: - '31358762' file: - access_level: open_access checksum: 70c6e5d6fbea0932b0669505ab6633ec content_type: application/pdf creator: cziletti date_created: 2021-02-02T13:47:21Z date_updated: 2021-02-02T13:47:21Z file_id: '9061' file_name: 2019_NatureComm_Ramananarivo.pdf file_size: 2820337 relation: main_file success: 1 file_date_updated: 2021-02-02T13:47:21Z has_accepted_license: '1' intvolume: ' 10' issue: '1' keyword: - General Biochemistry - Genetics and Molecular Biology - General Physics and Astronomy - General Chemistry language: - iso: eng month: '07' oa: 1 oa_version: Published Version pmid: 1 publication: Nature Communications publication_identifier: issn: - 2041-1723 publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: Activity-controlled annealing of colloidal monolayers 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: D865714E-FA4E-11E9-B85B-F5C5E5697425 volume: 10 year: '2019' ... --- _id: '9460' abstract: - lang: eng text: Epigenetic reprogramming is required for proper regulation of gene expression in eukaryotic organisms. In Arabidopsis, active DNA demethylation is crucial for seed viability, pollen function, and successful reproduction. The DEMETER (DME) DNA glycosylase initiates localized DNA demethylation in vegetative and central cells, so-called companion cells that are adjacent to sperm and egg gametes, respectively. In rice, the central cell genome displays local DNA hypomethylation, suggesting that active DNA demethylation also occurs in rice; however, the enzyme responsible for this process is unknown. One candidate is the rice REPRESSOR OF SILENCING 1a (ROS1a) gene, which is related to DME and is essential for rice seed viability and pollen function. Here, we report genome-wide analyses of DNA methylation in wild-type and ros1a mutant sperm and vegetative cells. We find that the rice vegetative cell genome is locally hypomethylated compared with sperm by a process that requires ROS1a activity. We show that many ROS1a target sequences in the vegetative cell are hypomethylated in the rice central cell, suggesting that ROS1a also demethylates the central cell genome. Similar to Arabidopsis, we show that sperm non-CG methylation is indirectly promoted by DNA demethylation in the vegetative cell. These results reveal that DNA glycosylase-mediated DNA demethylation processes are conserved in Arabidopsis and rice, plant species that diverged 150 million years ago. Finally, although global non-CG methylation levels of sperm and egg differ, the maternal and paternal embryo genomes show similar non-CG methylation levels, suggesting that rice gamete genomes undergo dynamic DNA methylation reprogramming after cell fusion. article_processing_charge: No article_type: original author: - first_name: M. Yvonne full_name: Kim, M. Yvonne last_name: Kim - first_name: Akemi full_name: Ono, Akemi last_name: Ono - first_name: Stefan full_name: Scholten, Stefan last_name: Scholten - first_name: Tetsu full_name: Kinoshita, Tetsu last_name: Kinoshita - first_name: Daniel full_name: Zilberman, Daniel id: 6973db13-dd5f-11ea-814e-b3e5455e9ed1 last_name: Zilberman orcid: 0000-0002-0123-8649 - first_name: Takashi full_name: Okamoto, Takashi last_name: Okamoto - first_name: Robert L. full_name: Fischer, Robert L. last_name: Fischer citation: ama: Kim MY, Ono A, Scholten S, et al. DNA demethylation by ROS1a in rice vegetative cells promotes methylation in sperm. Proceedings of the National Academy of Sciences. 2019;116(19):9652-9657. doi:10.1073/pnas.1821435116 apa: Kim, M. Y., Ono, A., Scholten, S., Kinoshita, T., Zilberman, D., Okamoto, T., & Fischer, R. L. (2019). DNA demethylation by ROS1a in rice vegetative cells promotes methylation in sperm. Proceedings of the National Academy of Sciences. National Academy of Sciences. https://doi.org/10.1073/pnas.1821435116 chicago: Kim, M. Yvonne, Akemi Ono, Stefan Scholten, Tetsu Kinoshita, Daniel Zilberman, Takashi Okamoto, and Robert L. Fischer. “DNA Demethylation by ROS1a in Rice Vegetative Cells Promotes Methylation in Sperm.” Proceedings of the National Academy of Sciences. National Academy of Sciences, 2019. https://doi.org/10.1073/pnas.1821435116. ieee: M. Y. Kim et al., “DNA demethylation by ROS1a in rice vegetative cells promotes methylation in sperm,” Proceedings of the National Academy of Sciences, vol. 116, no. 19. National Academy of Sciences, pp. 9652–9657, 2019. ista: Kim MY, Ono A, Scholten S, Kinoshita T, Zilberman D, Okamoto T, Fischer RL. 2019. DNA demethylation by ROS1a in rice vegetative cells promotes methylation in sperm. Proceedings of the National Academy of Sciences. 116(19), 9652–9657. mla: Kim, M. Yvonne, et al. “DNA Demethylation by ROS1a in Rice Vegetative Cells Promotes Methylation in Sperm.” Proceedings of the National Academy of Sciences, vol. 116, no. 19, National Academy of Sciences, 2019, pp. 9652–57, doi:10.1073/pnas.1821435116. short: M.Y. Kim, A. Ono, S. Scholten, T. Kinoshita, D. Zilberman, T. Okamoto, R.L. Fischer, Proceedings of the National Academy of Sciences 116 (2019) 9652–9657. date_created: 2021-06-04T12:38:20Z date_published: 2019-05-07T00:00:00Z date_updated: 2021-12-14T07:52:30Z day: '07' ddc: - '580' department: - _id: DaZi doi: 10.1073/pnas.1821435116 extern: '1' external_id: pmid: - '31000601' file: - access_level: open_access checksum: 5b0ae3779b8b21b5223bd2d3cceede3a content_type: application/pdf creator: asandaue date_created: 2021-06-04T12:50:47Z date_updated: 2021-06-04T12:50:47Z file_id: '9461' file_name: 2019_PNAS_Kim.pdf file_size: 1142540 relation: main_file success: 1 file_date_updated: 2021-06-04T12:50:47Z has_accepted_license: '1' intvolume: ' 116' issue: '19' keyword: - Multidisciplinary language: - iso: eng month: '05' oa: 1 oa_version: Published Version page: 9652-9657 pmid: 1 publication: Proceedings of the National Academy of Sciences publication_identifier: eissn: - 1091-6490 issn: - 0027-8424 publication_status: published publisher: National Academy of Sciences quality_controlled: '1' scopus_import: '1' status: public title: DNA demethylation by ROS1a in rice vegetative cells promotes methylation in sperm tmp: image: /images/cc_by_nc_nd.png legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0) short: CC BY-NC-ND (4.0) type: journal_article user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 volume: 116 year: '2019' ... --- _id: '9689' abstract: - lang: eng text: A central goal of computational physics and chemistry is to predict material properties by using first-principles methods based on the fundamental laws of quantum mechanics. However, the high computational costs of these methods typically prevent rigorous predictions of macroscopic quantities at finite temperatures, such as heat capacity, density, and chemical potential. Here, we enable such predictions by marrying advanced free-energy methods with data-driven machine-learning interatomic potentials. We show that, for the ubiquitous and technologically essential system of water, a first-principles thermodynamic description not only leads to excellent agreement with experiments, but also reveals the crucial role of nuclear quantum fluctuations in modulating the thermodynamic stabilities of different phases of water. article_processing_charge: No article_type: original author: - first_name: Bingqing full_name: Cheng, Bingqing id: cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9 last_name: Cheng orcid: 0000-0002-3584-9632 - first_name: Edgar A. full_name: Engel, Edgar A. last_name: Engel - first_name: Jörg full_name: Behler, Jörg last_name: Behler - first_name: Christoph full_name: Dellago, Christoph last_name: Dellago - first_name: Michele full_name: Ceriotti, Michele last_name: Ceriotti citation: ama: Cheng B, Engel EA, Behler J, Dellago C, Ceriotti M. Ab initio thermodynamics of liquid and solid water. Proceedings of the National Academy of Sciences. 2019;116(4):1110-1115. doi:10.1073/pnas.1815117116 apa: Cheng, B., Engel, E. A., Behler, J., Dellago, C., & Ceriotti, M. (2019). Ab initio thermodynamics of liquid and solid water. Proceedings of the National Academy of Sciences. National Academy of Sciences. https://doi.org/10.1073/pnas.1815117116 chicago: Cheng, Bingqing, Edgar A. Engel, Jörg Behler, Christoph Dellago, and Michele Ceriotti. “Ab Initio Thermodynamics of Liquid and Solid Water.” Proceedings of the National Academy of Sciences. National Academy of Sciences, 2019. https://doi.org/10.1073/pnas.1815117116. ieee: B. Cheng, E. A. Engel, J. Behler, C. Dellago, and M. Ceriotti, “Ab initio thermodynamics of liquid and solid water,” Proceedings of the National Academy of Sciences, vol. 116, no. 4. National Academy of Sciences, pp. 1110–1115, 2019. ista: Cheng B, Engel EA, Behler J, Dellago C, Ceriotti M. 2019. Ab initio thermodynamics of liquid and solid water. Proceedings of the National Academy of Sciences. 116(4), 1110–1115. mla: Cheng, Bingqing, et al. “Ab Initio Thermodynamics of Liquid and Solid Water.” Proceedings of the National Academy of Sciences, vol. 116, no. 4, National Academy of Sciences, 2019, pp. 1110–15, doi:10.1073/pnas.1815117116. short: B. Cheng, E.A. Engel, J. Behler, C. Dellago, M. Ceriotti, Proceedings of the National Academy of Sciences 116 (2019) 1110–1115. date_created: 2021-07-19T10:17:09Z date_published: 2019-01-22T00:00:00Z date_updated: 2023-02-23T14:05:08Z day: '22' doi: 10.1073/pnas.1815117116 extern: '1' external_id: arxiv: - '1811.08630' pmid: - '30610171' intvolume: ' 116' issue: '4' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1073/pnas.1815117116 month: '01' oa: 1 oa_version: Published Version page: 1110-1115 pmid: 1 publication: Proceedings of the National Academy of Sciences publication_identifier: eissn: - 1091-6490 issn: - 0027-8424 publication_status: published publisher: National Academy of Sciences quality_controlled: '1' scopus_import: '1' status: public title: Ab initio thermodynamics of liquid and solid water type: journal_article user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf volume: 116 year: '2019' ... --- _id: '6819' abstract: - lang: eng text: Glyphosate (N-phosphonomethyl glycine) and its commercial herbicide formulations have been shown to exert toxicity via various mechanisms. It has been asserted that glyphosate substitutes for glycine in polypeptide chains leading to protein misfolding and toxicity. However, as no direct evidence exists for glycine to glyphosate substitution in proteins, including in mammalian organisms, we tested this claim by conducting a proteomics analysis of MDA-MB-231 human breast cancer cells grown in the presence of 100 mg/L glyphosate for 6 days. Protein extracts from three treated and three untreated cell cultures were analysed as one TMT-6plex labelled sample, to highlight a specific pattern (+/+/+/−/−/−) of reporter intensities for peptides bearing true glyphosate treatment induced-post translational modifications as well as allowing an investigation of the total proteome. article_number: '494' article_processing_charge: No author: - first_name: Michael N. full_name: Antoniou, Michael N. last_name: Antoniou - first_name: Armel full_name: Nicolas, Armel id: 2A103192-F248-11E8-B48F-1D18A9856A87 last_name: Nicolas - first_name: Robin full_name: Mesnage, Robin last_name: Mesnage - first_name: Martina full_name: Biserni, Martina last_name: Biserni - first_name: Francesco V. full_name: Rao, Francesco V. last_name: Rao - first_name: Cristina Vazquez full_name: Martin, Cristina Vazquez last_name: Martin citation: ama: Antoniou MN, Nicolas A, Mesnage R, Biserni M, Rao FV, Martin CV. Glyphosate does not substitute for glycine in proteins of actively dividing mammalian cells. BMC Research Notes. 2019;12. doi:10.1186/s13104-019-4534-3 apa: Antoniou, M. N., Nicolas, A., Mesnage, R., Biserni, M., Rao, F. V., & Martin, C. V. (2019). Glyphosate does not substitute for glycine in proteins of actively dividing mammalian cells. BMC Research Notes. BioMed Central. https://doi.org/10.1186/s13104-019-4534-3 chicago: Antoniou, Michael N., Armel Nicolas, Robin Mesnage, Martina Biserni, Francesco V. Rao, and Cristina Vazquez Martin. “Glyphosate Does Not Substitute for Glycine in Proteins of Actively Dividing Mammalian Cells.” BMC Research Notes. BioMed Central, 2019. https://doi.org/10.1186/s13104-019-4534-3. ieee: M. N. Antoniou, A. Nicolas, R. Mesnage, M. Biserni, F. V. Rao, and C. V. Martin, “Glyphosate does not substitute for glycine in proteins of actively dividing mammalian cells,” BMC Research Notes, vol. 12. BioMed Central, 2019. ista: Antoniou MN, Nicolas A, Mesnage R, Biserni M, Rao FV, Martin CV. 2019. Glyphosate does not substitute for glycine in proteins of actively dividing mammalian cells. BMC Research Notes. 12, 494. mla: Antoniou, Michael N., et al. “Glyphosate Does Not Substitute for Glycine in Proteins of Actively Dividing Mammalian Cells.” BMC Research Notes, vol. 12, 494, BioMed Central, 2019, doi:10.1186/s13104-019-4534-3. short: M.N. Antoniou, A. Nicolas, R. Mesnage, M. Biserni, F.V. Rao, C.V. Martin, BMC Research Notes 12 (2019). date_created: 2019-08-18T22:00:39Z date_published: 2019-08-08T00:00:00Z date_updated: 2023-02-23T14:08:14Z day: '08' ddc: - '570' department: - _id: LifeSc doi: 10.1186/s13104-019-4534-3 external_id: pmid: - '31395095' file: - access_level: open_access checksum: 4a2bb7994b7f2c432bf44f5127ea3102 content_type: application/pdf creator: dernst date_created: 2019-08-23T11:10:35Z date_updated: 2020-07-14T12:47:40Z file_id: '6829' file_name: 2019_BMC_Antoniou.pdf file_size: 1177482 relation: main_file file_date_updated: 2020-07-14T12:47:40Z has_accepted_license: '1' intvolume: ' 12' language: - iso: eng month: '08' oa: 1 oa_version: Published Version pmid: 1 publication: BMC Research Notes publication_identifier: eissn: - 1756-0500 publication_status: published publisher: BioMed Central quality_controlled: '1' related_material: record: - id: '9784' relation: research_data status: public scopus_import: 1 status: public title: Glyphosate does not substitute for glycine in proteins of actively dividing mammalian 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: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 12 year: '2019' ... --- _id: '9784' abstract: - lang: eng text: 'Additional file 1: Table S1. Kinetics of MDA-MB-231 cell growth in either the presence or absence of 100Â mg/L glyphosate. Cell counts are given at day-1 of seeding flasks and following 6-days of continuous culture. Note: no differences in cell numbers were observed between negative control and glyphosate treated cultures.' article_processing_charge: No author: - first_name: Michael N. full_name: Antoniou, Michael N. last_name: Antoniou - first_name: Armel full_name: Nicolas, Armel id: 2A103192-F248-11E8-B48F-1D18A9856A87 last_name: Nicolas - first_name: Robin full_name: Mesnage, Robin last_name: Mesnage - first_name: Martina full_name: Biserni, Martina last_name: Biserni - first_name: Francesco V. full_name: Rao, Francesco V. last_name: Rao - first_name: Cristina Vazquez full_name: Martin, Cristina Vazquez last_name: Martin citation: ama: Antoniou MN, Nicolas A, Mesnage R, Biserni M, Rao FV, Martin CV. MOESM1 of Glyphosate does not substitute for glycine in proteins of actively dividing mammalian cells. 2019. doi:10.6084/m9.figshare.9411761.v1 apa: Antoniou, M. N., Nicolas, A., Mesnage, R., Biserni, M., Rao, F. V., & Martin, C. V. (2019). MOESM1 of Glyphosate does not substitute for glycine in proteins of actively dividing mammalian cells. Springer Nature. https://doi.org/10.6084/m9.figshare.9411761.v1 chicago: Antoniou, Michael N., Armel Nicolas, Robin Mesnage, Martina Biserni, Francesco V. Rao, and Cristina Vazquez Martin. “MOESM1 of Glyphosate Does Not Substitute for Glycine in Proteins of Actively Dividing Mammalian Cells.” Springer Nature, 2019. https://doi.org/10.6084/m9.figshare.9411761.v1. ieee: M. N. Antoniou, A. Nicolas, R. Mesnage, M. Biserni, F. V. Rao, and C. V. Martin, “MOESM1 of Glyphosate does not substitute for glycine in proteins of actively dividing mammalian cells.” Springer Nature, 2019. ista: Antoniou MN, Nicolas A, Mesnage R, Biserni M, Rao FV, Martin CV. 2019. MOESM1 of Glyphosate does not substitute for glycine in proteins of actively dividing mammalian cells, Springer Nature, 10.6084/m9.figshare.9411761.v1. mla: Antoniou, Michael N., et al. MOESM1 of Glyphosate Does Not Substitute for Glycine in Proteins of Actively Dividing Mammalian Cells. Springer Nature, 2019, doi:10.6084/m9.figshare.9411761.v1. short: M.N. Antoniou, A. Nicolas, R. Mesnage, M. Biserni, F.V. Rao, C.V. Martin, (2019). date_created: 2021-08-06T08:14:05Z date_published: 2019-08-09T00:00:00Z date_updated: 2023-02-23T12:52:29Z day: '09' department: - _id: LifeSc doi: 10.6084/m9.figshare.9411761.v1 main_file_link: - open_access: '1' url: https://doi.org/10.6084/m9.figshare.9411761.v1 month: '08' oa: 1 oa_version: Published Version publisher: Springer Nature related_material: record: - id: '6819' relation: used_in_publication status: public status: public title: MOESM1 of Glyphosate does not substitute for glycine in proteins of actively dividing mammalian cells type: research_data_reference user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf year: '2019' ... --- _id: '9839' abstract: - lang: eng text: 'More than 100 years after Grigg’s influential analysis of species’ borders, the causes of limits to species’ ranges still represent a puzzle that has never been understood with clarity. The topic has become especially important recently as many scientists have become interested in the potential for species’ ranges to shift in response to climate change—and yet nearly all of those studies fail to recognise or incorporate evolutionary genetics in a way that relates to theoretical developments. I show that range margins can be understood based on just two measurable parameters: (i) the fitness cost of dispersal—a measure of environmental heterogeneity—and (ii) the strength of genetic drift, which reduces genetic diversity. Together, these two parameters define an ‘expansion threshold’: adaptation fails when genetic drift reduces genetic diversity below that required for adaptation to a heterogeneous environment. When the key parameters drop below this expansion threshold locally, a sharp range margin forms. When they drop below this threshold throughout the species’ range, adaptation collapses everywhere, resulting in either extinction or formation of a fragmented metapopulation. Because the effects of dispersal differ fundamentally with dimension, the second parameter—the strength of genetic drift—is qualitatively different compared to a linear habitat. In two-dimensional habitats, genetic drift becomes effectively independent of selection. It decreases with ‘neighbourhood size’—the number of individuals accessible by dispersal within one generation. Moreover, in contrast to earlier predictions, which neglected evolution of genetic variance and/or stochasticity in two dimensions, dispersal into small marginal populations aids adaptation. This is because the reduction of both genetic and demographic stochasticity has a stronger effect than the cost of dispersal through increased maladaptation. The expansion threshold thus provides a novel, theoretically justified, and testable prediction for formation of the range margin and collapse of the species’ range.' article_processing_charge: No author: - first_name: Jitka full_name: Polechova, Jitka id: 3BBFB084-F248-11E8-B48F-1D18A9856A87 last_name: Polechova orcid: 0000-0003-0951-3112 citation: ama: 'Polechova J. Data from: Is the sky the limit? On the expansion threshold of a species’ range. 2019. doi:10.5061/dryad.5vv37' apa: 'Polechova, J. (2019). Data from: Is the sky the limit? On the expansion threshold of a species’ range. Dryad. https://doi.org/10.5061/dryad.5vv37' chicago: 'Polechova, Jitka. “Data from: Is the Sky the Limit? On the Expansion Threshold of a Species’ Range.” Dryad, 2019. https://doi.org/10.5061/dryad.5vv37.' ieee: 'J. Polechova, “Data from: Is the sky the limit? On the expansion threshold of a species’ range.” Dryad, 2019.' ista: 'Polechova J. 2019. Data from: Is the sky the limit? On the expansion threshold of a species’ range, Dryad, 10.5061/dryad.5vv37.' mla: 'Polechova, Jitka. Data from: Is the Sky the Limit? On the Expansion Threshold of a Species’ Range. Dryad, 2019, doi:10.5061/dryad.5vv37.' short: J. Polechova, (2019). date_created: 2021-08-09T13:07:28Z date_published: 2019-06-22T00:00:00Z date_updated: 2023-02-23T11:14:30Z day: '22' department: - _id: NiBa doi: 10.5061/dryad.5vv37 main_file_link: - open_access: '1' url: https://doi.org/10.5061/dryad.5vv37 month: '06' oa: 1 oa_version: Published Version publisher: Dryad related_material: record: - id: '315' relation: used_in_publication status: public status: public title: 'Data from: Is the sky the limit? On the expansion threshold of a species'' range' type: research_data_reference user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf year: '2019' ... --- _id: '8408' abstract: - lang: eng text: Aromatic residues are located at structurally important sites of many proteins. Probing their interactions and dynamics can provide important functional insight but is challenging in large proteins. Here, we introduce approaches to characterize dynamics of phenylalanine residues using 1H-detected fast magic-angle spinning (MAS) NMR combined with a tailored isotope-labeling scheme. Our approach yields isolated two-spin systems that are ideally suited for artefact-free dynamics measurements, and allows probing motions effectively without molecular-weight limitations. The application to the TET2 enzyme assembly of ~0.5 MDa size, the currently largest protein assigned by MAS NMR, provides insights into motions occurring on a wide range of time scales (ps-ms). We quantitatively probe ring flip motions, and show the temperature dependence by MAS NMR measurements down to 100 K. Interestingly, favorable line widths are observed down to 100 K, with potential implications for DNP NMR. Furthermore, we report the first 13C R1ρ MAS NMR relaxation-dispersion measurements and detect structural excursions occurring on a microsecond time scale in the entry pore to the catalytic chamber and at a trimer interface that was proposed as exit pore. We show that the labeling scheme with deuteration at ca. 50 kHz MAS provides superior resolution compared to 100 kHz MAS experiments with protonated, uniformly 13C-labeled samples. article_processing_charge: No article_type: original author: - first_name: Diego F. full_name: Gauto, Diego F. last_name: Gauto - first_name: Pavel full_name: Macek, Pavel last_name: Macek - first_name: Alessandro full_name: Barducci, Alessandro last_name: Barducci - first_name: Hugo full_name: Fraga, Hugo last_name: Fraga - first_name: Audrey full_name: Hessel, Audrey last_name: Hessel - first_name: Tsutomu full_name: Terauchi, Tsutomu last_name: Terauchi - first_name: David full_name: Gajan, David last_name: Gajan - first_name: Yohei full_name: Miyanoiri, Yohei last_name: Miyanoiri - first_name: Jerome full_name: Boisbouvier, Jerome last_name: Boisbouvier - first_name: Roman full_name: Lichtenecker, Roman last_name: Lichtenecker - first_name: Masatsune full_name: Kainosho, Masatsune last_name: Kainosho - first_name: Paul full_name: Schanda, Paul id: 7B541462-FAF6-11E9-A490-E8DFE5697425 last_name: Schanda orcid: 0000-0002-9350-7606 citation: ama: Gauto DF, Macek P, Barducci A, et al. Aromatic ring dynamics, thermal activation, and transient conformations of a 468 kDa enzyme by specific 1H–13C labeling and fast magic-angle spinning NMR. Journal of the American Chemical Society. 2019;141(28):11183-11195. doi:10.1021/jacs.9b04219 apa: Gauto, D. F., Macek, P., Barducci, A., Fraga, H., Hessel, A., Terauchi, T., … Schanda, P. (2019). Aromatic ring dynamics, thermal activation, and transient conformations of a 468 kDa enzyme by specific 1H–13C labeling and fast magic-angle spinning NMR. Journal of the American Chemical Society. American Chemical Society. https://doi.org/10.1021/jacs.9b04219 chicago: Gauto, Diego F., Pavel Macek, Alessandro Barducci, Hugo Fraga, Audrey Hessel, Tsutomu Terauchi, David Gajan, et al. “Aromatic Ring Dynamics, Thermal Activation, and Transient Conformations of a 468 KDa Enzyme by Specific 1H–13C Labeling and Fast Magic-Angle Spinning NMR.” Journal of the American Chemical Society. American Chemical Society, 2019. https://doi.org/10.1021/jacs.9b04219. ieee: D. F. Gauto et al., “Aromatic ring dynamics, thermal activation, and transient conformations of a 468 kDa enzyme by specific 1H–13C labeling and fast magic-angle spinning NMR,” Journal of the American Chemical Society, vol. 141, no. 28. American Chemical Society, pp. 11183–11195, 2019. ista: Gauto DF, Macek P, Barducci A, Fraga H, Hessel A, Terauchi T, Gajan D, Miyanoiri Y, Boisbouvier J, Lichtenecker R, Kainosho M, Schanda P. 2019. Aromatic ring dynamics, thermal activation, and transient conformations of a 468 kDa enzyme by specific 1H–13C labeling and fast magic-angle spinning NMR. Journal of the American Chemical Society. 141(28), 11183–11195. mla: Gauto, Diego F., et al. “Aromatic Ring Dynamics, Thermal Activation, and Transient Conformations of a 468 KDa Enzyme by Specific 1H–13C Labeling and Fast Magic-Angle Spinning NMR.” Journal of the American Chemical Society, vol. 141, no. 28, American Chemical Society, 2019, pp. 11183–95, doi:10.1021/jacs.9b04219. short: D.F. Gauto, P. Macek, A. Barducci, H. Fraga, A. Hessel, T. Terauchi, D. Gajan, Y. Miyanoiri, J. Boisbouvier, R. Lichtenecker, M. Kainosho, P. Schanda, Journal of the American Chemical Society 141 (2019) 11183–11195. date_created: 2020-09-17T10:29:00Z date_published: 2019-06-14T00:00:00Z date_updated: 2021-01-12T08:19:04Z day: '14' doi: 10.1021/jacs.9b04219 extern: '1' external_id: pmid: - '31199882' intvolume: ' 141' issue: '28' keyword: - Colloid and Surface Chemistry - Biochemistry - General Chemistry - Catalysis language: - iso: eng month: '06' oa_version: Submitted Version page: 11183-11195 pmid: 1 publication: Journal of the American Chemical Society publication_identifier: issn: - 0002-7863 - 1520-5126 publication_status: published publisher: American Chemical Society quality_controlled: '1' status: public title: Aromatic ring dynamics, thermal activation, and transient conformations of a 468 kDa enzyme by specific 1H–13C labeling and fast magic-angle spinning NMR type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 141 year: '2019' ... --- _id: '8418' abstract: - lang: eng text: For the Restricted Circular Planar 3 Body Problem, we show that there exists an open set U in phase space of fixed measure, where the set of initial points which lead to collision is O(μ120) dense as μ→0. article_processing_charge: No article_type: original author: - first_name: Marcel full_name: Guardia, Marcel last_name: Guardia - first_name: Vadim full_name: Kaloshin, Vadim id: FE553552-CDE8-11E9-B324-C0EBE5697425 last_name: Kaloshin orcid: 0000-0002-6051-2628 - first_name: Jianlu full_name: Zhang, Jianlu last_name: Zhang citation: ama: Guardia M, Kaloshin V, Zhang J. Asymptotic density of collision orbits in the Restricted Circular Planar 3 Body Problem. Archive for Rational Mechanics and Analysis. 2019;233(2):799-836. doi:10.1007/s00205-019-01368-7 apa: Guardia, M., Kaloshin, V., & Zhang, J. (2019). Asymptotic density of collision orbits in the Restricted Circular Planar 3 Body Problem. Archive for Rational Mechanics and Analysis. Springer Nature. https://doi.org/10.1007/s00205-019-01368-7 chicago: Guardia, Marcel, Vadim Kaloshin, and Jianlu Zhang. “Asymptotic Density of Collision Orbits in the Restricted Circular Planar 3 Body Problem.” Archive for Rational Mechanics and Analysis. Springer Nature, 2019. https://doi.org/10.1007/s00205-019-01368-7. ieee: M. Guardia, V. Kaloshin, and J. Zhang, “Asymptotic density of collision orbits in the Restricted Circular Planar 3 Body Problem,” Archive for Rational Mechanics and Analysis, vol. 233, no. 2. Springer Nature, pp. 799–836, 2019. ista: Guardia M, Kaloshin V, Zhang J. 2019. Asymptotic density of collision orbits in the Restricted Circular Planar 3 Body Problem. Archive for Rational Mechanics and Analysis. 233(2), 799–836. mla: Guardia, Marcel, et al. “Asymptotic Density of Collision Orbits in the Restricted Circular Planar 3 Body Problem.” Archive for Rational Mechanics and Analysis, vol. 233, no. 2, Springer Nature, 2019, pp. 799–836, doi:10.1007/s00205-019-01368-7. short: M. Guardia, V. Kaloshin, J. Zhang, Archive for Rational Mechanics and Analysis 233 (2019) 799–836. date_created: 2020-09-17T10:41:51Z date_published: 2019-03-12T00:00:00Z date_updated: 2021-01-12T08:19:09Z day: '12' doi: 10.1007/s00205-019-01368-7 extern: '1' intvolume: ' 233' issue: '2' keyword: - Mechanical Engineering - Mathematics (miscellaneous) - Analysis language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1007/s00205-019-01368-7 month: '03' oa: 1 oa_version: Published Version page: 799-836 publication: Archive for Rational Mechanics and Analysis publication_identifier: issn: - 0003-9527 - 1432-0673 publication_status: published publisher: Springer Nature quality_controlled: '1' status: public title: Asymptotic density of collision orbits in the Restricted Circular Planar 3 Body Problem type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 233 year: '2019' ... --- _id: '8416' abstract: - lang: eng text: In this paper, we show that any smooth one-parameter deformations of a strictly convex integrable billiard table Ω0 preserving the integrability near the boundary have to be tangent to a finite dimensional space passing through Ω0. article_processing_charge: No article_type: original author: - first_name: Guan full_name: Huang, Guan last_name: Huang - first_name: Vadim full_name: Kaloshin, Vadim id: FE553552-CDE8-11E9-B324-C0EBE5697425 last_name: Kaloshin orcid: 0000-0002-6051-2628 citation: ama: Huang G, Kaloshin V. On the finite dimensionality of integrable deformations of strictly convex integrable billiard tables. Moscow Mathematical Journal. 2019;19(2):307-327. doi:10.17323/1609-4514-2019-19-2-307-327 apa: Huang, G., & Kaloshin, V. (2019). On the finite dimensionality of integrable deformations of strictly convex integrable billiard tables. Moscow Mathematical Journal. American Mathematical Society. https://doi.org/10.17323/1609-4514-2019-19-2-307-327 chicago: Huang, Guan, and Vadim Kaloshin. “On the Finite Dimensionality of Integrable Deformations of Strictly Convex Integrable Billiard Tables.” Moscow Mathematical Journal. American Mathematical Society, 2019. https://doi.org/10.17323/1609-4514-2019-19-2-307-327. ieee: G. Huang and V. Kaloshin, “On the finite dimensionality of integrable deformations of strictly convex integrable billiard tables,” Moscow Mathematical Journal, vol. 19, no. 2. American Mathematical Society, pp. 307–327, 2019. ista: Huang G, Kaloshin V. 2019. On the finite dimensionality of integrable deformations of strictly convex integrable billiard tables. Moscow Mathematical Journal. 19(2), 307–327. mla: Huang, Guan, and Vadim Kaloshin. “On the Finite Dimensionality of Integrable Deformations of Strictly Convex Integrable Billiard Tables.” Moscow Mathematical Journal, vol. 19, no. 2, American Mathematical Society, 2019, pp. 307–27, doi:10.17323/1609-4514-2019-19-2-307-327. short: G. Huang, V. Kaloshin, Moscow Mathematical Journal 19 (2019) 307–327. date_created: 2020-09-17T10:41:36Z date_published: 2019-04-01T00:00:00Z date_updated: 2021-01-12T08:19:08Z day: '01' doi: 10.17323/1609-4514-2019-19-2-307-327 extern: '1' external_id: arxiv: - '1809.09341' intvolume: ' 19' issue: '2' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1809.09341 month: '04' oa: 1 oa_version: Preprint page: 307-327 publication: Moscow Mathematical Journal publication_identifier: issn: - 1609-4514 publication_status: published publisher: American Mathematical Society quality_controlled: '1' status: public title: On the finite dimensionality of integrable deformations of strictly convex integrable billiard tables type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 19 year: '2019' ... --- _id: '8693' abstract: - lang: eng text: We review V. I. Arnold’s 1963 celebrated paper [1] Proof of A. N. Kolmogorov’s Theorem on the Conservation of Conditionally Periodic Motions with a Small Variation in the Hamiltonian, and prove that, optimising Arnold’s scheme, one can get “sharp” asymptotic quantitative conditions (as ε → 0, ε being the strength of the perturbation). All constants involved are explicitly computed. article_processing_charge: No article_type: original author: - first_name: Luigi full_name: Chierchia, Luigi last_name: Chierchia - first_name: Edmond full_name: Koudjinan, Edmond id: 52DF3E68-AEFA-11EA-95A4-124A3DDC885E last_name: Koudjinan orcid: 0000-0003-2640-4049 citation: ama: Chierchia L, Koudjinan E. V. I. Arnold’s “pointwise” KAM theorem. Regular and Chaotic Dynamics. 2019;24:583–606. doi:10.1134/S1560354719060017 apa: Chierchia, L., & Koudjinan, E. (2019). V. I. Arnold’s “pointwise” KAM theorem. Regular and Chaotic Dynamics. Springer. https://doi.org/10.1134/S1560354719060017 chicago: Chierchia, Luigi, and Edmond Koudjinan. “V. I. Arnold’s ‘Pointwise’ KAM Theorem.” Regular and Chaotic Dynamics. Springer, 2019. https://doi.org/10.1134/S1560354719060017. ieee: L. Chierchia and E. Koudjinan, “V. I. Arnold’s ‘pointwise’ KAM theorem,” Regular and Chaotic Dynamics, vol. 24. Springer, pp. 583–606, 2019. ista: Chierchia L, Koudjinan E. 2019. V. I. Arnold’s “pointwise” KAM theorem. Regular and Chaotic Dynamics. 24, 583–606. mla: Chierchia, Luigi, and Edmond Koudjinan. “V. I. Arnold’s ‘Pointwise’ KAM Theorem.” Regular and Chaotic Dynamics, vol. 24, Springer, 2019, pp. 583–606, doi:10.1134/S1560354719060017. short: L. Chierchia, E. Koudjinan, Regular and Chaotic Dynamics 24 (2019) 583–606. date_created: 2020-10-21T15:25:45Z date_published: 2019-12-10T00:00:00Z date_updated: 2021-01-12T08:20:34Z day: '10' doi: 10.1134/S1560354719060017 extern: '1' external_id: arxiv: - '1908.02523' intvolume: ' 24' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1908.02523 month: '12' oa: 1 oa_version: Preprint page: 583–606 publication: Regular and Chaotic Dynamics publication_status: published publisher: Springer quality_controlled: '1' status: public title: V. I. Arnold’s “pointwise” KAM theorem type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 24 year: '2019' ... --- _id: '9018' abstract: - lang: eng text: Anti-silencing function 1 (ASF1) is a conserved H3-H4 histone chaperone involved in histone dynamics during replication, transcription, and DNA repair. Overexpressed in proliferating tissues including many tumors, ASF1 has emerged as a promising therapeutic target. Here, we combine structural, computational, and biochemical approaches to design peptides that inhibit the ASF1-histone interaction. Starting from the structure of the human ASF1-histone complex, we developed a rational design strategy combining epitope tethering and optimization of interface contacts to identify a potent peptide inhibitor with a dissociation constant of 3 nM. When introduced into cultured cells, the inhibitors impair cell proliferation, perturb cell-cycle progression, and reduce cell migration and invasion in a manner commensurate with their affinity for ASF1. Finally, we find that direct injection of the most potent ASF1 peptide inhibitor in mouse allografts reduces tumor growth. Our results open new avenues to use ASF1 inhibitors as promising leads for cancer therapy. article_processing_charge: No article_type: original author: - first_name: May M full_name: Bakail, May M id: FB3C3F8E-522F-11EA-B186-22963DDC885E last_name: Bakail orcid: 0000-0002-9592-1587 - first_name: Albane full_name: Gaubert, Albane last_name: Gaubert - first_name: Jessica full_name: Andreani, Jessica last_name: Andreani - first_name: Gwenaëlle full_name: Moal, Gwenaëlle last_name: Moal - first_name: Guillaume full_name: Pinna, Guillaume last_name: Pinna - first_name: Ekaterina full_name: Boyarchuk, Ekaterina last_name: Boyarchuk - first_name: Marie-Cécile full_name: Gaillard, Marie-Cécile last_name: Gaillard - first_name: Regis full_name: Courbeyrette, Regis last_name: Courbeyrette - first_name: Carl full_name: Mann, Carl last_name: Mann - first_name: Jean-Yves full_name: Thuret, Jean-Yves last_name: Thuret - first_name: Bérengère full_name: Guichard, Bérengère last_name: Guichard - first_name: Brice full_name: Murciano, Brice last_name: Murciano - first_name: Nicolas full_name: Richet, Nicolas last_name: Richet - first_name: Adeline full_name: Poitou, Adeline last_name: Poitou - first_name: Claire full_name: Frederic, Claire last_name: Frederic - first_name: Marie-Hélène full_name: Le Du, Marie-Hélène last_name: Le Du - first_name: Morgane full_name: Agez, Morgane last_name: Agez - first_name: Caroline full_name: Roelants, Caroline last_name: Roelants - first_name: Zachary A. full_name: Gurard-Levin, Zachary A. last_name: Gurard-Levin - first_name: Geneviève full_name: Almouzni, Geneviève last_name: Almouzni - first_name: Nadia full_name: Cherradi, Nadia last_name: Cherradi - first_name: Raphael full_name: Guerois, Raphael last_name: Guerois - first_name: Françoise full_name: Ochsenbein, Françoise last_name: Ochsenbein citation: ama: Bakail MM, Gaubert A, Andreani J, et al. Design on a rational basis of high-affinity peptides inhibiting the histone chaperone ASF1. Cell Chemical Biology. 2019;26(11):1573-1585.e10. doi:10.1016/j.chembiol.2019.09.002 apa: Bakail, M. M., Gaubert, A., Andreani, J., Moal, G., Pinna, G., Boyarchuk, E., … Ochsenbein, F. (2019). Design on a rational basis of high-affinity peptides inhibiting the histone chaperone ASF1. Cell Chemical Biology. Elsevier. https://doi.org/10.1016/j.chembiol.2019.09.002 chicago: Bakail, May M, Albane Gaubert, Jessica Andreani, Gwenaëlle Moal, Guillaume Pinna, Ekaterina Boyarchuk, Marie-Cécile Gaillard, et al. “Design on a Rational Basis of High-Affinity Peptides Inhibiting the Histone Chaperone ASF1.” Cell Chemical Biology. Elsevier, 2019. https://doi.org/10.1016/j.chembiol.2019.09.002. ieee: M. M. Bakail et al., “Design on a rational basis of high-affinity peptides inhibiting the histone chaperone ASF1,” Cell Chemical Biology, vol. 26, no. 11. Elsevier, p. 1573–1585.e10, 2019. ista: Bakail MM, Gaubert A, Andreani J, Moal G, Pinna G, Boyarchuk E, Gaillard M-C, Courbeyrette R, Mann C, Thuret J-Y, Guichard B, Murciano B, Richet N, Poitou A, Frederic C, Le Du M-H, Agez M, Roelants C, Gurard-Levin ZA, Almouzni G, Cherradi N, Guerois R, Ochsenbein F. 2019. Design on a rational basis of high-affinity peptides inhibiting the histone chaperone ASF1. Cell Chemical Biology. 26(11), 1573–1585.e10. mla: Bakail, May M., et al. “Design on a Rational Basis of High-Affinity Peptides Inhibiting the Histone Chaperone ASF1.” Cell Chemical Biology, vol. 26, no. 11, Elsevier, 2019, p. 1573–1585.e10, doi:10.1016/j.chembiol.2019.09.002. short: M.M. Bakail, A. Gaubert, J. Andreani, G. Moal, G. Pinna, E. Boyarchuk, M.-C. Gaillard, R. Courbeyrette, C. Mann, J.-Y. Thuret, B. Guichard, B. Murciano, N. Richet, A. Poitou, C. Frederic, M.-H. Le Du, M. Agez, C. Roelants, Z.A. Gurard-Levin, G. Almouzni, N. Cherradi, R. Guerois, F. Ochsenbein, Cell Chemical Biology 26 (2019) 1573–1585.e10. date_created: 2021-01-19T11:04:50Z date_published: 2019-11-21T00:00:00Z date_updated: 2023-02-23T13:46:53Z day: '21' doi: 10.1016/j.chembiol.2019.09.002 extern: '1' external_id: pmid: - '31543461' intvolume: ' 26' issue: '11' keyword: - Clinical Biochemistry - Molecular Medicine - Biochemistry - Molecular Biology - Pharmacology - Drug Discovery language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1016/j.chembiol.2019.09.002 month: '11' oa: 1 oa_version: Published Version page: 1573-1585.e10 pmid: 1 publication: Cell Chemical Biology publication_identifier: issn: - 2451-9456 publication_status: published publisher: Elsevier quality_controlled: '1' status: public title: Design on a rational basis of high-affinity peptides inhibiting the histone chaperone ASF1 type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 26 year: '2019' ... --- _id: '9530' abstract: - lang: eng text: "Background\r\nDNA methylation of active genes, also known as gene body methylation, is found in many animal and plant genomes. Despite this, the transcriptional and developmental role of such methylation remains poorly understood. Here, we explore the dynamic range of DNA methylation in honey bee, a model organism for gene body methylation.\r\n\r\nResults\r\nOur data show that CG methylation in gene bodies globally fluctuates during honey bee development. However, these changes cause no gene expression alterations. Intriguingly, despite the global alterations, tissue-specific CG methylation patterns of complete genes or exons are rare, implying robust maintenance of genic methylation during development. Additionally, we show that CG methylation maintenance fluctuates in somatic cells, while reaching maximum fidelity in sperm cells. Finally, unlike universally present CG methylation, we discovered non-CG methylation specifically in bee heads that resembles such methylation in mammalian brain tissue.\r\n\r\nConclusions\r\nBased on these results, we propose that gene body CG methylation can oscillate during development if it is kept to a level adequate to preserve function. Additionally, our data suggest that heightened non-CG methylation is a conserved regulator of animal nervous systems." article_number: '62' article_processing_charge: No article_type: original author: - first_name: Keith D. full_name: Harris, Keith D. last_name: Harris - first_name: James P. B. full_name: Lloyd, James P. B. last_name: Lloyd - first_name: Katherine full_name: Domb, Katherine last_name: Domb - first_name: Daniel full_name: Zilberman, Daniel id: 6973db13-dd5f-11ea-814e-b3e5455e9ed1 last_name: Zilberman orcid: 0000-0002-0123-8649 - first_name: Assaf full_name: Zemach, Assaf last_name: Zemach citation: ama: Harris KD, Lloyd JPB, Domb K, Zilberman D, Zemach A. DNA methylation is maintained with high fidelity in the honey bee germline and exhibits global non-functional fluctuations during somatic development. Epigenetics and Chromatin. 2019;12. doi:10.1186/s13072-019-0307-4 apa: Harris, K. D., Lloyd, J. P. B., Domb, K., Zilberman, D., & Zemach, A. (2019). DNA methylation is maintained with high fidelity in the honey bee germline and exhibits global non-functional fluctuations during somatic development. Epigenetics and Chromatin. Springer Nature. https://doi.org/10.1186/s13072-019-0307-4 chicago: Harris, Keith D., James P. B. Lloyd, Katherine Domb, Daniel Zilberman, and Assaf Zemach. “DNA Methylation Is Maintained with High Fidelity in the Honey Bee Germline and Exhibits Global Non-Functional Fluctuations during Somatic Development.” Epigenetics and Chromatin. Springer Nature, 2019. https://doi.org/10.1186/s13072-019-0307-4. ieee: K. D. Harris, J. P. B. Lloyd, K. Domb, D. Zilberman, and A. Zemach, “DNA methylation is maintained with high fidelity in the honey bee germline and exhibits global non-functional fluctuations during somatic development,” Epigenetics and Chromatin, vol. 12. Springer Nature, 2019. ista: Harris KD, Lloyd JPB, Domb K, Zilberman D, Zemach A. 2019. DNA methylation is maintained with high fidelity in the honey bee germline and exhibits global non-functional fluctuations during somatic development. Epigenetics and Chromatin. 12, 62. mla: Harris, Keith D., et al. “DNA Methylation Is Maintained with High Fidelity in the Honey Bee Germline and Exhibits Global Non-Functional Fluctuations during Somatic Development.” Epigenetics and Chromatin, vol. 12, 62, Springer Nature, 2019, doi:10.1186/s13072-019-0307-4. short: K.D. Harris, J.P.B. Lloyd, K. Domb, D. Zilberman, A. Zemach, Epigenetics and Chromatin 12 (2019). date_created: 2021-06-08T09:21:51Z date_published: 2019-10-10T00:00:00Z date_updated: 2021-12-14T07:53:00Z day: '10' ddc: - '570' department: - _id: DaZi doi: 10.1186/s13072-019-0307-4 extern: '1' external_id: pmid: - '31601251' file: - access_level: open_access checksum: 86ff50a7517891511af2733c76c81b67 content_type: application/pdf creator: asandaue date_created: 2021-06-08T09:29:19Z date_updated: 2021-06-08T09:29:19Z file_id: '9531' file_name: 2019_EpigeneticsAndChromatin_Harris.pdf file_size: 3221067 relation: main_file success: 1 file_date_updated: 2021-06-08T09:29:19Z has_accepted_license: '1' intvolume: ' 12' language: - iso: eng month: '10' oa: 1 oa_version: Published Version pmid: 1 publication: Epigenetics and Chromatin publication_identifier: eissn: - 1756-8935 publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: DNA methylation is maintained with high fidelity in the honey bee germline and exhibits global non-functional fluctuations during somatic development 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: 8b945eb4-e2f2-11eb-945a-df72226e66a9 volume: 12 year: '2019' ... --- _id: '9586' abstract: - lang: eng text: "Consider integers \U0001D458,ℓ such that 0⩽ℓ⩽(\U0001D4582) . Given a large graph \U0001D43A , what is the fraction of \U0001D458 -vertex subsets of \U0001D43A \ which span exactly ℓ edges? When \U0001D43A is empty or complete, and ℓ \ is zero or (\U0001D4582) , this fraction can be exactly 1. On the other hand, if ℓ is far from these extreme values, one might expect that this fraction is substantially smaller than 1. This was recently proved by Alon, Hefetz, Krivelevich, and Tyomkyn who initiated the systematic study of this question and proposed several natural conjectures.\r\nLet ℓ∗=min{ℓ,(\U0001D4582)−ℓ} . Our main result is that for any \U0001D458 and ℓ , the fraction of \U0001D458 -vertex subsets that span ℓ edges is at most log\U0001D442(1)(ℓ∗/\U0001D458)√ \U0001D458/ℓ∗, which is best-possible up to the logarithmic factor. This improves on multiple results of Alon, Hefetz, Krivelevich, and Tyomkyn, and resolves one of their conjectures. In addition, we also make some first steps towards some analogous questions for hypergraphs.\r\nOur proofs involve some Ramsey-type arguments, and a number of different probabilistic tools, such as polynomial anticoncentration inequalities, hypercontractivity, and a coupling trick for random variables defined on a ‘slice’ of the Boolean hypercube." article_processing_charge: No article_type: original author: - first_name: Matthew Alan full_name: Kwan, Matthew Alan id: 5fca0887-a1db-11eb-95d1-ca9d5e0453b3 last_name: Kwan orcid: 0000-0002-4003-7567 - first_name: Benny full_name: Sudakov, Benny last_name: Sudakov - first_name: Tuan full_name: Tran, Tuan last_name: Tran citation: ama: Kwan MA, Sudakov B, Tran T. Anticoncentration for subgraph statistics. Journal of the London Mathematical Society. 2019;99(3):757-777. doi:10.1112/jlms.12192 apa: Kwan, M. A., Sudakov, B., & Tran, T. (2019). Anticoncentration for subgraph statistics. Journal of the London Mathematical Society. Wiley. https://doi.org/10.1112/jlms.12192 chicago: Kwan, Matthew Alan, Benny Sudakov, and Tuan Tran. “Anticoncentration for Subgraph Statistics.” Journal of the London Mathematical Society. Wiley, 2019. https://doi.org/10.1112/jlms.12192. ieee: M. A. Kwan, B. Sudakov, and T. Tran, “Anticoncentration for subgraph statistics,” Journal of the London Mathematical Society, vol. 99, no. 3. Wiley, pp. 757–777, 2019. ista: Kwan MA, Sudakov B, Tran T. 2019. Anticoncentration for subgraph statistics. Journal of the London Mathematical Society. 99(3), 757–777. mla: Kwan, Matthew Alan, et al. “Anticoncentration for Subgraph Statistics.” Journal of the London Mathematical Society, vol. 99, no. 3, Wiley, 2019, pp. 757–77, doi:10.1112/jlms.12192. short: M.A. Kwan, B. Sudakov, T. Tran, Journal of the London Mathematical Society 99 (2019) 757–777. date_created: 2021-06-22T09:46:03Z date_published: 2019-05-03T00:00:00Z date_updated: 2023-02-23T14:01:53Z day: '03' doi: 10.1112/jlms.12192 extern: '1' external_id: arxiv: - '1807.05202' intvolume: ' 99' issue: '3' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1807.05202 month: '05' oa: 1 oa_version: Preprint page: 757-777 publication: Journal of the London Mathematical Society publication_identifier: eissn: - 1469-7750 issn: - 0024-6107 publication_status: published publisher: Wiley quality_controlled: '1' scopus_import: '1' status: public title: Anticoncentration for subgraph statistics type: journal_article user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf volume: 99 year: '2019' ... --- _id: '9580' abstract: - lang: eng text: An r-cut of a k-uniform hypergraph H is a partition of the vertex set of H into r parts and the size of the cut is the number of edges which have a vertex in each part. A classical result of Edwards says that every m-edge graph has a 2-cut of size m/2+Ω)(m−−√) and this is best possible. That is, there exist cuts which exceed the expected size of a random cut by some multiple of the standard deviation. We study analogues of this and related results in hypergraphs. First, we observe that similarly to graphs, every m-edge k-uniform hypergraph has an r-cut whose size is Ω(m−−√) larger than the expected size of a random r-cut. Moreover, in the case where k = 3 and r = 2 this bound is best possible and is attained by Steiner triple systems. Surprisingly, for all other cases (that is, if k ≥ 4 or r ≥ 3), we show that every m-edge k-uniform hypergraph has an r-cut whose size is Ω(m5/9) larger than the expected size of a random r-cut. This is a significant difference in behaviour, since the amount by which the size of the largest cut exceeds the expected size of a random cut is now considerably larger than the standard deviation. article_processing_charge: No article_type: original author: - first_name: David full_name: Conlon, David last_name: Conlon - first_name: Jacob full_name: Fox, Jacob last_name: Fox - first_name: Matthew Alan full_name: Kwan, Matthew Alan id: 5fca0887-a1db-11eb-95d1-ca9d5e0453b3 last_name: Kwan orcid: 0000-0002-4003-7567 - first_name: Benny full_name: Sudakov, Benny last_name: Sudakov citation: ama: Conlon D, Fox J, Kwan MA, Sudakov B. Hypergraph cuts above the average. Israel Journal of Mathematics. 2019;233(1):67-111. doi:10.1007/s11856-019-1897-z apa: Conlon, D., Fox, J., Kwan, M. A., & Sudakov, B. (2019). Hypergraph cuts above the average. Israel Journal of Mathematics. Springer. https://doi.org/10.1007/s11856-019-1897-z chicago: Conlon, David, Jacob Fox, Matthew Alan Kwan, and Benny Sudakov. “Hypergraph Cuts above the Average.” Israel Journal of Mathematics. Springer, 2019. https://doi.org/10.1007/s11856-019-1897-z. ieee: D. Conlon, J. Fox, M. A. Kwan, and B. Sudakov, “Hypergraph cuts above the average,” Israel Journal of Mathematics, vol. 233, no. 1. Springer, pp. 67–111, 2019. ista: Conlon D, Fox J, Kwan MA, Sudakov B. 2019. Hypergraph cuts above the average. Israel Journal of Mathematics. 233(1), 67–111. mla: Conlon, David, et al. “Hypergraph Cuts above the Average.” Israel Journal of Mathematics, vol. 233, no. 1, Springer, 2019, pp. 67–111, doi:10.1007/s11856-019-1897-z. short: D. Conlon, J. Fox, M.A. Kwan, B. Sudakov, Israel Journal of Mathematics 233 (2019) 67–111. date_created: 2021-06-21T13:36:02Z date_published: 2019-08-01T00:00:00Z date_updated: 2023-02-23T14:01:41Z day: '01' doi: 10.1007/s11856-019-1897-z extern: '1' external_id: arxiv: - '1803.08462' intvolume: ' 233' issue: '1' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1803.08462 month: '08' oa: 1 oa_version: Preprint page: 67-111 publication: Israel Journal of Mathematics publication_identifier: eissn: - 1565-8511 issn: - 0021-2172 publication_status: published publisher: Springer quality_controlled: '1' scopus_import: '1' status: public title: Hypergraph cuts above the average type: journal_article user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf volume: 233 year: '2019' ... --- _id: '9585' abstract: - lang: eng text: An n-vertex graph is called C-Ramsey if it has no clique or independent set of size C log n. All known constructions of Ramsey graphs involve randomness in an essential way, and there is an ongoing line of research towards showing that in fact all Ramsey graphs must obey certain “richness” properties characteristic of random graphs. More than 25 years ago, Erdős, Faudree and Sós conjectured that in any C-Ramsey graph there are Ω(n^5/2) induced subgraphs, no pair of which have the same numbers of vertices and edges. Improving on earlier results of Alon, Balogh, Kostochka and Samotij, in this paper we prove this conjecture. article_processing_charge: No article_type: original author: - first_name: Matthew Alan full_name: Kwan, Matthew Alan id: 5fca0887-a1db-11eb-95d1-ca9d5e0453b3 last_name: Kwan orcid: 0000-0002-4003-7567 - first_name: Benny full_name: Sudakov, Benny last_name: Sudakov citation: ama: Kwan MA, Sudakov B. Proof of a conjecture on induced subgraphs of Ramsey graphs. Transactions of the American Mathematical Society. 2019;372(8):5571-5594. doi:10.1090/tran/7729 apa: Kwan, M. A., & Sudakov, B. (2019). Proof of a conjecture on induced subgraphs of Ramsey graphs. Transactions of the American Mathematical Society. American Mathematical Society. https://doi.org/10.1090/tran/7729 chicago: Kwan, Matthew Alan, and Benny Sudakov. “Proof of a Conjecture on Induced Subgraphs of Ramsey Graphs.” Transactions of the American Mathematical Society. American Mathematical Society, 2019. https://doi.org/10.1090/tran/7729. ieee: M. A. Kwan and B. Sudakov, “Proof of a conjecture on induced subgraphs of Ramsey graphs,” Transactions of the American Mathematical Society, vol. 372, no. 8. American Mathematical Society, pp. 5571–5594, 2019. ista: Kwan MA, Sudakov B. 2019. Proof of a conjecture on induced subgraphs of Ramsey graphs. Transactions of the American Mathematical Society. 372(8), 5571–5594. mla: Kwan, Matthew Alan, and Benny Sudakov. “Proof of a Conjecture on Induced Subgraphs of Ramsey Graphs.” Transactions of the American Mathematical Society, vol. 372, no. 8, American Mathematical Society, 2019, pp. 5571–94, doi:10.1090/tran/7729. short: M.A. Kwan, B. Sudakov, Transactions of the American Mathematical Society 372 (2019) 5571–5594. date_created: 2021-06-22T09:31:45Z date_published: 2019-10-15T00:00:00Z date_updated: 2023-02-23T14:01:50Z day: '15' doi: 10.1090/tran/7729 extern: '1' external_id: arxiv: - '1712.05656' intvolume: ' 372' issue: '8' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1090/tran/7729 month: '10' oa: 1 oa_version: Submitted Version page: 5571-5594 publication: Transactions of the American Mathematical Society publication_identifier: eissn: - 1088-6850 issn: - 0002-9947 publication_status: published publisher: American Mathematical Society quality_controlled: '1' scopus_import: '1' status: public title: Proof of a conjecture on induced subgraphs of Ramsey graphs type: journal_article user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf volume: 372 year: '2019' ... --- _id: '9677' abstract: - lang: eng text: Progress in the atomic-scale modeling of matter over the past decade has been tremendous. This progress has been brought about by improvements in methods for evaluating interatomic forces that work by either solving the electronic structure problem explicitly, or by computing accurate approximations of the solution and by the development of techniques that use the Born–Oppenheimer (BO) forces to move the atoms on the BO potential energy surface. As a consequence of these developments it is now possible to identify stable or metastable states, to sample configurations consistent with the appropriate thermodynamic ensemble, and to estimate the kinetics of reactions and phase transitions. All too often, however, progress is slowed down by the bottleneck associated with implementing new optimization algorithms and/or sampling techniques into the many existing electronic-structure and empirical-potential codes. To address this problem, we are thus releasing a new version of the i-PI software. This piece of software is an easily extensible framework for implementing advanced atomistic simulation techniques using interatomic potentials and forces calculated by an external driver code. While the original version of the code (Ceriotti et al., 2014) was developed with a focus on path integral molecular dynamics techniques, this second release of i-PI not only includes several new advanced path integral methods, but also offers other classes of algorithms. In other words, i-PI is moving towards becoming a universal force engine that is both modular and tightly coupled to the driver codes that evaluate the potential energy surface and its derivatives. article_processing_charge: No article_type: original author: - first_name: Venkat full_name: Kapil, Venkat last_name: Kapil - first_name: Mariana full_name: Rossi, Mariana last_name: Rossi - first_name: Ondrej full_name: Marsalek, Ondrej last_name: Marsalek - first_name: Riccardo full_name: Petraglia, Riccardo last_name: Petraglia - first_name: Yair full_name: Litman, Yair last_name: Litman - first_name: Thomas full_name: Spura, Thomas last_name: Spura - first_name: Bingqing full_name: Cheng, Bingqing id: cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9 last_name: Cheng orcid: 0000-0002-3584-9632 - first_name: Alice full_name: Cuzzocrea, Alice last_name: Cuzzocrea - first_name: Robert H. full_name: Meißner, Robert H. last_name: Meißner - first_name: David M. full_name: Wilkins, David M. last_name: Wilkins - first_name: Benjamin A. full_name: Helfrecht, Benjamin A. last_name: Helfrecht - first_name: Przemysław full_name: Juda, Przemysław last_name: Juda - first_name: Sébastien P. full_name: Bienvenue, Sébastien P. last_name: Bienvenue - first_name: Wei full_name: Fang, Wei last_name: Fang - first_name: Jan full_name: Kessler, Jan last_name: Kessler - first_name: Igor full_name: Poltavsky, Igor last_name: Poltavsky - first_name: Steven full_name: Vandenbrande, Steven last_name: Vandenbrande - first_name: Jelle full_name: Wieme, Jelle last_name: Wieme - first_name: Clemence full_name: Corminboeuf, Clemence last_name: Corminboeuf - first_name: Thomas D. full_name: Kühne, Thomas D. last_name: Kühne - first_name: David E. full_name: Manolopoulos, David E. last_name: Manolopoulos - first_name: Thomas E. full_name: Markland, Thomas E. last_name: Markland - first_name: Jeremy O. full_name: Richardson, Jeremy O. last_name: Richardson - first_name: Alexandre full_name: Tkatchenko, Alexandre last_name: Tkatchenko - first_name: Gareth A. full_name: Tribello, Gareth A. last_name: Tribello - first_name: Veronique full_name: Van Speybroeck, Veronique last_name: Van Speybroeck - first_name: Michele full_name: Ceriotti, Michele last_name: Ceriotti citation: ama: 'Kapil V, Rossi M, Marsalek O, et al. i-PI 2.0: A universal force engine for advanced molecular simulations. Computer Physics Communications. 2019;236:214-223. doi:10.1016/j.cpc.2018.09.020' apa: 'Kapil, V., Rossi, M., Marsalek, O., Petraglia, R., Litman, Y., Spura, T., … Ceriotti, M. (2019). i-PI 2.0: A universal force engine for advanced molecular simulations. Computer Physics Communications. Elsevier. https://doi.org/10.1016/j.cpc.2018.09.020' chicago: 'Kapil, Venkat, Mariana Rossi, Ondrej Marsalek, Riccardo Petraglia, Yair Litman, Thomas Spura, Bingqing Cheng, et al. “I-PI 2.0: A Universal Force Engine for Advanced Molecular Simulations.” Computer Physics Communications. Elsevier, 2019. https://doi.org/10.1016/j.cpc.2018.09.020.' ieee: 'V. Kapil et al., “i-PI 2.0: A universal force engine for advanced molecular simulations,” Computer Physics Communications, vol. 236. Elsevier, pp. 214–223, 2019.' ista: 'Kapil V, Rossi M, Marsalek O, Petraglia R, Litman Y, Spura T, Cheng B, Cuzzocrea A, Meißner RH, Wilkins DM, Helfrecht BA, Juda P, Bienvenue SP, Fang W, Kessler J, Poltavsky I, Vandenbrande S, Wieme J, Corminboeuf C, Kühne TD, Manolopoulos DE, Markland TE, Richardson JO, Tkatchenko A, Tribello GA, Van Speybroeck V, Ceriotti M. 2019. i-PI 2.0: A universal force engine for advanced molecular simulations. Computer Physics Communications. 236, 214–223.' mla: 'Kapil, Venkat, et al. “I-PI 2.0: A Universal Force Engine for Advanced Molecular Simulations.” Computer Physics Communications, vol. 236, Elsevier, 2019, pp. 214–23, doi:10.1016/j.cpc.2018.09.020.' short: V. Kapil, M. Rossi, O. Marsalek, R. Petraglia, Y. Litman, T. Spura, B. Cheng, A. Cuzzocrea, R.H. Meißner, D.M. Wilkins, B.A. Helfrecht, P. Juda, S.P. Bienvenue, W. Fang, J. Kessler, I. Poltavsky, S. Vandenbrande, J. Wieme, C. Corminboeuf, T.D. Kühne, D.E. Manolopoulos, T.E. Markland, J.O. Richardson, A. Tkatchenko, G.A. Tribello, V. Van Speybroeck, M. Ceriotti, Computer Physics Communications 236 (2019) 214–223. date_created: 2021-07-16T08:53:01Z date_published: 2019-03-01T00:00:00Z date_updated: 2021-08-09T12:37:16Z day: '01' doi: 10.1016/j.cpc.2018.09.020 extern: '1' external_id: arxiv: - '1808.03824' intvolume: ' 236' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1808.03824 month: '03' oa: 1 oa_version: Preprint page: 214-223 publication: Computer Physics Communications publication_identifier: issn: - 0010-4655 publication_status: published publisher: Elsevier quality_controlled: '1' scopus_import: '1' status: public title: 'i-PI 2.0: A universal force engine for advanced molecular simulations' type: journal_article user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf volume: 236 year: '2019' ... --- _id: '9680' abstract: - lang: eng text: Atomistic modeling of phase transitions, chemical reactions, or other rare events that involve overcoming high free energy barriers usually entails prohibitively long simulation times. Introducing a bias potential as a function of an appropriately chosen set of collective variables can significantly accelerate the exploration of phase space, albeit at the price of distorting the distribution of microstates. Efficient reweighting to recover the unbiased distribution can be nontrivial when employing adaptive sampling techniques such as metadynamics, variationally enhanced sampling, or parallel bias metadynamics, in which the system evolves in a quasi-equilibrium manner under a time-dependent bias. We introduce an iterative unbiasing scheme that makes efficient use of all the trajectory data and that does not require the distribution to be evaluated on a grid. The method can thus be used even when the bias has a high dimensionality. We benchmark this approach against some of the existing schemes on model systems with different complexity and dimensionality. article_processing_charge: No article_type: original author: - first_name: F. full_name: Giberti, F. last_name: Giberti - first_name: Bingqing full_name: Cheng, Bingqing id: cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9 last_name: Cheng orcid: 0000-0002-3584-9632 - first_name: G. A. full_name: Tribello, G. A. last_name: Tribello - first_name: M. full_name: Ceriotti, M. last_name: Ceriotti citation: ama: Giberti F, Cheng B, Tribello GA, Ceriotti M. Iterative unbiasing of quasi-equilibrium sampling. Journal of Chemical Theory and Computation. 2019;16(1):100-107. doi:10.1021/acs.jctc.9b00907 apa: Giberti, F., Cheng, B., Tribello, G. A., & Ceriotti, M. (2019). Iterative unbiasing of quasi-equilibrium sampling. Journal of Chemical Theory and Computation. American Chemical Society. https://doi.org/10.1021/acs.jctc.9b00907 chicago: Giberti, F., Bingqing Cheng, G. A. Tribello, and M. Ceriotti. “Iterative Unbiasing of Quasi-Equilibrium Sampling.” Journal of Chemical Theory and Computation. American Chemical Society, 2019. https://doi.org/10.1021/acs.jctc.9b00907. ieee: F. Giberti, B. Cheng, G. A. Tribello, and M. Ceriotti, “Iterative unbiasing of quasi-equilibrium sampling,” Journal of Chemical Theory and Computation, vol. 16, no. 1. American Chemical Society, pp. 100–107, 2019. ista: Giberti F, Cheng B, Tribello GA, Ceriotti M. 2019. Iterative unbiasing of quasi-equilibrium sampling. Journal of Chemical Theory and Computation. 16(1), 100–107. mla: Giberti, F., et al. “Iterative Unbiasing of Quasi-Equilibrium Sampling.” Journal of Chemical Theory and Computation, vol. 16, no. 1, American Chemical Society, 2019, pp. 100–07, doi:10.1021/acs.jctc.9b00907. short: F. Giberti, B. Cheng, G.A. Tribello, M. Ceriotti, Journal of Chemical Theory and Computation 16 (2019) 100–107. date_created: 2021-07-19T06:56:45Z date_published: 2019-01-14T00:00:00Z date_updated: 2021-08-09T12:37:37Z day: '14' doi: 10.1021/acs.jctc.9b00907 extern: '1' external_id: arxiv: - '1911.01140' pmid: - '31743021' intvolume: ' 16' issue: '1' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1911.01140 month: '01' oa: 1 oa_version: Preprint page: 100-107 pmid: 1 publication: Journal of Chemical Theory and Computation publication_identifier: eissn: - 1549-9626 issn: - 1549-9618 publication_status: published publisher: American Chemical Society quality_controlled: '1' scopus_import: '1' status: public title: Iterative unbiasing of quasi-equilibrium sampling type: journal_article user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf volume: 16 year: '2019' ... --- _id: '12600' abstract: - lang: eng text: The snow cover dynamics of High Mountain Asia are usually assessed at spatial resolutions of 250 m or greater, but this scale is too coarse to clearly represent the rugged topography common to the region. Higher-resolution measurement of snow-covered area often results in biased sampling due to cloud cover and deep shadows. We therefore develop a Normalized Difference Snow Index-based workflow to delineate snow lines from Landsat Thematic Mapper/Enhanced Thematic Mapper+ imagery and apply it to the upper Langtang Valley in Nepal, processing 194 scenes spanning 1999 to 2013. For each scene, we determine the spatial distribution of snow line altitudes (SLAs) with respect to aspect and across six subcatchments. Our results show that the mean SLA exhibits distinct seasonal behavior based on aspect and subcatchment position. We find that SLA dynamics respond to spatial and seasonal trade-offs in precipitation, temperature, and solar radiation, which act as primary controls. We identify two SLA spatial gradients, which we attribute to the effect of spatially variable precipitation. Our results also reveal that aspect-related SLA differences vary seasonally and are influenced by solar radiation. In terms of seasonal dominant controls, we demonstrate that the snow line is controlled by snow precipitation in winter, melt in premonsoon, a combination of both in postmonsoon, and temperature in monsoon, explaining to a large extent the spatial and seasonal variability of the SLA in the upper Langtang Valley. We conclude that while SLA and snow-covered area are complementary metrics, the SLA has a strong potential for understanding local-scale snow cover dynamics and their controlling mechanisms. article_processing_charge: No article_type: original author: - first_name: Marc full_name: Girona‐Mata, Marc last_name: Girona‐Mata - first_name: Evan S. full_name: Miles, Evan S. last_name: Miles - first_name: Silvan full_name: Ragettli, Silvan last_name: Ragettli - first_name: Francesca full_name: Pellicciotti, Francesca id: b28f055a-81ea-11ed-b70c-a9fe7f7b0e70 last_name: Pellicciotti citation: ama: Girona‐Mata M, Miles ES, Ragettli S, Pellicciotti F. High‐resolution snowline delineation from Landsat imagery to infer snow cover controls in a Himalayan catchment. Water Resources Research. 2019;55(8):6754-6772. doi:10.1029/2019wr024935 apa: Girona‐Mata, M., Miles, E. S., Ragettli, S., & Pellicciotti, F. (2019). High‐resolution snowline delineation from Landsat imagery to infer snow cover controls in a Himalayan catchment. Water Resources Research. American Geophysical Union. https://doi.org/10.1029/2019wr024935 chicago: Girona‐Mata, Marc, Evan S. Miles, Silvan Ragettli, and Francesca Pellicciotti. “High‐resolution Snowline Delineation from Landsat Imagery to Infer Snow Cover Controls in a Himalayan Catchment.” Water Resources Research. American Geophysical Union, 2019. https://doi.org/10.1029/2019wr024935. ieee: M. Girona‐Mata, E. S. Miles, S. Ragettli, and F. Pellicciotti, “High‐resolution snowline delineation from Landsat imagery to infer snow cover controls in a Himalayan catchment,” Water Resources Research, vol. 55, no. 8. American Geophysical Union, pp. 6754–6772, 2019. ista: Girona‐Mata M, Miles ES, Ragettli S, Pellicciotti F. 2019. High‐resolution snowline delineation from Landsat imagery to infer snow cover controls in a Himalayan catchment. Water Resources Research. 55(8), 6754–6772. mla: Girona‐Mata, Marc, et al. “High‐resolution Snowline Delineation from Landsat Imagery to Infer Snow Cover Controls in a Himalayan Catchment.” Water Resources Research, vol. 55, no. 8, American Geophysical Union, 2019, pp. 6754–72, doi:10.1029/2019wr024935. short: M. Girona‐Mata, E.S. Miles, S. Ragettli, F. Pellicciotti, Water Resources Research 55 (2019) 6754–6772. date_created: 2023-02-20T08:12:59Z date_published: 2019-08-01T00:00:00Z date_updated: 2023-02-28T12:14:18Z day: '01' doi: 10.1029/2019wr024935 extern: '1' intvolume: ' 55' issue: '8' keyword: - Water Science and Technology language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1029/2019WR024935 month: '08' oa: 1 oa_version: Published Version page: 6754-6772 publication: Water Resources Research publication_identifier: eissn: - 1944-7973 issn: - 0043-1397 publication_status: published publisher: American Geophysical Union quality_controlled: '1' scopus_import: '1' status: public title: High‐resolution snowline delineation from Landsat imagery to infer snow cover controls in a Himalayan catchment type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 55 year: '2019' ... --- _id: '12602' abstract: - lang: eng text: 'This study aims at developing and applying a spatially-distributed coupled glacier mass balance and ice-flow model to attribute the response of glaciers to natural and anthropogenic climate change. We focus on two glaciers with contrasting surface characteristics: a debris-covered glacier (Langtang Glacier in Nepal) and a clean-ice glacier (Hintereisferner in Austria). The model is applied from the end of the Little Ice Age (1850) to the present-day (2016) and is forced with four bias-corrected General Circulation Models (GCMs) from the historical experiment of the CMIP5 archive. The selected GCMs represent region-specific warm-dry, warm-wet, cold-dry, and cold-wet climate conditions. To isolate the effects of anthropogenic climate change on glacier mass balance and flow runs from these GCMs with and without further anthropogenic forcing after 1970 until 2016 are selected. The outcomes indicate that both glaciers experience the largest reduction in area and volume under warm climate conditions, whereas area and volume reductions are smaller under cold climate conditions. Simultaneously with changes in glacier area and volume, surface velocities generally decrease over time. Without further anthropogenic forcing the results reveal a 3% (9%) smaller decline in glacier area (volume) for the debris-covered glacier and a 18% (39%) smaller decline in glacier area (volume) for the clean-ice glacier. The difference in the magnitude between the two glaciers can mainly be attributed to differences in the response time of the glaciers, where the clean-ice glacier shows a much faster response to climate change. We conclude that the response of the two glaciers can mainly be attributed to anthropogenic climate change and that the impact is larger on the clean-ice glacier. The outcomes show that the model performs well under different climate conditions and that the developed approach can be used for regional-scale glacio-hydrological modeling.' article_number: '143' article_processing_charge: No article_type: original author: - first_name: René R. full_name: Wijngaard, René R. last_name: Wijngaard - first_name: Jakob F. full_name: Steiner, Jakob F. last_name: Steiner - first_name: Philip D. A. full_name: Kraaijenbrink, Philip D. A. last_name: Kraaijenbrink - first_name: Christoph full_name: Klug, Christoph last_name: Klug - first_name: Surendra full_name: Adhikari, Surendra last_name: Adhikari - first_name: Argha full_name: Banerjee, Argha last_name: Banerjee - first_name: Francesca full_name: Pellicciotti, Francesca id: b28f055a-81ea-11ed-b70c-a9fe7f7b0e70 last_name: Pellicciotti - first_name: Ludovicus P. H. full_name: van Beek, Ludovicus P. H. last_name: van Beek - first_name: Marc F. P. full_name: Bierkens, Marc F. P. last_name: Bierkens - first_name: Arthur F. full_name: Lutz, Arthur F. last_name: Lutz - first_name: Walter W. full_name: Immerzeel, Walter W. last_name: Immerzeel citation: ama: Wijngaard RR, Steiner JF, Kraaijenbrink PDA, et al. Modeling the response of the Langtang Glacier and the Hintereisferner to a changing climate since the Little Ice Age. Frontiers in Earth Science. 2019;7. doi:10.3389/feart.2019.00143 apa: Wijngaard, R. R., Steiner, J. F., Kraaijenbrink, P. D. A., Klug, C., Adhikari, S., Banerjee, A., … Immerzeel, W. W. (2019). Modeling the response of the Langtang Glacier and the Hintereisferner to a changing climate since the Little Ice Age. Frontiers in Earth Science. Frontiers Media. https://doi.org/10.3389/feart.2019.00143 chicago: Wijngaard, René R., Jakob F. Steiner, Philip D. A. Kraaijenbrink, Christoph Klug, Surendra Adhikari, Argha Banerjee, Francesca Pellicciotti, et al. “Modeling the Response of the Langtang Glacier and the Hintereisferner to a Changing Climate since the Little Ice Age.” Frontiers in Earth Science. Frontiers Media, 2019. https://doi.org/10.3389/feart.2019.00143. ieee: R. R. Wijngaard et al., “Modeling the response of the Langtang Glacier and the Hintereisferner to a changing climate since the Little Ice Age,” Frontiers in Earth Science, vol. 7. Frontiers Media, 2019. ista: Wijngaard RR, Steiner JF, Kraaijenbrink PDA, Klug C, Adhikari S, Banerjee A, Pellicciotti F, van Beek LPH, Bierkens MFP, Lutz AF, Immerzeel WW. 2019. Modeling the response of the Langtang Glacier and the Hintereisferner to a changing climate since the Little Ice Age. Frontiers in Earth Science. 7, 143. mla: Wijngaard, René R., et al. “Modeling the Response of the Langtang Glacier and the Hintereisferner to a Changing Climate since the Little Ice Age.” Frontiers in Earth Science, vol. 7, 143, Frontiers Media, 2019, doi:10.3389/feart.2019.00143. short: R.R. Wijngaard, J.F. Steiner, P.D.A. Kraaijenbrink, C. Klug, S. Adhikari, A. Banerjee, F. Pellicciotti, L.P.H. van Beek, M.F.P. Bierkens, A.F. Lutz, W.W. Immerzeel, Frontiers in Earth Science 7 (2019). date_created: 2023-02-20T08:13:08Z date_published: 2019-06-04T00:00:00Z date_updated: 2023-02-28T12:04:48Z day: '04' doi: 10.3389/feart.2019.00143 extern: '1' intvolume: ' 7' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.3389/feart.2019.00143 month: '06' oa: 1 oa_version: Published Version publication: Frontiers in Earth Science publication_identifier: issn: - 2296-6463 publication_status: published publisher: Frontiers Media quality_controlled: '1' scopus_import: '1' status: public title: Modeling the response of the Langtang Glacier and the Hintereisferner to a changing climate since the Little Ice Age type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 7 year: '2019' ... --- _id: '12601' abstract: - lang: eng text: Ice cliffs and ponds on debris-covered glaciers have received increased attention due to their role in amplifying local melt. However, very few studies have looked at these features on the catchment scale to determine their patterns and changes in space and time. We have compiled a detailed inventory of cliffs and ponds in the Langtang catchment, central Himalaya, from six high-resolution satellite orthoimages and DEMs between 2006 and 2015, and a historic orthophoto from 1974. Cliffs cover between 1.4% (± 0.4%) in the dry and 3.4% (± 0.9%) in the wet seasons and ponds between 0.6% (± 0.1%) and 1.6% (± 0.3%) of the total debris-covered tongues. We find large variations between seasons, as cliffs and ponds tend to grow in the wetter monsoon period, but there is no obvious trend in total area over the study period. The inventory further shows that cliffs are predominately north-facing irrespective of the glacier flow direction. Both cliffs and ponds appear in higher densities several hundred metres from the terminus in areas where tributaries reach the main glacier tongue. On the largest glacier in the catchment ~10% of all cliffs and ponds persisted over nearly a decade. article_processing_charge: No article_type: original author: - first_name: JAKOB F. full_name: STEINER, JAKOB F. last_name: STEINER - first_name: PASCAL full_name: BURI, PASCAL last_name: BURI - first_name: EVAN S. full_name: MILES, EVAN S. last_name: MILES - first_name: SILVAN full_name: RAGETTLI, SILVAN last_name: RAGETTLI - first_name: Francesca full_name: Pellicciotti, Francesca id: b28f055a-81ea-11ed-b70c-a9fe7f7b0e70 last_name: Pellicciotti citation: ama: 'STEINER JF, BURI P, MILES ES, RAGETTLI S, Pellicciotti F. Supraglacial ice cliffs and ponds on debris-covered glaciers: Spatio-temporal distribution and characteristics. Journal of Glaciology. 2019;65(252):617-632. doi:10.1017/jog.2019.40' apa: 'STEINER, J. F., BURI, P., MILES, E. S., RAGETTLI, S., & Pellicciotti, F. (2019). Supraglacial ice cliffs and ponds on debris-covered glaciers: Spatio-temporal distribution and characteristics. Journal of Glaciology. Cambridge University Press. https://doi.org/10.1017/jog.2019.40' chicago: 'STEINER, JAKOB F., PASCAL BURI, EVAN S. MILES, SILVAN RAGETTLI, and Francesca Pellicciotti. “Supraglacial Ice Cliffs and Ponds on Debris-Covered Glaciers: Spatio-Temporal Distribution and Characteristics.” Journal of Glaciology. Cambridge University Press, 2019. https://doi.org/10.1017/jog.2019.40.' ieee: 'J. F. STEINER, P. BURI, E. S. MILES, S. RAGETTLI, and F. Pellicciotti, “Supraglacial ice cliffs and ponds on debris-covered glaciers: Spatio-temporal distribution and characteristics,” Journal of Glaciology, vol. 65, no. 252. Cambridge University Press, pp. 617–632, 2019.' ista: 'STEINER JF, BURI P, MILES ES, RAGETTLI S, Pellicciotti F. 2019. Supraglacial ice cliffs and ponds on debris-covered glaciers: Spatio-temporal distribution and characteristics. Journal of Glaciology. 65(252), 617–632.' mla: 'STEINER, JAKOB F., et al. “Supraglacial Ice Cliffs and Ponds on Debris-Covered Glaciers: Spatio-Temporal Distribution and Characteristics.” Journal of Glaciology, vol. 65, no. 252, Cambridge University Press, 2019, pp. 617–32, doi:10.1017/jog.2019.40.' short: J.F. STEINER, P. BURI, E.S. MILES, S. RAGETTLI, F. Pellicciotti, Journal of Glaciology 65 (2019) 617–632. date_created: 2023-02-20T08:13:03Z date_published: 2019-08-01T00:00:00Z date_updated: 2023-02-28T12:11:07Z day: '01' doi: 10.1017/jog.2019.40 extern: '1' intvolume: ' 65' issue: '252' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1017/jog.2019.40 month: '08' oa: 1 oa_version: Published Version page: 617-632 publication: Journal of Glaciology publication_identifier: eissn: - 1727-5652 issn: - 0022-1430 publication_status: published publisher: Cambridge University Press quality_controlled: '1' scopus_import: '1' status: public title: 'Supraglacial ice cliffs and ponds on debris-covered glaciers: Spatio-temporal distribution and characteristics' type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 65 year: '2019' ... --- _id: '12192' abstract: - lang: eng text: Transposable elements (TEs), the movement of which can damage the genome, are epigenetically silenced in eukaryotes. Intriguingly, TEs are activated in the sperm companion cell – vegetative cell (VC) – of the flowering plant Arabidopsis thaliana. However, the extent and mechanism of this activation are unknown. Here we show that about 100 heterochromatic TEs are activated in VCs, mostly by DEMETER-catalyzed DNA demethylation. We further demonstrate that DEMETER access to some of these TEs is permitted by the natural depletion of linker histone H1 in VCs. Ectopically expressed H1 suppresses TEs in VCs by reducing DNA demethylation and via a methylation-independent mechanism. We demonstrate that H1 is required for heterochromatin condensation in plant cells and show that H1 overexpression creates heterochromatic foci in the VC progenitor cell. Taken together, our results demonstrate that the natural depletion of H1 during male gametogenesis facilitates DEMETER-directed DNA demethylation, heterochromatin relaxation, and TE activation. acknowledgement: We thank David Twell for the pDONR-P4-P1R-pLAT52 and pDONR-P2R-P3-mRFP vectors, the John Innes Centre Bioimaging Facility (Elaine Barclay and Grant Calder) for their assistance with microscopy, and the Norwich BioScience Institute Partnership Computing infrastructure for Science Group for High Performance Computing resources. This work was funded by a Biotechnology and Biological Sciences Research Council (BBSRC) David Phillips Fellowship (BB/L025043/1; SH, JZ and XF), a European Research Council Starting Grant ('SexMeth' 804981; XF) and a Grant to Exceptional Researchers by the Gatsby Charitable Foundation (SH and XF). article_number: '42530' article_processing_charge: No article_type: original author: - first_name: Shengbo full_name: He, Shengbo last_name: He - first_name: Martin full_name: Vickers, Martin last_name: Vickers - first_name: Jingyi full_name: Zhang, Jingyi last_name: Zhang - first_name: Xiaoqi full_name: Feng, Xiaoqi id: e0164712-22ee-11ed-b12a-d80fcdf35958 last_name: Feng orcid: 0000-0002-4008-1234 citation: ama: He S, Vickers M, Zhang J, Feng X. Natural depletion of histone H1 in sex cells causes DNA demethylation, heterochromatin decondensation and transposon activation. eLife. 2019;8. doi:10.7554/elife.42530 apa: He, S., Vickers, M., Zhang, J., & Feng, X. (2019). Natural depletion of histone H1 in sex cells causes DNA demethylation, heterochromatin decondensation and transposon activation. ELife. eLife Sciences Publications, Ltd. https://doi.org/10.7554/elife.42530 chicago: He, Shengbo, Martin Vickers, Jingyi Zhang, and Xiaoqi Feng. “Natural Depletion of Histone H1 in Sex Cells Causes DNA Demethylation, Heterochromatin Decondensation and Transposon Activation.” ELife. eLife Sciences Publications, Ltd, 2019. https://doi.org/10.7554/elife.42530. ieee: S. He, M. Vickers, J. Zhang, and X. Feng, “Natural depletion of histone H1 in sex cells causes DNA demethylation, heterochromatin decondensation and transposon activation,” eLife, vol. 8. eLife Sciences Publications, Ltd, 2019. ista: He S, Vickers M, Zhang J, Feng X. 2019. Natural depletion of histone H1 in sex cells causes DNA demethylation, heterochromatin decondensation and transposon activation. eLife. 8, 42530. mla: He, Shengbo, et al. “Natural Depletion of Histone H1 in Sex Cells Causes DNA Demethylation, Heterochromatin Decondensation and Transposon Activation.” ELife, vol. 8, 42530, eLife Sciences Publications, Ltd, 2019, doi:10.7554/elife.42530. short: S. He, M. Vickers, J. Zhang, X. Feng, ELife 8 (2019). date_created: 2023-01-16T09:17:21Z date_published: 2019-05-28T00:00:00Z date_updated: 2023-05-08T10:54:12Z day: '28' ddc: - '580' department: - _id: XiFe doi: 10.7554/elife.42530 extern: '1' external_id: unknown: - '31135340' file: - access_level: open_access checksum: ea6b89c20d59e5eb3646916fe5d568ad content_type: application/pdf creator: alisjak date_created: 2023-02-07T09:42:46Z date_updated: 2023-02-07T09:42:46Z file_id: '12525' file_name: 2019_elife_He.pdf file_size: 2493837 relation: main_file success: 1 file_date_updated: 2023-02-07T09:42:46Z has_accepted_license: '1' intvolume: ' 8' keyword: - General Immunology and Microbiology - General Biochemistry - Genetics and Molecular Biology - General Medicine - General Neuroscience language: - iso: eng main_file_link: - open_access: '1' url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6594752/ month: '05' oa: 1 oa_version: Published Version publication: eLife publication_identifier: issn: - 2050-084X publication_status: published publisher: eLife Sciences Publications, Ltd quality_controlled: '1' scopus_import: '1' status: public title: Natural depletion of histone H1 in sex cells causes DNA demethylation, heterochromatin decondensation and transposon activation 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: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 8 year: '2019' ... --- _id: '12190' abstract: - lang: eng text: Meiotic crossover frequency varies within genomes, which influences genetic diversity and adaptation. In turn, genetic variation within populations can act to modify crossover frequency in cis and trans. To identify genetic variation that controls meiotic crossover frequency, we screened Arabidopsis accessions using fluorescent recombination reporters. We mapped a genetic modifier of crossover frequency in Col × Bur populations of Arabidopsis to a premature stop codon within TBP-ASSOCIATED FACTOR 4b (TAF4b), which encodes a subunit of the RNA polymerase II general transcription factor TFIID. The Arabidopsis taf4b mutation is a rare variant found in the British Isles, originating in South-West Ireland. Using genetics, genomics, and immunocytology, we demonstrate a genome-wide decrease in taf4b crossovers, with strongest reduction in the sub-telomeric regions. Using RNA sequencing (RNA-seq) from purified meiocytes, we show that TAF4b expression is meiocyte enriched, whereas its paralog TAF4 is broadly expressed. Consistent with the role of TFIID in promoting gene expression, RNA-seq of wild-type and taf4b meiocytes identified widespread transcriptional changes, including in genes that regulate the meiotic cell cycle and recombination. Therefore, TAF4b duplication is associated with acquisition of meiocyte-specific expression and promotion of germline transcription, which act directly or indirectly to elevate crossovers. This identifies a novel mode of meiotic recombination control via a general transcription factor. acknowledgement: "We thank Gregory Copenhaver (University of North Carolina), Avraham Levy (The Weizmann Institute), and Scott Poethig (University of Pennsylvania) for FTLs; Piotr Ziolkowski for Col-420/Bur seed; Sureshkumar Balasubramanian\r\n(Monash University) for providing British and Irish Arabidopsis accessions; Mathilde Grelon (INRA, Versailles) for providing the MLH1 antibody; and the Gurdon Institute for access to microscopes. This work was supported by a BBSRC DTP studentship (E.J.L.), European Research Area Network for Coordinating Action in Plant Sciences/BBSRC ‘‘DeCOP’’ (BB/M004937/1; C.L.), a BBSRC David Phillips Fellowship (BB/L025043/1; H.G. and X.F.), the European Research Council (CoG ‘‘SynthHotspot,’’ A.J.T., C.L., and I.R.H.; StG ‘‘SexMeth,’’ X.F.), and a Sainsbury Charitable Foundation Studentship (A.R.B.)." article_processing_charge: No article_type: original author: - first_name: Emma J. full_name: Lawrence, Emma J. last_name: Lawrence - first_name: Hongbo full_name: Gao, Hongbo last_name: Gao - first_name: Andrew J. full_name: Tock, Andrew J. last_name: Tock - first_name: Christophe full_name: Lambing, Christophe last_name: Lambing - first_name: Alexander R. full_name: Blackwell, Alexander R. last_name: Blackwell - first_name: Xiaoqi full_name: Feng, Xiaoqi id: e0164712-22ee-11ed-b12a-d80fcdf35958 last_name: Feng orcid: 0000-0002-4008-1234 - first_name: Ian R. full_name: Henderson, Ian R. last_name: Henderson citation: ama: Lawrence EJ, Gao H, Tock AJ, et al. Natural variation in TBP-ASSOCIATED FACTOR 4b controls meiotic crossover and germline transcription in Arabidopsis. Current Biology. 2019;29(16):2676-2686.e3. doi:10.1016/j.cub.2019.06.084 apa: Lawrence, E. J., Gao, H., Tock, A. J., Lambing, C., Blackwell, A. R., Feng, X., & Henderson, I. R. (2019). Natural variation in TBP-ASSOCIATED FACTOR 4b controls meiotic crossover and germline transcription in Arabidopsis. Current Biology. Elsevier BV. https://doi.org/10.1016/j.cub.2019.06.084 chicago: Lawrence, Emma J., Hongbo Gao, Andrew J. Tock, Christophe Lambing, Alexander R. Blackwell, Xiaoqi Feng, and Ian R. Henderson. “Natural Variation in TBP-ASSOCIATED FACTOR 4b Controls Meiotic Crossover and Germline Transcription in Arabidopsis.” Current Biology. Elsevier BV, 2019. https://doi.org/10.1016/j.cub.2019.06.084. ieee: E. J. Lawrence et al., “Natural variation in TBP-ASSOCIATED FACTOR 4b controls meiotic crossover and germline transcription in Arabidopsis,” Current Biology, vol. 29, no. 16. Elsevier BV, p. 2676–2686.e3, 2019. ista: Lawrence EJ, Gao H, Tock AJ, Lambing C, Blackwell AR, Feng X, Henderson IR. 2019. Natural variation in TBP-ASSOCIATED FACTOR 4b controls meiotic crossover and germline transcription in Arabidopsis. Current Biology. 29(16), 2676–2686.e3. mla: Lawrence, Emma J., et al. “Natural Variation in TBP-ASSOCIATED FACTOR 4b Controls Meiotic Crossover and Germline Transcription in Arabidopsis.” Current Biology, vol. 29, no. 16, Elsevier BV, 2019, p. 2676–2686.e3, doi:10.1016/j.cub.2019.06.084. short: E.J. Lawrence, H. Gao, A.J. Tock, C. Lambing, A.R. Blackwell, X. Feng, I.R. Henderson, Current Biology 29 (2019) 2676–2686.e3. date_created: 2023-01-16T09:16:33Z date_published: 2019-08-19T00:00:00Z date_updated: 2023-05-08T10:54:54Z day: '19' department: - _id: XiFe doi: 10.1016/j.cub.2019.06.084 extern: '1' external_id: pmid: - '31378616' intvolume: ' 29' issue: '16' keyword: - General Agricultural and Biological Sciences - General Biochemistry - Genetics and Molecular Biology language: - iso: eng month: '08' oa_version: None page: 2676-2686.e3 pmid: 1 publication: Current Biology publication_identifier: issn: - 0960-9822 publication_status: published publisher: Elsevier BV quality_controlled: '1' scopus_import: '1' status: public title: Natural variation in TBP-ASSOCIATED FACTOR 4b controls meiotic crossover and germline transcription in Arabidopsis type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 29 year: '2019' ... --- _id: '8305' abstract: - lang: eng text: In this paper, we present the first fully asynchronous distributed key generation (ADKG) algorithm as well as the first distributed key generation algorithm that can create keys with a dual (f,2f+1)−threshold that are necessary for scalable consensus (which so far needs a trusted dealer assumption). In order to create a DKG with a dual (f,2f+1)− threshold we first answer in the affirmative the open question posed by Cachin et al. how to create an AVSS protocol with recovery thresholds f+1