--- _id: '7280' abstract: - lang: eng text: Non-aqueous lithium-oxygen batteries cycle by forming lithium peroxide during discharge and oxidizing it during recharge. The significant problem of oxidizing the solid insulating lithium peroxide can greatly be facilitated by incorporating redox mediators that shuttle electron-holes between the porous substrate and lithium peroxide. Redox mediator stability is thus key for energy efficiency, reversibility, and cycle life. However, the gradual deactivation of redox mediators during repeated cycling has not conclusively been explained. Here, we show that organic redox mediators are predominantly decomposed by singlet oxygen that forms during cycling. Their reaction with superoxide, previously assumed to mainly trigger their degradation, peroxide, and dioxygen, is orders of magnitude slower in comparison. The reduced form of the mediator is markedly more reactive towards singlet oxygen than the oxidized form, from which we derive reaction mechanisms supported by density functional theory calculations. Redox mediators must thus be designed for stability against singlet oxygen. article_number: '1380' article_processing_charge: No article_type: original author: - first_name: Won-Jin full_name: Kwak, Won-Jin last_name: Kwak - first_name: Hun full_name: Kim, Hun last_name: Kim - first_name: Yann K. full_name: Petit, Yann K. last_name: Petit - first_name: Christian full_name: Leypold, Christian last_name: Leypold - first_name: Trung Thien full_name: Nguyen, Trung Thien last_name: Nguyen - first_name: Nika full_name: Mahne, Nika last_name: Mahne - first_name: Paul full_name: Redfern, Paul last_name: Redfern - first_name: Larry A. full_name: Curtiss, Larry A. last_name: Curtiss - first_name: Hun-Gi full_name: Jung, Hun-Gi last_name: Jung - first_name: Sergey M. full_name: Borisov, Sergey M. last_name: Borisov - first_name: Stefan Alexander full_name: Freunberger, Stefan Alexander id: A8CA28E6-CE23-11E9-AD2D-EC27E6697425 last_name: Freunberger orcid: 0000-0003-2902-5319 - first_name: Yang-Kook full_name: Sun, Yang-Kook last_name: Sun citation: ama: Kwak W-J, Kim H, Petit YK, et al. Deactivation of redox mediators in lithium-oxygen batteries by singlet oxygen. Nature Communications. 2019;10. doi:10.1038/s41467-019-09399-0 apa: Kwak, W.-J., Kim, H., Petit, Y. K., Leypold, C., Nguyen, T. T., Mahne, N., … Sun, Y.-K. (2019). Deactivation of redox mediators in lithium-oxygen batteries by singlet oxygen. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-019-09399-0 chicago: Kwak, Won-Jin, Hun Kim, Yann K. Petit, Christian Leypold, Trung Thien Nguyen, Nika Mahne, Paul Redfern, et al. “Deactivation of Redox Mediators in Lithium-Oxygen Batteries by Singlet Oxygen.” Nature Communications. Springer Nature, 2019. https://doi.org/10.1038/s41467-019-09399-0. ieee: W.-J. Kwak et al., “Deactivation of redox mediators in lithium-oxygen batteries by singlet oxygen,” Nature Communications, vol. 10. Springer Nature, 2019. ista: Kwak W-J, Kim H, Petit YK, Leypold C, Nguyen TT, Mahne N, Redfern P, Curtiss LA, Jung H-G, Borisov SM, Freunberger SA, Sun Y-K. 2019. Deactivation of redox mediators in lithium-oxygen batteries by singlet oxygen. Nature Communications. 10, 1380. mla: Kwak, Won-Jin, et al. “Deactivation of Redox Mediators in Lithium-Oxygen Batteries by Singlet Oxygen.” Nature Communications, vol. 10, 1380, Springer Nature, 2019, doi:10.1038/s41467-019-09399-0. short: W.-J. Kwak, H. Kim, Y.K. Petit, C. Leypold, T.T. Nguyen, N. Mahne, P. Redfern, L.A. Curtiss, H.-G. Jung, S.M. Borisov, S.A. Freunberger, Y.-K. Sun, Nature Communications 10 (2019). date_created: 2020-01-15T12:12:26Z date_published: 2019-03-26T00:00:00Z date_updated: 2021-01-12T08:12:44Z day: '26' ddc: - '540' doi: 10.1038/s41467-019-09399-0 extern: '1' file: - access_level: open_access checksum: 123dd33e7f26761c82c74e10811a1e4d content_type: application/pdf creator: dernst date_created: 2020-01-22T15:58:54Z date_updated: 2020-07-14T12:47:55Z file_id: '7355' file_name: 2019_NatureComm_Kwak.pdf file_size: 1003676 relation: main_file file_date_updated: 2020-07-14T12:47:55Z has_accepted_license: '1' intvolume: ' 10' language: - iso: eng license: https://creativecommons.org/licenses/by/4.0/ month: '03' oa: 1 oa_version: Published Version publication: Nature Communications publication_identifier: issn: - 2041-1723 publication_status: published publisher: Springer Nature quality_controlled: '1' status: public title: Deactivation of redox mediators in lithium-oxygen batteries by singlet oxygen 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: 10 year: '2019' ... --- _id: '7276' abstract: - lang: eng text: Singlet oxygen (1O2) causes a major fraction of the parasitic chemistry during the cycling of non‐aqueous alkali metal‐O2 batteries and also contributes to interfacial reactivity of transition‐metal oxide intercalation compounds. We introduce DABCOnium, the mono alkylated form of 1,4‐diazabicyclo[2.2.2]octane (DABCO), as an efficient 1O2 quencher with an unusually high oxidative stability of ca. 4.2 V vs. Li/Li+. Previous quenchers are strongly Lewis basic amines with too low oxidative stability. DABCOnium is an ionic liquid, non‐volatile, highly soluble in the electrolyte, stable against superoxide and peroxide, and compatible with lithium metal. The electrochemical stability covers the required range for metal–O2 batteries and greatly reduces 1O2 related parasitic chemistry as demonstrated for the Li–O2 cell. article_processing_charge: No article_type: original author: - first_name: Yann K. full_name: Petit, Yann K. last_name: Petit - first_name: Christian full_name: Leypold, Christian last_name: Leypold - first_name: Nika full_name: Mahne, Nika last_name: Mahne - first_name: Eléonore full_name: Mourad, Eléonore last_name: Mourad - first_name: Lukas full_name: Schafzahl, Lukas last_name: Schafzahl - first_name: Christian full_name: Slugovc, Christian last_name: Slugovc - first_name: Sergey M. full_name: Borisov, Sergey M. last_name: Borisov - first_name: Stefan Alexander full_name: Freunberger, Stefan Alexander id: A8CA28E6-CE23-11E9-AD2D-EC27E6697425 last_name: Freunberger orcid: 0000-0003-2902-5319 citation: ama: 'Petit YK, Leypold C, Mahne N, et al. DABCOnium: An efficient and high-voltage stable singlet oxygen quencher for metal-O2 cells. Angewandte Chemie International Edition. 2019;58(20):6535-6539. doi:10.1002/anie.201901869' apa: 'Petit, Y. K., Leypold, C., Mahne, N., Mourad, E., Schafzahl, L., Slugovc, C., … Freunberger, S. A. (2019). DABCOnium: An efficient and high-voltage stable singlet oxygen quencher for metal-O2 cells. Angewandte Chemie International Edition. Wiley. https://doi.org/10.1002/anie.201901869' chicago: 'Petit, Yann K., Christian Leypold, Nika Mahne, Eléonore Mourad, Lukas Schafzahl, Christian Slugovc, Sergey M. Borisov, and Stefan Alexander Freunberger. “DABCOnium: An Efficient and High-Voltage Stable Singlet Oxygen Quencher for Metal-O2 Cells.” Angewandte Chemie International Edition. Wiley, 2019. https://doi.org/10.1002/anie.201901869.' ieee: 'Y. K. Petit et al., “DABCOnium: An efficient and high-voltage stable singlet oxygen quencher for metal-O2 cells,” Angewandte Chemie International Edition, vol. 58, no. 20. Wiley, pp. 6535–6539, 2019.' ista: 'Petit YK, Leypold C, Mahne N, Mourad E, Schafzahl L, Slugovc C, Borisov SM, Freunberger SA. 2019. DABCOnium: An efficient and high-voltage stable singlet oxygen quencher for metal-O2 cells. Angewandte Chemie International Edition. 58(20), 6535–6539.' mla: 'Petit, Yann K., et al. “DABCOnium: An Efficient and High-Voltage Stable Singlet Oxygen Quencher for Metal-O2 Cells.” Angewandte Chemie International Edition, vol. 58, no. 20, Wiley, 2019, pp. 6535–39, doi:10.1002/anie.201901869.' short: Y.K. Petit, C. Leypold, N. Mahne, E. Mourad, L. Schafzahl, C. Slugovc, S.M. Borisov, S.A. Freunberger, Angewandte Chemie International Edition 58 (2019) 6535–6539. date_created: 2020-01-15T07:19:27Z date_published: 2019-05-13T00:00:00Z date_updated: 2021-01-12T08:12:42Z day: '13' ddc: - '540' doi: 10.1002/anie.201901869 extern: '1' file: - access_level: open_access checksum: 9620b6a511a910d7abe1f26c42dc7f83 content_type: application/pdf creator: dernst date_created: 2020-01-22T16:16:54Z date_updated: 2020-07-14T12:47:55Z file_id: '7356' file_name: 2019_AngewChemie_Petit.pdf file_size: 952737 relation: main_file file_date_updated: 2020-07-14T12:47:55Z has_accepted_license: '1' intvolume: ' 58' issue: '20' language: - iso: eng license: https://creativecommons.org/licenses/by-nc-nd/4.0/ month: '05' oa: 1 oa_version: Published Version page: 6535-6539 publication: Angewandte Chemie International Edition publication_identifier: issn: - 1433-7851 publication_status: published publisher: Wiley quality_controlled: '1' status: public title: 'DABCOnium: An efficient and high-voltage stable singlet oxygen quencher for metal-O2 cells' 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: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 58 year: '2019' ... --- _id: '7281' abstract: - lang: eng text: Li–O2 batteries are plagued by side reactions that cause poor rechargeability and efficiency. These reactions were recently revealed to be predominantly caused by singlet oxygen, which can be neutralized by chemical traps or physical quenchers. However, traps are irreversibly consumed and thus only active for a limited time, and so far identified quenchers lack oxidative stability to be suitable for typically required recharge potentials. Thus, reducing the charge potential within the stability limit of the quencher and/or finding more stable quenchers is required. Here, we show that dimethylphenazine as a redox mediator decreases the charge potential well within the stability limit of the quencher 1,4-diazabicyclo[2.2.2]octane. The quencher can thus mitigate the parasitic reactions without being oxidatively decomposed. At the same time the quencher protects the redox mediator from singlet oxygen attack. The mutual conservation of the redox mediator and the quencher is rational for stable and effective Li–O2 batteries. article_processing_charge: No article_type: original author: - first_name: Won-Jin full_name: Kwak, Won-Jin last_name: Kwak - first_name: Stefan Alexander full_name: Freunberger, Stefan Alexander id: A8CA28E6-CE23-11E9-AD2D-EC27E6697425 last_name: Freunberger orcid: 0000-0003-2902-5319 - first_name: Hun full_name: Kim, Hun last_name: Kim - first_name: Jiwon full_name: Park, Jiwon last_name: Park - first_name: Trung Thien full_name: Nguyen, Trung Thien last_name: Nguyen - first_name: Hun-Gi full_name: Jung, Hun-Gi last_name: Jung - first_name: Hye Ryung full_name: Byon, Hye Ryung last_name: Byon - first_name: Yang-Kook full_name: Sun, Yang-Kook last_name: Sun citation: ama: Kwak W-J, Freunberger SA, Kim H, et al. Mutual conservation of redox mediator and singlet oxygen quencher in Lithium–Oxygen batteries. ACS Catalysis. 2019;9(11):9914-9922. doi:10.1021/acscatal.9b01337 apa: Kwak, W.-J., Freunberger, S. A., Kim, H., Park, J., Nguyen, T. T., Jung, H.-G., … Sun, Y.-K. (2019). Mutual conservation of redox mediator and singlet oxygen quencher in Lithium–Oxygen batteries. ACS Catalysis. ACS. https://doi.org/10.1021/acscatal.9b01337 chicago: Kwak, Won-Jin, Stefan Alexander Freunberger, Hun Kim, Jiwon Park, Trung Thien Nguyen, Hun-Gi Jung, Hye Ryung Byon, and Yang-Kook Sun. “Mutual Conservation of Redox Mediator and Singlet Oxygen Quencher in Lithium–Oxygen Batteries.” ACS Catalysis. ACS, 2019. https://doi.org/10.1021/acscatal.9b01337. ieee: W.-J. Kwak et al., “Mutual conservation of redox mediator and singlet oxygen quencher in Lithium–Oxygen batteries,” ACS Catalysis, vol. 9, no. 11. ACS, pp. 9914–9922, 2019. ista: Kwak W-J, Freunberger SA, Kim H, Park J, Nguyen TT, Jung H-G, Byon HR, Sun Y-K. 2019. Mutual conservation of redox mediator and singlet oxygen quencher in Lithium–Oxygen batteries. ACS Catalysis. 9(11), 9914–9922. mla: Kwak, Won-Jin, et al. “Mutual Conservation of Redox Mediator and Singlet Oxygen Quencher in Lithium–Oxygen Batteries.” ACS Catalysis, vol. 9, no. 11, ACS, 2019, pp. 9914–22, doi:10.1021/acscatal.9b01337. short: W.-J. Kwak, S.A. Freunberger, H. Kim, J. Park, T.T. Nguyen, H.-G. Jung, H.R. Byon, Y.-K. Sun, ACS Catalysis 9 (2019) 9914–9922. date_created: 2020-01-15T12:12:40Z date_published: 2019-11-01T00:00:00Z date_updated: 2021-01-12T08:12:44Z day: '01' ddc: - '540' doi: 10.1021/acscatal.9b01337 extern: '1' file: - access_level: open_access checksum: bbaebfe5ff0bcab6235821ba3460b7de content_type: application/pdf creator: sfreunbe date_created: 2020-06-29T15:19:30Z date_updated: 2020-07-14T12:47:55Z file_id: '8053' file_name: Revised Manuscript.pdf file_size: 1199086 relation: main_file file_date_updated: 2020-07-14T12:47:55Z has_accepted_license: '1' intvolume: ' 9' issue: '11' language: - iso: eng month: '11' oa: 1 oa_version: Submitted Version page: 9914-9922 publication: ACS Catalysis publication_identifier: issn: - 2155-5435 publication_status: published publisher: ACS quality_controlled: '1' status: public title: Mutual conservation of redox mediator and singlet oxygen quencher in Lithium–Oxygen batteries type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 9 year: '2019' ... --- _id: '7282' abstract: - lang: eng text: Interphases that form on the anode surface of lithium-ion batteries are critical for performance and lifetime, but are poorly understood. Now, a decade-old misconception regarding a main component of the interphase has been revealed, which could potentially lead to improved devices. article_processing_charge: No article_type: letter_note author: - first_name: Stefan Alexander full_name: Freunberger, Stefan Alexander id: A8CA28E6-CE23-11E9-AD2D-EC27E6697425 last_name: Freunberger orcid: 0000-0003-2902-5319 citation: ama: Freunberger SA. Interphase identity crisis. Nature Chemistry. 2019;11(9):761-763. doi:10.1038/s41557-019-0311-0 apa: Freunberger, S. A. (2019). Interphase identity crisis. Nature Chemistry. Springer Nature. https://doi.org/10.1038/s41557-019-0311-0 chicago: Freunberger, Stefan Alexander. “Interphase Identity Crisis.” Nature Chemistry. Springer Nature, 2019. https://doi.org/10.1038/s41557-019-0311-0. ieee: S. A. Freunberger, “Interphase identity crisis,” Nature Chemistry, vol. 11, no. 9. Springer Nature, pp. 761–763, 2019. ista: Freunberger SA. 2019. Interphase identity crisis. Nature Chemistry. 11(9), 761–763. mla: Freunberger, Stefan Alexander. “Interphase Identity Crisis.” Nature Chemistry, vol. 11, no. 9, Springer Nature, 2019, pp. 761–63, doi:10.1038/s41557-019-0311-0. short: S.A. Freunberger, Nature Chemistry 11 (2019) 761–763. date_created: 2020-01-15T12:12:53Z date_published: 2019-08-19T00:00:00Z date_updated: 2021-01-12T08:12:44Z day: '19' ddc: - '540' - '547' doi: 10.1038/s41557-019-0311-0 extern: '1' file: - access_level: open_access checksum: 76806cff3d5b62f846499a8617cee7ef content_type: application/pdf creator: sfreunbe date_created: 2020-06-29T15:38:21Z date_updated: 2020-07-14T12:47:55Z file_id: '8054' file_name: Freunberger on Eichhorn.pdf file_size: 286805 relation: main_file file_date_updated: 2020-07-14T12:47:55Z has_accepted_license: '1' intvolume: ' 11' issue: '9' language: - iso: eng month: '08' oa: 1 oa_version: Submitted Version page: 761-763 publication: Nature Chemistry publication_identifier: issn: - 1755-4330 - 1755-4349 publication_status: published publisher: Springer Nature quality_controlled: '1' status: public title: Interphase identity crisis type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 11 year: '2019' ... --- _id: '7283' abstract: - lang: eng text: Potassium–air batteries, which suffer from oxygen cathode and potassium metal anode degradation, can be cycled thousands of times when an organic anode replaces the metal. article_processing_charge: No article_type: letter_note author: - first_name: Yann K. full_name: Petit, Yann K. last_name: Petit - first_name: Stefan Alexander full_name: Freunberger, Stefan Alexander id: A8CA28E6-CE23-11E9-AD2D-EC27E6697425 last_name: Freunberger orcid: 0000-0003-2902-5319 citation: ama: Petit YK, Freunberger SA. Thousands of cycles. Nature Materials. 2019;18(4):301-302. doi:10.1038/s41563-019-0313-8 apa: Petit, Y. K., & Freunberger, S. A. (2019). Thousands of cycles. Nature Materials. Springer Nature. https://doi.org/10.1038/s41563-019-0313-8 chicago: Petit, Yann K., and Stefan Alexander Freunberger. “Thousands of Cycles.” Nature Materials. Springer Nature, 2019. https://doi.org/10.1038/s41563-019-0313-8. ieee: Y. K. Petit and S. A. Freunberger, “Thousands of cycles,” Nature Materials, vol. 18, no. 4. Springer Nature, pp. 301–302, 2019. ista: Petit YK, Freunberger SA. 2019. Thousands of cycles. Nature Materials. 18(4), 301–302. mla: Petit, Yann K., and Stefan Alexander Freunberger. “Thousands of Cycles.” Nature Materials, vol. 18, no. 4, Springer Nature, 2019, pp. 301–02, doi:10.1038/s41563-019-0313-8. short: Y.K. Petit, S.A. Freunberger, Nature Materials 18 (2019) 301–302. date_created: 2020-01-15T12:13:05Z date_published: 2019-03-20T00:00:00Z date_updated: 2021-01-12T08:12:45Z day: '20' ddc: - '540' - '541' doi: 10.1038/s41563-019-0313-8 extern: '1' file: - access_level: open_access checksum: 4c9a0314327028a22dd902bc109b8798 content_type: application/pdf creator: sfreunbe date_created: 2020-06-29T16:26:54Z date_updated: 2020-07-14T12:47:55Z file_id: '8059' file_name: NaV_final.pdf file_size: 398123 relation: main_file file_date_updated: 2020-07-14T12:47:55Z has_accepted_license: '1' intvolume: ' 18' issue: '4' language: - iso: eng month: '03' oa: 1 oa_version: Submitted Version page: 301-302 publication: Nature Materials publication_identifier: issn: - 1476-1122 - 1476-4660 publication_status: published publisher: Springer Nature quality_controlled: '1' status: public title: Thousands of cycles type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 18 year: '2019' ... --- _id: '7284' abstract: - lang: eng text: In this issue of Joule, Dongmin Im and coworkers from Samsung in South Korea describe a prototype lithium-O2 battery that reaches ∼700 Wh kg–1 and ∼600 Wh L–1 on the cell level. They cut all components to the minimum to reach this value. Difficulties filling the pores with discharge product and inhomogeneous cell utilization turn out to limit the achievable energy. Their work underlines the importance of reporting performance with respect to full cell weight and volume. article_processing_charge: No article_type: review author: - first_name: Christian full_name: Prehal, Christian last_name: Prehal - first_name: Stefan Alexander full_name: Freunberger, Stefan Alexander id: A8CA28E6-CE23-11E9-AD2D-EC27E6697425 last_name: Freunberger orcid: 0000-0003-2902-5319 citation: ama: Prehal C, Freunberger SA. Li-O2 cell-scale energy densities. Joule. 2019;3(2):321-323. doi:10.1016/j.joule.2019.01.020 apa: Prehal, C., & Freunberger, S. A. (2019). Li-O2 cell-scale energy densities. Joule. Elsevier. https://doi.org/10.1016/j.joule.2019.01.020 chicago: Prehal, Christian, and Stefan Alexander Freunberger. “Li-O2 Cell-Scale Energy Densities.” Joule. Elsevier, 2019. https://doi.org/10.1016/j.joule.2019.01.020. ieee: C. Prehal and S. A. Freunberger, “Li-O2 cell-scale energy densities,” Joule, vol. 3, no. 2. Elsevier, pp. 321–323, 2019. ista: Prehal C, Freunberger SA. 2019. Li-O2 cell-scale energy densities. Joule. 3(2), 321–323. mla: Prehal, Christian, and Stefan Alexander Freunberger. “Li-O2 Cell-Scale Energy Densities.” Joule, vol. 3, no. 2, Elsevier, 2019, pp. 321–23, doi:10.1016/j.joule.2019.01.020. short: C. Prehal, S.A. Freunberger, Joule 3 (2019) 321–323. date_created: 2020-01-15T12:13:15Z date_published: 2019-02-20T00:00:00Z date_updated: 2021-01-12T08:12:45Z day: '20' doi: 10.1016/j.joule.2019.01.020 extern: '1' intvolume: ' 3' issue: '2' language: - iso: eng main_file_link: - open_access: '1' url: https://www.doi.org/10.1016/j.joule.2019.01.020 month: '02' oa: 1 oa_version: Published Version page: 321-323 publication: Joule publication_identifier: issn: - 2542-4351 publication_status: published publisher: Elsevier quality_controlled: '1' status: public title: Li-O2 cell-scale energy densities type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 3 year: '2019' ... --- _id: '7358' abstract: - lang: eng text: Telencephalic organoids generated from human pluripotent stem cells (hPSCs) are emerging as an effective system to study the distinct features of the developing human brain and the underlying causes of many neurological disorders. While progress in organoid technology has been steadily advancing, many challenges remain including rampant batch-to-batch and cell line-to-cell line variability and irreproducibility. Here, we demonstrate that a major contributor to successful cortical organoid production is the manner in which hPSCs are maintained prior to differentiation. Optimal results were achieved using fibroblast-feeder-supported hPSCs compared to feeder-independent cells, related to differences in their transcriptomic states. Feeder-supported hPSCs display elevated activation of diverse TGFβ superfamily signaling pathways and increased expression of genes associated with naïve pluripotency. We further identify combinations of TGFβ-related growth factors that are necessary and together sufficient to impart broad telencephalic organoid competency to feeder-free hPSCs and enable reproducible formation of brain structures suitable for disease modeling. article_processing_charge: No author: - first_name: Momoko full_name: Watanabe, Momoko last_name: Watanabe - first_name: Jillian R. full_name: Haney, Jillian R. last_name: Haney - first_name: Neda full_name: Vishlaghi, Neda last_name: Vishlaghi - first_name: Felix full_name: Turcios, Felix last_name: Turcios - first_name: Jessie E. full_name: Buth, Jessie E. last_name: Buth - first_name: Wen full_name: Gu, Wen last_name: Gu - first_name: Amanda J. full_name: Collier, Amanda J. last_name: Collier - first_name: Osvaldo full_name: Miranda, Osvaldo id: 862A3C56-A8BF-11E9-B4FA-D9E3E5697425 last_name: Miranda orcid: 0000-0001-6618-6889 - first_name: Di full_name: Chen, Di last_name: Chen - first_name: Shan full_name: Sabri, Shan last_name: Sabri - first_name: Amander T. full_name: Clark, Amander T. last_name: Clark - first_name: Kathrin full_name: Plath, Kathrin last_name: Plath - first_name: Heather R. full_name: Christofk, Heather R. last_name: Christofk - first_name: Michael J. full_name: Gandal, Michael J. last_name: Gandal - first_name: Bennett G. full_name: Novitch, Bennett G. last_name: Novitch citation: ama: Watanabe M, Haney JR, Vishlaghi N, et al. TGFβ superfamily signaling regulates the state of human stem cell pluripotency and competency to create telencephalic organoids. bioRxiv. 2019. doi:10.1101/2019.12.13.875773 apa: Watanabe, M., Haney, J. R., Vishlaghi, N., Turcios, F., Buth, J. E., Gu, W., … Novitch, B. G. (2019). TGFβ superfamily signaling regulates the state of human stem cell pluripotency and competency to create telencephalic organoids. bioRxiv. Cold Spring Harbor Laboratory. https://doi.org/10.1101/2019.12.13.875773 chicago: Watanabe, Momoko, Jillian R. Haney, Neda Vishlaghi, Felix Turcios, Jessie E. Buth, Wen Gu, Amanda J. Collier, et al. “TGFβ Superfamily Signaling Regulates the State of Human Stem Cell Pluripotency and Competency to Create Telencephalic Organoids.” BioRxiv. Cold Spring Harbor Laboratory, 2019. https://doi.org/10.1101/2019.12.13.875773. ieee: M. Watanabe et al., “TGFβ superfamily signaling regulates the state of human stem cell pluripotency and competency to create telencephalic organoids,” bioRxiv. Cold Spring Harbor Laboratory, 2019. ista: Watanabe M, Haney JR, Vishlaghi N, Turcios F, Buth JE, Gu W, Collier AJ, Miranda O, Chen D, Sabri S, Clark AT, Plath K, Christofk HR, Gandal MJ, Novitch BG. 2019. TGFβ superfamily signaling regulates the state of human stem cell pluripotency and competency to create telencephalic organoids. bioRxiv, 10.1101/2019.12.13.875773. mla: Watanabe, Momoko, et al. “TGFβ Superfamily Signaling Regulates the State of Human Stem Cell Pluripotency and Competency to Create Telencephalic Organoids.” BioRxiv, Cold Spring Harbor Laboratory, 2019, doi:10.1101/2019.12.13.875773. short: M. Watanabe, J.R. Haney, N. Vishlaghi, F. Turcios, J.E. Buth, W. Gu, A.J. Collier, O. Miranda, D. Chen, S. Sabri, A.T. Clark, K. Plath, H.R. Christofk, M.J. Gandal, B.G. Novitch, BioRxiv (2019). date_created: 2020-01-23T09:53:40Z date_published: 2019-12-13T00:00:00Z date_updated: 2022-06-17T08:03:32Z day: '13' doi: 10.1101/2019.12.13.875773 extern: '1' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1101/2019.12.13.875773 month: '12' oa: 1 oa_version: Preprint page: '75' publication: bioRxiv publication_status: published publisher: Cold Spring Harbor Laboratory status: public title: TGFβ superfamily signaling regulates the state of human stem cell pluripotency and competency to create telencephalic organoids type: preprint user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2019' ... --- _id: '7401' abstract: - lang: eng text: 'The genus g(G) of a graph G is the minimum g such that G has an embedding on the orientable surface M_g of genus g. A drawing of a graph on a surface is independently even if every pair of nonadjacent edges in the drawing crosses an even number of times. The Z_2-genus of a graph G, denoted by g_0(G), is the minimum g such that G has an independently even drawing on M_g. By a result of Battle, Harary, Kodama and Youngs from 1962, the graph genus is additive over 2-connected blocks. In 2013, Schaefer and Stefankovic proved that the Z_2-genus of a graph is additive over 2-connected blocks as well, and asked whether this result can be extended to so-called 2-amalgamations, as an analogue of results by Decker, Glover, Huneke, and Stahl for the genus. We give the following partial answer. If G=G_1 cup G_2, G_1 and G_2 intersect in two vertices u and v, and G-u-v has k connected components (among which we count the edge uv if present), then |g_0(G)-(g_0(G_1)+g_0(G_2))|<=k+1. For complete bipartite graphs K_{m,n}, with n >= m >= 3, we prove that g_0(K_{m,n})/g(K_{m,n})=1-O(1/n). Similar results are proved also for the Euler Z_2-genus. We express the Z_2-genus of a graph using the minimum rank of partial symmetric matrices over Z_2; a problem that might be of independent interest. ' alternative_title: - LIPIcs article_number: '39' article_processing_charge: No author: - first_name: Radoslav full_name: Fulek, Radoslav id: 39F3FFE4-F248-11E8-B48F-1D18A9856A87 last_name: Fulek orcid: 0000-0001-8485-1774 - first_name: Jan full_name: Kyncl, Jan last_name: Kyncl citation: ama: 'Fulek R, Kyncl J. Z_2-Genus of graphs and minimum rank of partial symmetric matrices. In: 35th International Symposium on Computational Geometry (SoCG 2019). Vol 129. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2019. doi:10.4230/LIPICS.SOCG.2019.39' apa: 'Fulek, R., & Kyncl, J. (2019). Z_2-Genus of graphs and minimum rank of partial symmetric matrices. In 35th International Symposium on Computational Geometry (SoCG 2019) (Vol. 129). Portland, OR, United States: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPICS.SOCG.2019.39' chicago: Fulek, Radoslav, and Jan Kyncl. “Z_2-Genus of Graphs and Minimum Rank of Partial Symmetric Matrices.” In 35th International Symposium on Computational Geometry (SoCG 2019), Vol. 129. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2019. https://doi.org/10.4230/LIPICS.SOCG.2019.39. ieee: R. Fulek and J. Kyncl, “Z_2-Genus of graphs and minimum rank of partial symmetric matrices,” in 35th International Symposium on Computational Geometry (SoCG 2019), Portland, OR, United States, 2019, vol. 129. ista: 'Fulek R, Kyncl J. 2019. Z_2-Genus of graphs and minimum rank of partial symmetric matrices. 35th International Symposium on Computational Geometry (SoCG 2019). SoCG: Symposium on Computational Geometry, LIPIcs, vol. 129, 39.' mla: Fulek, Radoslav, and Jan Kyncl. “Z_2-Genus of Graphs and Minimum Rank of Partial Symmetric Matrices.” 35th International Symposium on Computational Geometry (SoCG 2019), vol. 129, 39, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2019, doi:10.4230/LIPICS.SOCG.2019.39. short: R. Fulek, J. Kyncl, in:, 35th International Symposium on Computational Geometry (SoCG 2019), Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2019. conference: end_date: 2019-06-21 location: Portland, OR, United States name: 'SoCG: Symposium on Computational Geometry' start_date: 2019-06-18 date_created: 2020-01-29T16:17:05Z date_published: 2019-06-01T00:00:00Z date_updated: 2021-01-12T08:13:24Z day: '01' ddc: - '000' department: - _id: UlWa doi: 10.4230/LIPICS.SOCG.2019.39 external_id: arxiv: - '1903.08637' file: - access_level: open_access checksum: aac37b09118cc0ab58cf77129e691f8c content_type: application/pdf creator: dernst date_created: 2020-02-04T09:14:31Z date_updated: 2020-07-14T12:47:57Z file_id: '7445' file_name: 2019_LIPIcs_Fulek.pdf file_size: 628347 relation: main_file file_date_updated: 2020-07-14T12:47:57Z has_accepted_license: '1' intvolume: ' 129' language: - iso: eng month: '06' oa: 1 oa_version: Published Version project: - _id: 261FA626-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: M02281 name: Eliminating intersections in drawings of graphs publication: 35th International Symposium on Computational Geometry (SoCG 2019) publication_identifier: isbn: - 978-3-95977-104-7 issn: - 1868-8969 publication_status: published publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik quality_controlled: '1' scopus_import: 1 status: public title: Z_2-Genus of graphs and minimum rank of partial symmetric matrices 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: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 129 year: '2019' ... --- _id: '7453' abstract: - lang: eng text: We illustrate the ingredients of the state-of-the-art of model-based approach for the formal design and verification of cyber-physical systems. To capture the interaction between a discrete controller and its continuously evolving environment, we use the formal models of timed and hybrid automata. We explain the steps of modeling and verification in the tools Uppaal and SpaceEx using a case study based on a dual-chamber implantable pacemaker monitoring a human heart. We show how to design a model as a composition of components, how to construct models at varying levels of detail, how to establish that one model is an abstraction of another, how to specify correctness requirements using temporal logic, and how to verify that a model satisfies a logical requirement. acknowledgement: This research was supported in part by the Austrian Science Fund (FWF) under grants S11402-N23(RiSE/SHiNE) and Z211-N23 (Wittgenstein Award). This research has received funding from the Sino-Danish Basic Research Centre, IDEA4CPS, funded by the Danish National Research Foundation and the National Science Foundation, China, the Innovation Fund Denmark centre DiCyPS, as well as the ERC Advanced Grant LASSO. alternative_title: - Lecture Notes in Computer Science article_processing_charge: No author: - first_name: Rajeev full_name: Alur, Rajeev last_name: Alur - first_name: Mirco full_name: Giacobbe, Mirco id: 3444EA5E-F248-11E8-B48F-1D18A9856A87 last_name: Giacobbe orcid: 0000-0001-8180-0904 - first_name: Thomas A full_name: Henzinger, Thomas A id: 40876CD8-F248-11E8-B48F-1D18A9856A87 last_name: Henzinger orcid: 0000−0002−2985−7724 - first_name: Kim G. full_name: Larsen, Kim G. last_name: Larsen - first_name: Marius full_name: Mikučionis, Marius last_name: Mikučionis citation: ama: 'Alur R, Giacobbe M, Henzinger TA, Larsen KG, Mikučionis M. Continuous-time models for system design and analysis. In: Steffen B, Woeginger G, eds. Computing and Software Science. Vol 10000. LNCS. Springer Nature; 2019:452-477. doi:10.1007/978-3-319-91908-9_22' apa: Alur, R., Giacobbe, M., Henzinger, T. A., Larsen, K. G., & Mikučionis, M. (2019). Continuous-time models for system design and analysis. In B. Steffen & G. Woeginger (Eds.), Computing and Software Science (Vol. 10000, pp. 452–477). Springer Nature. https://doi.org/10.1007/978-3-319-91908-9_22 chicago: Alur, Rajeev, Mirco Giacobbe, Thomas A Henzinger, Kim G. Larsen, and Marius Mikučionis. “Continuous-Time Models for System Design and Analysis.” In Computing and Software Science, edited by Bernhard Steffen and Gerhard Woeginger, 10000:452–77. LNCS. Springer Nature, 2019. https://doi.org/10.1007/978-3-319-91908-9_22. ieee: R. Alur, M. Giacobbe, T. A. Henzinger, K. G. Larsen, and M. Mikučionis, “Continuous-time models for system design and analysis,” in Computing and Software Science, vol. 10000, B. Steffen and G. Woeginger, Eds. Springer Nature, 2019, pp. 452–477. ista: 'Alur R, Giacobbe M, Henzinger TA, Larsen KG, Mikučionis M. 2019.Continuous-time models for system design and analysis. In: Computing and Software Science. Lecture Notes in Computer Science, vol. 10000, 452–477.' mla: Alur, Rajeev, et al. “Continuous-Time Models for System Design and Analysis.” Computing and Software Science, edited by Bernhard Steffen and Gerhard Woeginger, vol. 10000, Springer Nature, 2019, pp. 452–77, doi:10.1007/978-3-319-91908-9_22. short: R. Alur, M. Giacobbe, T.A. Henzinger, K.G. Larsen, M. Mikučionis, in:, B. Steffen, G. Woeginger (Eds.), Computing and Software Science, Springer Nature, 2019, pp. 452–477. date_created: 2020-02-05T10:51:44Z date_published: 2019-10-05T00:00:00Z date_updated: 2022-09-06T08:25:52Z day: '05' department: - _id: ToHe doi: 10.1007/978-3-319-91908-9_22 editor: - first_name: Bernhard full_name: Steffen, Bernhard last_name: Steffen - first_name: Gerhard full_name: Woeginger, Gerhard last_name: Woeginger intvolume: ' 10000' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1007/978-3-319-91908-9_22 month: '10' oa: 1 oa_version: Published Version page: 452-477 project: - _id: 25F2ACDE-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S11402-N23 name: Rigorous Systems Engineering - _id: 25F42A32-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: Z211 name: The Wittgenstein Prize publication: Computing and Software Science publication_identifier: eisbn: - '9783319919089' eissn: - 0302-9743 isbn: - '9783319919072' issn: - 1611-3349 publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' series_title: LNCS status: public title: Continuous-time models for system design and analysis type: book_chapter user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 10000 year: '2019' ... --- _id: '7459' abstract: - lang: eng text: We report the fabrication of BaTiO3-Ni magnetoelectric nanocomposites comprising of BaTiO3 nanotubes surrounded by Ni matrix. BaTiO3 nanotubes obtained from the hydrothermal transformation of TiO2 have both inner and outer surfaces, which facilitates greater magnetoelectric coupling with the surrounding Ni matrix. The magnetoelectric coupling was studied by measuring the piezoelectric behavior in the presence of an in-plane direct magnetic field. A higher magnetoelectric voltage coefficient of 110 mV/cm·Oe was obtained, because of better coupling between Ni and BaTiO3 through the walls of the nanotubes. Such nanocomposite developed directly on Ti substrate may lead to efficient fabrication of magnetoelectric devices. article_processing_charge: No article_type: original author: - first_name: Samba Siva full_name: Vadla, Samba Siva last_name: Vadla - first_name: Tommaso full_name: Costanzo, Tommaso id: D93824F4-D9BA-11E9-BB12-F207E6697425 last_name: Costanzo orcid: 0000-0001-9732-3815 - first_name: Subish full_name: John, Subish last_name: John - first_name: Gabriel full_name: Caruntu, Gabriel last_name: Caruntu - first_name: Somnath C. full_name: Roy, Somnath C. last_name: Roy citation: ama: Vadla SS, Costanzo T, John S, Caruntu G, Roy SC. Local probing of magnetoelectric coupling in BaTiO3-Ni 1–3 composites. Scripta Materialia. 2019;159:33-36. doi:10.1016/j.scriptamat.2018.09.003 apa: Vadla, S. S., Costanzo, T., John, S., Caruntu, G., & Roy, S. C. (2019). Local probing of magnetoelectric coupling in BaTiO3-Ni 1–3 composites. Scripta Materialia. Elsevier. https://doi.org/10.1016/j.scriptamat.2018.09.003 chicago: Vadla, Samba Siva, Tommaso Costanzo, Subish John, Gabriel Caruntu, and Somnath C. Roy. “Local Probing of Magnetoelectric Coupling in BaTiO3-Ni 1–3 Composites.” Scripta Materialia. Elsevier, 2019. https://doi.org/10.1016/j.scriptamat.2018.09.003. ieee: S. S. Vadla, T. Costanzo, S. John, G. Caruntu, and S. C. Roy, “Local probing of magnetoelectric coupling in BaTiO3-Ni 1–3 composites,” Scripta Materialia, vol. 159. Elsevier, pp. 33–36, 2019. ista: Vadla SS, Costanzo T, John S, Caruntu G, Roy SC. 2019. Local probing of magnetoelectric coupling in BaTiO3-Ni 1–3 composites. Scripta Materialia. 159, 33–36. mla: Vadla, Samba Siva, et al. “Local Probing of Magnetoelectric Coupling in BaTiO3-Ni 1–3 Composites.” Scripta Materialia, vol. 159, Elsevier, 2019, pp. 33–36, doi:10.1016/j.scriptamat.2018.09.003. short: S.S. Vadla, T. Costanzo, S. John, G. Caruntu, S.C. Roy, Scripta Materialia 159 (2019) 33–36. date_created: 2020-02-05T14:19:17Z date_published: 2019-01-15T00:00:00Z date_updated: 2023-02-23T13:08:31Z day: '15' doi: 10.1016/j.scriptamat.2018.09.003 extern: '1' intvolume: ' 159' language: - iso: eng month: '01' oa_version: None page: 33-36 publication: Scripta Materialia publication_identifier: issn: - 1359-6462 publication_status: published publisher: Elsevier quality_controlled: '1' status: public title: Local probing of magnetoelectric coupling in BaTiO3-Ni 1–3 composites type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 159 year: '2019' ... --- _id: '7476' abstract: - lang: eng text: The sebaceous gland (SG) is an essential component of the skin, and SG dysfunction is debilitating1,2. Yet, the cellular bases for its origin, development and subsequent maintenance remain poorly understood. Here, we apply large-scale quantitative fate mapping to define the patterns of cell fate behaviour during SG development and maintenance. We show that the SG develops from a defined number of lineage-restricted progenitors that undergo a programme of independent and stochastic cell fate decisions. Following an expansion phase, equipotent progenitors transition into a phase of homeostatic turnover, which is correlated with changes in the mechanical properties of the stroma and spatial restrictions on gland size. Expression of the oncogene KrasG12D results in a release from these constraints and unbridled gland expansion. Quantitative clonal fate analysis reveals that, during this phase, the primary effect of the Kras oncogene is to drive a constant fate bias with little effect on cell division rates. These findings provide insight into the developmental programme of the SG, as well as the mechanisms that drive tumour progression and gland dysfunction. article_processing_charge: No article_type: original author: - first_name: Marianne Stemann full_name: Andersen, Marianne Stemann last_name: Andersen - first_name: Edouard B full_name: Hannezo, Edouard B id: 3A9DB764-F248-11E8-B48F-1D18A9856A87 last_name: Hannezo orcid: 0000-0001-6005-1561 - first_name: Svetlana full_name: Ulyanchenko, Svetlana last_name: Ulyanchenko - first_name: Soline full_name: Estrach, Soline last_name: Estrach - first_name: Yasuko full_name: Antoku, Yasuko last_name: Antoku - first_name: Sabrina full_name: Pisano, Sabrina last_name: Pisano - first_name: Kim E. full_name: Boonekamp, Kim E. last_name: Boonekamp - first_name: Sarah full_name: Sendrup, Sarah last_name: Sendrup - first_name: Martti full_name: Maimets, Martti last_name: Maimets - first_name: Marianne Terndrup full_name: Pedersen, Marianne Terndrup last_name: Pedersen - first_name: Jens V. full_name: Johansen, Jens V. last_name: Johansen - first_name: Ditte L. full_name: Clement, Ditte L. last_name: Clement - first_name: Chloe C. full_name: Feral, Chloe C. last_name: Feral - first_name: Benjamin D. full_name: Simons, Benjamin D. last_name: Simons - first_name: Kim B. full_name: Jensen, Kim B. last_name: Jensen citation: ama: Andersen MS, Hannezo EB, Ulyanchenko S, et al. Tracing the cellular dynamics of sebaceous gland development in normal and perturbed states. Nature Cell Biology. 2019;21(8):924-932. doi:10.1038/s41556-019-0362-x apa: Andersen, M. S., Hannezo, E. B., Ulyanchenko, S., Estrach, S., Antoku, Y., Pisano, S., … Jensen, K. B. (2019). Tracing the cellular dynamics of sebaceous gland development in normal and perturbed states. Nature Cell Biology. Springer Nature. https://doi.org/10.1038/s41556-019-0362-x chicago: Andersen, Marianne Stemann, Edouard B Hannezo, Svetlana Ulyanchenko, Soline Estrach, Yasuko Antoku, Sabrina Pisano, Kim E. Boonekamp, et al. “Tracing the Cellular Dynamics of Sebaceous Gland Development in Normal and Perturbed States.” Nature Cell Biology. Springer Nature, 2019. https://doi.org/10.1038/s41556-019-0362-x. ieee: M. S. Andersen et al., “Tracing the cellular dynamics of sebaceous gland development in normal and perturbed states,” Nature Cell Biology, vol. 21, no. 8. Springer Nature, pp. 924–932, 2019. ista: Andersen MS, Hannezo EB, Ulyanchenko S, Estrach S, Antoku Y, Pisano S, Boonekamp KE, Sendrup S, Maimets M, Pedersen MT, Johansen JV, Clement DL, Feral CC, Simons BD, Jensen KB. 2019. Tracing the cellular dynamics of sebaceous gland development in normal and perturbed states. Nature Cell Biology. 21(8), 924–932. mla: Andersen, Marianne Stemann, et al. “Tracing the Cellular Dynamics of Sebaceous Gland Development in Normal and Perturbed States.” Nature Cell Biology, vol. 21, no. 8, Springer Nature, 2019, pp. 924–32, doi:10.1038/s41556-019-0362-x. short: M.S. Andersen, E.B. Hannezo, S. Ulyanchenko, S. Estrach, Y. Antoku, S. Pisano, K.E. Boonekamp, S. Sendrup, M. Maimets, M.T. Pedersen, J.V. Johansen, D.L. Clement, C.C. Feral, B.D. Simons, K.B. Jensen, Nature Cell Biology 21 (2019) 924–932. date_created: 2020-02-11T08:43:49Z date_published: 2019-08-01T00:00:00Z date_updated: 2021-01-12T08:13:47Z day: '01' doi: 10.1038/s41556-019-0362-x extern: '1' external_id: pmid: - '31358966' intvolume: ' 21' issue: '8' language: - iso: eng main_file_link: - open_access: '1' url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6978139/ month: '08' oa: 1 oa_version: Submitted Version page: 924-932 pmid: 1 publication: Nature Cell Biology publication_identifier: issn: - 1465-7392 - 1476-4679 publication_status: published publisher: Springer Nature quality_controlled: '1' status: public title: Tracing the cellular dynamics of sebaceous gland development in normal and perturbed states type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 21 year: '2019' ... --- _id: '7548' abstract: - lang: eng text: Although the aggregation of the amyloid-β peptide (Aβ) into amyloid fibrils is a well-established hallmark of Alzheimer’s disease, the complex mechanisms linking this process to neurodegeneration are still incompletely understood. The nematode worm C. elegans is a valuable model organism through which to study these mechanisms because of its simple nervous system and its relatively short lifespan. Standard Aβ-based C. elegans models of Alzheimer’s disease are designed to study the toxic effects of the overexpression of Aβ in the muscle or nervous systems. However, the wide variety of effects associated with the tissue-level overexpression of Aβ makes it difficult to single out and study specific cellular mechanisms related to the onset of Alzheimer’s disease. Here, to better understand how to investigate the early events affecting neuronal signalling, we created a C. elegans model expressing Aβ42, the 42-residue form of Aβ, from a single-copy gene insertion in just one pair of glutamatergic sensory neurons, the BAG neurons. In behavioural assays, we found that the Aβ42-expressing animals displayed a subtle modulation of the response to CO2, compared to controls. Ca2+ imaging revealed that the BAG neurons in young Aβ42-expressing nematodes were activated more strongly than in control animals, and that neuronal activation remained intact until old age. Taken together, our results suggest that Aβ42-expression in this very subtle model of AD is sufficient to modulate the behavioural response but not strong enough to generate significant neurotoxicity, suggesting that slightly more aggressive perturbations will enable effectively studies of the links between the modulation of a physiological response and its associated neurotoxicity. article_number: e0217746 article_processing_charge: No article_type: original author: - first_name: Tessa full_name: Sinnige, Tessa last_name: Sinnige - first_name: Prashanth full_name: Ciryam, Prashanth last_name: Ciryam - first_name: Samuel full_name: Casford, Samuel last_name: Casford - first_name: Christopher M. full_name: Dobson, Christopher M. last_name: Dobson - first_name: Mario full_name: de Bono, Mario id: 4E3FF80E-F248-11E8-B48F-1D18A9856A87 last_name: de Bono orcid: 0000-0001-8347-0443 - first_name: Michele full_name: Vendruscolo, Michele last_name: Vendruscolo citation: ama: Sinnige T, Ciryam P, Casford S, Dobson CM, de Bono M, Vendruscolo M. Expression of the amyloid-β peptide in a single pair of C. elegans sensory neurons modulates the associated behavioural response. PLOS ONE. 2019;14(5). doi:10.1371/journal.pone.0217746 apa: Sinnige, T., Ciryam, P., Casford, S., Dobson, C. M., de Bono, M., & Vendruscolo, M. (2019). Expression of the amyloid-β peptide in a single pair of C. elegans sensory neurons modulates the associated behavioural response. PLOS ONE. Public Library of Science. https://doi.org/10.1371/journal.pone.0217746 chicago: Sinnige, Tessa, Prashanth Ciryam, Samuel Casford, Christopher M. Dobson, Mario de Bono, and Michele Vendruscolo. “Expression of the Amyloid-β Peptide in a Single Pair of C. Elegans Sensory Neurons Modulates the Associated Behavioural Response.” PLOS ONE. Public Library of Science, 2019. https://doi.org/10.1371/journal.pone.0217746. ieee: T. Sinnige, P. Ciryam, S. Casford, C. M. Dobson, M. de Bono, and M. Vendruscolo, “Expression of the amyloid-β peptide in a single pair of C. elegans sensory neurons modulates the associated behavioural response,” PLOS ONE, vol. 14, no. 5. Public Library of Science, 2019. ista: Sinnige T, Ciryam P, Casford S, Dobson CM, de Bono M, Vendruscolo M. 2019. Expression of the amyloid-β peptide in a single pair of C. elegans sensory neurons modulates the associated behavioural response. PLOS ONE. 14(5), e0217746. mla: Sinnige, Tessa, et al. “Expression of the Amyloid-β Peptide in a Single Pair of C. Elegans Sensory Neurons Modulates the Associated Behavioural Response.” PLOS ONE, vol. 14, no. 5, e0217746, Public Library of Science, 2019, doi:10.1371/journal.pone.0217746. short: T. Sinnige, P. Ciryam, S. Casford, C.M. Dobson, M. de Bono, M. Vendruscolo, PLOS ONE 14 (2019). date_created: 2020-02-28T10:45:13Z date_published: 2019-05-31T00:00:00Z date_updated: 2021-01-12T08:14:08Z day: '31' doi: 10.1371/journal.pone.0217746 extern: '1' intvolume: ' 14' issue: '5' language: - iso: eng month: '05' oa_version: Published Version publication: PLOS ONE publication_identifier: issn: - 1932-6203 publication_status: published publisher: Public Library of Science quality_controlled: '1' status: public title: Expression of the amyloid-β peptide in a single pair of C. elegans sensory neurons modulates the associated behavioural response type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 14 year: '2019' ... --- _id: '7547' abstract: - lang: eng text: The BH3-only family of proteins is key for initiating apoptosis in a variety of contexts, and may also contribute to non-apoptotic cellular processes. Historically, the nematode Caenorhabditis elegans has provided a powerful system for studying and identifying conserved regulators of BH3-only proteins. In C. elegans, the BH3-only protein egl-1 is expressed during development to cell-autonomously trigger most developmental cell deaths. Here we provide evidence that egl-1 is also transcribed after development in the sensory neuron pair URX without inducing apoptosis. We used genetic screening and epistasis analysis to determine that its transcription is regulated in URX by neuronal activity and/or in parallel by orthologs of Protein Kinase G and the Salt-Inducible Kinase family. Because several BH3-only family proteins are also expressed in the adult nervous system of mammals, we suggest that studying egl-1 expression in URX may shed light on mechanisms that regulate conserved family members in higher organisms. article_processing_charge: No article_type: original author: - first_name: Jesse full_name: Cohn, Jesse last_name: Cohn - first_name: Vivek full_name: Dwivedi, Vivek last_name: Dwivedi - first_name: Giulio full_name: Valperga, Giulio last_name: Valperga - first_name: Nicole full_name: Zarate, Nicole last_name: Zarate - first_name: Mario full_name: de Bono, Mario id: 4E3FF80E-F248-11E8-B48F-1D18A9856A87 last_name: de Bono orcid: 0000-0001-8347-0443 - first_name: H. Robert full_name: Horvitz, H. Robert last_name: Horvitz - first_name: Jonathan T. full_name: Pierce, Jonathan T. last_name: Pierce citation: ama: 'Cohn J, Dwivedi V, Valperga G, et al. Activity-dependent regulation of the proapoptotic BH3-only gene egl-1 in a living neuron pair in Caenorhabditis elegans. G3: Genes, Genomes, Genetics. 2019;9(11):3703-3714. doi:10.1534/g3.119.400654' apa: 'Cohn, J., Dwivedi, V., Valperga, G., Zarate, N., de Bono, M., Horvitz, H. R., & Pierce, J. T. (2019). Activity-dependent regulation of the proapoptotic BH3-only gene egl-1 in a living neuron pair in Caenorhabditis elegans. G3: Genes, Genomes, Genetics. Genetics Society of America. https://doi.org/10.1534/g3.119.400654' chicago: 'Cohn, Jesse, Vivek Dwivedi, Giulio Valperga, Nicole Zarate, Mario de Bono, H. Robert Horvitz, and Jonathan T. Pierce. “Activity-Dependent Regulation of the Proapoptotic BH3-Only Gene Egl-1 in a Living Neuron Pair in Caenorhabditis Elegans.” G3: Genes, Genomes, Genetics. Genetics Society of America, 2019. https://doi.org/10.1534/g3.119.400654.' ieee: 'J. Cohn et al., “Activity-dependent regulation of the proapoptotic BH3-only gene egl-1 in a living neuron pair in Caenorhabditis elegans,” G3: Genes, Genomes, Genetics, vol. 9, no. 11. Genetics Society of America, pp. 3703–3714, 2019.' ista: 'Cohn J, Dwivedi V, Valperga G, Zarate N, de Bono M, Horvitz HR, Pierce JT. 2019. Activity-dependent regulation of the proapoptotic BH3-only gene egl-1 in a living neuron pair in Caenorhabditis elegans. G3: Genes, Genomes, Genetics. 9(11), 3703–3714.' mla: 'Cohn, Jesse, et al. “Activity-Dependent Regulation of the Proapoptotic BH3-Only Gene Egl-1 in a Living Neuron Pair in Caenorhabditis Elegans.” G3: Genes, Genomes, Genetics, vol. 9, no. 11, Genetics Society of America, 2019, pp. 3703–14, doi:10.1534/g3.119.400654.' short: 'J. Cohn, V. Dwivedi, G. Valperga, N. Zarate, M. de Bono, H.R. Horvitz, J.T. Pierce, G3: Genes, Genomes, Genetics 9 (2019) 3703–3714.' date_created: 2020-02-28T10:44:27Z date_published: 2019-11-01T00:00:00Z date_updated: 2021-01-12T08:14:07Z day: '01' doi: 10.1534/g3.119.400654 extern: '1' external_id: pmid: - '31519744' intvolume: ' 9' issue: '11' language: - iso: eng month: '11' oa_version: Published Version page: 3703-3714 pmid: 1 publication: 'G3: Genes, Genomes, Genetics' publication_identifier: issn: - 2160-1836 publication_status: published publisher: Genetics Society of America quality_controlled: '1' status: public title: Activity-dependent regulation of the proapoptotic BH3-only gene egl-1 in a living neuron pair in Caenorhabditis elegans type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 9 year: '2019' ... --- _id: '7550' abstract: - lang: eng text: 'We consider an optimal control problem for an abstract nonlinear dissipative evolution equation. The differential constraint is penalized by augmenting the target functional by a nonnegative global-in-time functional which is null-minimized in the evolution equation is satisfied. Different variational settings are presented, leading to the convergence of the penalization method for gradient flows, noncyclic and semimonotone flows, doubly nonlinear evolutions, and GENERIC systems. ' acknowledgement: This work is supported by Vienna Science and Technology Fund (WWTF) through Project MA14-009 and by the Austrian Science Fund (FWF) projects F 65 and I 2375. article_processing_charge: No article_type: original author: - first_name: Lorenzo full_name: Portinale, Lorenzo id: 30AD2CBC-F248-11E8-B48F-1D18A9856A87 last_name: Portinale - first_name: Ulisse full_name: Stefanelli, Ulisse last_name: Stefanelli citation: ama: Portinale L, Stefanelli U. Penalization via global functionals of optimal-control problems for dissipative evolution. Advances in Mathematical Sciences and Applications. 2019;28(2):425-447. apa: Portinale, L., & Stefanelli, U. (2019). Penalization via global functionals of optimal-control problems for dissipative evolution. Advances in Mathematical Sciences and Applications. Gakko Tosho. chicago: Portinale, Lorenzo, and Ulisse Stefanelli. “Penalization via Global Functionals of Optimal-Control Problems for Dissipative Evolution.” Advances in Mathematical Sciences and Applications. Gakko Tosho, 2019. ieee: L. Portinale and U. Stefanelli, “Penalization via global functionals of optimal-control problems for dissipative evolution,” Advances in Mathematical Sciences and Applications, vol. 28, no. 2. Gakko Tosho, pp. 425–447, 2019. ista: Portinale L, Stefanelli U. 2019. Penalization via global functionals of optimal-control problems for dissipative evolution. Advances in Mathematical Sciences and Applications. 28(2), 425–447. mla: Portinale, Lorenzo, and Ulisse Stefanelli. “Penalization via Global Functionals of Optimal-Control Problems for Dissipative Evolution.” Advances in Mathematical Sciences and Applications, vol. 28, no. 2, Gakko Tosho, 2019, pp. 425–47. short: L. Portinale, U. Stefanelli, Advances in Mathematical Sciences and Applications 28 (2019) 425–447. date_created: 2020-02-28T10:54:41Z date_published: 2019-10-22T00:00:00Z date_updated: 2022-06-17T07:52:41Z day: '22' department: - _id: JaMa external_id: arxiv: - '1910.10050' intvolume: ' 28' issue: '2' language: - iso: eng main_file_link: - open_access: '1' url: ' https://doi.org/10.48550/arXiv.1910.10050' month: '10' oa: 1 oa_version: Preprint page: 425-447 project: - _id: fc31cba2-9c52-11eb-aca3-ff467d239cd2 grant_number: F6504 name: Taming Complexity in Partial Differential Systems publication: Advances in Mathematical Sciences and Applications publication_identifier: issn: - 1343-4373 publication_status: published publisher: Gakko Tosho quality_controlled: '1' status: public title: Penalization via global functionals of optimal-control problems for dissipative evolution type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 28 year: '2019' ... --- _id: '7552' abstract: - lang: eng text: 'There is increasing evidence that protein binding to specific sites along DNA can activate the reading out of genetic information without coming into direct physical contact with the gene. There also is evidence that these distant but interacting sites are embedded in a liquid droplet of proteins which condenses out of the surrounding solution. We argue that droplet-mediated interactions can account for crucial features of gene regulation only if the droplet is poised at a non-generic point in its phase diagram. We explore a minimal model that embodies this idea, show that this model has a natural mechanism for self-tuning, and suggest direct experimental tests. ' article_processing_charge: No author: - first_name: William full_name: Bialek, William last_name: Bialek - first_name: Thomas full_name: Gregor, Thomas last_name: Gregor - first_name: Gašper full_name: Tkačik, Gašper id: 3D494DCA-F248-11E8-B48F-1D18A9856A87 last_name: Tkačik orcid: 0000-0002-6699-1455 citation: ama: Bialek W, Gregor T, Tkačik G. Action at a distance in transcriptional regulation. arXiv:191208579. apa: Bialek, W., Gregor, T., & Tkačik, G. (n.d.). Action at a distance in transcriptional regulation. arXiv:1912.08579. ArXiv. chicago: Bialek, William, Thomas Gregor, and Gašper Tkačik. “Action at a Distance in Transcriptional Regulation.” ArXiv:1912.08579. ArXiv, n.d. ieee: W. Bialek, T. Gregor, and G. Tkačik, “Action at a distance in transcriptional regulation,” arXiv:1912.08579. ArXiv. ista: Bialek W, Gregor T, Tkačik G. Action at a distance in transcriptional regulation. arXiv:1912.08579, . mla: Bialek, William, et al. “Action at a Distance in Transcriptional Regulation.” ArXiv:1912.08579, ArXiv. short: W. Bialek, T. Gregor, G. Tkačik, ArXiv:1912.08579 (n.d.). date_created: 2020-02-28T10:57:08Z date_published: 2019-12-18T00:00:00Z date_updated: 2021-01-12T08:14:09Z day: '18' department: - _id: GaTk external_id: arxiv: - '1912.08579' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1912.08579 month: '12' oa: 1 oa_version: Preprint page: '5' project: - _id: 254E9036-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P28844-B27 name: Biophysics of information processing in gene regulation publication: arXiv:1912.08579 publication_status: submitted publisher: ArXiv status: public title: Action at a distance in transcriptional regulation type: preprint user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2019' ... --- _id: '7576' abstract: - lang: eng text: We present the results of a friendly competition for formal verification of continuous and hybrid systems with nonlinear continuous dynamics. The friendly competition took place as part of the workshop Applied Verification for Continuous and Hybrid Systems (ARCH) in 2019. In this year, 6 tools Ariadne, CORA, DynIbex, Flow*, Isabelle/HOL, and JuliaReach (in alphabetic order) participated. They are applied to solve reachability analysis problems on four benchmark problems, one of them with hybrid dynamics. We do not rank the tools based on the results, but show the current status and discover the potential advantages of different tools. article_processing_charge: No author: - first_name: Fabian full_name: Immler, Fabian last_name: Immler - first_name: Matthias full_name: Althoff, Matthias last_name: Althoff - first_name: Luis full_name: Benet, Luis last_name: Benet - first_name: Alexandre full_name: Chapoutot, Alexandre last_name: Chapoutot - first_name: Xin full_name: Chen, Xin last_name: Chen - first_name: Marcelo full_name: Forets, Marcelo last_name: Forets - first_name: Luca full_name: Geretti, Luca last_name: Geretti - first_name: Niklas full_name: Kochdumper, Niklas last_name: Kochdumper - first_name: David P. full_name: Sanders, David P. last_name: Sanders - first_name: Christian full_name: Schilling, Christian id: 3A2F4DCE-F248-11E8-B48F-1D18A9856A87 last_name: Schilling orcid: 0000-0003-3658-1065 citation: ama: 'Immler F, Althoff M, Benet L, et al. ARCH-COMP19 Category Report: Continuous and hybrid systems with nonlinear dynamics. In: EPiC Series in Computing. Vol 61. EasyChair Publications; 2019:41-61. doi:10.29007/m75b' apa: 'Immler, F., Althoff, M., Benet, L., Chapoutot, A., Chen, X., Forets, M., … Schilling, C. (2019). ARCH-COMP19 Category Report: Continuous and hybrid systems with nonlinear dynamics. In EPiC Series in Computing (Vol. 61, pp. 41–61). Montreal, Canada: EasyChair Publications. https://doi.org/10.29007/m75b' chicago: 'Immler, Fabian, Matthias Althoff, Luis Benet, Alexandre Chapoutot, Xin Chen, Marcelo Forets, Luca Geretti, Niklas Kochdumper, David P. Sanders, and Christian Schilling. “ARCH-COMP19 Category Report: Continuous and Hybrid Systems with Nonlinear Dynamics.” In EPiC Series in Computing, 61:41–61. EasyChair Publications, 2019. https://doi.org/10.29007/m75b.' ieee: 'F. Immler et al., “ARCH-COMP19 Category Report: Continuous and hybrid systems with nonlinear dynamics,” in EPiC Series in Computing, Montreal, Canada, 2019, vol. 61, pp. 41–61.' ista: 'Immler F, Althoff M, Benet L, Chapoutot A, Chen X, Forets M, Geretti L, Kochdumper N, Sanders DP, Schilling C. 2019. ARCH-COMP19 Category Report: Continuous and hybrid systems with nonlinear dynamics. EPiC Series in Computing. ARCH: International Workshop on Applied Verification on Continuous and Hybrid Systems vol. 61, 41–61.' mla: 'Immler, Fabian, et al. “ARCH-COMP19 Category Report: Continuous and Hybrid Systems with Nonlinear Dynamics.” EPiC Series in Computing, vol. 61, EasyChair Publications, 2019, pp. 41–61, doi:10.29007/m75b.' short: F. Immler, M. Althoff, L. Benet, A. Chapoutot, X. Chen, M. Forets, L. Geretti, N. Kochdumper, D.P. Sanders, C. Schilling, in:, EPiC Series in Computing, EasyChair Publications, 2019, pp. 41–61. 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: 2020-03-08T23:00:49Z date_published: 2019-05-25T00:00:00Z date_updated: 2021-01-12T08:14:17Z day: '25' ddc: - '000' department: - _id: ToHe doi: 10.29007/m75b file: - access_level: open_access checksum: 9138977a06fcd6a95976eb4bca875f0c content_type: application/pdf creator: dernst date_created: 2020-03-24T07:36:36Z date_updated: 2020-07-14T12:48:00Z file_id: '7617' file_name: 2019_ARCH19_Immler.pdf file_size: 1934830 relation: main_file file_date_updated: 2020-07-14T12:48:00Z has_accepted_license: '1' intvolume: ' 61' language: - iso: eng month: '05' oa: 1 oa_version: Published Version page: 41-61 publication: EPiC Series in Computing publication_identifier: eissn: - '23987340' publication_status: published publisher: EasyChair Publications quality_controlled: '1' scopus_import: 1 status: public title: 'ARCH-COMP19 Category Report: Continuous and hybrid systems with nonlinear dynamics' type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 61 year: '2019' ... --- _id: '7627' abstract: - lang: eng text: 'Electrodepositing insulating and insoluble Li2O2 is the key process during discharge of aprotic Li-O2 batteries and determines rate, capacity, and reversibility. Current understanding states that the partition between surface adsorbed and solvated LiO2 governs whether Li2O2 grows as surface film, leading to low capacity even at low rates, or in solution, leading to particles and high capacities. Here we show that Li2O2 forms to the widest extent as particles via solution mediated LiO2 disproportionation. We describe a unified Li2O2 growth model that conclusively explains capacity limitations across the whole range of electrolytes. Deciding for particle morphology, achievable rate and capacities are species mobilities, electrode specific surface area (determining true areal rate) and the concentration distribution of associated LiO2 in solution. Provided that species mobilities and surface are high, high, capacities are possible even with low-donor-number electrolytes, previously considered prototypical for low capacity via surface growth. The tools for these insights are microscopy, hydrodynamic voltammetry, a numerical reaction model, and in situ small/wide angle X-ray scattering (SAXS/WAXS). Combined with sophisticated data analysis, SAXS allows retrieving rich quantitative information from complex multi-phase systems. On a wider perspective, this SAXS method is a powerful in situ metrology with atomic to sub-micron resolution to study mechanisms in complex electrochemical systems and beyond. ' article_processing_charge: No author: - first_name: Christian full_name: Prehal, Christian last_name: Prehal - first_name: Aleksej full_name: Samojlov, Aleksej last_name: Samojlov - first_name: Manfred full_name: Nachtnebel, Manfred last_name: Nachtnebel - first_name: Manfred full_name: Kriechbaum, Manfred last_name: Kriechbaum - first_name: Heinz full_name: Amenitsch, Heinz last_name: Amenitsch - first_name: Stefan Alexander full_name: Freunberger, Stefan Alexander id: A8CA28E6-CE23-11E9-AD2D-EC27E6697425 last_name: Freunberger orcid: 0000-0003-2902-5319 citation: ama: Prehal C, Samojlov A, Nachtnebel M, Kriechbaum M, Amenitsch H, Freunberger SA. A revised O2 reduction model in Li-O2 batteries as revealed by in situ small angle X-ray scattering. apa: Prehal, C., Samojlov, A., Nachtnebel, M., Kriechbaum, M., Amenitsch, H., & Freunberger, S. A. (n.d.). A revised O2 reduction model in Li-O2 batteries as revealed by in situ small angle X-ray scattering. ChemRxiv. chicago: Prehal, Christian, Aleksej Samojlov, Manfred Nachtnebel, Manfred Kriechbaum, Heinz Amenitsch, and Stefan Alexander Freunberger. “A Revised O2 Reduction Model in Li-O2 Batteries as Revealed by in Situ Small Angle X-Ray Scattering.” ChemRxiv, n.d. ieee: C. Prehal, A. Samojlov, M. Nachtnebel, M. Kriechbaum, H. Amenitsch, and S. A. Freunberger, “A revised O2 reduction model in Li-O2 batteries as revealed by in situ small angle X-ray scattering.” ChemRxiv. ista: Prehal C, Samojlov A, Nachtnebel M, Kriechbaum M, Amenitsch H, Freunberger SA. A revised O2 reduction model in Li-O2 batteries as revealed by in situ small angle X-ray scattering. mla: Prehal, Christian, et al. A Revised O2 Reduction Model in Li-O2 Batteries as Revealed by in Situ Small Angle X-Ray Scattering. ChemRxiv. short: C. Prehal, A. Samojlov, M. Nachtnebel, M. Kriechbaum, H. Amenitsch, S.A. Freunberger, (n.d.). date_created: 2020-04-01T10:10:21Z date_published: 2019-12-26T00:00:00Z date_updated: 2020-04-06T10:36:21Z day: '26' extern: '1' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.26434/chemrxiv.11447775.v1 month: '12' oa: 1 oa_version: Preprint page: '50' publication_status: submitted publisher: ChemRxiv status: public title: A revised O2 reduction model in Li-O2 batteries as revealed by in situ small angle X-ray scattering type: preprint user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2019' ... --- _id: '7710' abstract: - lang: eng text: 'The number of human genomes being genotyped or sequenced increases exponentially and efficient haplotype estimation methods able to handle this amount of data are now required. Here we present a method, SHAPEIT4, which substantially improves upon other methods to process large genotype and high coverage sequencing datasets. It notably exhibits sub-linear running times with sample size, provides highly accurate haplotypes and allows integrating external phasing information such as large reference panels of haplotypes, collections of pre-phased variants and long sequencing reads. We provide SHAPEIT4 in an open source format and demonstrate its performance in terms of accuracy and running times on two gold standard datasets: the UK Biobank data and the Genome In A Bottle.' article_number: '5436' article_processing_charge: No article_type: original author: - first_name: Olivier full_name: Delaneau, Olivier last_name: Delaneau - first_name: Jean-François full_name: Zagury, Jean-François last_name: Zagury - 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: Jonathan L. full_name: Marchini, Jonathan L. last_name: Marchini - first_name: Emmanouil T. full_name: Dermitzakis, Emmanouil T. last_name: Dermitzakis citation: ama: Delaneau O, Zagury J-F, Robinson MR, Marchini JL, Dermitzakis ET. Accurate, scalable and integrative haplotype estimation. Nature Communications. 2019;10. doi:10.1038/s41467-019-13225-y apa: Delaneau, O., Zagury, J.-F., Robinson, M. R., Marchini, J. L., & Dermitzakis, E. T. (2019). Accurate, scalable and integrative haplotype estimation. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-019-13225-y chicago: Delaneau, Olivier, Jean-François Zagury, Matthew Richard Robinson, Jonathan L. Marchini, and Emmanouil T. Dermitzakis. “Accurate, Scalable and Integrative Haplotype Estimation.” Nature Communications. Springer Nature, 2019. https://doi.org/10.1038/s41467-019-13225-y. ieee: O. Delaneau, J.-F. Zagury, M. R. Robinson, J. L. Marchini, and E. T. Dermitzakis, “Accurate, scalable and integrative haplotype estimation,” Nature Communications, vol. 10. Springer Nature, 2019. ista: Delaneau O, Zagury J-F, Robinson MR, Marchini JL, Dermitzakis ET. 2019. Accurate, scalable and integrative haplotype estimation. Nature Communications. 10, 5436. mla: Delaneau, Olivier, et al. “Accurate, Scalable and Integrative Haplotype Estimation.” Nature Communications, vol. 10, 5436, Springer Nature, 2019, doi:10.1038/s41467-019-13225-y. short: O. Delaneau, J.-F. Zagury, M.R. Robinson, J.L. Marchini, E.T. Dermitzakis, Nature Communications 10 (2019). date_created: 2020-04-30T10:40:32Z date_published: 2019-11-28T00:00:00Z date_updated: 2021-01-12T08:15:01Z day: '28' doi: 10.1038/s41467-019-13225-y extern: '1' intvolume: ' 10' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1038/s41467-019-13225-y month: '11' oa: 1 oa_version: Published Version publication: Nature Communications publication_identifier: issn: - 2041-1723 publication_status: published publisher: Springer Nature quality_controlled: '1' status: public title: Accurate, scalable and integrative haplotype estimation type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 10 year: '2019' ... --- _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' ...