--- _id: '8834' abstract: - lang: eng text: "This data collection contains the transport data for figures presented in the supplementary material of \"Enhancement of Proximity Induced Superconductivity in Planar Germanium\" by K. Aggarwal, et. al. \r\nThe measurements were done using Labber Software and the data is stored in the hdf5 file format. The files can be opened using either the Labber Log Browser (https://labber.org/overview/) or Labber Python API (http://labber.org/online-doc/api/LogFile.html).\r\n" article_processing_charge: No author: - first_name: Georgios full_name: Katsaros, Georgios id: 38DB5788-F248-11E8-B48F-1D18A9856A87 last_name: Katsaros orcid: 0000-0001-8342-202X citation: ama: Katsaros G. Enhancement of proximity induced superconductivity in planar Germanium. 2020. doi:10.15479/AT:ISTA:8834 apa: Katsaros, G. (2020). Enhancement of proximity induced superconductivity in planar Germanium. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:8834 chicago: Katsaros, Georgios. “Enhancement of Proximity Induced Superconductivity in Planar Germanium.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:8834. ieee: G. Katsaros, “Enhancement of proximity induced superconductivity in planar Germanium.” Institute of Science and Technology Austria, 2020. ista: Katsaros G. 2020. Enhancement of proximity induced superconductivity in planar Germanium, Institute of Science and Technology Austria, 10.15479/AT:ISTA:8834. mla: Katsaros, Georgios. Enhancement of Proximity Induced Superconductivity in Planar Germanium. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:8834. short: G. Katsaros, (2020). contributor: - contributor_type: project_member first_name: Kushagra id: b22ab905-3539-11eb-84c3-fc159dcd79cb last_name: Aggarwal - contributor_type: project_member first_name: Andrea C id: 340F461A-F248-11E8-B48F-1D18A9856A87 last_name: Hofmann - contributor_type: project_member first_name: Daniel id: 4C473F58-F248-11E8-B48F-1D18A9856A87 last_name: Jirovec - contributor_type: project_member first_name: Ivan id: 2A307FE2-F248-11E8-B48F-1D18A9856A87 last_name: Prieto Gonzalez - contributor_type: project_member first_name: Amir last_name: Sammak - contributor_type: project_member first_name: Marc last_name: Botifoll - contributor_type: project_member first_name: Sara last_name: Marti-Sanchez - contributor_type: project_member first_name: Menno last_name: Veldhorst - contributor_type: project_member first_name: Jordi last_name: Arbiol - contributor_type: project_member first_name: Giordano last_name: Scappucci - contributor_type: project_leader first_name: Georgios id: 38DB5788-F248-11E8-B48F-1D18A9856A87 last_name: Katsaros date_created: 2020-12-02T10:49:30Z date_published: 2020-12-02T00:00:00Z date_updated: 2024-02-21T12:41:26Z day: '02' ddc: - 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access_level: open_access checksum: 618f507780343c6b9145c40d3d5b0ff0 content_type: application/octet-stream creator: gkatsaro date_created: 2020-12-02T10:46:27Z date_updated: 2020-12-02T10:46:27Z file_id: '8904' file_name: dev2-jj2-ICvsVG-Tdependence_850mK.hdf5 file_size: 145282 relation: main_file success: 1 - access_level: open_access checksum: 7547c3607280c7eedca3168854976cc9 content_type: application/octet-stream creator: gkatsaro date_created: 2020-12-02T10:46:27Z date_updated: 2020-12-02T10:46:27Z file_id: '8905' file_name: dev2-jj2-ICvsVG-Tdependence_900mK.hdf5 file_size: 143681 relation: main_file success: 1 - access_level: open_access checksum: 514d9a43ed3888ce7d8b26ca772cadc3 content_type: application/octet-stream creator: gkatsaro date_created: 2020-12-02T10:46:27Z date_updated: 2020-12-02T10:46:27Z file_id: '8906' file_name: dev2-jj2-ICvsVG-Tdependence_90mK.hdf5 file_size: 167184 relation: main_file success: 1 - access_level: open_access checksum: 77285471178fa68c1eade48761b2aba5 content_type: application/octet-stream creator: gkatsaro date_created: 2020-12-02T10:46:27Z date_updated: 2020-12-02T10:46:27Z file_id: '8907' file_name: dev2-jj2-ICvsVG-Tdependence_930mK.hdf5 file_size: 143491 relation: main_file success: 1 - access_level: open_access checksum: bf8da09fcfa20196fb7e65528a581297 content_type: application/octet-stream creator: gkatsaro date_created: 2020-12-02T10:46:27Z date_updated: 2020-12-02T10:46:27Z file_id: '8908' file_name: dev2-jj2-ICvsVG-Tdependence_965mK.hdf5 file_size: 144057 relation: main_file success: 1 file_date_updated: 2020-12-02T10:46:27Z has_accepted_license: '1' month: '12' oa: 1 oa_version: Published Version publisher: Institute of Science and Technology Austria related_material: record: - id: '10559' relation: used_in_publication status: public - id: '8831' relation: used_in_publication status: public status: public title: Enhancement of proximity induced superconductivity in planar Germanium tmp: image: /images/cc_0.png legal_code_url: https://creativecommons.org/publicdomain/zero/1.0/legalcode name: Creative Commons Public Domain Dedication (CC0 1.0) short: CC0 (1.0) type: research_data user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2020' ... --- _id: '8914' abstract: - lang: eng text: Amyotrophic lateral sclerosis (ALS) leads to a loss of specific motor neuron populations in the spinal cord and cortex. Emerging evidence suggests that interneurons may also be affected, but a detailed characterization of interneuron loss and its potential impacts on motor neuron loss and disease progression is lacking. To examine this issue, the fate of V1 inhibitory neurons during ALS was assessed in the ventral spinal cord using the SODG93A mouse model. The V1 population makes up ∼30% of all ventral inhibitory neurons, ∼50% of direct inhibitory synaptic contacts onto motor neuron cell bodies, and is thought to play a key role in modulating motor output, in part through recurrent and reciprocal inhibitory circuits. We find that approximately half of V1 inhibitory neurons are lost in SODG93A mice at late disease stages, but that this loss is delayed relative to the loss of motor neurons and V2a excitatory neurons. We further identify V1 subpopulations based on transcription factor expression that are differentially susceptible to degeneration in SODG93A mice. At an early disease stage, we show that V1 synaptic contacts with motor neuron cell bodies increase, suggesting an upregulation of inhibition before V1 neurons are lost in substantial numbers. These data support a model in which progressive changes in V1 synaptic contacts early in disease, and in select V1 subpopulations at later stages, represent a compensatory upregulation and then deleterious breakdown of specific interneuron circuits within the spinal cord. acknowledgement: This work was made possible by the generous support of Project ALS. Imaging and related analyses were facilitated by The Waitt Advanced Biophotonics Center Core at the Salk Institute, supported by grants from NIH-NCI CCSG (P30 014195) and NINDS Neuroscience Center (NS072031). The authors would like to additionally thank Drs. Jane Dodd, Robert Brownstone, and Laskaro Zagoraiou for helpful comments on the manuscript. This manuscript is dedicated to Tom Jessell, an inspirational scientist, friend and mentor. article_processing_charge: Yes (via OA deal) article_type: original author: - first_name: Alina full_name: Salamatina, Alina last_name: Salamatina - first_name: Jerry H full_name: Yang, Jerry H last_name: Yang - first_name: Susan full_name: Brenner-Morton, Susan last_name: Brenner-Morton - first_name: 'Jay B ' full_name: 'Bikoff, Jay B ' last_name: Bikoff - first_name: Linjing full_name: Fang, Linjing last_name: Fang - first_name: Christopher R full_name: Kintner, Christopher R last_name: Kintner - first_name: Thomas M full_name: Jessell, Thomas M last_name: Jessell - first_name: Lora Beatrice Jaeger full_name: Sweeney, Lora Beatrice Jaeger id: 56BE8254-C4F0-11E9-8E45-0B23E6697425 last_name: Sweeney orcid: 0000-0001-9242-5601 citation: ama: Salamatina A, Yang JH, Brenner-Morton S, et al. Differential loss of spinal interneurons in a mouse model of ALS. Neuroscience. 2020;450:81-95. doi:10.1016/j.neuroscience.2020.08.011 apa: Salamatina, A., Yang, J. H., Brenner-Morton, S., Bikoff, J. B., Fang, L., Kintner, C. R., … Sweeney, L. B. (2020). Differential loss of spinal interneurons in a mouse model of ALS. Neuroscience. Elsevier. https://doi.org/10.1016/j.neuroscience.2020.08.011 chicago: Salamatina, Alina, Jerry H Yang, Susan Brenner-Morton, Jay B Bikoff, Linjing Fang, Christopher R Kintner, Thomas M Jessell, and Lora B. Sweeney. “Differential Loss of Spinal Interneurons in a Mouse Model of ALS.” Neuroscience. Elsevier, 2020. https://doi.org/10.1016/j.neuroscience.2020.08.011. ieee: A. Salamatina et al., “Differential loss of spinal interneurons in a mouse model of ALS,” Neuroscience, vol. 450. Elsevier, pp. 81–95, 2020. ista: Salamatina A, Yang JH, Brenner-Morton S, Bikoff JB, Fang L, Kintner CR, Jessell TM, Sweeney LB. 2020. Differential loss of spinal interneurons in a mouse model of ALS. Neuroscience. 450, 81–95. mla: Salamatina, Alina, et al. “Differential Loss of Spinal Interneurons in a Mouse Model of ALS.” Neuroscience, vol. 450, Elsevier, 2020, pp. 81–95, doi:10.1016/j.neuroscience.2020.08.011. short: A. Salamatina, J.H. Yang, S. Brenner-Morton, J.B. Bikoff, L. Fang, C.R. Kintner, T.M. Jessell, L.B. Sweeney, Neuroscience 450 (2020) 81–95. date_created: 2020-12-03T11:47:31Z date_published: 2020-12-01T00:00:00Z date_updated: 2024-01-31T10:15:34Z day: '01' ddc: - '570' department: - _id: LoSw doi: 10.1016/j.neuroscience.2020.08.011 external_id: isi: - '000595588700008' pmid: - '32858144' file: - access_level: open_access checksum: da7413c819e079720669c82451b49294 content_type: application/pdf creator: dernst date_created: 2020-12-03T11:45:26Z date_updated: 2020-12-03T11:45:26Z file_id: '8915' file_name: 2020_Neuroscience_Salamatina.pdf file_size: 4071247 relation: main_file success: 1 file_date_updated: 2020-12-03T11:45:26Z has_accepted_license: '1' intvolume: ' 450' isi: 1 language: - iso: eng month: '12' oa: 1 oa_version: Published Version page: 81-95 pmid: 1 publication: Neuroscience publication_identifier: issn: - 0306-4522 publication_status: published publisher: Elsevier quality_controlled: '1' scopus_import: '1' status: public title: Differential loss of spinal interneurons in a mouse model of ALS 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: 450 year: '2020' ... --- _id: '8924' abstract: - lang: eng text: 'Maintaining fertility in a fluctuating environment is key to the reproductive success of flowering plants. Meiosis and pollen formation are particularly sensitive to changes in growing conditions, especially temperature. We have previously identified cyclin-dependent kinase G1 (CDKG1) as a master regulator of temperature-dependent meiosis and this may involve the regulation of alternative splicing (AS), including of its own transcript. CDKG1 mRNA can undergo several AS events, potentially producing two protein variants: CDKG1L and CDKG1S, differing in their N-terminal domain which may be involved in co-factor interaction. In leaves, both isoforms have distinct temperature-dependent functions on target mRNA processing, but their role in pollen development is unknown. In the present study, we characterize the role of CDKG1L and CDKG1S in maintaining Arabidopsis fertility. We show that the long (L) form is necessary and sufficient to rescue the fertility defects of the cdkg1-1 mutant, while the short (S) form is unable to rescue fertility. On the other hand, an extra copy of CDKG1L reduces fertility. In addition, mutation of the ATP binding pocket of the kinase indicates that kinase activity is necessary for the function of CDKG1. Kinase mutants of CDKG1L and CDKG1S correctly localize to the cell nucleus and nucleus and cytoplasm, respectively, but are unable to rescue either the fertility or the splicing defects of the cdkg1-1 mutant. Furthermore, we show that there is partial functional overlap between CDKG1 and its paralog CDKG2 that could in part be explained by overlapping gene expression.' acknowledgement: CN, DD, NF-F, and JD were funded by the BBSRC (grant number BB/M009459/1). NK and AM were funded through the ERASMUS+Program. NC was funded by the VIPS Program of the Austrian Federal Ministry of Science and Research and the City of Vienna. article_number: '586870' article_processing_charge: No article_type: original author: - first_name: Candida full_name: Nibau, Candida last_name: Nibau - first_name: Despoina full_name: Dadarou, Despoina last_name: Dadarou - first_name: Nestoras full_name: Kargios, Nestoras last_name: Kargios - first_name: Areti full_name: Mallioura, Areti last_name: Mallioura - first_name: Narcis full_name: Fernandez-Fuentes, Narcis last_name: Fernandez-Fuentes - first_name: Nicola full_name: Cavallari, Nicola id: 457160E6-F248-11E8-B48F-1D18A9856A87 last_name: Cavallari - first_name: John H. full_name: Doonan, John H. last_name: Doonan citation: ama: Nibau C, Dadarou D, Kargios N, et al. A functional kinase is necessary for cyclin-dependent kinase G1 (CDKG1) to maintain fertility at high ambient temperature in Arabidopsis. Frontiers in Plant Science. 2020;11. doi:10.3389/fpls.2020.586870 apa: Nibau, C., Dadarou, D., Kargios, N., Mallioura, A., Fernandez-Fuentes, N., Cavallari, N., & Doonan, J. H. (2020). A functional kinase is necessary for cyclin-dependent kinase G1 (CDKG1) to maintain fertility at high ambient temperature in Arabidopsis. Frontiers in Plant Science. Frontiers. https://doi.org/10.3389/fpls.2020.586870 chicago: Nibau, Candida, Despoina Dadarou, Nestoras Kargios, Areti Mallioura, Narcis Fernandez-Fuentes, Nicola Cavallari, and John H. Doonan. “A Functional Kinase Is Necessary for Cyclin-Dependent Kinase G1 (CDKG1) to Maintain Fertility at High Ambient Temperature in Arabidopsis.” Frontiers in Plant Science. Frontiers, 2020. https://doi.org/10.3389/fpls.2020.586870. ieee: C. Nibau et al., “A functional kinase is necessary for cyclin-dependent kinase G1 (CDKG1) to maintain fertility at high ambient temperature in Arabidopsis,” Frontiers in Plant Science, vol. 11. Frontiers, 2020. ista: Nibau C, Dadarou D, Kargios N, Mallioura A, Fernandez-Fuentes N, Cavallari N, Doonan JH. 2020. A functional kinase is necessary for cyclin-dependent kinase G1 (CDKG1) to maintain fertility at high ambient temperature in Arabidopsis. Frontiers in Plant Science. 11, 586870. mla: Nibau, Candida, et al. “A Functional Kinase Is Necessary for Cyclin-Dependent Kinase G1 (CDKG1) to Maintain Fertility at High Ambient Temperature in Arabidopsis.” Frontiers in Plant Science, vol. 11, 586870, Frontiers, 2020, doi:10.3389/fpls.2020.586870. short: C. Nibau, D. Dadarou, N. Kargios, A. Mallioura, N. Fernandez-Fuentes, N. Cavallari, J.H. Doonan, Frontiers in Plant Science 11 (2020). date_created: 2020-12-06T23:01:14Z date_published: 2020-11-10T00:00:00Z date_updated: 2023-08-24T10:50:00Z day: '10' ddc: - '580' department: - _id: EvBe doi: 10.3389/fpls.2020.586870 external_id: isi: - '000591637000001' file: - access_level: open_access checksum: 1c0ee6ce9950aa665d6a5cc64aa6b752 content_type: application/pdf creator: dernst date_created: 2020-12-09T09:14:19Z date_updated: 2020-12-09T09:14:19Z file_id: '8929' file_name: 2020_Frontiers_Nibau.pdf file_size: 1833244 relation: main_file success: 1 file_date_updated: 2020-12-09T09:14:19Z has_accepted_license: '1' intvolume: ' 11' isi: 1 language: - iso: eng month: '11' oa: 1 oa_version: Published Version publication: Frontiers in Plant Science publication_identifier: eissn: - 1664-462X publication_status: published publisher: Frontiers quality_controlled: '1' scopus_import: '1' status: public title: A functional kinase is necessary for cyclin-dependent kinase G1 (CDKG1) to maintain fertility at high ambient temperature in Arabidopsis tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 11 year: '2020' ... --- _id: '8926' abstract: - lang: eng text: 'Bimetallic nanoparticles with tailored size and specific composition have shown promise as stable and selective catalysts for electrochemical reduction of CO2 (CO2R) in batch systems. Yet, limited effort was devoted to understand the effect of ligand coverage and postsynthesis treatments on CO2 reduction, especially under industrially applicable conditions, such as at high currents (>100 mA/cm2) using gas diffusion electrodes (GDE) and flow reactors. In this work, Cu–Ag core–shell nanoparticles (11 ± 2 nm) were prepared with three different surface modes: (i) capped with oleylamine, (ii) capped with monoisopropylamine, and (iii) surfactant-free with a reducing borohydride agent; Cu–Ag (OAm), Cu–Ag (MIPA), and Cu–Ag (NaBH4), respectively. The ligand exchange and removal was evidenced by infrared spectroscopy (ATR-FTIR) analysis, whereas high-resolution scanning transmission electron microscopy (HAADF-STEM) showed their effect on the interparticle distance and nanoparticle rearrangement. Later on, we developed a process-on-substrate method to track these effects on CO2R. Cu–Ag (OAm) gave a lower on-set potential for hydrocarbon production, whereas Cu–Ag (MIPA) and Cu–Ag (NaBH4) promoted syngas production. The electrochemical impedance and surface area analysis on the well-controlled electrodes showed gradual increases in the electrical conductivity and active surface area after each surface treatment. We found that the increasing amount of the triple phase boundaries (the meeting point for the electron–electrolyte–CO2 reactant) affect the required electrode potential and eventually the C+2e̅/C2e̅ product ratio. This study highlights the importance of the electron transfer to those active sites affected by the capping agents—particularly on larger substrates that are crucial for their industrial application.' acknowledgement: The authors also acknowledge financial support from the University Research Fund (BOF-GOA-PS ID No. 33928). S.L. has received funding from the European Union’s Horizon 2020 research and innovation program under the Marie Skłodowska-Curie Grant Agreement No. 665385. article_processing_charge: No article_type: original author: - first_name: Erdem full_name: Irtem, Erdem last_name: Irtem - first_name: Daniel full_name: Arenas Esteban, Daniel last_name: Arenas Esteban - first_name: Miguel full_name: Duarte, Miguel last_name: Duarte - first_name: Daniel full_name: Choukroun, Daniel last_name: Choukroun - first_name: Seungho full_name: Lee, Seungho id: BB243B88-D767-11E9-B658-BC13E6697425 last_name: Lee orcid: 0000-0002-6962-8598 - first_name: Maria full_name: Ibáñez, Maria id: 43C61214-F248-11E8-B48F-1D18A9856A87 last_name: Ibáñez orcid: 0000-0001-5013-2843 - first_name: Sara full_name: Bals, Sara last_name: Bals - first_name: Tom full_name: Breugelmans, Tom last_name: Breugelmans citation: ama: Irtem E, Arenas Esteban D, Duarte M, et al. Ligand-mode directed selectivity in Cu-Ag core-shell based gas diffusion electrodes for CO2 electroreduction. ACS Catalysis. 2020;10(22):13468-13478. doi:10.1021/acscatal.0c03210 apa: Irtem, E., Arenas Esteban, D., Duarte, M., Choukroun, D., Lee, S., Ibáñez, M., … Breugelmans, T. (2020). Ligand-mode directed selectivity in Cu-Ag core-shell based gas diffusion electrodes for CO2 electroreduction. ACS Catalysis. American Chemical Society. https://doi.org/10.1021/acscatal.0c03210 chicago: Irtem, Erdem, Daniel Arenas Esteban, Miguel Duarte, Daniel Choukroun, Seungho Lee, Maria Ibáñez, Sara Bals, and Tom Breugelmans. “Ligand-Mode Directed Selectivity in Cu-Ag Core-Shell Based Gas Diffusion Electrodes for CO2 Electroreduction.” ACS Catalysis. American Chemical Society, 2020. https://doi.org/10.1021/acscatal.0c03210. ieee: E. Irtem et al., “Ligand-mode directed selectivity in Cu-Ag core-shell based gas diffusion electrodes for CO2 electroreduction,” ACS Catalysis, vol. 10, no. 22. American Chemical Society, pp. 13468–13478, 2020. ista: Irtem E, Arenas Esteban D, Duarte M, Choukroun D, Lee S, Ibáñez M, Bals S, Breugelmans T. 2020. Ligand-mode directed selectivity in Cu-Ag core-shell based gas diffusion electrodes for CO2 electroreduction. ACS Catalysis. 10(22), 13468–13478. mla: Irtem, Erdem, et al. “Ligand-Mode Directed Selectivity in Cu-Ag Core-Shell Based Gas Diffusion Electrodes for CO2 Electroreduction.” ACS Catalysis, vol. 10, no. 22, American Chemical Society, 2020, pp. 13468–78, doi:10.1021/acscatal.0c03210. short: E. Irtem, D. Arenas Esteban, M. Duarte, D. Choukroun, S. Lee, M. Ibáñez, S. Bals, T. Breugelmans, ACS Catalysis 10 (2020) 13468–13478. date_created: 2020-12-06T23:01:15Z date_published: 2020-11-20T00:00:00Z date_updated: 2023-08-24T10:52:32Z day: '20' department: - _id: MaIb doi: 10.1021/acscatal.0c03210 ec_funded: 1 external_id: isi: - '000592978900031' intvolume: ' 10' isi: 1 issue: '22' language: - iso: eng month: '11' oa_version: None page: 13468-13478 project: - _id: 2564DBCA-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '665385' name: International IST Doctoral Program publication: ACS Catalysis publication_identifier: eissn: - '21555435' publication_status: published publisher: American Chemical Society quality_controlled: '1' scopus_import: '1' status: public title: Ligand-mode directed selectivity in Cu-Ag core-shell based gas diffusion electrodes for CO2 electroreduction type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 10 year: '2020' ... --- _id: '8930' abstract: - lang: eng text: Phenomenological relations such as Ohm’s or Fourier’s law have a venerable history in physics but are still scarce in biology. This situation restrains predictive theory. Here, we build on bacterial “growth laws,” which capture physiological feedback between translation and cell growth, to construct a minimal biophysical model for the combined action of ribosome-targeting antibiotics. Our model predicts drug interactions like antagonism or synergy solely from responses to individual drugs. We provide analytical results for limiting cases, which agree well with numerical results. We systematically refine the model by including direct physical interactions of different antibiotics on the ribosome. In a limiting case, our model provides a mechanistic underpinning for recent predictions of higher-order interactions that were derived using entropy maximization. We further refine the model to include the effects of antibiotics that mimic starvation and the presence of resistance genes. We describe the impact of a starvation-mimicking antibiotic on drug interactions analytically and verify it experimentally. Our extended model suggests a change in the type of drug interaction that depends on the strength of resistance, which challenges established rescaling paradigms. We experimentally show that the presence of unregulated resistance genes can lead to altered drug interaction, which agrees with the prediction of the model. While minimal, the model is readily adaptable and opens the door to predicting interactions of second and higher-order in a broad range of biological systems. article_processing_charge: No author: - first_name: Bor full_name: Kavcic, Bor id: 350F91D2-F248-11E8-B48F-1D18A9856A87 last_name: Kavcic orcid: 0000-0001-6041-254X citation: ama: Kavcic B. Analysis scripts and research data for the paper “Minimal biophysical model of combined antibiotic action.” 2020. doi:10.15479/AT:ISTA:8930 apa: Kavcic, B. (2020). Analysis scripts and research data for the paper “Minimal biophysical model of combined antibiotic action.” Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:8930 chicago: Kavcic, Bor. “Analysis Scripts and Research Data for the Paper ‘Minimal Biophysical Model of Combined Antibiotic Action.’” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:8930. ieee: B. Kavcic, “Analysis scripts and research data for the paper ‘Minimal biophysical model of combined antibiotic action.’” Institute of Science and Technology Austria, 2020. ista: Kavcic B. 2020. Analysis scripts and research data for the paper ‘Minimal biophysical model of combined antibiotic action’, Institute of Science and Technology Austria, 10.15479/AT:ISTA:8930. mla: Kavcic, Bor. Analysis Scripts and Research Data for the Paper “Minimal Biophysical Model of Combined Antibiotic Action.” Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:8930. short: B. Kavcic, (2020). contributor: - contributor_type: supervisor first_name: Gašper id: 3D494DCA-F248-11E8-B48F-1D18A9856A87 last_name: Tkačik orcid: 0000-0002-6699-1455 - contributor_type: supervisor first_name: Tobias id: 3E6DB97A-F248-11E8-B48F-1D18A9856A87 last_name: Bollenbach date_created: 2020-12-09T15:04:02Z date_published: 2020-12-10T00:00:00Z date_updated: 2024-02-21T12:41:42Z day: '10' ddc: - '570' department: - _id: GaTk doi: 10.15479/AT:ISTA:8930 file: - access_level: open_access checksum: 60a818edeffaa7da1ebf5f8fbea9ba18 content_type: application/zip creator: bkavcic date_created: 2020-12-09T15:00:19Z date_updated: 2020-12-09T15:00:19Z file_id: '8932' file_name: PLoSCompBiol2020_datarep.zip file_size: 315494370 relation: main_file success: 1 file_date_updated: 2020-12-09T15:00:19Z has_accepted_license: '1' keyword: - Escherichia coli - antibiotic combinations - translation - growth laws - drug interactions - bacterial physiology - translation inhibitors month: '12' oa: 1 oa_version: Published Version publisher: Institute of Science and Technology Austria related_material: record: - id: '8997' relation: used_in_publication status: public status: public title: Analysis scripts and research data for the paper "Minimal biophysical model of combined antibiotic action" 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: research_data user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2020' ... --- _id: '8943' abstract: - lang: eng text: The widely used non-steroidal anti-inflammatory drugs (NSAIDs) are derivatives of the phytohormone salicylic acid (SA). SA is well known to regulate plant immunity and development, whereas there have been few reports focusing on the effects of NSAIDs in plants. Our studies here reveal that NSAIDs exhibit largely overlapping physiological activities to SA in the model plant Arabidopsis. NSAID treatments lead to shorter and agravitropic primary roots and inhibited lateral root organogenesis. Notably, in addition to the SA-like action, which in roots involves binding to the protein phosphatase 2A (PP2A), NSAIDs also exhibit PP2A-independent effects. Cell biological and biochemical analyses reveal that many NSAIDs bind directly to and inhibit the chaperone activity of TWISTED DWARF1, thereby regulating actin cytoskeleton dynamics and subsequent endosomal trafficking. Our findings uncover an unexpected bioactivity of human pharmaceuticals in plants and provide insights into the molecular mechanism underlying the cellular action of this class of anti-inflammatory compounds. acknowledged_ssus: - _id: LifeSc - _id: Bio acknowledgement: "We thank Drs. Sebastian Bednarek (University of Wisconsin-Madison), Niko Geldner (University of Lausanne), and Karin Schumacher (Heidelberg University) for kindly sharing published Arabidopsis lines; Dr. Satoshi Naramoto for the pPIN2::PIN2-GFP; pVHA-a1::VHA-a1-mRFP reporter; the staff at the Life Science Facility and Bioimaging Facility, Monika Hrtyan, and Dorota Jaworska at IST Austria for technical support; and Drs. Su Tang (Texas A&M University),\r\nMelinda Abas (BOKU), Eva Benkova´ (IST Austria), Christian Luschnig (BOKU), Bartel Vanholme (Gent University), and the Friml group for valuable discussions. The research leading to these findings was funded by the European Union’s Horizon 2020 program (ERC grant agreement no. 742985, to J.F.), the People Programme (Marie Curie Actions) of the European Union’s Seventh Framework Programme (FP7/2007-2013) under REA grant agreement no.\r\n291734, the Swiss National Funds (31003A_165877, to M.G.), the Ministry of Education, Youth, and Sports of the Czech Republic (project no. CZ.02.1.01/0.0/0.0/16_019/0000738, EU Operational Programme ‘‘Research, development and education and Centre for Plant Experimental Biology’’), and the EU Operational Programme Prague - Competitiveness (project no. CZ.2.16/3.1.00/21519). S.T. was funded by a European Molecular Biology Organization (EMBO) long-term postdoctoral fellowship (ALTF 723-2015). X.Z. was partly supported by a PhD scholarship from the China Scholarship Council." article_number: '108463' article_processing_charge: Yes article_type: original author: - first_name: Shutang full_name: Tan, Shutang id: 2DE75584-F248-11E8-B48F-1D18A9856A87 last_name: Tan orcid: 0000-0002-0471-8285 - first_name: Martin full_name: Di Donato, Martin last_name: Di Donato - first_name: Matous full_name: Glanc, Matous id: 1AE1EA24-02D0-11E9-9BAA-DAF4881429F2 last_name: Glanc orcid: 0000-0003-0619-7783 - first_name: Xixi full_name: Zhang, Xixi id: 61A66458-47E9-11EA-85BA-8AEAAF14E49A last_name: Zhang orcid: 0000-0001-7048-4627 - first_name: Petr full_name: Klíma, Petr last_name: Klíma - first_name: Jie full_name: Liu, Jie last_name: Liu - first_name: Aurélien full_name: Bailly, Aurélien last_name: Bailly - first_name: Noel full_name: Ferro, Noel last_name: Ferro - first_name: Jan full_name: Petrášek, Jan last_name: Petrášek - first_name: Markus full_name: Geisler, Markus last_name: Geisler - first_name: Jiří full_name: Friml, Jiří id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 citation: ama: Tan S, Di Donato M, Glanc M, et al. Non-steroidal anti-inflammatory drugs target TWISTED DWARF1-regulated actin dynamics and auxin transport-mediated plant development. Cell Reports. 2020;33(9). doi:10.1016/j.celrep.2020.108463 apa: Tan, S., Di Donato, M., Glanc, M., Zhang, X., Klíma, P., Liu, J., … Friml, J. (2020). Non-steroidal anti-inflammatory drugs target TWISTED DWARF1-regulated actin dynamics and auxin transport-mediated plant development. Cell Reports. Elsevier. https://doi.org/10.1016/j.celrep.2020.108463 chicago: Tan, Shutang, Martin Di Donato, Matous Glanc, Xixi Zhang, Petr Klíma, Jie Liu, Aurélien Bailly, et al. “Non-Steroidal Anti-Inflammatory Drugs Target TWISTED DWARF1-Regulated Actin Dynamics and Auxin Transport-Mediated Plant Development.” Cell Reports. Elsevier, 2020. https://doi.org/10.1016/j.celrep.2020.108463. ieee: S. Tan et al., “Non-steroidal anti-inflammatory drugs target TWISTED DWARF1-regulated actin dynamics and auxin transport-mediated plant development,” Cell Reports, vol. 33, no. 9. Elsevier, 2020. ista: Tan S, Di Donato M, Glanc M, Zhang X, Klíma P, Liu J, Bailly A, Ferro N, Petrášek J, Geisler M, Friml J. 2020. Non-steroidal anti-inflammatory drugs target TWISTED DWARF1-regulated actin dynamics and auxin transport-mediated plant development. Cell Reports. 33(9), 108463. mla: Tan, Shutang, et al. “Non-Steroidal Anti-Inflammatory Drugs Target TWISTED DWARF1-Regulated Actin Dynamics and Auxin Transport-Mediated Plant Development.” Cell Reports, vol. 33, no. 9, 108463, Elsevier, 2020, doi:10.1016/j.celrep.2020.108463. short: S. Tan, M. Di Donato, M. Glanc, X. Zhang, P. Klíma, J. Liu, A. Bailly, N. Ferro, J. Petrášek, M. Geisler, J. Friml, Cell Reports 33 (2020). date_created: 2020-12-13T23:01:21Z date_published: 2020-12-01T00:00:00Z date_updated: 2023-11-16T13:03:31Z day: '01' ddc: - '580' department: - _id: JiFr doi: 10.1016/j.celrep.2020.108463 ec_funded: 1 external_id: isi: - '000595658100018' pmid: - '33264621' file: - access_level: open_access checksum: ed18cba0fb48ed2e789381a54cc21904 content_type: application/pdf creator: dernst date_created: 2020-12-14T07:33:39Z date_updated: 2020-12-14T07:33:39Z file_id: '8948' file_name: 2020_CellReports_Tan.pdf file_size: 8056434 relation: main_file success: 1 file_date_updated: 2020-12-14T07:33:39Z has_accepted_license: '1' intvolume: ' 33' isi: 1 issue: '9' language: - iso: eng month: '12' oa: 1 oa_version: Published Version pmid: 1 project: - _id: 261099A6-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '742985' name: Tracing Evolution of Auxin Transport and Polarity in Plants - _id: 25681D80-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '291734' name: International IST Postdoc Fellowship Programme - _id: 256FEF10-B435-11E9-9278-68D0E5697425 grant_number: 723-2015 name: Long Term Fellowship publication: Cell Reports publication_identifier: eissn: - '22111247' publication_status: published publisher: Elsevier quality_controlled: '1' related_material: link: - description: News on IST Homepage relation: press_release url: https://ist.ac.at/en/news/plants-on-aspirin/ scopus_import: '1' status: public title: Non-steroidal anti-inflammatory drugs target TWISTED DWARF1-regulated actin dynamics and auxin transport-mediated plant development tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 33 year: '2020' ... --- _id: '8944' abstract: - lang: eng text: "Superconductor insulator transition in transverse magnetic field is studied in the highly disordered MoC film with the product of the Fermi momentum and the mean free path kF*l close to unity. Surprisingly, the Zeeman paramagnetic effects dominate over orbital coupling on both sides of the transition. In superconducting state it is evidenced by a high upper critical magnetic field \U0001D435\U0001D4502, by its square root dependence on temperature, as well as by the Zeeman splitting of the quasiparticle density of states (DOS) measured by scanning tunneling microscopy. At \U0001D435\U0001D4502 a logarithmic anomaly in DOS is observed. This anomaly is further enhanced in increasing magnetic field, which is explained by the Zeeman splitting of the Altshuler-Aronov DOS driving\r\nthe system into a more insulating or resistive state. Spin dependent Altshuler-Aronov correction is also needed to explain the transport behavior above \U0001D435\U0001D4502." acknowledgement: 'We gratefully acknowledge helpful conversations with B.L. Altshuler and R. Hlubina. The work was supported by the projects APVV-18-0358, VEGA 2/0058/20, VEGA 1/0743/19 the European Microkelvin Platform, the COST action CA16218 (Nanocohybri) and by U.S. Steel Košice. ' article_number: '180508' article_processing_charge: No article_type: original arxiv: 1 author: - first_name: Martin full_name: Zemlicka, Martin id: 2DCF8DE6-F248-11E8-B48F-1D18A9856A87 last_name: Zemlicka - first_name: M. full_name: Kopčík, M. last_name: Kopčík - first_name: P. full_name: Szabó, P. last_name: Szabó - first_name: T. full_name: Samuely, T. last_name: Samuely - first_name: J. full_name: Kačmarčík, J. last_name: Kačmarčík - first_name: P. full_name: Neilinger, P. last_name: Neilinger - first_name: M. full_name: Grajcar, M. last_name: Grajcar - first_name: P. full_name: Samuely, P. last_name: Samuely citation: ama: 'Zemlicka M, Kopčík M, Szabó P, et al. Zeeman-driven superconductor-insulator transition in strongly disordered MoC films: Scanning tunneling microscopy and transport studies in a transverse magnetic field. Physical Review B. 2020;102(18). doi:10.1103/PhysRevB.102.180508' apa: 'Zemlicka, M., Kopčík, M., Szabó, P., Samuely, T., Kačmarčík, J., Neilinger, P., … Samuely, P. (2020). Zeeman-driven superconductor-insulator transition in strongly disordered MoC films: Scanning tunneling microscopy and transport studies in a transverse magnetic field. Physical Review B. American Physical Society. https://doi.org/10.1103/PhysRevB.102.180508' chicago: 'Zemlicka, Martin, M. Kopčík, P. Szabó, T. Samuely, J. Kačmarčík, P. Neilinger, M. Grajcar, and P. Samuely. “Zeeman-Driven Superconductor-Insulator Transition in Strongly Disordered MoC Films: Scanning Tunneling Microscopy and Transport Studies in a Transverse Magnetic Field.” Physical Review B. American Physical Society, 2020. https://doi.org/10.1103/PhysRevB.102.180508.' ieee: 'M. Zemlicka et al., “Zeeman-driven superconductor-insulator transition in strongly disordered MoC films: Scanning tunneling microscopy and transport studies in a transverse magnetic field,” Physical Review B, vol. 102, no. 18. American Physical Society, 2020.' ista: 'Zemlicka M, Kopčík M, Szabó P, Samuely T, Kačmarčík J, Neilinger P, Grajcar M, Samuely P. 2020. Zeeman-driven superconductor-insulator transition in strongly disordered MoC films: Scanning tunneling microscopy and transport studies in a transverse magnetic field. Physical Review B. 102(18), 180508.' mla: 'Zemlicka, Martin, et al. “Zeeman-Driven Superconductor-Insulator Transition in Strongly Disordered MoC Films: Scanning Tunneling Microscopy and Transport Studies in a Transverse Magnetic Field.” Physical Review B, vol. 102, no. 18, 180508, American Physical Society, 2020, doi:10.1103/PhysRevB.102.180508.' short: M. Zemlicka, M. Kopčík, P. Szabó, T. Samuely, J. Kačmarčík, P. Neilinger, M. Grajcar, P. Samuely, Physical Review B 102 (2020). date_created: 2020-12-13T23:01:21Z date_published: 2020-11-01T00:00:00Z date_updated: 2023-08-24T10:53:36Z day: '01' department: - _id: JoFi doi: 10.1103/PhysRevB.102.180508 external_id: arxiv: - '2011.04329' isi: - '000591509900003' intvolume: ' 102' isi: 1 issue: '18' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/2011.04329 month: '11' oa: 1 oa_version: Preprint publication: Physical Review B publication_identifier: eissn: - '24699969' issn: - '24699950' publication_status: published publisher: American Physical Society quality_controlled: '1' scopus_import: '1' status: public title: 'Zeeman-driven superconductor-insulator transition in strongly disordered MoC films: Scanning tunneling microscopy and transport studies in a transverse magnetic field' type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 102 year: '2020' ... --- _id: '8949' abstract: - lang: eng text: Development of the nervous system undergoes important transitions, including one from neurogenesis to gliogenesis which occurs late during embryonic gestation. Here we report on clonal analysis of gliogenesis in mice using Mosaic Analysis with Double Markers (MADM) with quantitative and computational methods. Results reveal that developmental gliogenesis in the cerebral cortex occurs in a fraction of earlier neurogenic clones, accelerating around E16.5, and giving rise to both astrocytes and oligodendrocytes. Moreover, MADM-based genetic deletion of the epidermal growth factor receptor (Egfr) in gliogenic clones revealed that Egfr is cell autonomously required for gliogenesis in the mouse dorsolateral cortices. A broad range in the proliferation capacity, symmetry of clones, and competitive advantage of MADM cells was evident in clones that contained one cellular lineage with double dosage of Egfr relative to their environment, while their sibling Egfr-null cells failed to generate glia. Remarkably, the total numbers of glia in MADM clones balance out regardless of significant alterations in clonal symmetries. The variability in glial clones shows stochastic patterns that we define mathematically, which are different from the deterministic patterns in neuronal clones. This study sets a foundation for studying the biological significance of stochastic and deterministic clonal principles underlying tissue development, and identifying mechanisms that differentiate between neurogenesis and gliogenesis. acknowledgement: This research was funded by grants from the National Institutes of Health to H.T.G. (R01NS098370 and R01NS089795). C.V.M. was supported by a National Science Foundation Graduate Research Fellowship (DGE-1746939). R.B. was supported by the FWF Lise-Meitner program (M 2416), and S.H. was supported by the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement No 725780 LinPro).The authors thank members of the Ghashghaei lab for discussions, technical support, and help with preparation of the manuscript. article_number: '2662' article_processing_charge: No article_type: original author: - first_name: Xuying full_name: Zhang, Xuying last_name: Zhang - first_name: Christine V. full_name: Mennicke, Christine V. last_name: Mennicke - first_name: Guanxi full_name: Xiao, Guanxi last_name: Xiao - first_name: Robert J full_name: Beattie, Robert J id: 2E26DF60-F248-11E8-B48F-1D18A9856A87 last_name: Beattie orcid: 0000-0002-8483-8753 - first_name: Mansoor full_name: Haider, Mansoor last_name: Haider - first_name: Simon full_name: Hippenmeyer, Simon id: 37B36620-F248-11E8-B48F-1D18A9856A87 last_name: Hippenmeyer orcid: 0000-0003-2279-1061 - first_name: H. Troy full_name: Ghashghaei, H. Troy last_name: Ghashghaei citation: ama: Zhang X, Mennicke CV, Xiao G, et al. Clonal analysis of gliogenesis in the cerebral cortex reveals stochastic expansion of glia and cell autonomous responses to Egfr dosage. Cells. 2020;9(12). doi:10.3390/cells9122662 apa: Zhang, X., Mennicke, C. V., Xiao, G., Beattie, R. J., Haider, M., Hippenmeyer, S., & Ghashghaei, H. T. (2020). Clonal analysis of gliogenesis in the cerebral cortex reveals stochastic expansion of glia and cell autonomous responses to Egfr dosage. Cells. MDPI. https://doi.org/10.3390/cells9122662 chicago: Zhang, Xuying, Christine V. Mennicke, Guanxi Xiao, Robert J Beattie, Mansoor Haider, Simon Hippenmeyer, and H. Troy Ghashghaei. “Clonal Analysis of Gliogenesis in the Cerebral Cortex Reveals Stochastic Expansion of Glia and Cell Autonomous Responses to Egfr Dosage.” Cells. MDPI, 2020. https://doi.org/10.3390/cells9122662. ieee: X. Zhang et al., “Clonal analysis of gliogenesis in the cerebral cortex reveals stochastic expansion of glia and cell autonomous responses to Egfr dosage,” Cells, vol. 9, no. 12. MDPI, 2020. ista: Zhang X, Mennicke CV, Xiao G, Beattie RJ, Haider M, Hippenmeyer S, Ghashghaei HT. 2020. Clonal analysis of gliogenesis in the cerebral cortex reveals stochastic expansion of glia and cell autonomous responses to Egfr dosage. Cells. 9(12), 2662. mla: Zhang, Xuying, et al. “Clonal Analysis of Gliogenesis in the Cerebral Cortex Reveals Stochastic Expansion of Glia and Cell Autonomous Responses to Egfr Dosage.” Cells, vol. 9, no. 12, 2662, MDPI, 2020, doi:10.3390/cells9122662. short: X. Zhang, C.V. Mennicke, G. Xiao, R.J. Beattie, M. Haider, S. Hippenmeyer, H.T. Ghashghaei, Cells 9 (2020). date_created: 2020-12-14T08:04:03Z date_published: 2020-12-11T00:00:00Z date_updated: 2023-08-24T10:57:48Z day: '11' ddc: - '570' department: - _id: SiHi doi: 10.3390/cells9122662 ec_funded: 1 external_id: isi: - '000601787300001' file: - access_level: open_access checksum: 5095cbdc728c9a510c5761cf60a8861c content_type: application/pdf creator: dernst date_created: 2020-12-14T08:09:43Z date_updated: 2020-12-14T08:09:43Z file_id: '8950' file_name: 2020_Cells_Zhang.pdf file_size: 3504525 relation: main_file success: 1 file_date_updated: 2020-12-14T08:09:43Z has_accepted_license: '1' intvolume: ' 9' isi: 1 issue: '12' language: - iso: eng month: '12' oa: 1 oa_version: Published Version project: - _id: 264E56E2-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: M02416 name: Molecular Mechanisms Regulating Gliogenesis in the Cerebral Cortex - _id: 260018B0-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '725780' name: Principles of Neural Stem Cell Lineage Progression in Cerebral Cortex Development publication: Cells publication_identifier: issn: - 2073-4409 publication_status: published publisher: MDPI quality_controlled: '1' status: public title: Clonal analysis of gliogenesis in the cerebral cortex reveals stochastic expansion of glia and cell autonomous responses to Egfr dosage tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 9 year: '2020' ... --- _id: '8951' abstract: - lang: eng text: Gene expression levels are influenced by multiple coexisting molecular mechanisms. Some of these interactions, such as those of transcription factors and promoters have been studied extensively. However, predicting phenotypes of gene regulatory networks remains a major challenge. Here, we use a well-defined synthetic gene regulatory network to study how network phenotypes depend on local genetic context, i.e. the genetic neighborhood of a transcription factor and its relative position. We show that one gene regulatory network with fixed topology can display not only quantitatively but also qualitatively different phenotypes, depending solely on the local genetic context of its components. Our results demonstrate that changes in local genetic context can place a single transcriptional unit within two separate regulons without the need for complex regulatory sequences. We propose that relative order of individual transcriptional units, with its potential for combinatorial complexity, plays an important role in shaping phenotypes of gene regulatory networks. article_processing_charge: No author: - first_name: Anna A full_name: Nagy-Staron, Anna A id: 3ABC5BA6-F248-11E8-B48F-1D18A9856A87 last_name: Nagy-Staron orcid: 0000-0002-1391-8377 citation: ama: Nagy-Staron AA. Sequences of gene regulatory network permutations for the article “Local genetic context shapes the function of a gene regulatory network.” 2020. doi:10.15479/AT:ISTA:8951 apa: Nagy-Staron, A. A. (2020). Sequences of gene regulatory network permutations for the article “Local genetic context shapes the function of a gene regulatory network.” Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:8951 chicago: Nagy-Staron, Anna A. “Sequences of Gene Regulatory Network Permutations for the Article ‘Local Genetic Context Shapes the Function of a Gene Regulatory Network.’” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:8951. ieee: A. A. Nagy-Staron, “Sequences of gene regulatory network permutations for the article ‘Local genetic context shapes the function of a gene regulatory network.’” Institute of Science and Technology Austria, 2020. ista: Nagy-Staron AA. 2020. Sequences of gene regulatory network permutations for the article ‘Local genetic context shapes the function of a gene regulatory network’, Institute of Science and Technology Austria, 10.15479/AT:ISTA:8951. mla: Nagy-Staron, Anna A. Sequences of Gene Regulatory Network Permutations for the Article “Local Genetic Context Shapes the Function of a Gene Regulatory Network.” Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:8951. short: A.A. Nagy-Staron, (2020). contributor: - contributor_type: project_member first_name: Anna A id: 3ABC5BA6-F248-11E8-B48F-1D18A9856A87 last_name: Nagy-Staron - contributor_type: project_member first_name: Kathrin id: 3AEC8556-F248-11E8-B48F-1D18A9856A87 last_name: Tomasek - contributor_type: project_member first_name: Caroline last_name: Caruso Carter - contributor_type: project_member first_name: Elisabeth last_name: Sonnleitner - contributor_type: project_member first_name: Bor id: 350F91D2-F248-11E8-B48F-1D18A9856A87 last_name: Kavcic orcid: 0000-0001-6041-254X - contributor_type: project_member first_name: Tiago last_name: Paixão - contributor_type: project_manager first_name: Calin C id: 47F8433E-F248-11E8-B48F-1D18A9856A87 last_name: Guet orcid: 0000-0001-6220-2052 date_created: 2020-12-20T10:00:26Z date_published: 2020-12-21T00:00:00Z date_updated: 2024-02-21T12:41:57Z day: '21' ddc: - '570' department: - _id: CaGu doi: 10.15479/AT:ISTA:8951 file: - access_level: open_access checksum: f57862aeee1690c7effd2b1117d40ed1 content_type: text/plain creator: bkavcic date_created: 2020-12-20T09:52:52Z date_updated: 2020-12-20T09:52:52Z file_id: '8952' file_name: readme.txt file_size: 523 relation: main_file success: 1 - access_level: open_access checksum: f2c6d5232ec6d551b6993991e8689e9f content_type: application/octet-stream creator: bkavcic date_created: 2020-12-20T22:01:44Z date_updated: 2020-12-20T22:01:44Z file_id: '8954' file_name: GRNs Research depository.gb file_size: 379228 relation: main_file success: 1 file_date_updated: 2020-12-20T22:01:44Z has_accepted_license: '1' keyword: - Gene regulatory networks - Gene expression - Escherichia coli - Synthetic Biology month: '12' oa: 1 oa_version: Published Version publisher: Institute of Science and Technology Austria related_material: record: - id: '9283' relation: used_in_publication status: public status: public title: Sequences of gene regulatory network permutations for the article "Local genetic context shapes the function of a gene regulatory network" 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: research_data user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2020' ... --- _id: '8955' abstract: - lang: eng text: Skeletal muscle activity is continuously modulated across physiologic states to provide coordination, flexibility and responsiveness to body tasks and external inputs. Despite the central role the muscular system plays in facilitating vital body functions, the network of brain-muscle interactions required to control hundreds of muscles and synchronize their activation in relation to distinct physiologic states has not been investigated. Recent approaches have focused on general associations between individual brain rhythms and muscle activation during movement tasks. However, the specific forms of coupling, the functional network of cortico-muscular coordination, and how network structure and dynamics are modulated by autonomic regulation across physiologic states remains unknown. To identify and quantify the cortico-muscular interaction network and uncover basic features of neuro-autonomic control of muscle function, we investigate the coupling between synchronous bursts in cortical rhythms and peripheral muscle activation during sleep and wake. Utilizing the concept of time delay stability and a novel network physiology approach, we find that the brain-muscle network exhibits complex dynamic patterns of communication involving multiple brain rhythms across cortical locations and different electromyographic frequency bands. Moreover, our results show that during each physiologic state the cortico-muscular network is characterized by a specific profile of network links strength, where particular brain rhythms play role of main mediators of interaction and control. Further, we discover a hierarchical reorganization in network structure across physiologic states, with high connectivity and network link strength during wake, intermediate during REM and light sleep, and low during deep sleep, a sleep-stage stratification that demonstrates a unique association between physiologic states and cortico-muscular network structure. The reported empirical observations are consistent across individual subjects, indicating universal behavior in network structure and dynamics, and high sensitivity of cortico-muscular control to changes in autonomic regulation, even at low levels of physical activity and muscle tone during sleep. Our findings demonstrate previously unrecognized basic principles of brain-muscle network communication and control, and provide new perspectives on the regulatory mechanisms of brain dynamics and locomotor activation, with potential clinical implications for neurodegenerative, movement and sleep disorders, and for developing efficient treatment strategies. acknowledgement: We acknowledge support from the W. M. Keck Foundation, National Institutes of Health (NIH Grant 1R01-HL098437), the US-Israel Binational Science Foundation (BSF Grant 2012219), and the Office of Naval Research (ONR Grant 000141010078). FL acknowledges support also from the European Union's Horizon 2020 research and innovation program under the Marie Sklodowska-Curie Grant Agreement No. 754411. article_number: '558070' article_processing_charge: No article_type: original author: - first_name: Rossella full_name: Rizzo, Rossella last_name: Rizzo - first_name: Xiyun full_name: Zhang, Xiyun last_name: Zhang - first_name: Jilin W.J.L. full_name: Wang, Jilin W.J.L. last_name: Wang - first_name: Fabrizio full_name: Lombardi, Fabrizio id: A057D288-3E88-11E9-986D-0CF4E5697425 last_name: Lombardi orcid: 0000-0003-2623-5249 - first_name: Plamen Ch full_name: Ivanov, Plamen Ch last_name: Ivanov citation: ama: Rizzo R, Zhang X, Wang JWJL, Lombardi F, Ivanov PC. Network physiology of cortico–muscular interactions. Frontiers in Physiology. 2020;11. doi:10.3389/fphys.2020.558070 apa: Rizzo, R., Zhang, X., Wang, J. W. J. L., Lombardi, F., & Ivanov, P. C. (2020). Network physiology of cortico–muscular interactions. Frontiers in Physiology. Frontiers. https://doi.org/10.3389/fphys.2020.558070 chicago: Rizzo, Rossella, Xiyun Zhang, Jilin W.J.L. Wang, Fabrizio Lombardi, and Plamen Ch Ivanov. “Network Physiology of Cortico–Muscular Interactions.” Frontiers in Physiology. Frontiers, 2020. https://doi.org/10.3389/fphys.2020.558070. ieee: R. Rizzo, X. Zhang, J. W. J. L. Wang, F. Lombardi, and P. C. Ivanov, “Network physiology of cortico–muscular interactions,” Frontiers in Physiology, vol. 11. Frontiers, 2020. ista: Rizzo R, Zhang X, Wang JWJL, Lombardi F, Ivanov PC. 2020. Network physiology of cortico–muscular interactions. Frontiers in Physiology. 11, 558070. mla: Rizzo, Rossella, et al. “Network Physiology of Cortico–Muscular Interactions.” Frontiers in Physiology, vol. 11, 558070, Frontiers, 2020, doi:10.3389/fphys.2020.558070. short: R. Rizzo, X. Zhang, J.W.J.L. Wang, F. Lombardi, P.C. Ivanov, Frontiers in Physiology 11 (2020). date_created: 2020-12-20T23:01:18Z date_published: 2020-11-26T00:00:00Z date_updated: 2023-08-24T11:00:45Z day: '26' ddc: - '570' department: - _id: GaTk doi: 10.3389/fphys.2020.558070 ec_funded: 1 external_id: isi: - '000596849400001' pmid: - '33324233' file: - access_level: open_access checksum: ef9515b28c5619b7126c0f347958bcb3 content_type: application/pdf creator: dernst date_created: 2020-12-21T10:37:50Z date_updated: 2020-12-21T10:37:50Z file_id: '8961' file_name: 2020_Frontiers_Rizzo.pdf file_size: 13380030 relation: main_file success: 1 file_date_updated: 2020-12-21T10:37:50Z has_accepted_license: '1' intvolume: ' 11' isi: 1 language: - iso: eng month: '11' oa: 1 oa_version: Published Version pmid: 1 project: - _id: 260C2330-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '754411' name: ISTplus - Postdoctoral Fellowships publication: Frontiers in Physiology publication_identifier: eissn: - 1664042X publication_status: published publisher: Frontiers quality_controlled: '1' scopus_import: '1' status: public title: Network physiology of cortico–muscular interactions tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 11 year: '2020' ... --- _id: '8957' abstract: - lang: eng text: Global tissue tension anisotropy has been shown to trigger stereotypical cell division orientation by elongating mitotic cells along the main tension axis. Yet, how tissue tension elongates mitotic cells despite those cells undergoing mitotic rounding (MR) by globally upregulating cortical actomyosin tension remains unclear. We addressed this question by taking advantage of ascidian embryos, consisting of a small number of interphasic and mitotic blastomeres and displaying an invariant division pattern. We found that blastomeres undergo MR by locally relaxing cortical tension at their apex, thereby allowing extrinsic pulling forces from neighboring interphasic blastomeres to polarize their shape and thus division orientation. Consistently, interfering with extrinsic forces by reducing the contractility of interphasic blastomeres or disrupting the establishment of asynchronous mitotic domains leads to aberrant mitotic cell division orientations. Thus, apical relaxation during MR constitutes a key mechanism by which tissue tension anisotropy controls stereotypical cell division orientation. acknowledged_ssus: - _id: Bio - _id: NanoFab acknowledgement: 'We thank members of the Heisenberg and McDougall groups for technical advice and discussion, Hitoyoshi Yasuo for sharing lab equipment, Lucas Leclère and Hitoyoshi Yasuo for their comments on a preliminary version of the manuscript, and Philippe Dru for the Rose plots. We are grateful to the Bioimaging and Nanofabrication facilities of IST Austria and the Imaging Platform (PIM) and animal facility (CRB) of Institut de la Mer de Villefranche (IMEV), which is supported by EMBRC-France, whose French state funds are managed by the ANR within the Investments of the Future program under reference ANR-10-INBS-0, for continuous support. This work was supported by a grant from the French Government funding agency Agence National de la Recherche (ANR “MorCell”: ANR-17-CE 13-002 8).' article_processing_charge: No article_type: original author: - first_name: Benoit G full_name: Godard, Benoit G id: 33280250-F248-11E8-B48F-1D18A9856A87 last_name: Godard - first_name: Rémi full_name: Dumollard, Rémi last_name: Dumollard - first_name: Edwin full_name: Munro, Edwin last_name: Munro - first_name: Janet full_name: Chenevert, Janet last_name: Chenevert - first_name: Céline full_name: Hebras, Céline last_name: Hebras - first_name: Alex full_name: Mcdougall, Alex last_name: Mcdougall - first_name: Carl-Philipp J full_name: Heisenberg, Carl-Philipp J id: 39427864-F248-11E8-B48F-1D18A9856A87 last_name: Heisenberg orcid: 0000-0002-0912-4566 citation: ama: Godard BG, Dumollard R, Munro E, et al. Apical relaxation during mitotic rounding promotes tension-oriented cell division. Developmental Cell. 2020;55(6):695-706. doi:10.1016/j.devcel.2020.10.016 apa: Godard, B. G., Dumollard, R., Munro, E., Chenevert, J., Hebras, C., Mcdougall, A., & Heisenberg, C.-P. J. (2020). Apical relaxation during mitotic rounding promotes tension-oriented cell division. Developmental Cell. Elsevier. https://doi.org/10.1016/j.devcel.2020.10.016 chicago: Godard, Benoit G, Rémi Dumollard, Edwin Munro, Janet Chenevert, Céline Hebras, Alex Mcdougall, and Carl-Philipp J Heisenberg. “Apical Relaxation during Mitotic Rounding Promotes Tension-Oriented Cell Division.” Developmental Cell. Elsevier, 2020. https://doi.org/10.1016/j.devcel.2020.10.016. ieee: B. G. Godard et al., “Apical relaxation during mitotic rounding promotes tension-oriented cell division,” Developmental Cell, vol. 55, no. 6. Elsevier, pp. 695–706, 2020. ista: Godard BG, Dumollard R, Munro E, Chenevert J, Hebras C, Mcdougall A, Heisenberg C-PJ. 2020. Apical relaxation during mitotic rounding promotes tension-oriented cell division. Developmental Cell. 55(6), 695–706. mla: Godard, Benoit G., et al. “Apical Relaxation during Mitotic Rounding Promotes Tension-Oriented Cell Division.” Developmental Cell, vol. 55, no. 6, Elsevier, 2020, pp. 695–706, doi:10.1016/j.devcel.2020.10.016. short: B.G. Godard, R. Dumollard, E. Munro, J. Chenevert, C. Hebras, A. Mcdougall, C.-P.J. Heisenberg, Developmental Cell 55 (2020) 695–706. date_created: 2020-12-20T23:01:19Z date_published: 2020-12-21T00:00:00Z date_updated: 2023-08-24T11:01:22Z day: '21' department: - _id: CaHe doi: 10.1016/j.devcel.2020.10.016 external_id: isi: - '000600665700008' pmid: - '33207225' intvolume: ' 55' isi: 1 issue: '6' language: - iso: eng month: '12' oa_version: None page: 695-706 pmid: 1 publication: Developmental Cell publication_identifier: eissn: - '18781551' issn: - '15345807' publication_status: published publisher: Elsevier quality_controlled: '1' related_material: link: - description: News on IST Homepage relation: press_release url: https://ist.ac.at/en/news/relaxing-cell-divisions/ scopus_import: '1' status: public title: Apical relaxation during mitotic rounding promotes tension-oriented cell division type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 55 year: '2020' ... --- _id: '8958' abstract: - lang: eng text: "The oft-quoted dictum by Arthur Schawlow: ``A diatomic molecule has one atom too many'' has been disavowed. Inspired by the possibility to experimentally manipulate and enhance chemical reactivity in helium nanodroplets, we investigate the rotation of coupled cold molecules in the presence of a many-body environment.\r\nIn this thesis, we introduce new variational approaches to quantum impurities and apply them to the Fröhlich polaron - a quasiparticle formed out of an electron (or other point-like impurity) in a polar medium, and to the angulon - a quasiparticle formed out of a rotating molecule in a bosonic bath.\r\nWith this theoretical toolbox, we reveal the self-localization transition for the angulon quasiparticle. We show that, unlike for polarons, self-localization of angulons occurs at finite impurity-bath coupling already at the mean-field level. The transition is accompanied by the spherical-symmetry breaking of the angulon ground state and a discontinuity in the first derivative of the ground-state energy. Moreover, the type of symmetry breaking is dictated by the symmetry of the microscopic impurity-bath interaction, which leads to a number of distinct self-localized states. \r\nFor the system containing multiple impurities, by analogy with the bipolaron, we introduce the biangulon quasiparticle describing two rotating molecules that align with respect to each other due to the effective attractive interaction mediated by the excitations of the bath. We study this system from the strong-coupling regime to the weak molecule-bath interaction regime. We show that the molecules tend to have a strong alignment in the ground state, the biangulon shows shifted angulon instabilities and an additional spectral instability, where resonant angular momentum transfer between the molecules and the bath takes place. Finally, we introduce a diagonalization scheme that allows us to describe the transition from two separated angulons to a biangulon as a function of the distance between the two molecules." alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Xiang full_name: Li, Xiang id: 4B7E523C-F248-11E8-B48F-1D18A9856A87 last_name: Li citation: ama: Li X. Rotation of coupled cold molecules in the presence of a many-body environment. 2020. doi:10.15479/AT:ISTA:8958 apa: Li, X. (2020). Rotation of coupled cold molecules in the presence of a many-body environment. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:8958 chicago: Li, Xiang. “Rotation of Coupled Cold Molecules in the Presence of a Many-Body Environment.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:8958. ieee: X. Li, “Rotation of coupled cold molecules in the presence of a many-body environment,” Institute of Science and Technology Austria, 2020. ista: Li X. 2020. Rotation of coupled cold molecules in the presence of a many-body environment. Institute of Science and Technology Austria. mla: Li, Xiang. Rotation of Coupled Cold Molecules in the Presence of a Many-Body Environment. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:8958. short: X. Li, Rotation of Coupled Cold Molecules in the Presence of a Many-Body Environment, Institute of Science and Technology Austria, 2020. date_created: 2020-12-21T09:44:30Z date_published: 2020-12-21T00:00:00Z date_updated: 2024-08-07T07:16:53Z day: '21' ddc: - '539' degree_awarded: PhD department: - _id: MiLe doi: 10.15479/AT:ISTA:8958 ec_funded: 1 file: - access_level: open_access checksum: 3994c54a1241451d561db1d4f43bad30 content_type: application/pdf creator: xli date_created: 2020-12-22T10:55:56Z date_updated: 2020-12-22T10:55:56Z file_id: '8967' file_name: THESIS_Xiang_Li.pdf file_size: 3622305 relation: main_file success: 1 - access_level: closed checksum: 0954ecfc5554c05615c14de803341f00 content_type: application/x-zip-compressed creator: xli date_created: 2020-12-22T10:56:03Z date_updated: 2020-12-30T07:18:03Z file_id: '8968' file_name: THESIS_Xiang_Li.zip file_size: 4018859 relation: source_file file_date_updated: 2020-12-30T07:18:03Z has_accepted_license: '1' language: - iso: eng month: '12' oa: 1 oa_version: Published Version page: '125' project: - _id: 26031614-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P29902 name: Quantum rotations in the presence of a many-body environment - _id: 2688CF98-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '801770' name: 'Angulon: physics and applications of a new quasiparticle' publication_identifier: issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '5886' relation: part_of_dissertation status: public - id: '1120' relation: part_of_dissertation status: public - id: '8587' relation: part_of_dissertation status: public status: public supervisor: - first_name: Mikhail full_name: Lemeshko, Mikhail id: 37CB05FA-F248-11E8-B48F-1D18A9856A87 last_name: Lemeshko orcid: 0000-0002-6990-7802 title: Rotation of coupled cold molecules in the presence of a many-body environment type: dissertation user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 year: '2020' ... --- _id: '8971' abstract: - lang: eng text: The actin-related protein (Arp)2/3 complex nucleates branched actin filament networks pivotal for cell migration, endocytosis and pathogen infection. Its activation is tightly regulated and involves complex structural rearrangements and actin filament binding, which are yet to be understood. Here, we report a 9.0 Å resolution structure of the actin filament Arp2/3 complex branch junction in cells using cryo-electron tomography and subtomogram averaging. This allows us to generate an accurate model of the active Arp2/3 complex in the branch junction and its interaction with actin filaments. Notably, our model reveals a previously undescribed set of interactions of the Arp2/3 complex with the mother filament, significantly different to the previous branch junction model. Our structure also indicates a central role for the ArpC3 subunit in stabilizing the active conformation. acknowledged_ssus: - _id: ScienComp - _id: LifeSc - _id: Bio - _id: EM-Fac acknowledgement: "This research was supported by the Scientific Service Units (SSUs) of IST Austria through resources provided by Scientific Computing (SciComp), the Life Science Facility (LSF), the BioImaging Facility (BIF), and the Electron Microscopy Facility (EMF). We also thank Dimitry Tegunov (MPI for Biophysical Chemistry) for helpful discussions\r\nabout the M software, and Michael Sixt (IST Austria) and Klemens Rottner (Technical University Braunschweig, HZI Braunschweig) for critical reading of the manuscript. We also thank Gregory Voth (University of Chicago) for providing us the MD-derived branch junction model for comparison. The authors acknowledge support from IST Austria and from the Austrian Science Fund (FWF): M02495 to G.D. and Austrian Science Fund (FWF): P33367 to F.K.M.S. " article_number: '6437' article_processing_charge: No article_type: original author: - first_name: Florian full_name: Fäßler, Florian id: 404F5528-F248-11E8-B48F-1D18A9856A87 last_name: Fäßler orcid: 0000-0001-7149-769X - first_name: Georgi A full_name: Dimchev, Georgi A id: 38C393BE-F248-11E8-B48F-1D18A9856A87 last_name: Dimchev orcid: 0000-0001-8370-6161 - first_name: Victor-Valentin full_name: Hodirnau, Victor-Valentin id: 3661B498-F248-11E8-B48F-1D18A9856A87 last_name: Hodirnau - first_name: William full_name: Wan, William last_name: Wan - first_name: Florian KM full_name: Schur, Florian KM id: 48AD8942-F248-11E8-B48F-1D18A9856A87 last_name: Schur orcid: 0000-0003-4790-8078 citation: ama: Fäßler F, Dimchev GA, Hodirnau V-V, Wan W, Schur FK. Cryo-electron tomography structure of Arp2/3 complex in cells reveals new insights into the branch junction. Nature Communications. 2020;11. doi:10.1038/s41467-020-20286-x apa: Fäßler, F., Dimchev, G. A., Hodirnau, V.-V., Wan, W., & Schur, F. K. (2020). Cryo-electron tomography structure of Arp2/3 complex in cells reveals new insights into the branch junction. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-020-20286-x chicago: Fäßler, Florian, Georgi A Dimchev, Victor-Valentin Hodirnau, William Wan, and Florian KM Schur. “Cryo-Electron Tomography Structure of Arp2/3 Complex in Cells Reveals New Insights into the Branch Junction.” Nature Communications. Springer Nature, 2020. https://doi.org/10.1038/s41467-020-20286-x. ieee: F. Fäßler, G. A. Dimchev, V.-V. Hodirnau, W. Wan, and F. K. Schur, “Cryo-electron tomography structure of Arp2/3 complex in cells reveals new insights into the branch junction,” Nature Communications, vol. 11. Springer Nature, 2020. ista: Fäßler F, Dimchev GA, Hodirnau V-V, Wan W, Schur FK. 2020. Cryo-electron tomography structure of Arp2/3 complex in cells reveals new insights into the branch junction. Nature Communications. 11, 6437. mla: Fäßler, Florian, et al. “Cryo-Electron Tomography Structure of Arp2/3 Complex in Cells Reveals New Insights into the Branch Junction.” Nature Communications, vol. 11, 6437, Springer Nature, 2020, doi:10.1038/s41467-020-20286-x. short: F. Fäßler, G.A. Dimchev, V.-V. Hodirnau, W. Wan, F.K. Schur, Nature Communications 11 (2020). date_created: 2020-12-23T08:25:45Z date_published: 2020-12-22T00:00:00Z date_updated: 2023-08-24T11:01:50Z day: '22' ddc: - '570' department: - _id: FlSc - _id: EM-Fac doi: 10.1038/s41467-020-20286-x external_id: isi: - '000603078000003' file: - access_level: open_access checksum: 55d43ea0061cc4027ba45e966e1db8cc content_type: application/pdf creator: dernst date_created: 2020-12-28T08:16:10Z date_updated: 2020-12-28T08:16:10Z file_id: '8975' file_name: 2020_NatureComm_Faessler.pdf file_size: 3958727 relation: main_file success: 1 file_date_updated: 2020-12-28T08:16:10Z has_accepted_license: '1' intvolume: ' 11' isi: 1 keyword: - General Biochemistry - Genetics and Molecular Biology - General Physics and Astronomy - General Chemistry language: - iso: eng month: '12' oa: 1 oa_version: Published Version project: - _id: 9B954C5C-BA93-11EA-9121-9846C619BF3A grant_number: P33367 name: Structure and isoform diversity of the Arp2/3 complex - _id: 2674F658-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: M02495 name: Protein structure and function in filopodia across scales publication: Nature Communications publication_identifier: issn: - 2041-1723 publication_status: published publisher: Springer Nature quality_controlled: '1' related_material: link: - description: News on IST Homepage relation: press_release url: https://ist.ac.at/en/news/cutting-edge-technology-reveals-structures-within-cells/ scopus_import: '1' status: public title: Cryo-electron tomography structure of Arp2/3 complex in cells reveals new insights into the branch junction tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 11 year: '2020' ... --- _id: '8973' abstract: - lang: eng text: We consider the symmetric simple exclusion process in Zd with quenched bounded dynamic random conductances and prove its hydrodynamic limit in path space. The main tool is the connection, due to the self-duality of the process, between the invariance principle for single particles starting from all points and the macroscopic behavior of the density field. While the hydrodynamic limit at fixed macroscopic times is obtained via a generalization to the time-inhomogeneous context of the strategy introduced in [41], in order to prove tightness for the sequence of empirical density fields we develop a new criterion based on the notion of uniform conditional stochastic continuity, following [50]. In conclusion, we show that uniform elliptic dynamic conductances provide an example of environments in which the so-called arbitrary starting point invariance principle may be derived from the invariance principle of a single particle starting from the origin. Therefore, our hydrodynamics result applies to the examples of quenched environments considered in, e.g., [1], [3], [6] in combination with the hypothesis of uniform ellipticity. acknowledgement: "We warmly thank S.R.S. Varadhan for many enlightening discussions at an early stage of this work. We are indebted to Francesca Collet for fruitful discussions and constant support all throughout this work. We thank Simone Floreani\r\nand Alberto Chiarini for helpful conversations on the final part of this paper as well as both referees for their careful reading and for raising relevant issues on some weak points contained in a previous version of this manuscript; we believe this helped us to improve it.\r\nPart of this work was done during the authors’ stay at the Institut Henri Poincaré (UMS 5208 CNRS-Sorbonne Université) – Centre Emile Borel during the trimester Stochastic Dynamics Out of Equilibrium. The authors thank this institution for hospitality and support (through LabEx CARMIN, ANR-10-LABX-59-01). F.S. thanks laboratoire\r\nMAP5 of Université de Paris, and E.S. thanks Delft University, for financial support and hospitality. F.S. acknowledges NWO for financial support via the TOP1 grant 613.001.552 as well as funding from the European Union’s Horizon 2020 research and innovation programme under the Marie-Skłodowska-Curie grant agreement No. 754411. This research has been conducted within the FP2M federation (CNRS FR 2036)." article_number: '138' article_processing_charge: No article_type: original arxiv: 1 author: - first_name: Frank full_name: Redig, Frank last_name: Redig - first_name: Ellen full_name: Saada, Ellen last_name: Saada - first_name: Federico full_name: Sau, Federico id: E1836206-9F16-11E9-8814-AEFDE5697425 last_name: Sau citation: ama: 'Redig F, Saada E, Sau F. Symmetric simple exclusion process in dynamic environment: Hydrodynamics. Electronic Journal of Probability. 2020;25. doi:10.1214/20-EJP536' apa: 'Redig, F., Saada, E., & Sau, F. (2020). Symmetric simple exclusion process in dynamic environment: Hydrodynamics. Electronic Journal of Probability. Institute of Mathematical Statistics. https://doi.org/10.1214/20-EJP536' chicago: 'Redig, Frank, Ellen Saada, and Federico Sau. “Symmetric Simple Exclusion Process in Dynamic Environment: Hydrodynamics.” Electronic Journal of Probability. Institute of Mathematical Statistics, 2020. https://doi.org/10.1214/20-EJP536.' ieee: 'F. Redig, E. Saada, and F. Sau, “Symmetric simple exclusion process in dynamic environment: Hydrodynamics,” Electronic Journal of Probability, vol. 25. Institute of Mathematical Statistics, 2020.' ista: 'Redig F, Saada E, Sau F. 2020. Symmetric simple exclusion process in dynamic environment: Hydrodynamics. Electronic Journal of Probability. 25, 138.' mla: 'Redig, Frank, et al. “Symmetric Simple Exclusion Process in Dynamic Environment: Hydrodynamics.” Electronic Journal of Probability, vol. 25, 138, Institute of Mathematical Statistics, 2020, doi:10.1214/20-EJP536.' short: F. Redig, E. Saada, F. Sau, Electronic Journal of Probability 25 (2020). date_created: 2020-12-27T23:01:17Z date_published: 2020-10-21T00:00:00Z date_updated: 2023-10-17T12:51:56Z day: '21' ddc: - '510' department: - _id: JaMa doi: 10.1214/20-EJP536 ec_funded: 1 external_id: arxiv: - '1811.01366' isi: - '000591737500001' file: - access_level: open_access checksum: d75359b9814e78d57c0a481b7cde3751 content_type: application/pdf creator: dernst date_created: 2020-12-28T08:24:08Z date_updated: 2020-12-28T08:24:08Z file_id: '8976' file_name: 2020_ElectronJProbab_Redig.pdf file_size: 696653 relation: main_file success: 1 file_date_updated: 2020-12-28T08:24:08Z has_accepted_license: '1' intvolume: ' 25' isi: 1 language: - iso: eng month: '10' oa: 1 oa_version: Published Version project: - _id: 260C2330-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '754411' name: ISTplus - Postdoctoral Fellowships publication: Electronic Journal of Probability publication_identifier: eissn: - 1083-6489 publication_status: published publisher: ' Institute of Mathematical Statistics' quality_controlled: '1' scopus_import: '1' status: public title: 'Symmetric simple exclusion process in dynamic environment: Hydrodynamics' type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 25 year: '2020' ... --- _id: '8978' abstract: - lang: eng text: "Mosaic analysis with double markers (MADM) technology enables concomitant fluorescent cell labeling and induction of uniparental chromosome disomy (UPD) with single-cell resolution. In UPD, imprinted genes are either overexpressed 2-fold or are not expressed. Here, the MADM platform is utilized to probe imprinting phenotypes at the transcriptional level. This protocol highlights major steps for the generation and isolation of projection neurons and astrocytes with MADM-induced UPD from mouse cerebral cortex for downstream single-cell and low-input sample RNA-sequencing experiments.\r\n\r\nFor complete details on the use and execution of this protocol, please refer to Laukoter et al. (2020b)." acknowledged_ssus: - _id: Bio - _id: PreCl acknowledgement: This research was supported by the Scientific Service Units (SSU) at IST Austria through resources provided by the Bioimaging (BIF) and Preclinical Facilities (PCF). N.A received support from the FWF Firnberg-Programm (T 1031). This work was also supported by IST Austria institutional funds; FWF SFB F78 to S.H.; NÖ Forschung und Bildung n[f+b] life science call grant (C13-002) to S.H.; the People Programme (Marie Curie Actions) of the European Union’s Seventh Framework Programme (FP7/2007-2013) under REA grant agreement no. 618444 to S.H.; and the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement no. 725780 LinPro) to S.H. article_number: '100215' article_processing_charge: No article_type: original author: - first_name: Susanne full_name: Laukoter, Susanne id: 2D6B7A9A-F248-11E8-B48F-1D18A9856A87 last_name: Laukoter - first_name: Nicole full_name: Amberg, Nicole id: 4CD6AAC6-F248-11E8-B48F-1D18A9856A87 last_name: Amberg orcid: 0000-0002-3183-8207 - first_name: Florian full_name: Pauler, Florian id: 48EA0138-F248-11E8-B48F-1D18A9856A87 last_name: Pauler - first_name: Simon full_name: Hippenmeyer, Simon id: 37B36620-F248-11E8-B48F-1D18A9856A87 last_name: Hippenmeyer orcid: 0000-0003-2279-1061 citation: ama: Laukoter S, Amberg N, Pauler F, Hippenmeyer S. Generation and isolation of single cells from mouse brain with mosaic analysis with double markers-induced uniparental chromosome disomy. STAR Protocols. 2020;1(3). doi:10.1016/j.xpro.2020.100215 apa: Laukoter, S., Amberg, N., Pauler, F., & Hippenmeyer, S. (2020). Generation and isolation of single cells from mouse brain with mosaic analysis with double markers-induced uniparental chromosome disomy. STAR Protocols. Elsevier. https://doi.org/10.1016/j.xpro.2020.100215 chicago: Laukoter, Susanne, Nicole Amberg, Florian Pauler, and Simon Hippenmeyer. “Generation and Isolation of Single Cells from Mouse Brain with Mosaic Analysis with Double Markers-Induced Uniparental Chromosome Disomy.” STAR Protocols. Elsevier, 2020. https://doi.org/10.1016/j.xpro.2020.100215. ieee: S. Laukoter, N. Amberg, F. Pauler, and S. Hippenmeyer, “Generation and isolation of single cells from mouse brain with mosaic analysis with double markers-induced uniparental chromosome disomy,” STAR Protocols, vol. 1, no. 3. Elsevier, 2020. ista: Laukoter S, Amberg N, Pauler F, Hippenmeyer S. 2020. Generation and isolation of single cells from mouse brain with mosaic analysis with double markers-induced uniparental chromosome disomy. STAR Protocols. 1(3), 100215. mla: Laukoter, Susanne, et al. “Generation and Isolation of Single Cells from Mouse Brain with Mosaic Analysis with Double Markers-Induced Uniparental Chromosome Disomy.” STAR Protocols, vol. 1, no. 3, 100215, Elsevier, 2020, doi:10.1016/j.xpro.2020.100215. short: S. Laukoter, N. Amberg, F. Pauler, S. Hippenmeyer, STAR Protocols 1 (2020). date_created: 2020-12-30T10:17:07Z date_published: 2020-12-18T00:00:00Z date_updated: 2021-01-12T08:21:36Z day: '18' ddc: - '570' department: - _id: SiHi doi: 10.1016/j.xpro.2020.100215 ec_funded: 1 external_id: pmid: - '33377108' file: - access_level: open_access checksum: f1e9a433e9cb0f41f7b6df6b76db1f6e content_type: application/pdf creator: dernst date_created: 2021-01-07T15:57:27Z date_updated: 2021-01-07T15:57:27Z file_id: '8996' file_name: 2020_STARProtocols_Laukoter.pdf file_size: 4031449 relation: main_file success: 1 file_date_updated: 2021-01-07T15:57:27Z has_accepted_license: '1' intvolume: ' 1' issue: '3' language: - iso: eng month: '12' oa: 1 oa_version: Published Version pmid: 1 project: - _id: 268F8446-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: T0101031 name: Role of Eed in neural stem cell lineage progression - _id: 059F6AB4-7A3F-11EA-A408-12923DDC885E grant_number: F07805 name: Molecular Mechanisms of Neural Stem Cell Lineage Progression - _id: 25D92700-B435-11E9-9278-68D0E5697425 grant_number: LS13-002 name: Mapping Cell-Type Specificity of the Genomic Imprintome in the Brain - _id: 25D61E48-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '618444' name: Molecular Mechanisms of Cerebral Cortex Development - _id: 260018B0-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '725780' name: Principles of Neural Stem Cell Lineage Progression in Cerebral Cortex Development publication: STAR Protocols publication_identifier: issn: - 2666-1667 publication_status: published publisher: Elsevier quality_controlled: '1' status: public title: Generation and isolation of single cells from mouse brain with mosaic analysis with double markers-induced uniparental chromosome disomy 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: 1 year: '2020' ... --- _id: '8983' abstract: - lang: eng text: Metabolic adaptation is a critical feature of migrating cells. It tunes the metabolic programs of migrating cells to allow them to efficiently exert their crucial roles in development, inflammatory responses and tumor metastasis. Cell migration through physically challenging contexts requires energy. However, how the metabolic reprogramming that underlies in vivo cell invasion is controlled is still unanswered. In my PhD project, I identify a novel conserved metabolic shift in Drosophila melanogaster immune cells that by modulating their bioenergetic potential controls developmentally programmed tissue invasion. We show that this regulation requires a novel conserved nuclear protein, named Atossa. Atossa enhances the transcription of a set of proteins, including an RNA helicase Porthos and two metabolic enzymes, each of which increases the tissue invasion of leading Drosophila macrophages and can rescue the atossa mutant phenotype. Porthos selectively regulates the translational efficiency of a subset of mRNAs containing a 5’-UTR cis-regulatory TOP-like sequence. These 5’TOPL mRNA targets encode mitochondrial-related proteins, including subunits of mitochondrial oxidative phosphorylation (OXPHOS) components III and V and other metabolic-related proteins. Porthos powers up mitochondrial OXPHOS to engender a sufficient ATP supply, which is required for tissue invasion of leading macrophages. Atossa’s two vertebrate orthologs rescue the invasion defect. In my PhD project, I elucidate that Atossa displays a conserved developmental metabolic control to modulate metabolic capacities and the cellular energy state, through altered transcription and translation, to aid the tissue infiltration of leading cells into energy demanding barriers. acknowledged_ssus: - _id: Bio - _id: LifeSc - _id: E-Lib - _id: CampIT acknowledgement: Also, I would like to express my appreciation and thanks to the Bioimaging facility, LSF, GSO, library, and IT people at IST Austria. alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Shamsi full_name: Emtenani, Shamsi id: 49D32318-F248-11E8-B48F-1D18A9856A87 last_name: Emtenani orcid: 0000-0001-6981-6938 citation: ama: Emtenani S. Metabolic regulation of Drosophila macrophage tissue invasion. 2020. doi:10.15479/AT:ISTA:8983 apa: Emtenani, S. (2020). Metabolic regulation of Drosophila macrophage tissue invasion. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:8983 chicago: Emtenani, Shamsi. “Metabolic Regulation of Drosophila Macrophage Tissue Invasion.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:8983. ieee: S. Emtenani, “Metabolic regulation of Drosophila macrophage tissue invasion,” Institute of Science and Technology Austria, 2020. ista: Emtenani S. 2020. Metabolic regulation of Drosophila macrophage tissue invasion. Institute of Science and Technology Austria. mla: Emtenani, Shamsi. Metabolic Regulation of Drosophila Macrophage Tissue Invasion. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:8983. short: S. Emtenani, Metabolic Regulation of Drosophila Macrophage Tissue Invasion, Institute of Science and Technology Austria, 2020. date_created: 2020-12-30T15:41:26Z date_published: 2020-12-30T00:00:00Z date_updated: 2023-09-07T13:24:17Z day: '30' ddc: - '570' degree_awarded: PhD department: - _id: DaSi doi: 10.15479/AT:ISTA:8983 file: - access_level: open_access checksum: ec2797ab7a6f253b35df0572b36d1b43 content_type: application/pdf creator: semtenan date_created: 2020-12-30T15:34:01Z date_updated: 2021-12-31T23:30:04Z embargo: 2021-12-30 file_id: '8984' file_name: Thesis_Shamsi_Emtenani_pdfA.pdf file_size: 10848175 relation: main_file - access_level: closed checksum: cc30e6608a9815414024cf548dff3b3a content_type: application/pdf creator: semtenan date_created: 2020-12-30T15:37:36Z date_updated: 2021-12-31T23:30:04Z embargo_to: open_access file_id: '8985' file_name: Thesis_Shamsi_Emtenani_source file.pdf file_size: 10073648 relation: source_file file_date_updated: 2021-12-31T23:30:04Z has_accepted_license: '1' language: - iso: eng month: '12' oa: 1 oa_version: Published Version page: '141' publication_identifier: issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '8557' relation: part_of_dissertation status: public - id: '6187' relation: part_of_dissertation status: public status: public supervisor: - first_name: Daria E full_name: Siekhaus, Daria E id: 3D224B9E-F248-11E8-B48F-1D18A9856A87 last_name: Siekhaus orcid: 0000-0001-8323-8353 title: Metabolic regulation of Drosophila macrophage tissue invasion type: dissertation user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 year: '2020' ... --- _id: '8986' abstract: - lang: eng text: 'Flowering plants display the highest diversity among plant species and have notably shaped terrestrial landscapes. Nonetheless, the evolutionary origin of their unprecedented morphological complexity remains largely an enigma. Here, we show that the coevolution of cis-regulatory and coding regions of PIN-FORMED (PIN) auxin transporters confined their expression to certain cell types and directed their subcellular localization to particular cell sides, which together enabled dynamic auxin gradients across tissues critical to the complex architecture of flowering plants. Extensive intraspecies and interspecies genetic complementation experiments with PINs from green alga up to flowering plant lineages showed that PIN genes underwent three subsequent, critical evolutionary innovations and thus acquired a triple function to regulate the development of three essential components of the flowering plant Arabidopsis: shoot/root, inflorescence, and floral organ. Our work highlights the critical role of functional innovations within the PIN gene family as essential prerequisites for the origin of flowering plants.' acknowledgement: 'We thank C.Löhne (Botanic Gardens, University of Bonn) for providing us with A. trichopoda. We would like to thank T.Han, A.Mally (IST, Austria), and C.Hartinger (University of Oxford) for constructive comment and careful reading. Funding: The research leading to these results has received funding from the European Union’s Horizon 2020 Research and Innovation Programme (ERC grant agreement number 742985), Austrian Science Fund (FWF, grant number I 3630-B25), DOC Fellowship of the Austrian Academy of Sciences, and IST Fellow program. ' article_number: eabc8895 article_processing_charge: No article_type: original author: - first_name: Yuzhou full_name: Zhang, Yuzhou id: 3B6137F2-F248-11E8-B48F-1D18A9856A87 last_name: Zhang orcid: 0000-0003-2627-6956 - first_name: Lesia full_name: Rodriguez Solovey, Lesia id: 3922B506-F248-11E8-B48F-1D18A9856A87 last_name: Rodriguez Solovey orcid: 0000-0002-7244-7237 - first_name: Lanxin full_name: Li, Lanxin id: 367EF8FA-F248-11E8-B48F-1D18A9856A87 last_name: Li orcid: 0000-0002-5607-272X - first_name: Xixi full_name: Zhang, Xixi id: 61A66458-47E9-11EA-85BA-8AEAAF14E49A last_name: Zhang orcid: 0000-0001-7048-4627 - first_name: Jiří full_name: Friml, Jiří id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 citation: ama: Zhang Y, Rodriguez Solovey L, Li L, Zhang X, Friml J. Functional innovations of PIN auxin transporters mark crucial evolutionary transitions during rise of flowering plants. Science Advances. 2020;6(50). doi:10.1126/sciadv.abc8895 apa: Zhang, Y., Rodriguez Solovey, L., Li, L., Zhang, X., & Friml, J. (2020). Functional innovations of PIN auxin transporters mark crucial evolutionary transitions during rise of flowering plants. Science Advances. AAAS. https://doi.org/10.1126/sciadv.abc8895 chicago: Zhang, Yuzhou, Lesia Rodriguez Solovey, Lanxin Li, Xixi Zhang, and Jiří Friml. “Functional Innovations of PIN Auxin Transporters Mark Crucial Evolutionary Transitions during Rise of Flowering Plants.” Science Advances. AAAS, 2020. https://doi.org/10.1126/sciadv.abc8895. ieee: Y. Zhang, L. Rodriguez Solovey, L. Li, X. Zhang, and J. Friml, “Functional innovations of PIN auxin transporters mark crucial evolutionary transitions during rise of flowering plants,” Science Advances, vol. 6, no. 50. AAAS, 2020. ista: Zhang Y, Rodriguez Solovey L, Li L, Zhang X, Friml J. 2020. Functional innovations of PIN auxin transporters mark crucial evolutionary transitions during rise of flowering plants. Science Advances. 6(50), eabc8895. mla: Zhang, Yuzhou, et al. “Functional Innovations of PIN Auxin Transporters Mark Crucial Evolutionary Transitions during Rise of Flowering Plants.” Science Advances, vol. 6, no. 50, eabc8895, AAAS, 2020, doi:10.1126/sciadv.abc8895. short: Y. Zhang, L. Rodriguez Solovey, L. Li, X. Zhang, J. Friml, Science Advances 6 (2020). date_created: 2021-01-03T23:01:23Z date_published: 2020-12-11T00:00:00Z date_updated: 2024-10-29T10:22:43Z day: '11' ddc: - '580' department: - _id: JiFr doi: 10.1126/sciadv.abc8895 ec_funded: 1 external_id: isi: - '000599903600014' pmid: - '33310852' file: - access_level: open_access checksum: 5ac2500b191c08ef6dab5327f40ff663 content_type: application/pdf creator: dernst date_created: 2021-01-07T12:44:33Z date_updated: 2021-01-07T12:44:33Z file_id: '8994' file_name: 2020_ScienceAdvances_Zhang.pdf file_size: 10578145 relation: main_file success: 1 file_date_updated: 2021-01-07T12:44:33Z has_accepted_license: '1' intvolume: ' 6' isi: 1 issue: '50' language: - iso: eng month: '12' oa: 1 oa_version: Published Version pmid: 1 project: - _id: 261099A6-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '742985' name: Tracing Evolution of Auxin Transport and Polarity in Plants - _id: 26538374-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: I03630 name: Molecular mechanisms of endocytic cargo recognition in plants - _id: 26B4D67E-B435-11E9-9278-68D0E5697425 grant_number: '25351' name: 'A Case Study of Plant Growth Regulation: Molecular Mechanism of Auxin-mediated Rapid Growth Inhibition in Arabidopsis Root' publication: Science Advances publication_identifier: eissn: - 2375-2548 publication_status: published publisher: AAAS quality_controlled: '1' related_material: record: - id: '10083' relation: dissertation_contains status: public scopus_import: '1' status: public title: Functional innovations of PIN auxin transporters mark crucial evolutionary transitions during rise of flowering plants tmp: image: /images/cc_by_nc.png legal_code_url: https://creativecommons.org/licenses/by-nc/4.0/legalcode name: Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0) short: CC BY-NC (4.0) type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 6 year: '2020' ... --- _id: '8987' abstract: - lang: eng text: "Currently several projects aim at designing and implementing protocols for privacy preserving automated contact tracing to help fight the current pandemic. Those proposal are quite similar, and in their most basic form basically propose an app for mobile phones which broadcasts frequently changing pseudorandom identifiers via (low energy) Bluetooth, and at the same time, the app stores IDs broadcast by phones in its proximity. Only if a user is tested positive, they upload either the beacons they did broadcast (which is the case in decentralized proposals as DP-3T, east and west coast PACT or Covid watch) or received (as in Popp-PT or ROBERT) during the last two weeks or so.\r\n\r\nVaudenay [eprint 2020/399] observes that this basic scheme (he considers the DP-3T proposal) succumbs to relay and even replay attacks, and proposes more complex interactive schemes which prevent those attacks without giving up too many privacy aspects. Unfortunately interaction is problematic for this application for efficiency and security reasons. The countermeasures that have been suggested so far are either not practical or give up on key privacy aspects. We propose a simple non-interactive variant of the basic protocol that\r\n(security) Provably prevents replay and (if location data is available) relay attacks.\r\n(privacy) The data of all parties (even jointly) reveals no information on the location or time where encounters happened.\r\n(efficiency) The broadcasted message can fit into 128 bits and uses only basic crypto (commitments and secret key authentication).\r\n\r\nTowards this end we introduce the concept of “delayed authentication”, which basically is a message authentication code where verification can be done in two steps, where the first doesn’t require the key, and the second doesn’t require the message." article_processing_charge: No author: - first_name: Krzysztof Z full_name: Pietrzak, Krzysztof Z id: 3E04A7AA-F248-11E8-B48F-1D18A9856A87 last_name: Pietrzak orcid: 0000-0002-9139-1654 citation: ama: 'Pietrzak KZ. Delayed authentication: Preventing replay and relay attacks in private contact tracing. In: Progress in Cryptology. Vol 12578. LNCS. Springer Nature; 2020:3-15. doi:10.1007/978-3-030-65277-7_1' apa: 'Pietrzak, K. Z. (2020). Delayed authentication: Preventing replay and relay attacks in private contact tracing. In Progress in Cryptology (Vol. 12578, pp. 3–15). Bangalore, India: Springer Nature. https://doi.org/10.1007/978-3-030-65277-7_1' chicago: 'Pietrzak, Krzysztof Z. “Delayed Authentication: Preventing Replay and Relay Attacks in Private Contact Tracing.” In Progress in Cryptology, 12578:3–15. LNCS. Springer Nature, 2020. https://doi.org/10.1007/978-3-030-65277-7_1.' ieee: 'K. Z. Pietrzak, “Delayed authentication: Preventing replay and relay attacks in private contact tracing,” in Progress in Cryptology, Bangalore, India, 2020, vol. 12578, pp. 3–15.' ista: 'Pietrzak KZ. 2020. Delayed authentication: Preventing replay and relay attacks in private contact tracing. Progress in Cryptology. INDOCRYPT: International Conference on Cryptology in IndiaLNCS vol. 12578, 3–15.' mla: 'Pietrzak, Krzysztof Z. “Delayed Authentication: Preventing Replay and Relay Attacks in Private Contact Tracing.” Progress in Cryptology, vol. 12578, Springer Nature, 2020, pp. 3–15, doi:10.1007/978-3-030-65277-7_1.' short: K.Z. Pietrzak, in:, Progress in Cryptology, Springer Nature, 2020, pp. 3–15. conference: end_date: 2020-12-16 location: Bangalore, India name: 'INDOCRYPT: International Conference on Cryptology in India' start_date: 2020-12-13 date_created: 2021-01-03T23:01:23Z date_published: 2020-12-08T00:00:00Z date_updated: 2023-08-24T11:08:58Z day: '08' department: - _id: KrPi doi: 10.1007/978-3-030-65277-7_1 ec_funded: 1 external_id: isi: - '000927592800001' intvolume: ' 12578' isi: 1 language: - iso: eng main_file_link: - open_access: '1' url: https://eprint.iacr.org/2020/418 month: '12' oa: 1 oa_version: Preprint page: 3-15 project: - _id: 258AA5B2-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '682815' name: Teaching Old Crypto New Tricks publication: Progress in Cryptology publication_identifier: eissn: - '16113349' isbn: - '9783030652760' issn: - '03029743' publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' series_title: LNCS status: public title: 'Delayed authentication: Preventing replay and relay attacks in private contact tracing' type: conference user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 12578 year: '2020' ... --- _id: '9000' abstract: - lang: eng text: 'In prokaryotes, thermodynamic models of gene regulation provide a highly quantitative mapping from promoter sequences to gene-expression levels that is compatible with in vivo and in vitro biophysical measurements. Such concordance has not been achieved for models of enhancer function in eukaryotes. In equilibrium models, it is difficult to reconcile the reported short transcription factor (TF) residence times on the DNA with the high specificity of regulation. In nonequilibrium models, progress is difficult due to an explosion in the number of parameters. Here, we navigate this complexity by looking for minimal nonequilibrium enhancer models that yield desired regulatory phenotypes: low TF residence time, high specificity, and tunable cooperativity. We find that a single extra parameter, interpretable as the “linking rate,” by which bound TFs interact with Mediator components, enables our models to escape equilibrium bounds and access optimal regulatory phenotypes, while remaining consistent with the reported phenomenology and simple enough to be inferred from upcoming experiments. We further find that high specificity in nonequilibrium models is in a trade-off with gene-expression noise, predicting bursty dynamics—an experimentally observed hallmark of eukaryotic transcription. By drastically reducing the vast parameter space of nonequilibrium enhancer models to a much smaller subspace that optimally realizes biological function, we deliver a rich class of models that could be tractably inferred from data in the near future.' acknowledgement: G.T. was supported by Human Frontiers Science Program Grant RGP0034/2018. R.G. was supported by the Austrian Academy of Sciences DOC Fellowship. R.G. thanks S. Avvakumov for helpful discussions. article_processing_charge: No article_type: original author: - first_name: Rok full_name: Grah, Rok id: 483E70DE-F248-11E8-B48F-1D18A9856A87 last_name: Grah orcid: 0000-0003-2539-3560 - first_name: Benjamin full_name: Zoller, Benjamin last_name: Zoller - first_name: Gašper full_name: Tkačik, Gašper id: 3D494DCA-F248-11E8-B48F-1D18A9856A87 last_name: Tkačik orcid: 0000-0002-6699-1455 citation: ama: Grah R, Zoller B, Tkačik G. Nonequilibrium models of optimal enhancer function. PNAS. 2020;117(50):31614-31622. doi:10.1073/pnas.2006731117 apa: Grah, R., Zoller, B., & Tkačik, G. (2020). Nonequilibrium models of optimal enhancer function. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.2006731117 chicago: Grah, Rok, Benjamin Zoller, and Gašper Tkačik. “Nonequilibrium Models of Optimal Enhancer Function.” PNAS. National Academy of Sciences, 2020. https://doi.org/10.1073/pnas.2006731117. ieee: R. Grah, B. Zoller, and G. Tkačik, “Nonequilibrium models of optimal enhancer function,” PNAS, vol. 117, no. 50. National Academy of Sciences, pp. 31614–31622, 2020. ista: Grah R, Zoller B, Tkačik G. 2020. Nonequilibrium models of optimal enhancer function. PNAS. 117(50), 31614–31622. mla: Grah, Rok, et al. “Nonequilibrium Models of Optimal Enhancer Function.” PNAS, vol. 117, no. 50, National Academy of Sciences, 2020, pp. 31614–22, doi:10.1073/pnas.2006731117. short: R. Grah, B. Zoller, G. Tkačik, PNAS 117 (2020) 31614–31622. date_created: 2021-01-10T23:01:17Z date_published: 2020-12-15T00:00:00Z date_updated: 2023-08-24T11:10:22Z day: '15' ddc: - '570' department: - _id: GaTk doi: 10.1073/pnas.2006731117 external_id: isi: - '000600608300015' pmid: - '33268497' file: - access_level: open_access checksum: 69039cd402a571983aa6cb4815ffa863 content_type: application/pdf creator: dernst date_created: 2021-01-11T08:37:31Z date_updated: 2021-01-11T08:37:31Z file_id: '9004' file_name: 2020_PNAS_Grah.pdf file_size: 1199247 relation: main_file success: 1 file_date_updated: 2021-01-11T08:37:31Z has_accepted_license: '1' intvolume: ' 117' isi: 1 issue: '50' language: - iso: eng month: '12' oa: 1 oa_version: Published Version page: 31614-31622 pmid: 1 project: - _id: 2665AAFE-B435-11E9-9278-68D0E5697425 grant_number: RGP0034/2018 name: Can evolution minimize spurious signaling crosstalk to reach optimal performance? - _id: 267C84F4-B435-11E9-9278-68D0E5697425 name: Biophysically realistic genotype-phenotype maps for regulatory networks publication: PNAS publication_identifier: eissn: - '10916490' issn: - '00278424' publication_status: published publisher: National Academy of Sciences quality_controlled: '1' related_material: link: - description: News on IST Homepage relation: press_release url: https://ist.ac.at/en/news/new-compact-model-for-gene-regulation-in-higher-organisms/ scopus_import: '1' status: public title: Nonequilibrium models of optimal enhancer function 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: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 117 year: '2020' ... --- _id: '177' abstract: - lang: eng text: We develop a geometric version of the circle method and use it to compute the compactly supported cohomology of the space of rational curves through a point on a smooth affine hypersurface of sufficiently low degree. article_processing_charge: No article_type: original arxiv: 1 author: - first_name: Timothy D full_name: Browning, Timothy D id: 35827D50-F248-11E8-B48F-1D18A9856A87 last_name: Browning orcid: 0000-0002-8314-0177 - first_name: Will full_name: Sawin, Will last_name: Sawin citation: ama: Browning TD, Sawin W. A geometric version of the circle method. Annals of Mathematics. 2020;191(3):893-948. doi:10.4007/annals.2020.191.3.4 apa: Browning, T. D., & Sawin, W. (2020). A geometric version of the circle method. Annals of Mathematics. Princeton University. https://doi.org/10.4007/annals.2020.191.3.4 chicago: Browning, Timothy D, and Will Sawin. “A Geometric Version of the Circle Method.” Annals of Mathematics. Princeton University, 2020. https://doi.org/10.4007/annals.2020.191.3.4. ieee: T. D. Browning and W. Sawin, “A geometric version of the circle method,” Annals of Mathematics, vol. 191, no. 3. Princeton University, pp. 893–948, 2020. ista: Browning TD, Sawin W. 2020. A geometric version of the circle method. Annals of Mathematics. 191(3), 893–948. mla: Browning, Timothy D., and Will Sawin. “A Geometric Version of the Circle Method.” Annals of Mathematics, vol. 191, no. 3, Princeton University, 2020, pp. 893–948, doi:10.4007/annals.2020.191.3.4. short: T.D. Browning, W. Sawin, Annals of Mathematics 191 (2020) 893–948. date_created: 2018-12-11T11:45:02Z date_published: 2020-05-01T00:00:00Z date_updated: 2023-08-17T07:12:37Z day: '01' department: - _id: TiBr doi: 10.4007/annals.2020.191.3.4 external_id: arxiv: - '1711.10451' isi: - '000526986300004' intvolume: ' 191' isi: 1 issue: '3' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1711.10451 month: '05' oa: 1 oa_version: Preprint page: 893-948 publication: Annals of Mathematics publication_status: published publisher: Princeton University publist_id: '7744' quality_controlled: '1' status: public title: A geometric version of the circle method type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 191 year: '2020' ...