--- _id: '14705' abstract: - lang: eng text: Since the commercialization of brine shrimp (genus Artemia) in the 1950s, this lineage, and in particular the model species Artemia franciscana, has been the subject of extensive research. However, our understanding of the genetic mechanisms underlying various aspects of their reproductive biology, including sex determination, are still lacking. This is partly due to the scarcity of genomic resources for Artemia species and crustaceans in general. Here, we present a chromosome-level genome assembly of Artemia franciscana (Kellogg 1906), from the Great Salt Lake, USA. The genome is 1GB, and the majority of the genome (81%) is scaffolded into 21 linkage groups using a previously published high-density linkage map. We performed coverage and FST analyses using male and female genomic and transcriptomic reads to quantify the extent of differentiation between the Z and W chromosomes. Additionally, we quantified the expression levels in male and female heads and gonads and found further evidence for dosage compensation in this species. article_processing_charge: No author: - first_name: Marwan N full_name: Elkrewi, Marwan N id: 0B46FACA-A8E1-11E9-9BD3-79D1E5697425 last_name: Elkrewi orcid: 0000-0002-5328-7231 citation: ama: Elkrewi MN. Data from “Chromosome-level assembly of Artemia franciscana sheds light on sex-chromosome differentiation.” 2024. doi:10.15479/AT:ISTA:14705 apa: Elkrewi, M. N. (2024). Data from “Chromosome-level assembly of Artemia franciscana sheds light on sex-chromosome differentiation.” Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:14705 chicago: Elkrewi, Marwan N. “Data from ‘Chromosome-Level Assembly of Artemia Franciscana Sheds Light on Sex-Chromosome Differentiation.’” Institute of Science and Technology Austria, 2024. https://doi.org/10.15479/AT:ISTA:14705. ieee: M. N. Elkrewi, “Data from ‘Chromosome-level assembly of Artemia franciscana sheds light on sex-chromosome differentiation.’” Institute of Science and Technology Austria, 2024. ista: Elkrewi MN. 2024. Data from ‘Chromosome-level assembly of Artemia franciscana sheds light on sex-chromosome differentiation’, Institute of Science and Technology Austria, 10.15479/AT:ISTA:14705. mla: Elkrewi, Marwan N. Data from “Chromosome-Level Assembly of Artemia Franciscana Sheds Light on Sex-Chromosome Differentiation.” Institute of Science and Technology Austria, 2024, doi:10.15479/AT:ISTA:14705. short: M.N. Elkrewi, (2024). contributor: - contributor_type: researcher first_name: Vincent K id: 57854184-AAE0-11E9-8D04-98D6E5697425 last_name: Bett - contributor_type: project_member first_name: Ariana id: 2A0848E2-F248-11E8-B48F-1D18A9856A87 last_name: Macon - contributor_type: supervisor first_name: Beatriz id: 49E1C5C6-F248-11E8-B48F-1D18A9856A87 last_name: Vicoso orcid: 0000-0002-4579-8306 - contributor_type: researcher first_name: Marwan N id: 0B46FACA-A8E1-11E9-9BD3-79D1E5697425 last_name: Elkrewi orcid: 0000-0002-5328-7231 date_created: 2023-12-22T13:40:48Z date_published: 2024-01-02T00:00:00Z date_updated: 2024-02-26T09:59:29Z day: '02' ddc: - '576' department: - _id: GradSch - _id: BeVi doi: 10.15479/AT:ISTA:14705 file: - access_level: open_access checksum: bdaf1392867786634ec5466d528c36ca content_type: text/plain creator: melkrewi date_created: 2023-12-22T13:54:21Z date_updated: 2023-12-22T13:54:21Z file_id: '14707' file_name: readme.txt.txt file_size: 847 relation: main_file success: 1 - access_level: open_access checksum: 973e1cbdab923a71709782177980829f content_type: application/x-zip-compressed creator: melkrewi date_created: 2023-12-22T14:14:06Z date_updated: 2023-12-22T14:14:06Z file_id: '14708' file_name: data_artemia_franciscana_genome.zip file_size: 343632753 relation: main_file success: 1 file_date_updated: 2023-12-22T14:14:06Z has_accepted_license: '1' keyword: - sex chromosome evolution - genome assembly - dosage compensation month: '01' oa: 1 oa_version: Published Version project: - _id: 34ae1506-11ca-11ed-8bc3-c14f4c474396 grant_number: F8810 name: The highjacking of meiosis for asexual reproduction publisher: Institute of Science and Technology Austria related_material: record: - id: '15009' relation: used_in_publication status: public status: public title: Data from "Chromosome-level assembly of Artemia franciscana sheds light on sex-chromosome differentiation" 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: '2024' ... --- _id: '15108' abstract: - lang: eng text: "in the research article \"Efficiency and resilience of cooperation in asymmetric social dilemmas\" (by Valentin Hübner, Manuel Staab, Christian Hilbe, Krishnendu Chatterjee, and Maria Kleshnina).\r\n\r\nWe used different implementations for the case of two and three players, both described below." article_processing_charge: No author: - first_name: Valentin full_name: Hübner, Valentin id: 2c8aa207-dc7d-11ea-9b2f-f22972ecd910 last_name: Hübner - first_name: Maria full_name: Kleshnina, Maria last_name: Kleshnina citation: ama: Hübner V, Kleshnina M. Computer code for “Efficiency and resilience of cooperation in asymmetric social dilemmas.” 2024. doi:10.5281/ZENODO.10639167 apa: Hübner, V., & Kleshnina, M. (2024). Computer code for “Efficiency and resilience of cooperation in asymmetric social dilemmas.” Zenodo. https://doi.org/10.5281/ZENODO.10639167 chicago: Hübner, Valentin, and Maria Kleshnina. “Computer Code for ‘Efficiency and Resilience of Cooperation in Asymmetric Social Dilemmas.’” Zenodo, 2024. https://doi.org/10.5281/ZENODO.10639167. ieee: V. Hübner and M. Kleshnina, “Computer code for ‘Efficiency and resilience of cooperation in asymmetric social dilemmas.’” Zenodo, 2024. ista: Hübner V, Kleshnina M. 2024. Computer code for ‘Efficiency and resilience of cooperation in asymmetric social dilemmas’, Zenodo, 10.5281/ZENODO.10639167. mla: Hübner, Valentin, and Maria Kleshnina. Computer Code for “Efficiency and Resilience of Cooperation in Asymmetric Social Dilemmas.” Zenodo, 2024, doi:10.5281/ZENODO.10639167. short: V. Hübner, M. Kleshnina, (2024). date_created: 2024-03-12T13:02:58Z date_published: 2024-02-09T00:00:00Z date_updated: 2024-03-12T13:29:26Z day: '09' ddc: - '000' department: - _id: KrCh doi: 10.5281/ZENODO.10639167 has_accepted_license: '1' main_file_link: - open_access: '1' url: https://10.5281/zenodo.10639167 month: '02' oa: 1 oa_version: Published Version publisher: Zenodo related_material: record: - id: '15083' relation: used_in_publication status: public status: public title: Computer code for "Efficiency and resilience of cooperation in asymmetric social dilemmas" 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_reference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2024' ... --- _id: '13275' abstract: - lang: eng text: We introduce a generic and accessible implementation of an exact diagonalization method for studying few-fermion models. Our aim is to provide a testbed for the newcomers to the field as well as a stepping stone for trying out novel optimizations and approximations. This userguide consists of a description of the algorithm, and several examples in varying orders of sophistication. In particular, we exemplify our routine using an effective-interaction approach that fixes the low-energy physics. We benchmark this approach against the existing data, and show that it is able to deliver state-of-the-art numerical results at a significantly reduced computational cost. article_processing_charge: No author: - first_name: Lukas full_name: Rammelmüller, Lukas last_name: Rammelmüller - first_name: David full_name: Huber, David last_name: Huber - first_name: Artem full_name: Volosniev, Artem id: 37D278BC-F248-11E8-B48F-1D18A9856A87 last_name: Volosniev orcid: 0000-0003-0393-5525 citation: ama: Rammelmüller L, Huber D, Volosniev A. Codebase release 1.0 for FermiFCI. 2023. doi:10.21468/scipostphyscodeb.12-r1.0 apa: Rammelmüller, L., Huber, D., & Volosniev, A. (2023). Codebase release 1.0 for FermiFCI. SciPost Foundation. https://doi.org/10.21468/scipostphyscodeb.12-r1.0 chicago: Rammelmüller, Lukas, David Huber, and Artem Volosniev. “Codebase Release 1.0 for FermiFCI.” SciPost Foundation, 2023. https://doi.org/10.21468/scipostphyscodeb.12-r1.0. ieee: L. Rammelmüller, D. Huber, and A. Volosniev, “Codebase release 1.0 for FermiFCI.” SciPost Foundation, 2023. ista: Rammelmüller L, Huber D, Volosniev A. 2023. Codebase release 1.0 for FermiFCI, SciPost Foundation, 10.21468/scipostphyscodeb.12-r1.0. mla: Rammelmüller, Lukas, et al. Codebase Release 1.0 for FermiFCI. SciPost Foundation, 2023, doi:10.21468/scipostphyscodeb.12-r1.0. short: L. Rammelmüller, D. Huber, A. Volosniev, (2023). date_created: 2023-07-24T10:46:23Z date_published: 2023-04-19T00:00:00Z date_updated: 2023-07-31T09:16:02Z day: '19' ddc: - '530' department: - _id: MiLe doi: 10.21468/scipostphyscodeb.12-r1.0 ec_funded: 1 main_file_link: - open_access: '1' url: https://doi.org/10.21468/SciPostPhysCodeb.12-r1.0 month: '04' oa: 1 oa_version: Published Version project: - _id: 260C2330-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '754411' name: ISTplus - Postdoctoral Fellowships publisher: SciPost Foundation related_material: record: - id: '13276' relation: used_in_publication status: public status: public title: Codebase release 1.0 for FermiFCI type: research_data_reference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2023' ... --- _id: '12820' abstract: - lang: eng text: "Disulfide bond formation is fundamentally important for protein structure, and constitutes a key mechanism by which cells regulate the intracellular oxidation state. Peroxiredoxins (PRDXs) eliminate reactive oxygen species such as hydrogen peroxide through a catalytic cycle of Cys oxidation and reduction. Additionally, upon Cys oxidation PRDXs undergo extensive conformational rearrangements that may underlie their presently structurally poorly defined functions as molecular chaperones. Rearrangements include high molecular-weight oligomerization, the dynamics of which are, however, poorly understood, as is the impact of disulfide bond formation on these properties. Here we show that formation of disulfide bonds along the catalytic cycle induces extensive microsecond time scale dynamics, as monitored by magic-angle spinning NMR of the 216 kDa-large Tsa1 decameric assembly and solution-NMR of a designed dimeric mutant. We ascribe the conformational dynamics to structural frustration, resulting from conflicts between the disulfide-constrained reduction of mobility and the desire to fulfil other favorable contacts. \r\n\r\nThis data repository contains NMR data presented in the associated manuscript" article_processing_charge: No author: - first_name: Paul full_name: Schanda, Paul id: 7B541462-FAF6-11E9-A490-E8DFE5697425 last_name: Schanda orcid: 0000-0002-9350-7606 citation: ama: Schanda P. Research data of the publication “Disulfide-bond-induced structural frustration and dynamic disorder in a peroxiredoxin from MAS NMR.” 2023. doi:10.15479/AT:ISTA:12820 apa: Schanda, P. (2023). Research data of the publication “Disulfide-bond-induced structural frustration and dynamic disorder in a peroxiredoxin from MAS NMR.” Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:12820 chicago: Schanda, Paul. “Research Data of the Publication ‘Disulfide-Bond-Induced Structural Frustration and Dynamic Disorder in a Peroxiredoxin from MAS NMR.’” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/AT:ISTA:12820. ieee: P. Schanda, “Research data of the publication ‘Disulfide-bond-induced structural frustration and dynamic disorder in a peroxiredoxin from MAS NMR.’” Institute of Science and Technology Austria, 2023. ista: Schanda P. 2023. Research data of the publication ‘Disulfide-bond-induced structural frustration and dynamic disorder in a peroxiredoxin from MAS NMR’, Institute of Science and Technology Austria, 10.15479/AT:ISTA:12820. mla: Schanda, Paul. Research Data of the Publication “Disulfide-Bond-Induced Structural Frustration and Dynamic Disorder in a Peroxiredoxin from MAS NMR.” Institute of Science and Technology Austria, 2023, doi:10.15479/AT:ISTA:12820. short: P. Schanda, (2023). contributor: - contributor_type: researcher first_name: Laura last_name: Troussicot - contributor_type: researcher first_name: Björn M. last_name: Burmann date_created: 2023-04-10T05:55:56Z date_published: 2023-04-18T00:00:00Z date_updated: 2023-08-01T14:48:08Z day: '18' ddc: - '570' department: - _id: PaSc doi: 10.15479/AT:ISTA:12820 file: - access_level: open_access checksum: 54a619605e44c871214fb0e07b05c6bf content_type: application/zip creator: pschanda date_created: 2023-04-14T09:39:33Z date_updated: 2023-04-14T09:39:33Z file_id: '12823' file_name: data_deposition.zip file_size: 54184807 relation: main_file success: 1 - access_level: open_access checksum: 8dede9fc78399d13144eb05c62bf5750 content_type: application/octet-stream creator: pschanda date_created: 2023-04-14T09:39:58Z date_updated: 2023-04-14T09:39:58Z file_id: '12824' file_name: README file_size: 4978 relation: main_file success: 1 file_date_updated: 2023-04-14T09:39:58Z has_accepted_license: '1' month: '04' oa: 1 oa_version: Published Version publisher: Institute of Science and Technology Austria related_material: record: - id: '13095' relation: used_in_publication status: public status: public title: Research data of the publication "Disulfide-bond-induced structural frustration and dynamic disorder in a peroxiredoxin from MAS NMR" 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: research_data user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2023' ... --- _id: '13124' abstract: - lang: eng text: This dataset comprises all data shown in the figures of the submitted article "Tunable directional photon scattering from a pair of superconducting qubits" at arXiv:2205.03293. Additional raw data are available from the corresponding author on reasonable request. article_processing_charge: No author: - first_name: Elena full_name: Redchenko, Elena id: 2C21D6E8-F248-11E8-B48F-1D18A9856A87 last_name: Redchenko - first_name: Alexander full_name: Poshakinskiy, Alexander last_name: Poshakinskiy - first_name: Riya full_name: Sett, Riya id: 2E6D040E-F248-11E8-B48F-1D18A9856A87 last_name: Sett - first_name: Martin full_name: Zemlicka, Martin id: 2DCF8DE6-F248-11E8-B48F-1D18A9856A87 last_name: Zemlicka - first_name: Alexander full_name: Poddubny, Alexander last_name: Poddubny - first_name: Johannes M full_name: Fink, Johannes M id: 4B591CBA-F248-11E8-B48F-1D18A9856A87 last_name: Fink orcid: 0000-0001-8112-028X citation: ama: Redchenko E, Poshakinskiy A, Sett R, Zemlicka M, Poddubny A, Fink JM. Tunable directional photon scattering from a pair of superconducting qubits. 2023. doi:10.5281/ZENODO.7858567 apa: Redchenko, E., Poshakinskiy, A., Sett, R., Zemlicka, M., Poddubny, A., & Fink, J. M. (2023). Tunable directional photon scattering from a pair of superconducting qubits. Zenodo. https://doi.org/10.5281/ZENODO.7858567 chicago: Redchenko, Elena, Alexander Poshakinskiy, Riya Sett, Martin Zemlicka, Alexander Poddubny, and Johannes M Fink. “Tunable Directional Photon Scattering from a Pair of Superconducting Qubits.” Zenodo, 2023. https://doi.org/10.5281/ZENODO.7858567. ieee: E. Redchenko, A. Poshakinskiy, R. Sett, M. Zemlicka, A. Poddubny, and J. M. Fink, “Tunable directional photon scattering from a pair of superconducting qubits.” Zenodo, 2023. ista: Redchenko E, Poshakinskiy A, Sett R, Zemlicka M, Poddubny A, Fink JM. 2023. Tunable directional photon scattering from a pair of superconducting qubits, Zenodo, 10.5281/ZENODO.7858567. mla: Redchenko, Elena, et al. Tunable Directional Photon Scattering from a Pair of Superconducting Qubits. Zenodo, 2023, doi:10.5281/ZENODO.7858567. short: E. Redchenko, A. Poshakinskiy, R. Sett, M. Zemlicka, A. Poddubny, J.M. Fink, (2023). date_created: 2023-06-06T07:36:50Z date_published: 2023-04-28T00:00:00Z date_updated: 2023-08-02T06:10:25Z day: '28' ddc: - '530' department: - _id: JoFi doi: 10.5281/ZENODO.7858567 main_file_link: - open_access: '1' url: https://doi.org/10.5281/zenodo.7858567 month: '04' oa: 1 oa_version: Published Version publisher: Zenodo related_material: record: - id: '13117' relation: used_in_publication status: public status: public title: Tunable directional photon scattering from a pair of superconducting qubits 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_reference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2023' ... --- _id: '13122' abstract: - lang: eng text: Data for submitted article "Entangling microwaves with light" at arXiv:2301.03315v1 article_processing_charge: No author: - first_name: Rishabh full_name: Sahu, Rishabh id: 47D26E34-F248-11E8-B48F-1D18A9856A87 last_name: Sahu orcid: 0000-0001-6264-2162 citation: ama: Sahu R. Entangling microwaves with light. 2023. doi:10.5281/ZENODO.7789417 apa: Sahu, R. (2023). Entangling microwaves with light. Zenodo. https://doi.org/10.5281/ZENODO.7789417 chicago: Sahu, Rishabh. “Entangling Microwaves with Light.” Zenodo, 2023. https://doi.org/10.5281/ZENODO.7789417. ieee: R. Sahu, “Entangling microwaves with light.” Zenodo, 2023. ista: Sahu R. 2023. Entangling microwaves with light, Zenodo, 10.5281/ZENODO.7789417. mla: Sahu, Rishabh. Entangling Microwaves with Light. Zenodo, 2023, doi:10.5281/ZENODO.7789417. short: R. Sahu, (2023). date_created: 2023-06-06T06:46:16Z date_published: 2023-03-31T00:00:00Z date_updated: 2023-08-02T06:08:56Z day: '31' department: - _id: JoFi doi: 10.5281/ZENODO.7789417 main_file_link: - open_access: '1' url: https://doi.org/10.5281/zenodo.7789418 month: '03' oa: 1 oa_version: Published Version publisher: Zenodo related_material: record: - id: '13106' relation: used_in_publication status: public status: public title: Entangling microwaves with light 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_reference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2023' ... --- _id: '12945' abstract: - lang: eng text: "basic data for use in code for experimental data analysis for manuscript under revision: \r\nDynamic pathogen detection and social feedback shape collective hygiene in ants\r\nCasillas-Pérez B, Boďová K, Grasse AV, Tkačik G, Cremer S" acknowledged_ssus: - _id: LifeSc acknowledgement: This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (Grant No. 771402; EPIDEMICSonCHIP) to SC, from the Scientific Grant Agency of the Slovak Republic (Grant No. 1/0521/20) to KB, and the Human Frontier Science Program (Grant No. RGP0065/2012) to GT. article_processing_charge: No author: - first_name: Sylvia full_name: Cremer, Sylvia id: 2F64EC8C-F248-11E8-B48F-1D18A9856A87 last_name: Cremer orcid: 0000-0002-2193-3868 citation: ama: 'Cremer S. Data from: “Dynamic pathogen detection and social feedback shape collective hygiene in ants” . 2023. doi:10.15479/AT:ISTA:12945' apa: 'Cremer, S. (2023). Data from: “Dynamic pathogen detection and social feedback shape collective hygiene in ants” . Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:12945' chicago: 'Cremer, Sylvia. “Data from: ‘Dynamic Pathogen Detection and Social Feedback Shape Collective Hygiene in Ants’ .” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/AT:ISTA:12945.' ieee: 'S. Cremer, “Data from: ‘Dynamic pathogen detection and social feedback shape collective hygiene in ants’ .” Institute of Science and Technology Austria, 2023.' ista: 'Cremer S. 2023. Data from: ‘Dynamic pathogen detection and social feedback shape collective hygiene in ants’ , Institute of Science and Technology Austria, 10.15479/AT:ISTA:12945.' mla: 'Cremer, Sylvia. Data from: “Dynamic Pathogen Detection and Social Feedback Shape Collective Hygiene in Ants” . Institute of Science and Technology Austria, 2023, doi:10.15479/AT:ISTA:12945.' short: S. Cremer, (2023). contributor: - contributor_type: data_collector first_name: Barbara E id: 351ED2AA-F248-11E8-B48F-1D18A9856A87 last_name: Casillas Perez - contributor_type: data_collector first_name: Anna V id: 406F989C-F248-11E8-B48F-1D18A9856A87 last_name: Grasse - contributor_type: researcher first_name: Katarina last_name: Bodova - contributor_type: supervisor first_name: Gašper id: 3D494DCA-F248-11E8-B48F-1D18A9856A87 last_name: Tkačik orcid: 0000-0002-6699-1455 date_created: 2023-05-11T21:35:17Z date_published: 2023-05-12T00:00:00Z date_updated: 2023-08-07T13:09:09Z day: '12' ddc: - '570' department: - _id: SyCr doi: 10.15479/AT:ISTA:12945 file: - access_level: open_access checksum: 3eadf17fd59ad8c98bf10bf63061863c content_type: application/zip creator: scremer date_created: 2023-05-12T08:04:04Z date_updated: 2023-05-12T08:04:04Z file_id: '12947' file_name: Experimental_data.zip file_size: 3414674 relation: main_file success: 1 - access_level: open_access checksum: 1b5e8e01a0989154a76b44e6d8d68f89 content_type: application/octet-stream creator: scremer date_created: 2023-05-12T08:04:08Z date_updated: 2023-05-12T08:04:08Z file_id: '12948' file_name: README_Experimental_Data.md file_size: 2113 relation: main_file success: 1 file_date_updated: 2023-05-12T08:04:08Z has_accepted_license: '1' keyword: - collective behavior - host-pathogen interactions - social immunity - epidemiology - social insects - probabilistic modeling month: '05' oa: 1 oa_version: None publisher: Institute of Science and Technology Austria related_material: record: - id: '13127' relation: used_in_publication status: public status: public title: 'Data from: "Dynamic pathogen detection and social feedback shape collective hygiene in ants" ' 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: research_data user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2023' ... --- _id: '14279' abstract: - lang: eng text: "The zip file includes source data used in the manuscript \"CCR7 acts as both a sensor and a sink for CCL19 to coordinate collective leukocyte migration\", as well as a representative Jupyter notebook to reproduce the main figures. Please see the preprint on bioRxiv and the DOI link there to access the final published version. Note the title change between the preprint and the published manuscript.\r\nA sample script for particle-based simulations of collective chemotaxis by self-generated gradients is also included (see Self-generated_chemotaxis_sample_script.ipynb) to generate exemplary cell trajectories. A detailed description of the simulation setup is provided in the supplementary information of the manuscipt." article_processing_charge: No author: - first_name: Mehmet C full_name: Ucar, Mehmet C id: 50B2A802-6007-11E9-A42B-EB23E6697425 last_name: Ucar orcid: 0000-0003-0506-4217 citation: ama: Ucar MC. Source data for the manuscript “CCR7 acts as both a sensor and a sink for CCL19 to coordinate collective leukocyte migration.” 2023. doi:10.5281/ZENODO.8133960 apa: Ucar, M. C. (2023). Source data for the manuscript “CCR7 acts as both a sensor and a sink for CCL19 to coordinate collective leukocyte migration.” Zenodo. https://doi.org/10.5281/ZENODO.8133960 chicago: Ucar, Mehmet C. “Source Data for the Manuscript ‘CCR7 Acts as Both a Sensor and a Sink for CCL19 to Coordinate Collective Leukocyte Migration.’” Zenodo, 2023. https://doi.org/10.5281/ZENODO.8133960. ieee: M. C. Ucar, “Source data for the manuscript ‘CCR7 acts as both a sensor and a sink for CCL19 to coordinate collective leukocyte migration.’” Zenodo, 2023. ista: Ucar MC. 2023. Source data for the manuscript ‘CCR7 acts as both a sensor and a sink for CCL19 to coordinate collective leukocyte migration’, Zenodo, 10.5281/ZENODO.8133960. mla: Ucar, Mehmet C. Source Data for the Manuscript “CCR7 Acts as Both a Sensor and a Sink for CCL19 to Coordinate Collective Leukocyte Migration.” Zenodo, 2023, doi:10.5281/ZENODO.8133960. short: M.C. Ucar, (2023). date_created: 2023-09-06T08:39:25Z date_published: 2023-07-11T00:00:00Z date_updated: 2023-10-03T11:42:58Z day: '11' ddc: - '570' department: - _id: EdHa doi: 10.5281/ZENODO.8133960 has_accepted_license: '1' main_file_link: - open_access: '1' url: https://doi.org/10.5281/zenodo.8133960 month: '07' oa: 1 oa_version: Published Version publisher: Zenodo related_material: record: - id: '14274' relation: used_in_publication status: public status: public title: Source data for the manuscript "CCR7 acts as both a sensor and a sink for CCL19 to coordinate collective leukocyte migration" 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_reference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2023' ... --- _id: '12370' abstract: - lang: eng text: 'Statistics of natural scenes are not uniform - their structure varies dramatically from ground to sky. It remains unknown whether these non-uniformities are reflected in the large-scale organization of the early visual system and what benefits such adaptations would confer. Here, by relying on the efficient coding hypothesis, we predict that changes in the structure of receptive fields across visual space increase the efficiency of sensory coding. We show experimentally that, in agreement with our predictions, receptive fields of retinal ganglion cells change their shape along the dorsoventral retinal axis, with a marked surround asymmetry at the visual horizon. Our work demonstrates that, according to principles of efficient coding, the panoramic structure of natural scenes is exploited by the retina across space and cell-types. ' acknowledged_ssus: - _id: ScienComp - _id: M-Shop - _id: Bio - _id: PreCl - _id: LifeSc article_processing_charge: No author: - first_name: Divyansh full_name: Gupta, Divyansh id: 2A485EBE-F248-11E8-B48F-1D18A9856A87 last_name: Gupta orcid: 0000-0001-7400-6665 - first_name: Anton L full_name: Sumser, Anton L id: 3320A096-F248-11E8-B48F-1D18A9856A87 last_name: Sumser orcid: 0000-0002-4792-1881 - first_name: Maximilian A full_name: Jösch, Maximilian A id: 2BD278E6-F248-11E8-B48F-1D18A9856A87 last_name: Jösch orcid: 0000-0002-3937-1330 citation: ama: 'Gupta D, Sumser AL, Jösch MA. Research Data for: Panoramic visual statistics shape retina-wide organization of receptive fields. 2023. doi:10.15479/AT:ISTA:12370' apa: 'Gupta, D., Sumser, A. L., & Jösch, M. A. (2023). Research Data for: Panoramic visual statistics shape retina-wide organization of receptive fields. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:12370' chicago: 'Gupta, Divyansh, Anton L Sumser, and Maximilian A Jösch. “Research Data for: Panoramic Visual Statistics Shape Retina-Wide Organization of Receptive Fields.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/AT:ISTA:12370.' ieee: 'D. Gupta, A. L. Sumser, and M. A. Jösch, “Research Data for: Panoramic visual statistics shape retina-wide organization of receptive fields.” Institute of Science and Technology Austria, 2023.' ista: 'Gupta D, Sumser AL, Jösch MA. 2023. Research Data for: Panoramic visual statistics shape retina-wide organization of receptive fields, Institute of Science and Technology Austria, 10.15479/AT:ISTA:12370.' mla: 'Gupta, Divyansh, et al. Research Data for: Panoramic Visual Statistics Shape Retina-Wide Organization of Receptive Fields. Institute of Science and Technology Austria, 2023, doi:10.15479/AT:ISTA:12370.' short: D. Gupta, A.L. Sumser, M.A. Jösch, (2023). contributor: - contributor_type: researcher first_name: Olga id: 3C0C7BC6-F248-11E8-B48F-1D18A9856A87 last_name: Symonova - contributor_type: researcher first_name: Wiktor F id: 358A453A-F248-11E8-B48F-1D18A9856A87 last_name: Mlynarski - contributor_type: researcher first_name: Jan id: f7f724c3-9d6f-11ed-9f44-e5c5f3a5bee2 last_name: Svaton date_created: 2023-01-25T12:45:18Z date_published: 2023-01-26T00:00:00Z date_updated: 2023-10-04T11:41:04Z day: '26' ddc: - '571' department: - _id: GradSch - _id: MaJö doi: 10.15479/AT:ISTA:12370 ec_funded: 1 file: - access_level: open_access checksum: 172cd1c315cbf063c122298396bc17a7 content_type: text/plain creator: dgupta date_created: 2023-01-26T10:51:34Z date_updated: 2023-01-26T10:51:34Z file_id: '12396' file_name: readme_exvivo.txt file_size: 1917 relation: main_file success: 1 - access_level: open_access checksum: d3cecda51cad86b1182195731c01a14f content_type: text/plain creator: dgupta date_created: 2023-01-26T10:50:50Z date_updated: 2023-01-26T10:50:50Z file_id: '12397' file_name: readme_invivo.txt file_size: 1585 relation: main_file success: 1 - access_level: open_access checksum: b85018b27f2c43a6d94ee0e8b841220d content_type: application/octet-stream creator: dgupta date_created: 2023-01-26T10:43:30Z date_updated: 2023-01-26T10:43:30Z file_id: '12398' file_name: exvivo_RFs.mat file_size: 5019459775 relation: main_file success: 1 - access_level: open_access checksum: f75dccd96a3f837cdeed65b5134e697e content_type: application/octet-stream creator: dgupta date_created: 2023-01-26T10:40:35Z date_updated: 2023-01-26T10:40:35Z file_id: '12399' file_name: RGC_in_vivo_RFs_selected.mat file_size: 94999721 relation: main_file success: 1 - access_level: open_access checksum: d41836ffe03ea0efb677de31287c8d2e content_type: application/octet-stream creator: dgupta date_created: 2023-01-25T16:03:49Z date_updated: 2023-01-25T16:03:49Z file_id: '12382' file_name: invivo_BL6-eyeGC8m-dC-3_210924_1534_Result.mat file_size: 720893739 relation: main_file success: 1 - access_level: open_access checksum: 0a0cba5208241a95f9bb7684d0a43afa content_type: application/octet-stream creator: dgupta date_created: 2023-01-25T16:03:30Z date_updated: 2023-01-25T16:03:30Z file_id: '12383' file_name: invivo_BL6-eyeGC8m-dC-3_211026_1235_Result.mat file_size: 248122209 relation: main_file success: 1 - 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access_level: open_access checksum: 9483686a44e69eadea428b705c33a9a2 content_type: application/octet-stream creator: dgupta date_created: 2023-01-25T16:23:02Z date_updated: 2023-01-25T16:23:02Z file_id: '12389' file_name: invivo_BL6-eyeGC8m-dC-5_220630_1518_Result.mat file_size: 1617777136 relation: main_file success: 1 file_date_updated: 2023-01-26T10:51:34Z has_accepted_license: '1' license: https://creativecommons.org/licenses/by-nc-sa/4.0/ month: '01' oa: 1 oa_version: Published Version project: - _id: 2564DBCA-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '665385' name: International IST Doctoral Program - _id: 626c45b5-2b32-11ec-9570-e509828c1ba6 grant_number: P34015 name: Efficient coding with biophysical realism - _id: 2634E9D2-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '756502' name: Circuits of Visual Attention - _id: 266D407A-B435-11E9-9278-68D0E5697425 grant_number: LT000256 name: Neuronal networks of salience and spatial detection in the murine superior colliculus - _id: 264FEA02-B435-11E9-9278-68D0E5697425 grant_number: ALTF 1098-2017 name: Connecting sensory with motor processing in the superior colliculus publisher: Institute of Science and Technology Austria related_material: record: - id: '12349' relation: used_in_publication status: public status: public title: 'Research Data for: Panoramic visual statistics shape retina-wide organization of receptive fields' tmp: image: /images/cc_by_nc_sa.png legal_code_url: https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode name: Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0) short: CC BY-NC-SA (4.0) type: research_data user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2023' ... --- _id: '12949' abstract: - lang: eng text: The classical infinitesimal model is a simple and robust model for the inheritance of quantitative traits. In this model, a quantitative trait is expressed as the sum of a genetic and a non-genetic (environmental) component and the genetic component of offspring traits within a family follows a normal distribution around the average of the parents’ trait values, and has a variance that is independent of the trait values of the parents. Although the trait distribution across the whole population can be far from normal, the trait distributions within families are normally distributed with a variance-covariance matrix that is determined entirely by that in the ancestral population and the probabilities of identity determined by the pedigree. Moreover, conditioning on some of the trait values within the pedigree has predictable effects on the mean and variance within and between families. In previous work, Barton et al. (2017), we showed that when trait values are determined by the sum of a large number of Mendelian factors, each of small effect, one can justify the infinitesimal model as limit of Mendelian inheritance. It was also shown that under some forms of epistasis, trait values within a family are still normally distributed. article_processing_charge: No author: - first_name: Nicholas H full_name: Barton, Nicholas H id: 4880FE40-F248-11E8-B48F-1D18A9856A87 last_name: Barton orcid: 0000-0002-8548-5240 citation: ama: Barton NH. The infinitesimal model with dominance. 2023. doi:10.15479/AT:ISTA:12949 apa: Barton, N. H. (2023). The infinitesimal model with dominance. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:12949 chicago: Barton, Nicholas H. “The Infinitesimal Model with Dominance.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/AT:ISTA:12949. ieee: N. H. Barton, “The infinitesimal model with dominance.” Institute of Science and Technology Austria, 2023. ista: Barton NH. 2023. The infinitesimal model with dominance, Institute of Science and Technology Austria, 10.15479/AT:ISTA:12949. mla: Barton, Nicholas H. The Infinitesimal Model with Dominance. Institute of Science and Technology Austria, 2023, doi:10.15479/AT:ISTA:12949. short: N.H. Barton, (2023). contributor: - contributor_type: researcher first_name: Amandine last_name: Veber - contributor_type: researcher first_name: Alison last_name: Etheridge date_created: 2023-05-13T09:49:09Z date_published: 2023-05-13T00:00:00Z date_updated: 2023-10-30T13:04:11Z day: '13' ddc: - '576' department: - _id: NiBa doi: 10.15479/AT:ISTA:12949 file: - access_level: open_access checksum: b0ce7d4b1ee7e7265430ceed36fc3336 content_type: application/octet-stream creator: nbarton date_created: 2023-05-13T09:36:33Z date_updated: 2023-05-13T09:36:33Z file_id: '12950' file_name: Neutral identities 16th Jan file_size: 13662 relation: main_file success: 1 - access_level: open_access checksum: ad5035ad4f7d3b150a252c79884f6a83 content_type: application/octet-stream creator: nbarton date_created: 2023-05-13T09:38:17Z date_updated: 2023-05-13T09:38:17Z file_id: '12951' file_name: p, zA, zD, N=30 neutral III file_size: 181619928 relation: main_file success: 1 - access_level: open_access checksum: 62182a1de796256edd6f4223704312ef content_type: application/octet-stream creator: nbarton date_created: 2023-05-13T09:41:59Z date_updated: 2023-05-13T09:41:59Z file_id: '12952' file_name: p, zA, zD, N=30 neutral IV file_size: 605902074 relation: main_file success: 1 - access_level: open_access checksum: af775dda5c4f6859cb1e5a81ec40a667 content_type: application/octet-stream creator: nbarton date_created: 2023-05-13T09:46:52Z date_updated: 2023-05-13T09:46:52Z file_id: '12953' file_name: p, zA, zD, N=30 selected k=5 file_size: 1018238746 relation: main_file success: 1 - access_level: open_access checksum: af26f3394c387d3ada14b434cd68b1e5 content_type: application/octet-stream creator: nbarton date_created: 2023-05-13T09:42:05Z date_updated: 2023-05-13T09:42:05Z file_id: '12954' file_name: Pairwise F N=30 neutral II file_size: 3197160 relation: main_file success: 1 - access_level: open_access checksum: d5da7dc0e7282dd48222e26d12e34220 content_type: application/octet-stream creator: nbarton date_created: 2023-05-13T09:42:06Z date_updated: 2023-05-13T09:42:06Z file_id: '12955' file_name: Pedigrees N=30 neutral II file_size: 55492 relation: main_file success: 1 - access_level: open_access checksum: 00f386d80677590e29f6235d49cba58d content_type: application/octet-stream creator: nbarton date_created: 2023-05-13T09:46:06Z date_updated: 2023-05-13T09:46:06Z file_id: '12956' file_name: selected reps N=30 selected k=1,2 300 reps III file_size: 474003467 relation: main_file success: 1 - access_level: open_access checksum: 658cef3eaea6136a4d24da4f074191d7 content_type: application/octet-stream creator: nbarton date_created: 2023-05-13T09:46:08Z date_updated: 2023-05-13T09:46:08Z file_id: '12957' file_name: Algorithm for caclulating identities.nb file_size: 121209 relation: main_file success: 1 - access_level: open_access checksum: db9b6dddd7a596d974e25f5e78f5c45c content_type: application/octet-stream creator: nbarton date_created: 2023-05-13T09:46:08Z date_updated: 2023-05-13T09:46:08Z file_id: '12958' file_name: Infinitesimal with dominance.nb file_size: 1803898 relation: main_file success: 1 - access_level: open_access checksum: 91f80a9fb58cae8eef2d8bf59fe30189 content_type: text/plain creator: nbarton date_created: 2023-05-16T04:09:08Z date_updated: 2023-05-16T04:09:08Z file_id: '12967' file_name: ReadMe.txt file_size: 990 relation: main_file success: 1 file_date_updated: 2023-05-16T04:09:08Z has_accepted_license: '1' keyword: - Quantitative genetics - infinitesimal model month: '05' oa: 1 oa_version: Published Version project: - _id: bd6958e0-d553-11ed-ba76-86eba6a76c00 grant_number: '101055327' name: Understanding the evolution of continuous genomes publisher: Institute of Science and Technology Austria related_material: record: - id: '14452' relation: used_in_publication status: public status: public title: The infinitesimal model with dominance 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: '2023' ... --- _id: '14494' abstract: - lang: eng text: "We provide i) gridded initial conditions (.tif), ii) modeled gridded monthly outputs (.tif), and iii) modeled hourly outputs at the station locations (.txt) for the hydrological year 2019. Information about the variables and units can be found in the figures (.png) associated to each dataset. Details about the datasets can be found in the original publication by Buri and others (2023).\r\n\r\nBuri, P., Fatichi, S., Shaw, T. E., Miles, E. S., McCarthy, M. J., Fyffe, C. L., ... & Pellicciotti, F. (2023). Land Surface Modeling in the Himalayas: On the Importance of Evaporative Fluxes for the Water Balance of a High‐Elevation Catchment. Water Resources Research, 59(10), e2022WR033841. DOI: 10.1029/2022WR033841" article_processing_charge: No author: - first_name: Pascal full_name: Buri, Pascal last_name: Buri - first_name: Simone full_name: Fatichi, Simone last_name: Fatichi - first_name: Thomas full_name: Shaw, Thomas id: 3caa3f91-1f03-11ee-96ce-e0e553054d6e last_name: Shaw - first_name: 'Evan ' full_name: 'Miles, Evan ' last_name: Miles - first_name: Michael full_name: McCarthy, Michael id: 22a2674a-61ce-11ee-94b5-d18813baf16f last_name: McCarthy - first_name: Catriona Louise full_name: Fyffe, Catriona Louise id: 001b0422-8d15-11ed-bc51-cab6c037a228 last_name: Fyffe - first_name: Stefan full_name: Fugger, Stefan last_name: Fugger - first_name: Shaoting full_name: Ren, Shaoting last_name: Ren - first_name: Marin full_name: Kneib, Marin last_name: Kneib - first_name: Achille full_name: Jouberton, Achille last_name: Jouberton - first_name: Jakob full_name: Steiner, Jakob last_name: Steiner - first_name: Koji full_name: Fujita, Koji last_name: Fujita - first_name: Francesca full_name: Pellicciotti, Francesca id: b28f055a-81ea-11ed-b70c-a9fe7f7b0e70 last_name: Pellicciotti orcid: 0000-0002-5554-8087 citation: ama: 'Buri P, Fatichi S, Shaw T, et al. Model output data to “Land surface modeling in the Himalayas: on the importance of evaporative fluxes for the water balance of a high elevation catchment.” 2023. doi:10.5281/ZENODO.8402426' apa: 'Buri, P., Fatichi, S., Shaw, T., Miles, E., McCarthy, M., Fyffe, C. L., … Pellicciotti, F. (2023). Model output data to “Land surface modeling in the Himalayas: on the importance of evaporative fluxes for the water balance of a high elevation catchment.” Zenodo. https://doi.org/10.5281/ZENODO.8402426' chicago: 'Buri, Pascal, Simone Fatichi, Thomas Shaw, Evan Miles, Michael McCarthy, Catriona Louise Fyffe, Stefan Fugger, et al. “Model Output Data to ‘Land Surface Modeling in the Himalayas: On the Importance of Evaporative Fluxes for the Water Balance of a High Elevation Catchment.’” Zenodo, 2023. https://doi.org/10.5281/ZENODO.8402426.' ieee: 'P. Buri et al., “Model output data to ‘Land surface modeling in the Himalayas: on the importance of evaporative fluxes for the water balance of a high elevation catchment.’” Zenodo, 2023.' ista: 'Buri P, Fatichi S, Shaw T, Miles E, McCarthy M, Fyffe CL, Fugger S, Ren S, Kneib M, Jouberton A, Steiner J, Fujita K, Pellicciotti F. 2023. Model output data to ‘Land surface modeling in the Himalayas: on the importance of evaporative fluxes for the water balance of a high elevation catchment’, Zenodo, 10.5281/ZENODO.8402426.' mla: 'Buri, Pascal, et al. Model Output Data to “Land Surface Modeling in the Himalayas: On the Importance of Evaporative Fluxes for the Water Balance of a High Elevation Catchment.” Zenodo, 2023, doi:10.5281/ZENODO.8402426.' short: P. Buri, S. Fatichi, T. Shaw, E. Miles, M. McCarthy, C.L. Fyffe, S. Fugger, S. Ren, M. Kneib, A. Jouberton, J. Steiner, K. Fujita, F. Pellicciotti, (2023). date_created: 2023-11-07T08:01:39Z date_published: 2023-10-03T00:00:00Z date_updated: 2023-11-07T08:12:35Z day: '03' ddc: - '550' department: - _id: FrPe doi: 10.5281/ZENODO.8402426 has_accepted_license: '1' main_file_link: - open_access: '1' url: https://10.5281/ZENODO.8402426 month: '10' oa: 1 oa_version: Published Version publisher: Zenodo related_material: record: - id: '14487' relation: used_in_publication status: public status: public title: 'Model output data to "Land surface modeling in the Himalayas: on the importance of evaporative fluxes for the water balance of a high elevation catchment"' 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_reference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2023' ... --- _id: '12869' abstract: - lang: eng text: 'We introduce a stochastic cellular automaton as a model for culture and border formation. The model can be conceptualized as a game where the expansion rate of cultures is quantified in terms of their area and perimeter in such a way that approximately round cultures get a competitive advantage. We first analyse the model with periodic boundary conditions, where we study how the model can end up in a fixed state, i.e. freezes. Then we implement the model on the European geography with mountains and rivers. We see how the model reproduces some qualitative features of European culture formation, namely that rivers and mountains are more frequently borders between cultures, mountainous regions tend to have higher cultural diversity and the central European plain has less clear cultural borders. ' acknowledgement: 'FRK acknowledges support from the Villum Foundation for support through the QMATH center of Excellence (Grant No. 10059) and the Villum Young Investigator (Grant No. 25452) programs. ' article_processing_charge: No author: - first_name: Frederik Ravn full_name: Klausen, Frederik Ravn last_name: Klausen - first_name: Asbjørn Bækgaard full_name: Lauritsen, Asbjørn Bækgaard id: e1a2682f-dc8d-11ea-abe3-81da9ac728f1 last_name: Lauritsen orcid: 0000-0003-4476-2288 citation: ama: 'Klausen FR, Lauritsen AB. Research data for: A stochastic cellular automaton model of culture formation. 2023. doi:10.15479/AT:ISTA:12869' apa: 'Klausen, F. R., & Lauritsen, A. B. (2023). Research data for: A stochastic cellular automaton model of culture formation. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:12869' chicago: 'Klausen, Frederik Ravn, and Asbjørn Bækgaard Lauritsen. “Research Data for: A Stochastic Cellular Automaton Model of Culture Formation.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/AT:ISTA:12869.' ieee: 'F. R. Klausen and A. B. Lauritsen, “Research data for: A stochastic cellular automaton model of culture formation.” Institute of Science and Technology Austria, 2023.' ista: 'Klausen FR, Lauritsen AB. 2023. Research data for: A stochastic cellular automaton model of culture formation, Institute of Science and Technology Austria, 10.15479/AT:ISTA:12869.' mla: 'Klausen, Frederik Ravn, and Asbjørn Bækgaard Lauritsen. Research Data for: A Stochastic Cellular Automaton Model of Culture Formation. Institute of Science and Technology Austria, 2023, doi:10.15479/AT:ISTA:12869.' short: F.R. Klausen, A.B. Lauritsen, (2023). date_created: 2023-04-26T12:34:49Z date_published: 2023-04-26T00:00:00Z date_updated: 2023-11-13T07:47:29Z day: '26' ddc: - '000' department: - _id: GradSch - _id: RoSe doi: 10.15479/AT:ISTA:12869 file: - access_level: open_access checksum: 85ede12d38bb8d944022a8cba4d719f5 content_type: application/octet-stream creator: alaurits date_created: 2023-04-26T12:30:06Z date_updated: 2023-04-26T12:30:06Z file_id: '12870' file_name: README.md file_size: 4567 relation: main_file success: 1 - access_level: open_access checksum: 25bf79452ae895f9c8a20571a096b4c3 content_type: application/x-zip-compressed creator: alaurits date_created: 2023-04-26T12:27:34Z date_updated: 2023-04-26T12:27:34Z file_id: '12871' file_name: simulations_era=10_flux_varied_europe.zip file_size: 732586731 relation: main_file success: 1 - access_level: open_access checksum: bca48d80ece73eb169aee7211a4a751a content_type: application/x-zip-compressed creator: alaurits date_created: 2023-04-26T12:29:53Z date_updated: 2023-04-26T12:29:53Z file_id: '12872' file_name: simulations_era=10_flux_varied_torus.zip file_size: 1743893150 relation: main_file success: 1 - access_level: open_access checksum: e77a655db15486a387a36362fbf0b665 content_type: application/x-zip-compressed creator: alaurits date_created: 2023-04-26T12:29:19Z date_updated: 2023-04-26T12:29:19Z file_id: '12873' file_name: simulations_era=10_R_varied_torus.zip file_size: 878391851 relation: main_file success: 1 - access_level: open_access checksum: 8556406513adc4aa2e0417f46680f627 content_type: application/x-zip-compressed creator: alaurits date_created: 2023-04-26T12:30:05Z date_updated: 2023-04-26T12:30:05Z file_id: '12874' file_name: simulations_era=100.zip file_size: 201652478 relation: main_file success: 1 file_date_updated: 2023-04-26T12:30:06Z has_accepted_license: '1' month: '04' oa: 1 oa_version: Published Version publisher: Institute of Science and Technology Austria related_material: record: - id: '14505' relation: used_in_publication status: for_moderation - id: '12890' relation: used_in_publication status: public status: public title: 'Research data for: A stochastic cellular automaton model of culture formation' 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: '2023' ... --- _id: '14523' abstract: - lang: eng text: see Readme file article_processing_charge: No author: - first_name: Jack full_name: Binysh, Jack last_name: Binysh - first_name: Indrajit full_name: Chakraborty, Indrajit last_name: Chakraborty - first_name: Mykyta full_name: Chubynsky, Mykyta last_name: Chubynsky - first_name: Vicente L full_name: Diaz Melian, Vicente L id: b6798902-eea0-11ea-9cbc-a8e14286c631 last_name: Diaz Melian - first_name: Scott R full_name: Waitukaitis, Scott R id: 3A1FFC16-F248-11E8-B48F-1D18A9856A87 last_name: Waitukaitis orcid: 0000-0002-2299-3176 - first_name: James full_name: Sprittles, James last_name: Sprittles - first_name: Anton full_name: Souslov, Anton last_name: Souslov citation: ama: 'Binysh J, Chakraborty I, Chubynsky M, et al. SouslovLab/PRL2023-ModellingLeidenfrostLevitationofSoftElasticSolids: v1.0.1. 2023. doi:10.5281/ZENODO.8329143' apa: 'Binysh, J., Chakraborty, I., Chubynsky, M., Diaz Melian, V. L., Waitukaitis, S. R., Sprittles, J., & Souslov, A. (2023). SouslovLab/PRL2023-ModellingLeidenfrostLevitationofSoftElasticSolids: v1.0.1. Zenodo. https://doi.org/10.5281/ZENODO.8329143' chicago: 'Binysh, Jack, Indrajit Chakraborty, Mykyta Chubynsky, Vicente L Diaz Melian, Scott R Waitukaitis, James Sprittles, and Anton Souslov. “SouslovLab/PRL2023-ModellingLeidenfrostLevitationofSoftElasticSolids: V1.0.1.” Zenodo, 2023. https://doi.org/10.5281/ZENODO.8329143.' ieee: 'J. Binysh et al., “SouslovLab/PRL2023-ModellingLeidenfrostLevitationofSoftElasticSolids: v1.0.1.” Zenodo, 2023.' ista: 'Binysh J, Chakraborty I, Chubynsky M, Diaz Melian VL, Waitukaitis SR, Sprittles J, Souslov A. 2023. SouslovLab/PRL2023-ModellingLeidenfrostLevitationofSoftElasticSolids: v1.0.1, Zenodo, 10.5281/ZENODO.8329143.' mla: 'Binysh, Jack, et al. SouslovLab/PRL2023-ModellingLeidenfrostLevitationofSoftElasticSolids: V1.0.1. Zenodo, 2023, doi:10.5281/ZENODO.8329143.' short: J. Binysh, I. Chakraborty, M. Chubynsky, V.L. Diaz Melian, S.R. Waitukaitis, J. Sprittles, A. Souslov, (2023). date_created: 2023-11-13T09:12:11Z date_published: 2023-09-08T00:00:00Z date_updated: 2023-11-13T09:21:31Z day: '08' ddc: - '530' department: - _id: ScWa doi: 10.5281/ZENODO.8329143 main_file_link: - open_access: '1' url: https://doi.org/10.5281/ZENODO.8329143 month: '09' oa: 1 oa_version: Published Version publisher: Zenodo related_material: record: - id: '14514' relation: used_in_publication status: public status: public title: 'SouslovLab/PRL2023-ModellingLeidenfrostLevitationofSoftElasticSolids: v1.0.1' type: research_data_reference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2023' ... --- _id: '14579' abstract: - lang: eng text: "This is associated with our paper \"Plant size, latitude, and phylogeny explain within-population variability in herbivory\" published in Science.\r\n" article_processing_charge: No author: - first_name: William full_name: Wetzel, William last_name: Wetzel citation: ama: 'Wetzel W. HerbVar-Network/HV-Large-Patterns-MS-public: v1.0.0. 2023. doi:10.5281/ZENODO.8133117' apa: 'Wetzel, W. (2023). HerbVar-Network/HV-Large-Patterns-MS-public: v1.0.0. Zenodo. https://doi.org/10.5281/ZENODO.8133117' chicago: 'Wetzel, William. “HerbVar-Network/HV-Large-Patterns-MS-Public: V1.0.0.” Zenodo, 2023. https://doi.org/10.5281/ZENODO.8133117.' ieee: 'W. Wetzel, “HerbVar-Network/HV-Large-Patterns-MS-public: v1.0.0.” Zenodo, 2023.' ista: 'Wetzel W. 2023. HerbVar-Network/HV-Large-Patterns-MS-public: v1.0.0, Zenodo, 10.5281/ZENODO.8133117.' mla: 'Wetzel, William. HerbVar-Network/HV-Large-Patterns-MS-Public: V1.0.0. Zenodo, 2023, doi:10.5281/ZENODO.8133117.' short: W. Wetzel, (2023). date_created: 2023-11-20T11:07:45Z date_published: 2023-07-11T00:00:00Z date_updated: 2023-11-20T11:17:33Z day: '11' ddc: - '570' department: - _id: NiBa doi: 10.5281/ZENODO.8133117 main_file_link: - open_access: '1' url: https://doi.org/10.5281/zenodo.8133118 month: '07' oa: 1 oa_version: Published Version publisher: Zenodo related_material: record: - id: '14552' relation: used_in_publication status: public status: public title: 'HerbVar-Network/HV-Large-Patterns-MS-public: v1.0.0' type: research_data_reference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2023' ... --- _id: '14562' abstract: - lang: eng text: "Regulation of the Arp2/3 complex is required for productive nucleation of branched actin networks. An emerging aspect of regulation is the incorporation of subunit isoforms into the Arp2/3 complex. Specifically, both ArpC5 subunit isoforms, ArpC5 and ArpC5L, have been reported to fine-tune nucleation activity and branch junction stability. We have combined reverse genetics and cellular structural biology to describe how ArpC5 and ArpC5L differentially affect cell migration. Both define the structural stability of ArpC1 in branch junctions and, in turn, by determining protrusion characteristics, affect protein dynamics and actin network ultrastructure. ArpC5 isoforms also affect the positioning of members of the Ena/Vasodilator-stimulated phosphoprotein (VASP) family of actin filament elongators, which mediate ArpC5 isoform–specific effects on the actin assembly level. Our results suggest that ArpC5 and Ena/VASP proteins are part of a signaling pathway enhancing cell migration.\r\n" acknowledged_ssus: - _id: LifeSc - _id: Bio - _id: ScienComp - _id: EM-Fac acknowledgement: "We would like to thank K. von Peinen and B. Denker (Helmholtz Centre for Infection Research, Braunschweig, Germany) for experimental and technical assistance, respectively.\r\nFunding: This research was supported by the Scientific Service Units (SSUs) of ISTA through resources provided by Scientific Computing (SciComp), the Life Science Facility (LSF), the Imaging and Optics facility (IOF), and the Electron Microscopy Facility (EMF). We acknowledge support from ISTA and from the Austrian Science Fund (FWF) (P33367) to F.K.M.S., from the Research Training Group GRK2223 and the Helmholtz Society to K.R,. and from the Deutsche Forschungsgemeinschaft (DFG) to J.F. and K.R." article_processing_charge: No author: - 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: Schur FK. Research data of the publication “ArpC5 isoforms regulate Arp2/3 complex-dependent protrusion through differential Ena/VASP positioning.” 2023. doi:10.15479/AT:ISTA:14562 apa: Schur, F. K. (2023). Research data of the publication “ArpC5 isoforms regulate Arp2/3 complex-dependent protrusion through differential Ena/VASP positioning.” Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:14562 chicago: Schur, Florian KM. “Research Data of the Publication ‘ArpC5 Isoforms Regulate Arp2/3 Complex-Dependent Protrusion through Differential Ena/VASP Positioning.’” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/AT:ISTA:14562. ieee: F. K. Schur, “Research data of the publication ‘ArpC5 isoforms regulate Arp2/3 complex-dependent protrusion through differential Ena/VASP positioning.’” Institute of Science and Technology Austria, 2023. ista: Schur FK. 2023. Research data of the publication ‘ArpC5 isoforms regulate Arp2/3 complex-dependent protrusion through differential Ena/VASP positioning’, Institute of Science and Technology Austria, 10.15479/AT:ISTA:14562. mla: Schur, Florian KM. Research Data of the Publication “ArpC5 Isoforms Regulate Arp2/3 Complex-Dependent Protrusion through Differential Ena/VASP Positioning.” Institute of Science and Technology Austria, 2023, doi:10.15479/AT:ISTA:14562. short: F.K. Schur, (2023). contributor: - contributor_type: researcher first_name: Florian id: 404F5528-F248-11E8-B48F-1D18A9856A87 last_name: Fäßler orcid: 0000-0001-7149-769X - contributor_type: researcher first_name: Manjunath id: 305ab18b-dc7d-11ea-9b2f-b58195228ea2 last_name: Javoor - contributor_type: researcher first_name: Julia id: 3B12E2E6-F248-11E8-B48F-1D18A9856A87 last_name: Datler orcid: 0000-0002-3616-8580 - contributor_type: researcher first_name: Hermann last_name: Döring - contributor_type: researcher first_name: Florian id: b9d234ba-9e33-11ed-95b6-cd561df280e6 last_name: Hofer - contributor_type: researcher first_name: Georgi A id: 38C393BE-F248-11E8-B48F-1D18A9856A87 last_name: Dimchev orcid: 0000-0001-8370-6161 - contributor_type: researcher first_name: Victor-Valentin id: 3661B498-F248-11E8-B48F-1D18A9856A87 last_name: Hodirnau - contributor_type: researcher first_name: Jan last_name: Faix - contributor_type: researcher first_name: Klemens last_name: Rottner - contributor_type: researcher first_name: Florian KM id: 48AD8942-F248-11E8-B48F-1D18A9856A87 last_name: Schur orcid: 0000-0003-4790-8078 date_created: 2023-11-20T09:22:33Z date_published: 2023-11-21T00:00:00Z date_updated: 2023-11-21T08:05:34Z day: '21' ddc: - '570' department: - _id: FlSc doi: 10.15479/AT:ISTA:14562 file: - access_level: open_access checksum: e9bab797b44614f144a5b02d9636f8c3 content_type: application/zip creator: fschur date_created: 2023-11-20T10:27:17Z date_updated: 2023-11-20T10:27:17Z file_id: '14570' file_name: Figure2.zip file_size: 1581687449 relation: main_file success: 1 - access_level: open_access checksum: 4efd388cccd03c549fc90f6e46d37006 content_type: application/zip creator: fschur date_created: 2023-11-20T10:29:18Z date_updated: 2023-11-20T10:29:18Z file_id: '14571' file_name: SupplementaryFigure3.zip file_size: 116088565 relation: main_file success: 1 - access_level: open_access checksum: bdeb232dc94d0c22a3f7e0d18189ce89 content_type: application/zip creator: fschur date_created: 2023-11-20T10:44:39Z date_updated: 2023-11-20T10:44:39Z file_id: '14572' file_name: Figure5.zip file_size: 5154614201 relation: main_file success: 1 - access_level: open_access checksum: 83aee17d621a05d865f68f39c8892d27 content_type: application/zip creator: fschur date_created: 2023-11-20T10:46:00Z date_updated: 2023-11-20T10:46:00Z file_id: '14573' file_name: SupplementaryFigure7.zip file_size: 1277893286 relation: main_file success: 1 - access_level: open_access checksum: fb9beb6fe15c8dac6679dd02044d2ea6 content_type: application/zip creator: fschur date_created: 2023-11-20T10:46:08Z date_updated: 2023-11-20T10:46:08Z file_id: '14574' file_name: SupplementaryFigure9.zip file_size: 228485124 relation: main_file success: 1 - access_level: open_access checksum: 4f3644e5feabe4824486d56885bb79fe content_type: application/zip creator: fschur date_created: 2023-11-20T10:46:32Z date_updated: 2023-11-20T10:46:32Z file_id: '14575' file_name: SupplementaryFigure10.zip file_size: 1226788198 relation: main_file success: 1 - access_level: open_access checksum: 96167f722ed0ca78e30681cd1573b9d7 content_type: application/zip creator: fschur date_created: 2023-11-20T10:46:17Z date_updated: 2023-11-20T10:46:17Z file_id: '14576' file_name: SupplementaryFigure11.zip file_size: 277577131 relation: main_file success: 1 - access_level: open_access checksum: d1e03c9805c18cfbc2e9fdf38a9f556f content_type: application/zip creator: fschur date_created: 2023-11-20T10:46:29Z date_updated: 2023-11-20T10:46:29Z file_id: '14577' file_name: SupplementaryFigure15.zip file_size: 591483468 relation: main_file success: 1 - access_level: open_access checksum: 4d437c04fdb3c1e699618063c4bd21c3 content_type: application/zip creator: fschur date_created: 2023-11-20T10:47:00Z date_updated: 2023-11-20T10:47:00Z file_id: '14578' file_name: SupplementaryFigure17.zip file_size: 1709528579 relation: main_file success: 1 - access_level: open_access checksum: 967b5378a4f16c43f490eae328afe50e content_type: application/zip creator: fschur date_created: 2023-11-20T11:26:36Z date_updated: 2023-11-20T11:26:36Z file_id: '14581' file_name: SupplementaryFigure4.zip file_size: 1920765280 relation: main_file success: 1 - access_level: open_access checksum: 11899986cf0b471d258fe168ee33a3ea content_type: application/zip creator: fschur date_created: 2023-11-20T11:38:12Z date_updated: 2023-11-20T11:38:12Z file_id: '14583' file_name: Figure1_partA.zip file_size: 3013566196 relation: main_file success: 1 - access_level: open_access checksum: c452afe1ab506d58d32e601d5b3878bb content_type: application/zip creator: fschur date_created: 2023-11-20T11:43:23Z date_updated: 2023-11-20T11:43:23Z file_id: '14584' file_name: Figure1_partB.zip file_size: 3250260203 relation: main_file success: 1 - access_level: open_access checksum: 223c98eceecbe65dd268f4f363a620d8 content_type: text/rtf creator: fschur date_created: 2023-11-20T11:49:58Z date_updated: 2023-11-20T11:49:58Z file_id: '14585' file_name: ReadMe.rtf file_size: 1460 relation: main_file success: 1 file_date_updated: 2023-11-20T11:49:58Z has_accepted_license: '1' license: https://creativecommons.org/licenses/by-sa/4.0/ month: '11' 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 publisher: Institute of Science and Technology Austria related_material: record: - id: '12334' relation: used_in_publication status: public status: public title: Research data of the publication "ArpC5 isoforms regulate Arp2/3 complex-dependent protrusion through differential Ena/VASP positioning" tmp: image: /images/cc_by_sa.png legal_code_url: https://creativecommons.org/licenses/by-sa/4.0/legalcode name: Creative Commons Attribution-ShareAlike 4.0 International Public License (CC BY-SA 4.0) short: CC BY-SA (4.0) type: research_data user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2023' ... --- _id: '14472' abstract: - lang: eng text: "Data related to the following paper:\r\n\"Stress granules plug and stabilize damaged endolysosomal membranes\" (https://doi.org/10.1038/s41586-023-06726-w)\r\n\r\nAbstract: \r\nEndomembrane damage represents a form of stress that is detrimental for eukaryotic cells. To cope with this threat, cells possess mechanisms that repair the damage and restore cellular homeostasis. Endomembrane damage also results in organelle instability and the mechanisms by which cells stabilize damaged endomembranes to enable membrane repair remains unknown. In this work we use a minimal coarse-grained molecular dynamics system to explore how lipid vesicles undergoing poration in a protein-rich medium can be plugged and stabilised by condensate formation. The solution of proteins in and out of the vesicle is described by beads dispersed in implicit solvent. The membrane is described as a one-bead-thick fluid elastic layer of mechanical properties that mimic biological membranes. We tune the interactions between solution beads in the different compartments to capture the differences between the cytoplasmic and endosomal protein solutions and explore how the system responds to different degrees of membrane poration. We find that, in the right interaction regime, condensates form rapidly at the damage site upon solution mixing and act as a plug that prevents futher mixing and destabilisation of the vesicle. Further, when the condensate can interact with the membrane (wetting interactions) we find that it mediates pore sealing and membrane repair. This research is part of the work published in \"Stress granules plug and stabilize damaged endolysosomal membranes\", Bussi et al, Nature, 2023 - 10.1038/s41586-023-06726-w." article_processing_charge: No author: - first_name: Christian Eduardo full_name: Vanhille-Campos, Christian Eduardo id: 3adeca52-9313-11ed-b1ac-c170b2505714 last_name: Vanhille-Campos - first_name: Anđela full_name: Šarić, Anđela id: bf63d406-f056-11eb-b41d-f263a6566d8b last_name: Šarić orcid: 0000-0002-7854-2139 citation: ama: Vanhille-Campos CE, Šarić A. Stress granules plug and stabilize damaged endolysosomal membranes. 2023. doi:10.15479/AT:ISTA:14472 apa: Vanhille-Campos, C. E., & Šarić, A. (2023). Stress granules plug and stabilize damaged endolysosomal membranes. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:14472 chicago: Vanhille-Campos, Christian Eduardo, and Anđela Šarić. “Stress Granules Plug and Stabilize Damaged Endolysosomal Membranes.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/AT:ISTA:14472. ieee: C. E. Vanhille-Campos and A. Šarić, “Stress granules plug and stabilize damaged endolysosomal membranes.” Institute of Science and Technology Austria, 2023. ista: Vanhille-Campos CE, Šarić A. 2023. Stress granules plug and stabilize damaged endolysosomal membranes, Institute of Science and Technology Austria, 10.15479/AT:ISTA:14472. mla: Vanhille-Campos, Christian Eduardo, and Anđela Šarić. Stress Granules Plug and Stabilize Damaged Endolysosomal Membranes. Institute of Science and Technology Austria, 2023, doi:10.15479/AT:ISTA:14472. short: C.E. Vanhille-Campos, A. Šarić, (2023). date_created: 2023-10-30T16:38:32Z date_published: 2023-10-31T00:00:00Z date_updated: 2023-11-27T09:05:07Z day: '31' ddc: - '570' department: - _id: AnSa doi: 10.15479/AT:ISTA:14472 file: - access_level: open_access checksum: a18706e952e8660c51ede52a167270b7 content_type: application/zip creator: ipalaia date_created: 2023-10-30T16:31:08Z date_updated: 2023-10-30T16:31:08Z file_id: '14473' file_name: SGporecondensation-main.zip file_size: 62821432 relation: main_file success: 1 - access_level: open_access checksum: 389eab31c6509dbc05795017fb618758 content_type: text/plain creator: dernst date_created: 2023-10-31T08:57:50Z date_updated: 2023-10-31T08:57:50Z file_id: '14474' file_name: README.txt file_size: 1697 relation: main_file success: 1 file_date_updated: 2023-10-31T08:57:50Z has_accepted_license: '1' month: '10' oa: 1 oa_version: Published Version publisher: Institute of Science and Technology Austria related_material: record: - id: '14610' relation: used_in_publication status: public status: public title: Stress granules plug and stabilize damaged endolysosomal membranes 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: '2023' ... --- _id: '14616' abstract: - lang: eng text: Sex chromosomes have evolved independently multiple times, but why some are conserved for more than 100 million years whereas others turnover rapidly remains an open question. Here, we examine the homology of sex chromosomes across nine orders of insects, plus the outgroup springtails. We find that the X chromosome is likely homologous across insects and springtails; the only exception is in the Lepidoptera, which has lost the X and now has a ZZ/ZW sex chromosome system. These results suggest the ancestral insect X chromosome has persisted for more than 450 million years – the oldest known sex chromosome to date. Further, we propose that the shrinking of gene content of the Dipteran X chromosome has allowed for a burst of sex-chromosome turnover that is absent from other speciose insect orders. article_processing_charge: No author: - first_name: Melissa A full_name: Toups, Melissa A id: 4E099E4E-F248-11E8-B48F-1D18A9856A87 last_name: Toups orcid: 0000-0002-9752-7380 - first_name: Beatriz full_name: Vicoso, Beatriz id: 49E1C5C6-F248-11E8-B48F-1D18A9856A87 last_name: Vicoso orcid: 0000-0002-4579-8306 citation: ama: Toups MA, Vicoso B. The X chromosome of insects likely predates the origin of Class Insecta. 2023. doi:10.5061/DRYAD.HX3FFBGKT apa: Toups, M. A., & Vicoso, B. (2023). The X chromosome of insects likely predates the origin of Class Insecta. Dryad. https://doi.org/10.5061/DRYAD.HX3FFBGKT chicago: Toups, Melissa A, and Beatriz Vicoso. “The X Chromosome of Insects Likely Predates the Origin of Class Insecta.” Dryad, 2023. https://doi.org/10.5061/DRYAD.HX3FFBGKT. ieee: M. A. Toups and B. Vicoso, “The X chromosome of insects likely predates the origin of Class Insecta.” Dryad, 2023. ista: Toups MA, Vicoso B. 2023. The X chromosome of insects likely predates the origin of Class Insecta, Dryad, 10.5061/DRYAD.HX3FFBGKT. mla: Toups, Melissa A., and Beatriz Vicoso. The X Chromosome of Insects Likely Predates the Origin of Class Insecta. Dryad, 2023, doi:10.5061/DRYAD.HX3FFBGKT. short: M.A. Toups, B. Vicoso, (2023). date_created: 2023-11-28T08:01:53Z date_published: 2023-09-15T00:00:00Z date_updated: 2023-11-28T08:17:31Z day: '15' ddc: - '570' department: - _id: BeVi doi: 10.5061/DRYAD.HX3FFBGKT has_accepted_license: '1' main_file_link: - open_access: '1' url: https://doi.org/10.5061/dryad.hx3ffbgkt month: '09' oa: 1 oa_version: Published Version publisher: Dryad related_material: record: - id: '14604' relation: used_in_publication status: public status: public title: The X chromosome of insects likely predates the origin of Class Insecta 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_reference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2023' ... --- _id: '14617' abstract: - lang: eng text: Sex chromosomes have evolved independently multiple times, but why some are conserved for more than 100 million years whereas others turnover rapidly remains an open question. Here, we examine the homology of sex chromosomes across nine orders of insects, plus the outgroup springtails. We find that the X chromosome is likely homologous across insects and springtails; the only exception is in the Lepidoptera, which has lost the X and now has a ZZ/ZW sex chromosome system. These results suggest the ancestral insect X chromosome has persisted for more than 450 million years – the oldest known sex chromosome to date. Further, we propose that the shrinking of gene content of the Dipteran X chromosome has allowed for a burst of sex-chromosome turnover that is absent from other speciose insect orders. article_processing_charge: No author: - first_name: Melissa A full_name: Toups, Melissa A id: 4E099E4E-F248-11E8-B48F-1D18A9856A87 last_name: Toups orcid: 0000-0002-9752-7380 - first_name: Beatriz full_name: Vicoso, Beatriz id: 49E1C5C6-F248-11E8-B48F-1D18A9856A87 last_name: Vicoso orcid: 0000-0002-4579-8306 citation: ama: Toups MA, Vicoso B. The X chromosome of insects likely predates the origin of Class Insecta. 2023. doi:10.5281/ZENODO.8138705 apa: Toups, M. A., & Vicoso, B. (2023). The X chromosome of insects likely predates the origin of Class Insecta. Zenodo. https://doi.org/10.5281/ZENODO.8138705 chicago: Toups, Melissa A, and Beatriz Vicoso. “The X Chromosome of Insects Likely Predates the Origin of Class Insecta.” Zenodo, 2023. https://doi.org/10.5281/ZENODO.8138705. ieee: M. A. Toups and B. Vicoso, “The X chromosome of insects likely predates the origin of Class Insecta.” Zenodo, 2023. ista: Toups MA, Vicoso B. 2023. The X chromosome of insects likely predates the origin of Class Insecta, Zenodo, 10.5281/ZENODO.8138705. mla: Toups, Melissa A., and Beatriz Vicoso. The X Chromosome of Insects Likely Predates the Origin of Class Insecta. Zenodo, 2023, doi:10.5281/ZENODO.8138705. short: M.A. Toups, B. Vicoso, (2023). date_created: 2023-11-28T08:04:03Z date_published: 2023-09-15T00:00:00Z date_updated: 2023-11-28T08:25:28Z day: '15' ddc: - '570' department: - _id: BeVi doi: 10.5281/ZENODO.8138705 has_accepted_license: '1' main_file_link: - open_access: '1' url: https://doi.org/10.5281/zenodo.8138705 month: '09' oa: 1 oa_version: Published Version other_data_license: MIT License publisher: Zenodo related_material: record: - id: '14604' relation: used_in_publication status: public status: public title: The X chromosome of insects likely predates the origin of Class Insecta type: research_data_reference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2023' ... --- _id: '14619' abstract: - lang: eng text: Data underlying the publication "A streamlined molecular-dynamics workflow for computing solubilities of molecular and ionic crystals" (DOI https://doi.org/10.1063/5.0173341). article_processing_charge: No author: - first_name: Bingqing full_name: Cheng, Bingqing id: cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9 last_name: Cheng orcid: 0000-0002-3584-9632 citation: ama: 'Cheng B. BingqingCheng/solubility: V1.0. 2023. doi:10.5281/ZENODO.8398094' apa: 'Cheng, B. (2023). BingqingCheng/solubility: V1.0. Zenodo. https://doi.org/10.5281/ZENODO.8398094' chicago: 'Cheng, Bingqing. “BingqingCheng/Solubility: V1.0.” Zenodo, 2023. https://doi.org/10.5281/ZENODO.8398094.' ieee: 'B. Cheng, “BingqingCheng/solubility: V1.0.” Zenodo, 2023.' ista: 'Cheng B. 2023. BingqingCheng/solubility: V1.0, Zenodo, 10.5281/ZENODO.8398094.' mla: 'Cheng, Bingqing. BingqingCheng/Solubility: V1.0. Zenodo, 2023, doi:10.5281/ZENODO.8398094.' short: B. Cheng, (2023). date_created: 2023-11-28T08:32:18Z date_published: 2023-10-02T00:00:00Z date_updated: 2023-11-28T08:39:22Z day: '02' ddc: - '530' department: - _id: BiCh doi: 10.5281/ZENODO.8398094 has_accepted_license: '1' main_file_link: - open_access: '1' url: https://doi.org/10.5281/zenodo.8398094 month: '10' oa: 1 oa_version: Published Version publisher: Zenodo related_material: record: - id: '14603' relation: used_in_publication status: public status: public title: 'BingqingCheng/solubility: V1.0' type: research_data_reference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2023' ... --- _id: '12693' abstract: - lang: eng text: See Readme File for further information. article_processing_charge: No author: - first_name: Sylvia full_name: Cremer, Sylvia id: 2F64EC8C-F248-11E8-B48F-1D18A9856A87 last_name: Cremer orcid: 0000-0002-2193-3868 citation: ama: 'Cremer S. Source data for Metzler et al, 2023: Trade-offs between immunity and competitive ability in fighting ant males . 2023. doi:10.15479/AT:ISTA:12693' apa: 'Cremer, S. (2023). Source data for Metzler et al, 2023: Trade-offs between immunity and competitive ability in fighting ant males . Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:12693' chicago: 'Cremer, Sylvia. “Source Data for Metzler et Al, 2023: Trade-Offs between Immunity and Competitive Ability in Fighting Ant Males .” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/AT:ISTA:12693.' ieee: 'S. Cremer, “Source data for Metzler et al, 2023: Trade-offs between immunity and competitive ability in fighting ant males .” Institute of Science and Technology Austria, 2023.' ista: 'Cremer S. 2023. Source data for Metzler et al, 2023: Trade-offs between immunity and competitive ability in fighting ant males , Institute of Science and Technology Austria, 10.15479/AT:ISTA:12693.' mla: 'Cremer, Sylvia. Source Data for Metzler et Al, 2023: Trade-Offs between Immunity and Competitive Ability in Fighting Ant Males . Institute of Science and Technology Austria, 2023, doi:10.15479/AT:ISTA:12693.' short: S. Cremer, (2023). contributor: - contributor_type: data_collector first_name: Sina id: 48204546-F248-11E8-B48F-1D18A9856A87 last_name: Metzler - contributor_type: data_collector first_name: Jessica id: 21516227-15aa-11ec-9fb2-c6e8ffc155d3 last_name: Kirchner - contributor_type: data_collector first_name: Anna V id: 406F989C-F248-11E8-B48F-1D18A9856A87 last_name: Grasse date_created: 2023-02-28T06:38:37Z date_published: 2023-02-28T00:00:00Z date_updated: 2023-12-13T11:13:13Z day: '28' ddc: - '570' department: - _id: SyCr doi: 10.15479/AT:ISTA:12693 file: - access_level: open_access checksum: c1565d655ca05601acfd84e0d12b8563 content_type: application/pdf creator: scremer date_created: 2023-02-28T06:34:08Z date_updated: 2023-02-28T06:34:08Z file_id: '12694' file_name: Metzler_ReadMe.pdf file_size: 77070 relation: main_file success: 1 - access_level: open_access checksum: 75c4c4948563d6261cb7548f80d909f1 content_type: application/vnd.openxmlformats-officedocument.spreadsheetml.sheet creator: scremer date_created: 2023-02-28T06:34:12Z date_updated: 2023-02-28T06:34:12Z file_id: '12695' file_name: Metzler_RepositoryData.xlsx file_size: 88001 relation: main_file success: 1 file_date_updated: 2023-02-28T06:34:12Z has_accepted_license: '1' month: '02' oa: 1 oa_version: Published Version publisher: Institute of Science and Technology Austria related_material: record: - id: '12696' relation: used_in_publication status: public status: public title: 'Source data for Metzler et al, 2023: Trade-offs between immunity and competitive ability in fighting ant males ' 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: research_data user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2023' ... --- _id: '13336' article_processing_charge: No author: - first_name: Maria full_name: Kleshnina, Maria id: 4E21749C-F248-11E8-B48F-1D18A9856A87 last_name: Kleshnina citation: ama: 'Kleshnina M. kleshnina/stochgames_info: The effect of environmental information on evolution of cooperation in stochastic games. 2023. doi:10.5281/ZENODO.8059564' apa: 'Kleshnina, M. (2023). kleshnina/stochgames_info: The effect of environmental information on evolution of cooperation in stochastic games. Zenodo. https://doi.org/10.5281/ZENODO.8059564' chicago: 'Kleshnina, Maria. “Kleshnina/Stochgames_info: The Effect of Environmental Information on Evolution of Cooperation in Stochastic Games.” Zenodo, 2023. https://doi.org/10.5281/ZENODO.8059564.' ieee: 'M. Kleshnina, “kleshnina/stochgames_info: The effect of environmental information on evolution of cooperation in stochastic games.” Zenodo, 2023.' ista: 'Kleshnina M. 2023. kleshnina/stochgames_info: The effect of environmental information on evolution of cooperation in stochastic games, Zenodo, 10.5281/ZENODO.8059564.' mla: 'Kleshnina, Maria. Kleshnina/Stochgames_info: The Effect of Environmental Information on Evolution of Cooperation in Stochastic Games. Zenodo, 2023, doi:10.5281/ZENODO.8059564.' short: M. Kleshnina, (2023). date_created: 2023-07-31T11:30:46Z date_published: 2023-06-20T00:00:00Z date_updated: 2023-12-13T11:42:37Z day: '20' ddc: - '000' department: - _id: KrCh doi: 10.5281/ZENODO.8059564 main_file_link: - open_access: '1' url: https://doi.org/10.5281/zenodo.8059564 month: '06' oa: 1 oa_version: Published Version publisher: Zenodo related_material: record: - id: '13258' relation: used_in_publication status: public status: public title: 'kleshnina/stochgames_info: The effect of environmental information on evolution of cooperation in stochastic games' type: research_data_reference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2023' ... --- _id: '12933' abstract: - lang: eng text: Datasets of the publication "Sex-specific estimation of cis and trans regulation of gene expression in heads and gonads of Drosophila melanogaster". article_processing_charge: No author: - first_name: Gemma full_name: Puixeu Sala, Gemma id: 33AB266C-F248-11E8-B48F-1D18A9856A87 last_name: Puixeu Sala orcid: 0000-0001-8330-1754 citation: ama: 'Puixeu Sala G. Data from: Sex-specific estimation of cis and trans regulation of gene expression in heads and gonads of Drosophila melanogaster. 2023. doi:10.15479/AT:ISTA:12933' apa: 'Puixeu Sala, G. (2023). Data from: Sex-specific estimation of cis and trans regulation of gene expression in heads and gonads of Drosophila melanogaster. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:12933' chicago: 'Puixeu Sala, Gemma. “Data from: Sex-Specific Estimation of Cis and Trans Regulation of Gene Expression in Heads and Gonads of Drosophila Melanogaster.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/AT:ISTA:12933.' ieee: 'G. Puixeu Sala, “Data from: Sex-specific estimation of cis and trans regulation of gene expression in heads and gonads of Drosophila melanogaster.” Institute of Science and Technology Austria, 2023.' ista: 'Puixeu Sala G. 2023. Data from: Sex-specific estimation of cis and trans regulation of gene expression in heads and gonads of Drosophila melanogaster, Institute of Science and Technology Austria, 10.15479/AT:ISTA:12933.' mla: 'Puixeu Sala, Gemma. Data from: Sex-Specific Estimation of Cis and Trans Regulation of Gene Expression in Heads and Gonads of Drosophila Melanogaster. Institute of Science and Technology Austria, 2023, doi:10.15479/AT:ISTA:12933.' short: G. Puixeu Sala, (2023). contributor: - first_name: Ariana id: 2A0848E2-F248-11E8-B48F-1D18A9856A87 last_name: Macon - first_name: Beatriz id: 49E1C5C6-F248-11E8-B48F-1D18A9856A87 last_name: Vicoso orcid: 0000-0002-4579-8306 date_created: 2023-05-10T10:00:49Z date_published: 2023-05-15T00:00:00Z date_updated: 2023-12-13T12:15:36Z day: '15' ddc: - '570' department: - _id: GradSch - _id: NiBa - _id: BeVi doi: 10.15479/AT:ISTA:12933 file: - access_level: open_access checksum: 0ba0bcd0bb8b18d84792136a4370df90 content_type: text/csv creator: gpuixeus date_created: 2023-05-10T09:41:43Z date_updated: 2023-05-10T09:41:43Z file_id: '12934' file_name: Dataset_S1.csv file_size: 8029982 relation: main_file success: 1 - access_level: open_access checksum: a62aa9a6d4904e0fdb699cf752640863 content_type: text/csv creator: gpuixeus date_created: 2023-05-10T09:41:43Z date_updated: 2023-05-10T09:41:43Z file_id: '12935' file_name: Dataset_S2.csv file_size: 13667640 relation: main_file success: 1 - access_level: open_access checksum: e20ea7f4f8a9bdf1b3849a44664ae58b content_type: text/csv creator: gpuixeus date_created: 2023-05-10T09:41:48Z date_updated: 2023-05-10T09:41:48Z file_id: '12936' file_name: Dataset_S3.csv file_size: 8369141 relation: main_file success: 1 - access_level: open_access checksum: f6156e5fc44446c907ddd0d7289d4cf8 content_type: text/csv creator: gpuixeus date_created: 2023-05-10T09:41:50Z date_updated: 2023-05-10T09:41:50Z file_id: '12937' file_name: Dataset_S4.csv file_size: 19543247 relation: main_file success: 1 - access_level: open_access checksum: ae9f54c77a1c42b666ae6c1dfd33ac86 content_type: text/plain creator: gpuixeus date_created: 2023-05-11T12:50:18Z date_updated: 2023-05-11T12:50:18Z file_id: '12944' file_name: readme.txt file_size: 4566 relation: main_file success: 1 file_date_updated: 2023-05-11T12:50:18Z has_accepted_license: '1' month: '05' oa: 1 oa_version: Published Version publisher: Institute of Science and Technology Austria related_material: record: - id: '14058' relation: used_in_publication status: public - id: '14077' relation: used_in_publication status: public status: public title: 'Data from: Sex-specific estimation of cis and trans regulation of gene expression in heads and gonads of Drosophila melanogaster' 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: '2023' ... --- _id: '12817' abstract: - lang: eng text: 3D-reconstruction of living brain tissue down to individual synapse level would create opportunities for decoding the dynamics and structure-function relationships of the brain’s complex and dense information processing network. However, it has been hindered by insufficient 3D-resolution, inadequate signal-to-noise-ratio, and prohibitive light burden in optical imaging, whereas electron microscopy is inherently static. Here we solved these challenges by developing an integrated optical/machine learning technology, LIONESS (Live Information-Optimized Nanoscopy Enabling Saturated Segmentation). It leverages optical modifications to stimulated emission depletion (STED) microscopy in comprehensively, extracellularly labelled tissue and prior information on sample structure via machine learning to simultaneously achieve isotropic super-resolution, high signal-to-noise-ratio, and compatibility with living tissue. This allows dense deep-learning-based instance segmentation and 3D-reconstruction at synapse level incorporating molecular, activity, and morphodynamic information. LIONESS opens up avenues for studying the dynamic functional (nano-)architecture of living brain tissue. acknowledged_ssus: - _id: ScienComp - _id: Bio - _id: PreCl - _id: LifeSc - _id: M-Shop - _id: E-Lib acknowledgement: 'We thank J. Vorlaufer, N. Agudelo, A. Wartak for microscope maintenance and troubleshooting, C. Kreuzinger and A. Freeman for technical assistance, and M. Šuplata for hardware control support, and Márcia Cunha dos Santos for initial exploration of software. We thank Paul Henderson for advice on deep-learning training and Michael Sixt, Scott Boyd, and Tamara Weiss for discussions and critical reading of the manuscript. Luke Lavis (Janelia Research Campus) generously provided JF585-HaloTag ligand. ' article_processing_charge: No author: - first_name: Johann G full_name: Danzl, Johann G id: 42EFD3B6-F248-11E8-B48F-1D18A9856A87 last_name: Danzl orcid: 0000-0001-8559-3973 citation: ama: Danzl JG. Research data for the publication “Dense 4D nanoscale reconstruction of living brain tissue.” 2023. doi:10.15479/AT:ISTA:12817 apa: Danzl, J. G. (2023). Research data for the publication “Dense 4D nanoscale reconstruction of living brain tissue.” Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:12817 chicago: Danzl, Johann G. “Research Data for the Publication ‘Dense 4D Nanoscale Reconstruction of Living Brain Tissue.’” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/AT:ISTA:12817. ieee: J. G. Danzl, “Research data for the publication ‘Dense 4D nanoscale reconstruction of living brain tissue.’” Institute of Science and Technology Austria, 2023. ista: Danzl JG. 2023. Research data for the publication ‘Dense 4D nanoscale reconstruction of living brain tissue’, Institute of Science and Technology Austria, 10.15479/AT:ISTA:12817. mla: Danzl, Johann G. Research Data for the Publication “Dense 4D Nanoscale Reconstruction of Living Brain Tissue.” Institute of Science and Technology Austria, 2023, doi:10.15479/AT:ISTA:12817. short: J.G. Danzl, (2023). contributor: - first_name: Philipp id: 39BDC62C-F248-11E8-B48F-1D18A9856A87 last_name: Velicky orcid: 0000-0002-2340-7431 - first_name: Eder id: 3FB91342-F248-11E8-B48F-1D18A9856A87 last_name: Miguel Villalba - first_name: Julia M id: 443DB6DE-F248-11E8-B48F-1D18A9856A87 last_name: Michalska - first_name: Julia id: 46E28B80-F248-11E8-B48F-1D18A9856A87 last_name: Lyudchik - first_name: Donglai last_name: Wei - first_name: Zudi last_name: Lin - first_name: Jake id: 63836096-4690-11EA-BD4E-32803DDC885E last_name: Watson orcid: 0000-0002-8698-3823 - first_name: Jakob last_name: Troidl - first_name: Johanna last_name: Beyer - first_name: Yoav id: 43DF3136-F248-11E8-B48F-1D18A9856A87 last_name: Ben Simon - first_name: Christoph M id: 4DF26D8C-F248-11E8-B48F-1D18A9856A87 last_name: Sommer orcid: 0000-0003-1216-9105 - first_name: Wiebke id: 425C1CE8-F248-11E8-B48F-1D18A9856A87 last_name: Jahr - first_name: Alban id: 9ac8f577-2357-11eb-997a-e566c5550886 last_name: Cenameri - first_name: Johannes last_name: Broichhagen - first_name: 'Seth G. 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S., Clopath, C. Dynamic and selective engrams emerge with memory consolidation. 2023.' article_processing_charge: No author: - first_name: Douglas full_name: Feitosa Tomé, Douglas id: 0eed2d40-3d48-11ec-8d38-f789cc2e40b2 last_name: Feitosa Tomé citation: ama: 'Feitosa Tomé D. douglastome/dynamic-engrams: Dynamic and selective engrams emerge with memory consolidation. 2023. doi:10.5281/ZENODO.10251087' apa: 'Feitosa Tomé, D. (2023). douglastome/dynamic-engrams: Dynamic and selective engrams emerge with memory consolidation. Zenodo. https://doi.org/10.5281/ZENODO.10251087' chicago: 'Feitosa Tomé, Douglas. “Douglastome/Dynamic-Engrams: Dynamic and Selective Engrams Emerge with Memory Consolidation.” Zenodo, 2023. https://doi.org/10.5281/ZENODO.10251087.' ieee: 'D. Feitosa Tomé, “douglastome/dynamic-engrams: Dynamic and selective engrams emerge with memory consolidation.” Zenodo, 2023.' ista: 'Feitosa Tomé D. 2023. douglastome/dynamic-engrams: Dynamic and selective engrams emerge with memory consolidation, Zenodo, 10.5281/ZENODO.10251087.' mla: 'Feitosa Tomé, Douglas. Douglastome/Dynamic-Engrams: Dynamic and Selective Engrams Emerge with Memory Consolidation. Zenodo, 2023, doi:10.5281/ZENODO.10251087.' short: D. Feitosa Tomé, (2023). date_created: 2024-01-29T09:06:43Z date_published: 2023-12-02T00:00:00Z date_updated: 2024-01-29T09:22:01Z day: '02' ddc: - '570' department: - _id: TiVo doi: 10.5281/ZENODO.10251087 has_accepted_license: '1' main_file_link: - open_access: '1' url: https://doi.org/10.5281/zenodo.10251087 month: '12' oa: 1 oa_version: None publisher: Zenodo related_material: record: - id: '14887' relation: used_in_publication status: public status: public title: 'douglastome/dynamic-engrams: Dynamic and selective engrams emerge with memory consolidation' 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_reference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2023' ... --- _id: '14919' abstract: - lang: eng text: "GLACIER METEOROLOGICAL DATA SWISS ALPS -2022\r\n" article_processing_charge: No author: - first_name: Thomas full_name: Shaw, Thomas id: 3caa3f91-1f03-11ee-96ce-e0e553054d6e last_name: Shaw orcid: 0000-0001-7640-6152 - first_name: Pascal full_name: Buri, Pascal id: 317987aa-9421-11ee-ac5a-b941b041abba last_name: Buri - first_name: Michael full_name: McCarthy, Michael last_name: McCarthy - first_name: Evan full_name: Miles, Evan last_name: Miles - first_name: Francesca full_name: Pellicciotti, Francesca id: b28f055a-81ea-11ed-b70c-a9fe7f7b0e70 last_name: Pellicciotti orcid: 0000-0002-5554-8087 citation: ama: Shaw T, Buri P, McCarthy M, Miles E, Pellicciotti F. Air temperature and near-surface meteorology datasets on three Swiss glaciers - Extreme 2022 Summer. 2023. doi:10.5281/ZENODO.8277285 apa: Shaw, T., Buri, P., McCarthy, M., Miles, E., & Pellicciotti, F. (2023). Air temperature and near-surface meteorology datasets on three Swiss glaciers - Extreme 2022 Summer. Zenodo. https://doi.org/10.5281/ZENODO.8277285 chicago: Shaw, Thomas, Pascal Buri, Michael McCarthy, Evan Miles, and Francesca Pellicciotti. “Air Temperature and Near-Surface Meteorology Datasets on Three Swiss Glaciers - Extreme 2022 Summer.” Zenodo, 2023. https://doi.org/10.5281/ZENODO.8277285. ieee: T. Shaw, P. Buri, M. McCarthy, E. Miles, and F. Pellicciotti, “Air temperature and near-surface meteorology datasets on three Swiss glaciers - Extreme 2022 Summer.” Zenodo, 2023. ista: Shaw T, Buri P, McCarthy M, Miles E, Pellicciotti F. 2023. Air temperature and near-surface meteorology datasets on three Swiss glaciers - Extreme 2022 Summer, Zenodo, 10.5281/ZENODO.8277285. mla: Shaw, Thomas, et al. Air Temperature and Near-Surface Meteorology Datasets on Three Swiss Glaciers - Extreme 2022 Summer. Zenodo, 2023, doi:10.5281/ZENODO.8277285. short: T. Shaw, P. Buri, M. McCarthy, E. Miles, F. Pellicciotti, (2023). date_created: 2024-01-31T12:08:26Z date_published: 2023-08-23T00:00:00Z date_updated: 2024-02-06T08:44:01Z day: '23' ddc: - '550' department: - _id: FrPe doi: 10.5281/ZENODO.8277285 main_file_link: - open_access: '1' url: https://doi.org/10.5281/ZENODO.8277285 month: '08' oa: 1 oa_version: Published Version publisher: Zenodo related_material: record: - id: '14885' relation: used_in_publication status: public status: public title: Air temperature and near-surface meteorology datasets on three Swiss glaciers - Extreme 2022 Summer type: research_data_reference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2023' ... --- _id: '12497' abstract: - lang: eng text: Aromatic side chains are important reporters of the plasticity of proteins, and often form important contacts in protein–protein interactions. We studied aromatic residues in the two structurally homologous cross-β amyloid fibrils HET-s, and HELLF by employing a specific isotope-labeling approach and magic-angle-spinning NMR. The dynamic behavior of the aromatic residues Phe and Tyr indicates that the hydrophobic amyloid core is rigid, without any sign of "breathing motions" over hundreds of milliseconds at least. Aromatic residues exposed at the fibril surface have a rigid ring axis but undergo ring flips on a variety of time scales from nanoseconds to microseconds. Our approach provides direct insight into hydrophobic-core motions, enabling a better evaluation of the conformational heterogeneity generated from an NMR structural ensemble of such amyloid cross-β architecture. article_processing_charge: No author: - first_name: Lea Marie full_name: Becker, Lea Marie id: 36336939-eb97-11eb-a6c2-c83f1214ca79 last_name: Becker orcid: 0000-0002-6401-5151 - first_name: Paul full_name: Schanda, Paul id: 7B541462-FAF6-11E9-A490-E8DFE5697425 last_name: Schanda orcid: 0000-0002-9350-7606 citation: ama: 'Becker LM, Schanda P. Research data to: The rigid core and flexible surface of amyloid fibrils probed by magic-angle-spinning NMR spectroscopy of aromatic residues. 2023. doi:10.15479/AT:ISTA:12497' apa: 'Becker, L. M., & Schanda, P. (2023). Research data to: The rigid core and flexible surface of amyloid fibrils probed by magic-angle-spinning NMR spectroscopy of aromatic residues. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:12497' chicago: 'Becker, Lea Marie, and Paul Schanda. “Research Data to: The Rigid Core and Flexible Surface of Amyloid Fibrils Probed by Magic-Angle-Spinning NMR Spectroscopy of Aromatic Residues.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/AT:ISTA:12497.' ieee: 'L. M. Becker and P. Schanda, “Research data to: The rigid core and flexible surface of amyloid fibrils probed by magic-angle-spinning NMR spectroscopy of aromatic residues.” Institute of Science and Technology Austria, 2023.' ista: 'Becker LM, Schanda P. 2023. Research data to: The rigid core and flexible surface of amyloid fibrils probed by magic-angle-spinning NMR spectroscopy of aromatic residues, Institute of Science and Technology Austria, 10.15479/AT:ISTA:12497.' mla: 'Becker, Lea Marie, and Paul Schanda. Research Data to: The Rigid Core and Flexible Surface of Amyloid Fibrils Probed by Magic-Angle-Spinning NMR Spectroscopy of Aromatic Residues. Institute of Science and Technology Austria, 2023, doi:10.15479/AT:ISTA:12497.' short: L.M. Becker, P. Schanda, (2023). contributor: - contributor_type: researcher first_name: Mélanie last_name: Berbon - contributor_type: researcher first_name: Alicia last_name: Vallet - contributor_type: researcher first_name: Axelle last_name: Grelard - contributor_type: researcher first_name: Estelle last_name: Morvan - contributor_type: researcher first_name: Benjamin last_name: Bardiaux - contributor_type: researcher first_name: Roman last_name: Lichtenecker - contributor_type: researcher first_name: Matthias last_name: Ernst - contributor_type: researcher first_name: Antoine last_name: Loquet - contributor_type: contact_person first_name: Paul id: 7B541462-FAF6-11E9-A490-E8DFE5697425 last_name: Schanda orcid: 0000-0002-9350-7606 - contributor_type: researcher first_name: Lea Marie id: 36336939-eb97-11eb-a6c2-c83f1214ca79 last_name: Becker orcid: 0000-0002-6401-5151 date_created: 2023-02-03T08:08:02Z date_published: 2023-03-23T00:00:00Z date_updated: 2024-02-21T12:14:06Z day: '23' ddc: - '572' department: - _id: GradSch - _id: PaSc doi: 10.15479/AT:ISTA:12497 file: - access_level: open_access checksum: fd9a28620a81a82991fb70f4fd6591d9 content_type: application/zip creator: lbecker date_created: 2023-03-23T10:03:16Z date_updated: 2023-03-24T09:34:20Z file_id: '12743' file_name: Research_Data.zip file_size: 87018103 relation: main_file - access_level: open_access checksum: 30ebdfb600af118fcf8518b6efe0b7e9 content_type: text/plain creator: dernst date_created: 2023-03-24T07:13:55Z date_updated: 2023-03-24T09:42:03Z file_id: '12755' file_name: README.txt file_size: 747 relation: main_file file_date_updated: 2023-03-24T09:42:03Z has_accepted_license: '1' keyword: - aromatic side chains - isotopic labeling - protein dynamics - ring flips - spin relaxation month: '03' oa: 1 oa_version: Published Version publisher: Institute of Science and Technology Austria related_material: record: - id: '12675' relation: used_in_publication status: public status: public title: 'Research data to: The rigid core and flexible surface of amyloid fibrils probed by magic-angle-spinning NMR spectroscopy of aromatic residues' 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: research_data user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2023' ... --- _id: '13126' abstract: - lang: eng text: Mapping the complex and dense arrangement of cells and their connectivity in brain tissue demands nanoscale spatial resolution imaging. Super-resolution optical microscopy excels at visualizing specific molecules and individual cells but fails to provide tissue context. Here, we developed Comprehensive Analysis of Tissues across Scales (CATS), a technology to densely map brain tissue architecture from millimeter regional to nanometer synaptic scales in diverse chemically fixed brain preparations, including rodent and human. CATS uses fixation-compatible extracellular labeling and optical imaging, including stimulated emission depletion or expansion microscopy, to comprehensively delineate cellular structures. It enables three-dimensional reconstruction of single synapses and mapping of synaptic connectivity by identification and analysis of putative synaptic cleft regions. Applying CATS to the mouse hippocampal mossy fiber circuitry, we reconstructed and quantified the synaptic input and output structure of identified neurons. We furthermore demonstrate applicability to clinically derived human tissue samples, including formalin-fixed paraffin-embedded routine diagnostic specimens, for visualizing the cellular architecture of brain tissue in health and disease. acknowledged_ssus: - _id: ScienComp - _id: Bio - _id: PreCl - _id: LifeSc - _id: M-Shop - _id: E-Lib acknowledgement: "We thank Jakob Vorlaufer, Nathalie Agudelo-Dueñas, Wiebke Jahr, Andreas Wartak for microscope maintenance and troubleshooting, Caroline Kreuzinger, Anna Freeman, and Irene Erber for technical assistance and Matthias Tomschik for support with obtaining human samples. We gratefully acknowledge Eder Miguel for setting up webKnossos and Marek Šuplata for computational support and hardware control. We are grateful to Ryuichi Shigemoto and Bernd Bickel for generous support, and Michael Sixt and Scott Boyd (Stanford University) for discussions and critical reading of the manuscript. PSD95-HaloTag mice were kindly provided by Seth Grant (University of Edinburgh). We acknowledge expert support by IST Austria’s scientific computing, imaging and optics, preclinical, and lab support facilities, and by the Library and Miba machine shop.\r\nWe gratefully acknowledge funding by the following sources: \r\nAustrian Science Fund (FWF) grant I3600-B27 (JGD)\r\nAustrian Science Fund (FWF) grant DK W1232 (JGD, JMM)\r\nAustrian Science Fund (FWF) grant Z 312-B27, Wittgenstein award (PJ)\r\nAustrian Science Funds (FWF) projects I4685-B, I6565-B (SYNABS) and DOC 33-B27 (RH)\r\nGesellschaft für Forschungsförderung NÖ (NFB) grant LSC18-022 (JGD)\r\nEuropean Union’s Horizon 2020 research and innovation programme, European Research Council (ERC) grant 715508 – REVERSEAUTISM (GN)\r\nEuropean Union’s Horizon 2020 research and innovation programme, European Research Council (ERC) grant 692692 – GIANTSYN (PJ)\r\nMarie Skłodowska-Curie Actions Fellowship GA no. 665385 under the EU Horizon 2020 program (JMM, JL)\r\nMarie Skłodowska-Curie Actions Individual Fellowship 101026635 under the EU Horizon 2020 program (JFW)" article_processing_charge: No author: - first_name: Johann G full_name: Danzl, Johann G id: 42EFD3B6-F248-11E8-B48F-1D18A9856A87 last_name: Danzl orcid: 0000-0001-8559-3973 citation: ama: Danzl JG. Research data for the publication “Imaging brain tissue architecture across millimeter to nanometer scales.” 2023. doi:10.15479/AT:ISTA:13126 apa: Danzl, J. G. (2023). Research data for the publication “Imaging brain tissue architecture across millimeter to nanometer scales.” Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:13126 chicago: Danzl, Johann G. “Research Data for the Publication ‘Imaging Brain Tissue Architecture across Millimeter to Nanometer Scales.’” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/AT:ISTA:13126. ieee: J. G. Danzl, “Research data for the publication ‘Imaging brain tissue architecture across millimeter to nanometer scales.’” Institute of Science and Technology Austria, 2023. ista: Danzl JG. 2023. Research data for the publication ‘Imaging brain tissue architecture across millimeter to nanometer scales’, Institute of Science and Technology Austria, 10.15479/AT:ISTA:13126. mla: Danzl, Johann G. Research Data for the Publication “Imaging Brain Tissue Architecture across Millimeter to Nanometer Scales.” Institute of Science and Technology Austria, 2023, doi:10.15479/AT:ISTA:13126. short: J.G. Danzl, (2023). contributor: - first_name: Julia M id: 443DB6DE-F248-11E8-B48F-1D18A9856A87 last_name: Michalska - first_name: Julia id: 46E28B80-F248-11E8-B48F-1D18A9856A87 last_name: Lyudchik - first_name: Philipp id: 39BDC62C-F248-11E8-B48F-1D18A9856A87 last_name: Velicky orcid: 0000-0002-2340-7431 - first_name: Hana id: ee3cb6ca-ec98-11ea-ae11-ff703e2254ed last_name: Stefanickova - first_name: Jake id: 63836096-4690-11EA-BD4E-32803DDC885E last_name: Watson orcid: 0000-0002-8698-3823 - first_name: Alban id: 9ac8f577-2357-11eb-997a-e566c5550886 last_name: Cenameri - first_name: Christoph M id: 4DF26D8C-F248-11E8-B48F-1D18A9856A87 last_name: Sommer orcid: 0000-0003-1216-9105 - first_name: Nicole id: 4CD6AAC6-F248-11E8-B48F-1D18A9856A87 last_name: Amberg orcid: 0000-0002-3183-8207 - first_name: Alessandro id: 41CB84B2-F248-11E8-B48F-1D18A9856A87 last_name: Venturino orcid: 0000-0003-2356-9403 - first_name: Karl last_name: Roessler - first_name: Thomas last_name: Czech - first_name: Romana last_name: Höftberger - first_name: Sandra id: 36ACD32E-F248-11E8-B48F-1D18A9856A87 last_name: Siegert orcid: 0000-0001-8635-0877 - first_name: Gaia id: 3E57A680-F248-11E8-B48F-1D18A9856A87 last_name: Novarino orcid: 0000-0002-7673-7178 - first_name: Peter M id: 353C1B58-F248-11E8-B48F-1D18A9856A87 last_name: Jonas orcid: 0000-0001-5001-4804 date_created: 2023-06-07T07:15:12Z date_published: 2023-08-04T00:00:00Z date_updated: 2024-02-21T12:18:19Z day: '04' ddc: - '610' department: - _id: JoDa - _id: SaSi - _id: GaNo - _id: PeJo - _id: Bio - _id: RySh doi: 10.15479/AT:ISTA:13126 ec_funded: 1 file: - access_level: open_access checksum: 6f18ce9b89b47ce5abeb379869ff5c49 content_type: text/plain creator: jdanzl date_created: 2023-08-04T13:19:47Z date_updated: 2023-08-04T13:19:47Z file_id: '13961' file_name: Readme_Michalska_2023.txt file_size: 541 relation: main_file success: 1 - access_level: open_access checksum: 2098e8c5285c5e86cb69075e1b5dcf39 content_type: image/tiff creator: jdanzl date_created: 2023-08-03T11:29:29Z date_updated: 2023-08-03T11:29:29Z file_id: '13482' file_name: Fig1_b_top-left.tif file_size: 64582744 relation: main_file success: 1 - 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_id: 265CB4D0-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: I03600 name: Optical control of synaptic function via adhesion molecules - _id: 26AA4EF2-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: W1232-B24 name: Molecular Drug Targets - _id: 25C5A090-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: Z00312 name: The Wittgenstein Prize - _id: 23889792-32DE-11EA-91FC-C7463DDC885E name: High content imaging to decode human immune cell interactions in health and allergic disease - _id: 25444568-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '715508' name: Probing the Reversibility of Autism Spectrum Disorders by Employing in vivo and in vitro Models - _id: 25B7EB9E-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '692692' name: Biophysics and circuit function of a giant cortical glumatergic synapse - _id: 2564DBCA-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '665385' name: International IST Doctoral Program - _id: fc2be41b-9c52-11eb-aca3-faa90aa144e9 call_identifier: H2020 grant_number: '101026635' name: Synaptic computations of the hippocampal CA3 circuitry publisher: Institute of Science and Technology Austria related_material: link: - description: 'Original data for Fig. 5d, Fig. 5d (N2V) and Fig. 5f-i, provided via an external link due to the large size (>10GB) of the datasets. ' relation: research_data url: https://pub.ista.ac.at/group_danzl/data/CATS/ record: - id: '14257' relation: used_in_publication status: public status: public title: Research data for the publication "Imaging brain tissue architecture across millimeter to nanometer scales" tmp: image: /images/cc_by_nc_sa.png legal_code_url: https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode name: Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0) short: CC BY-NC-SA (4.0) type: research_data user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2023' ... --- _id: '13116' abstract: - lang: eng text: 'The emergence of large-scale order in self-organized systems relies on local interactions between individual components. During bacterial cell division, FtsZ -- a prokaryotic homologue of the eukaryotic protein tubulin -- polymerizes into treadmilling filaments that further organize into a cytoskeletal ring. In vitro, FtsZ filaments can form dynamic chiral assemblies. However, how the active and passive properties of individual filaments relate to these large-scale self-organized structures remains poorly understood. Here, we connect single filament properties with the mesoscopic scale by combining minimal active matter simulations and biochemical reconstitution experiments. We show that density and flexibility of active chiral filaments define their global order. At intermediate densities, curved, flexible filaments organize into chiral rings and polar bands. An effectively nematic organization dominates for high densities and for straight, mutant filaments with increased rigidity. Our predicted phase diagram captures these features quantitatively, demonstrating how the flexibility, density and chirality of active filaments affect their collective behaviour. Our findings shed light on the fundamental properties of active chiral matter and explain how treadmilling FtsZ filaments organize during bacterial cell division. ' acknowledged_ssus: - _id: Bio - _id: LifeSc acknowledgement: 'This work was supported by the European Research Council through grant ERC 2015-StG-679239 and by the Austrian Science Fund (FWF) StandAlone P34607 to M.L., B. P.M. was also supported by the Kanazawa University WPI- NanoLSI Bio-SPM collaborative research program. Z.D. has received funding from Doctoral Programme of the Austrian Academy of Sciences (OeAW): Grant agreement 26360. We thank Jan Brugues (MPI CBG, Dresden, Germany), Andela Saric (ISTA, Klosterneuburg, Austria), Daniel Pearce (Uni Geneva, Switzerland) for valuable scientific input and comments on the manuscript. We are also thankful for the support by the Scientific Service Units (SSU) of IST Austria through resources provided by the Imaging and Optics Facility (IOF) and the Lab Support Facility (LSF). ' article_processing_charge: No author: - first_name: Zuzana full_name: Dunajova, Zuzana id: 4B39F286-F248-11E8-B48F-1D18A9856A87 last_name: Dunajova - first_name: Batirtze full_name: Prats Mateu, Batirtze id: 299FE892-F248-11E8-B48F-1D18A9856A87 last_name: Prats Mateu - first_name: Philipp full_name: Radler, Philipp id: 40136C2A-F248-11E8-B48F-1D18A9856A87 last_name: Radler orcid: '0000-0001-9198-2182 ' - first_name: Keesiang full_name: Lim, Keesiang last_name: Lim - first_name: Dörte full_name: Brandis, Dörte last_name: Brandis - first_name: Philipp full_name: Velicky, Philipp id: 39BDC62C-F248-11E8-B48F-1D18A9856A87 last_name: Velicky orcid: 0000-0002-2340-7431 - first_name: Johann G full_name: Danzl, Johann G id: 42EFD3B6-F248-11E8-B48F-1D18A9856A87 last_name: Danzl orcid: 0000-0001-8559-3973 - first_name: Richard W. full_name: Wong, Richard W. last_name: Wong - first_name: Jens full_name: Elgeti, Jens last_name: Elgeti - first_name: Edouard B full_name: Hannezo, Edouard B id: 3A9DB764-F248-11E8-B48F-1D18A9856A87 last_name: Hannezo orcid: 0000-0001-6005-1561 - first_name: Martin full_name: Loose, Martin id: 462D4284-F248-11E8-B48F-1D18A9856A87 last_name: Loose orcid: 0000-0001-7309-9724 citation: ama: Dunajova Z, Prats Mateu B, Radler P, et al. Chiral and nematic phases of flexible active filaments. 2023. doi:10.15479/AT:ISTA:13116 apa: Dunajova, Z., Prats Mateu, B., Radler, P., Lim, K., Brandis, D., Velicky, P., … Loose, M. (2023). Chiral and nematic phases of flexible active filaments. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:13116 chicago: Dunajova, Zuzana, Batirtze Prats Mateu, Philipp Radler, Keesiang Lim, Dörte Brandis, Philipp Velicky, Johann G Danzl, et al. “Chiral and Nematic Phases of Flexible Active Filaments.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/AT:ISTA:13116. ieee: Z. Dunajova et al., “Chiral and nematic phases of flexible active filaments.” Institute of Science and Technology Austria, 2023. ista: Dunajova Z, Prats Mateu B, Radler P, Lim K, Brandis D, Velicky P, Danzl JG, Wong RW, Elgeti J, Hannezo EB, Loose M. 2023. Chiral and nematic phases of flexible active filaments, Institute of Science and Technology Austria, 10.15479/AT:ISTA:13116. mla: Dunajova, Zuzana, et al. Chiral and Nematic Phases of Flexible Active Filaments. Institute of Science and Technology Austria, 2023, doi:10.15479/AT:ISTA:13116. short: Z. Dunajova, B. Prats Mateu, P. Radler, K. Lim, D. Brandis, P. Velicky, J.G. Danzl, R.W. Wong, J. Elgeti, E.B. Hannezo, M. 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access_level: open_access checksum: 848456b4230c086e8999f57d57dba7f1 content_type: text/csv creator: mloose date_created: 2023-08-03T19:51:54Z date_updated: 2023-08-03T19:51:54Z file_id: '13952' file_name: Fig3a_F200.csv file_size: 59166206 relation: main_file success: 1 file_date_updated: 2023-08-08T11:17:28Z has_accepted_license: '1' month: '07' oa: 1 oa_version: Published Version project: - _id: 2595697A-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '679239' name: Self-Organization of the Bacterial Cell - _id: fc38323b-9c52-11eb-aca3-ff8afb4a011d grant_number: P34607 name: "Understanding bacterial cell division by in vitro\r\nreconstitution" - _id: 34d75525-11ca-11ed-8bc3-89b6307fee9d grant_number: '26360' name: Motile active matter models of migrating cells and chiral filaments publisher: Institute of Science and Technology Austria related_material: record: - id: '13314' relation: used_in_publication status: public status: public title: Chiral and nematic phases of flexible active filaments 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: '2023' ... --- _id: '14614' abstract: - lang: eng text: 'Many insects carry an ancient X chromosome—the Drosophila Muller element F—that likely predates their origin. Interestingly, the X has undergone turnover in multiple fly species (Diptera) after being conserved for more than 450 My. The long evolutionary distance between Diptera and other sequenced insect clades makes it difficult to infer what could have contributed to this sudden increase in rate of turnover. Here, we produce the first genome and transcriptome of scorpionflies (genus Panorpa), an insect belonging to a long overlooked sister-order to Diptera: Mecoptera. Combining our genome assembly with genomic short-read data, we obtain genome coverage and identify X-linked super-scaffolds. We further perform a gene homology analysis between the Panorpa X and a closely related Diptera species, and we assess the conservation of the Panorpa X-linked gene content with that of more distantly related insect species. We explored the structure of the Panorpa X by determining its repeat content, GC content, and nucleotide diversity. Finally, we used RNAseq data to detect the presence of dosage compensation in somatic tissues, as well as to explore gene expression tissue-specificity, and sex-bias in gene expression. We find high conservation of gene content between the mecopteran X and the dipteran Muller F element, as well as several shared biological features, such as the presence of dosage compensation and a low amount of genetic diversity, consistent with a low recombination rate. However, the 2 homologous X chromosomes differ strikingly in their size and number of genes they carry. Our results therefore support a common ancestry of the mecopteran and ancestral dipteran X chromosomes, and suggest that Muller element F shrank in size and gene content after the split of Diptera and Mecoptera, which may have contributed to its turnover in dipteran insects.' article_processing_charge: No author: - first_name: Clementine full_name: Lasne, Clementine id: 02225f57-50d2-11eb-9ed8-8c92b9a34237 last_name: Lasne orcid: 0000-0002-1197-8616 - first_name: Marwan N full_name: Elkrewi, Marwan N id: 0B46FACA-A8E1-11E9-9BD3-79D1E5697425 last_name: Elkrewi orcid: 0000-0002-5328-7231 citation: ama: Lasne C, Elkrewi MN. The scorpionfly (Panorpa cognata) genome highlights conserved and derived features of the peculiar dipteran X chromosome. 2023. doi:10.15479/AT:ISTA:14614 apa: Lasne, C., & Elkrewi, M. N. (2023). The scorpionfly (Panorpa cognata) genome highlights conserved and derived features of the peculiar dipteran X chromosome. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:14614 chicago: Lasne, Clementine, and Marwan N Elkrewi. “The Scorpionfly (Panorpa Cognata) Genome Highlights Conserved and Derived Features of the Peculiar Dipteran X Chromosome.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/AT:ISTA:14614. ieee: C. Lasne and M. N. Elkrewi, “The scorpionfly (Panorpa cognata) genome highlights conserved and derived features of the peculiar dipteran X chromosome.” Institute of Science and Technology Austria, 2023. ista: Lasne C, Elkrewi MN. 2023. The scorpionfly (Panorpa cognata) genome highlights conserved and derived features of the peculiar dipteran X chromosome, Institute of Science and Technology Austria, 10.15479/AT:ISTA:14614. mla: Lasne, Clementine, and Marwan N. Elkrewi. The Scorpionfly (Panorpa Cognata) Genome Highlights Conserved and Derived Features of the Peculiar Dipteran X Chromosome. Institute of Science and Technology Austria, 2023, doi:10.15479/AT:ISTA:14614. short: C. Lasne, M.N. Elkrewi, (2023). contributor: - contributor_type: researcher first_name: Marwan N id: 0B46FACA-A8E1-11E9-9BD3-79D1E5697425 last_name: Elkrewi orcid: 0000-0002-5328-7231 date_created: 2023-11-27T16:39:19Z date_published: 2023-12-01T00:00:00Z date_updated: 2024-02-21T12:18:35Z day: '01' ddc: - '576' department: - _id: BeVi doi: 10.15479/AT:ISTA:14614 file: - access_level: open_access checksum: cd0f13322b5156819ecaebd2bc8e7d12 content_type: application/zip creator: clasne date_created: 2023-11-28T13:15:26Z date_updated: 2023-11-28T13:15:26Z file_id: '14625' file_name: panorpaX.zip file_size: 404968272 relation: main_file success: 1 - access_level: open_access checksum: 9ff600416577687a737cb3c96dfcb26c content_type: text/plain creator: clasne date_created: 2023-11-30T14:16:59Z date_updated: 2023-11-30T14:16:59Z file_id: '14634' file_name: panorpa_readme.txt file_size: 2625 relation: main_file success: 1 file_date_updated: 2023-11-30T14:16:59Z has_accepted_license: '1' keyword: - Panorpa - scorpionfly - genome - transcriptome month: '12' oa: 1 oa_version: Published Version publisher: Institute of Science and Technology Austria related_material: record: - id: '14613' relation: used_in_publication status: public status: public title: The scorpionfly (Panorpa cognata) genome highlights conserved and derived features of the peculiar dipteran X chromosome 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: '2023' ... --- _id: '15027' abstract: - lang: eng text: 'This data repository underpins the paper, published in PNAS (doi pending) and bioarxiv (doi: https://doi.org/10.1101/2023.07.05.547777).' article_processing_charge: No author: - first_name: Samo full_name: Curk, Samo id: 031eff0d-d481-11ee-8508-cd12a7a86e5b last_name: Curk orcid: 0000-0001-6160-9766 citation: ama: Curk S. aggregation_data. 2023. apa: Curk, S. (2023). aggregation_data. Figshare. chicago: Curk, Samo. “Aggregation_data.” Figshare, 2023. ieee: S. Curk, “aggregation_data.” Figshare, 2023. ista: Curk S. 2023. aggregation_data, Figshare. mla: Curk, Samo. Aggregation_data. Figshare, 2023. short: S. Curk, (2023). date_created: 2024-02-26T08:37:57Z date_published: 2023-12-13T00:00:00Z date_updated: 2024-02-26T08:45:55Z day: '13' ddc: - '570' department: - _id: AnSa has_accepted_license: '1' main_file_link: - open_access: '1' url: https://figshare.com/s/85798bba4ebc68d822ed month: '12' oa: 1 oa_version: Published Version publisher: Figshare related_material: record: - id: '15001' relation: used_in_publication status: public status: public title: aggregation_data 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_reference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2023' ... --- _id: '14991' abstract: - lang: eng text: This repository contains the data, scripts, WRF codes and files required to reproduce the results of the manuscript "Assessing Memory in Convection Schemes Using Idealized Tests" submitted to the Journal of Advances in Modeling Earth Systems (JAMES). article_processing_charge: No author: - first_name: Yi-Ling full_name: Hwong, Yi-Ling id: 1217aa61-4dd1-11ec-9ac3-f2ba3f17ee22 last_name: Hwong orcid: 0000-0001-9281-3479 - first_name: Maxime full_name: Colin, Maxime last_name: Colin - first_name: Philipp full_name: Aglas, Philipp id: 02eace56-97fc-11ee-b81a-f0939ca85a77 last_name: Aglas - first_name: Caroline J full_name: Muller, Caroline J id: f978ccb0-3f7f-11eb-b193-b0e2bd13182b last_name: Muller orcid: 0000-0001-5836-5350 - first_name: Steven C. full_name: Sherwood, Steven C. last_name: Sherwood citation: ama: Hwong Y-L, Colin M, Aglas P, Muller CJ, Sherwood SC. Data-assessing memory in convection schemes using idealized tests. 2023. doi:10.5281/ZENODO.7757041 apa: Hwong, Y.-L., Colin, M., Aglas, P., Muller, C. J., & Sherwood, S. C. (2023). Data-assessing memory in convection schemes using idealized tests. Zenodo. https://doi.org/10.5281/ZENODO.7757041 chicago: Hwong, Yi-Ling, Maxime Colin, Philipp Aglas, Caroline J Muller, and Steven C. Sherwood. “Data-Assessing Memory in Convection Schemes Using Idealized Tests.” Zenodo, 2023. https://doi.org/10.5281/ZENODO.7757041. ieee: Y.-L. Hwong, M. Colin, P. Aglas, C. J. Muller, and S. C. Sherwood, “Data-assessing memory in convection schemes using idealized tests.” Zenodo, 2023. ista: Hwong Y-L, Colin M, Aglas P, Muller CJ, Sherwood SC. 2023. Data-assessing memory in convection schemes using idealized tests, Zenodo, 10.5281/ZENODO.7757041. mla: Hwong, Yi-Ling, et al. Data-Assessing Memory in Convection Schemes Using Idealized Tests. Zenodo, 2023, doi:10.5281/ZENODO.7757041. short: Y.-L. Hwong, M. Colin, P. Aglas, C.J. Muller, S.C. Sherwood, (2023). date_created: 2024-02-14T14:37:57Z date_published: 2023-06-23T00:00:00Z date_updated: 2024-02-27T07:26:31Z day: '23' ddc: - '550' department: - _id: CaMu doi: 10.5281/ZENODO.7757041 ec_funded: 1 has_accepted_license: '1' main_file_link: - open_access: '1' url: https://doi.org/10.5281/zenodo.7757041 month: '06' oa: 1 oa_version: Published Version project: - _id: fc2ed2f7-9c52-11eb-aca3-c01059dda49c call_identifier: H2020 grant_number: '101034413' name: 'IST-BRIDGE: International postdoctoral program' publisher: Zenodo related_material: record: - id: '14654' relation: used_in_publication status: public status: public title: Data-assessing memory in convection schemes using idealized tests 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_reference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2023' ... --- _id: '14990' abstract: - lang: eng text: The software artefact to evaluate the approximation of stationary distributions implementation. article_processing_charge: No author: - first_name: Tobias full_name: Meggendorfer, Tobias id: b21b0c15-30a2-11eb-80dc-f13ca25802e1 last_name: Meggendorfer orcid: 0000-0002-1712-2165 citation: ama: 'Meggendorfer T. Artefact for: Correct Approximation of Stationary Distributions. 2023. doi:10.5281/ZENODO.7548214' apa: 'Meggendorfer, T. (2023). Artefact for: Correct Approximation of Stationary Distributions. Zenodo. https://doi.org/10.5281/ZENODO.7548214' chicago: 'Meggendorfer, Tobias. “Artefact for: Correct Approximation of Stationary Distributions.” Zenodo, 2023. https://doi.org/10.5281/ZENODO.7548214.' ieee: 'T. Meggendorfer, “Artefact for: Correct Approximation of Stationary Distributions.” Zenodo, 2023.' ista: 'Meggendorfer T. 2023. Artefact for: Correct Approximation of Stationary Distributions, Zenodo, 10.5281/ZENODO.7548214.' mla: 'Meggendorfer, Tobias. Artefact for: Correct Approximation of Stationary Distributions. Zenodo, 2023, doi:10.5281/ZENODO.7548214.' short: T. Meggendorfer, (2023). date_created: 2024-02-14T14:27:06Z date_published: 2023-01-18T00:00:00Z date_updated: 2024-02-27T07:19:32Z day: '18' ddc: - '000' department: - _id: KrCh doi: 10.5281/ZENODO.7548214 has_accepted_license: '1' main_file_link: - open_access: '1' url: https://doi.org/10.5281/zenodo.7548214 month: '01' oa: 1 oa_version: Published Version publisher: Zenodo related_material: record: - id: '13139' relation: used_in_publication status: public status: public title: 'Artefact for: Correct Approximation of Stationary Distributions' 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_reference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2023' ... --- _id: '14995' abstract: - lang: eng text: "Lincheck is a new practical and user-friendly framework for testing concurrent data structures on the Java Virtual Machine (JVM). It provides a simple and declarative way to write concurrent tests. Instead of describing how to perform the test, users specify what to test by declaring all the operations to examine; the framework automatically handles the rest. As a result, tests written with Lincheck are concise and easy to understand. \r\nThe artifact presents a collection of Lincheck tests that discover new bugs in popular libraries and implementations from the concurrency literature -- they are listed in Table 1, Section 3. To evaluate the performance of Lincheck analysis, the collection of tests also includes those which check correct data structures and, thus, always succeed. Similarly to Table 2, Section 3, the experiments demonstrate the reasonable time to perform a test. Finally, Lincheck provides user-friendly output with an easy-to-follow trace to reproduce a detected error, significantly simplifying further investigation." article_processing_charge: No author: - first_name: Nikita full_name: Koval, Nikita id: 2F4DB10C-F248-11E8-B48F-1D18A9856A87 last_name: Koval - first_name: Alexander full_name: Fedorov, Alexander id: 2e711909-896a-11ed-bdf8-eb0f5a2984c6 last_name: Fedorov - first_name: Maria full_name: Sokolova, Maria last_name: Sokolova - first_name: Dmitry full_name: Tsitelov, Dmitry last_name: Tsitelov - first_name: Dan-Adrian full_name: Alistarh, Dan-Adrian id: 4A899BFC-F248-11E8-B48F-1D18A9856A87 last_name: Alistarh orcid: 0000-0003-3650-940X citation: ama: 'Koval N, Fedorov A, Sokolova M, Tsitelov D, Alistarh D-A. Lincheck: A practical framework for testing concurrent data structures on JVM. 2023. doi:10.5281/ZENODO.7877757' apa: 'Koval, N., Fedorov, A., Sokolova, M., Tsitelov, D., & Alistarh, D.-A. (2023). Lincheck: A practical framework for testing concurrent data structures on JVM. Zenodo. https://doi.org/10.5281/ZENODO.7877757' chicago: 'Koval, Nikita, Alexander Fedorov, Maria Sokolova, Dmitry Tsitelov, and Dan-Adrian Alistarh. “Lincheck: A Practical Framework for Testing Concurrent Data Structures on JVM.” Zenodo, 2023. https://doi.org/10.5281/ZENODO.7877757.' ieee: 'N. Koval, A. Fedorov, M. Sokolova, D. Tsitelov, and D.-A. Alistarh, “Lincheck: A practical framework for testing concurrent data structures on JVM.” Zenodo, 2023.' ista: 'Koval N, Fedorov A, Sokolova M, Tsitelov D, Alistarh D-A. 2023. Lincheck: A practical framework for testing concurrent data structures on JVM, Zenodo, 10.5281/ZENODO.7877757.' mla: 'Koval, Nikita, et al. Lincheck: A Practical Framework for Testing Concurrent Data Structures on JVM. Zenodo, 2023, doi:10.5281/ZENODO.7877757.' short: N. Koval, A. Fedorov, M. Sokolova, D. Tsitelov, D.-A. Alistarh, (2023). date_created: 2024-02-14T15:14:13Z date_published: 2023-04-28T00:00:00Z date_updated: 2024-02-27T07:46:52Z day: '28' ddc: - '000' department: - _id: DaAl doi: 10.5281/ZENODO.7877757 main_file_link: - open_access: '1' url: https://doi.org/10.5281/zenodo.7877757 month: '04' oa: 1 oa_version: Published Version publisher: Zenodo related_material: record: - id: '14260' relation: used_in_publication status: public status: public title: 'Lincheck: A practical framework for testing concurrent data structures on JVM' type: research_data_reference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2023' ... --- _id: '14994' abstract: - lang: eng text: This resource contains the artifacts for reproducing the experimental results presented in the paper titled "A Flexible Toolchain for Symbolic Rabin Games under Fair and Stochastic Uncertainties" that has been submitted in CAV 2023. article_processing_charge: No author: - first_name: Rupak full_name: Majumdar, Rupak last_name: Majumdar - first_name: Kaushik full_name: Mallik, Kaushik id: 0834ff3c-6d72-11ec-94e0-b5b0a4fb8598 last_name: Mallik orcid: 0000-0001-9864-7475 - first_name: Mateusz full_name: Rychlicki, Mateusz last_name: Rychlicki - first_name: Anne-Kathrin full_name: Schmuck, Anne-Kathrin last_name: Schmuck - first_name: Sadegh full_name: Soudjani, Sadegh last_name: Soudjani citation: ama: Majumdar R, Mallik K, Rychlicki M, Schmuck A-K, Soudjani S. A flexible toolchain for symbolic rabin games under fair and stochastic uncertainties. 2023. doi:10.5281/ZENODO.7877790 apa: Majumdar, R., Mallik, K., Rychlicki, M., Schmuck, A.-K., & Soudjani, S. (2023). A flexible toolchain for symbolic rabin games under fair and stochastic uncertainties. Zenodo. https://doi.org/10.5281/ZENODO.7877790 chicago: Majumdar, Rupak, Kaushik Mallik, Mateusz Rychlicki, Anne-Kathrin Schmuck, and Sadegh Soudjani. “A Flexible Toolchain for Symbolic Rabin Games under Fair and Stochastic Uncertainties.” Zenodo, 2023. https://doi.org/10.5281/ZENODO.7877790. ieee: R. Majumdar, K. Mallik, M. Rychlicki, A.-K. Schmuck, and S. Soudjani, “A flexible toolchain for symbolic rabin games under fair and stochastic uncertainties.” Zenodo, 2023. ista: Majumdar R, Mallik K, Rychlicki M, Schmuck A-K, Soudjani S. 2023. A flexible toolchain for symbolic rabin games under fair and stochastic uncertainties, Zenodo, 10.5281/ZENODO.7877790. mla: Majumdar, Rupak, et al. A Flexible Toolchain for Symbolic Rabin Games under Fair and Stochastic Uncertainties. Zenodo, 2023, doi:10.5281/ZENODO.7877790. short: R. Majumdar, K. Mallik, M. Rychlicki, A.-K. Schmuck, S. Soudjani, (2023). date_created: 2024-02-14T15:13:00Z date_published: 2023-04-28T00:00:00Z date_updated: 2024-02-27T07:39:51Z day: '28' ddc: - '000' department: - _id: ToHe doi: 10.5281/ZENODO.7877790 has_accepted_license: '1' main_file_link: - open_access: '1' url: https://doi.org/10.5281/zenodo.7877790 month: '04' oa: 1 oa_version: Published Version publisher: Zenodo related_material: record: - id: '14758' relation: used_in_publication status: public status: public title: A flexible toolchain for symbolic rabin games under fair and stochastic uncertainties 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_reference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2023' ... --- _id: '15035' abstract: - lang: eng text: "This artifact aims to reproduce experiments from the paper Monitoring Hyperproperties With Prefix Transducers accepted at RV'23, and give further pointers to implementation of prefix transducers.\r\nIt has two parts: a pre-compiled docker image and sources that one can use to compile (locally or in docker) the software and run the experiments." article_processing_charge: No author: - first_name: Marek full_name: Chalupa, Marek id: 87e34708-d6c6-11ec-9f5b-9391e7be2463 last_name: Chalupa - first_name: Thomas A full_name: Henzinger, Thomas A id: 40876CD8-F248-11E8-B48F-1D18A9856A87 last_name: Henzinger orcid: 0000-0002-2985-7724 citation: ama: Chalupa M, Henzinger TA. Monitoring hyperproperties with prefix transducers. 2023. doi:10.5281/ZENODO.8191723 apa: Chalupa, M., & Henzinger, T. A. (2023). Monitoring hyperproperties with prefix transducers. Zenodo. https://doi.org/10.5281/ZENODO.8191723 chicago: Chalupa, Marek, and Thomas A Henzinger. “Monitoring Hyperproperties with Prefix Transducers.” Zenodo, 2023. https://doi.org/10.5281/ZENODO.8191723. ieee: M. Chalupa and T. A. Henzinger, “Monitoring hyperproperties with prefix transducers.” Zenodo, 2023. ista: Chalupa M, Henzinger TA. 2023. Monitoring hyperproperties with prefix transducers, Zenodo, 10.5281/ZENODO.8191723. mla: Chalupa, Marek, and Thomas A. Henzinger. Monitoring Hyperproperties with Prefix Transducers. Zenodo, 2023, doi:10.5281/ZENODO.8191723. short: M. Chalupa, T.A. Henzinger, (2023). date_created: 2024-02-28T07:34:34Z date_published: 2023-07-28T00:00:00Z date_updated: 2024-02-28T12:33:09Z day: '28' ddc: - '000' department: - _id: ToHe doi: 10.5281/ZENODO.8191723 ec_funded: 1 has_accepted_license: '1' main_file_link: - open_access: '1' url: https://doi.org/10.5281/zenodo.8191722 month: '07' oa: 1 oa_version: Published Version project: - _id: 62781420-2b32-11ec-9570-8d9b63373d4d call_identifier: H2020 grant_number: '101020093' name: Vigilant Algorithmic Monitoring of Software publisher: Zenodo related_material: record: - id: '14076' relation: used_in_publication status: public status: public title: Monitoring hyperproperties with prefix transducers 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_reference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2023' ... --- _id: '14812' abstract: - lang: eng text: This repository contains the code and VCF files needed to conduct the analyses in our MS. Each folder contains a readMe document explaining the nature of each file and dataset and the results and analyses that they relate to. The same anlaysis code (but not VCF files) is also available at https://github.com/seanstankowski/Littorina_reproductive_mode article_processing_charge: No author: - first_name: Sean full_name: Stankowski, Sean id: 43161670-5719-11EA-8025-FABC3DDC885E last_name: Stankowski citation: ama: 'Stankowski S. Data and code for: The genetic architecture of a recent transition to live-bearing in marine snails. 2023. doi:10.5281/ZENODO.8318995' apa: 'Stankowski, S. (2023). Data and code for: The genetic architecture of a recent transition to live-bearing in marine snails. Zenodo. https://doi.org/10.5281/ZENODO.8318995' chicago: 'Stankowski, Sean. “Data and Code for: The Genetic Architecture of a Recent Transition to Live-Bearing in Marine Snails.” Zenodo, 2023. https://doi.org/10.5281/ZENODO.8318995.' ieee: 'S. Stankowski, “Data and code for: The genetic architecture of a recent transition to live-bearing in marine snails.” Zenodo, 2023.' ista: 'Stankowski S. 2023. Data and code for: The genetic architecture of a recent transition to live-bearing in marine snails, Zenodo, 10.5281/ZENODO.8318995.' mla: 'Stankowski, Sean. Data and Code for: The Genetic Architecture of a Recent Transition to Live-Bearing in Marine Snails. Zenodo, 2023, doi:10.5281/ZENODO.8318995.' short: S. Stankowski, (2023). contributor: - first_name: Zusanna last_name: Zagrodzka - first_name: Martin last_name: Garlovsky - first_name: Arka id: 6AAB2240-CA9A-11E9-9C1A-D9D1E5697425 last_name: Pal orcid: 0000-0002-4530-8469 - first_name: Daria id: 428A94B0-F248-11E8-B48F-1D18A9856A87 last_name: Shipilina orcid: 0000-0002-1145-9226 - first_name: Diego Fernando id: ae681a14-dc74-11ea-a0a7-c6ef18161701 last_name: Garcia Castillo - first_name: Hila id: d6ab5470-2fb3-11ed-8633-986a9b84edac last_name: Lifchitz - first_name: Alan last_name: Le Moan - first_name: Erica last_name: Leder - first_name: James last_name: Reeve - first_name: Kerstin last_name: Johannesson - first_name: Anja M id: 3C147470-F248-11E8-B48F-1D18A9856A87 last_name: Westram orcid: 0000-0003-1050-4969 - first_name: Roger last_name: Butlin date_created: 2024-01-16T10:23:01Z date_published: 2023-09-05T00:00:00Z date_updated: 2024-03-05T09:35:25Z day: '05' ddc: - '570' department: - _id: NiBa doi: 10.5281/ZENODO.8318995 has_accepted_license: '1' main_file_link: - open_access: '1' url: https://doi.org/10.5281/zenodo.8318995 month: '09' oa: 1 oa_version: Published Version publisher: Zenodo related_material: record: - id: '14796' relation: used_in_publication status: public status: public title: 'Data and code for: The genetic architecture of a recent transition to live-bearing in marine snails' 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_reference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2023' ... --- _id: '13173' abstract: - lang: eng text: GABAB receptor (GBR) activation inhibits neurotransmitter release in axon terminals in the brain, except in medial habenula (MHb) terminals, which show robust potentiation. However, mechanisms underlying this enigmatic potentiation remain elusive. Here, we report that GBR activation on MHb terminals induces an activity-dependent transition from a facilitating, tonic to a depressing, phasic neurotransmitter release mode. This transition is accompanied by a 4.1-fold increase in readily releasable vesicle pool (RRP) size and a 3.5-fold increase of docked synaptic vesicles at the presynaptic active zone (AZ). Strikingly, tonic and phasic release exhibit distinct coupling distances and are selectively affected by deletion of synaptoporin (SPO) and Ca2+-dependent activator protein for secretion 2 (CAPS2), respectively. SPO modulates augmentation, the short-term plasticity associated with tonic release, and CAPS2 retains the increased RRP for initial responses in phasic response trains. Double pre-embedding immunolabeling confirmed the co-localization of CAPS2 and SPO inside the same terminal. The cytosolic protein CAPS2 showed a synaptic vesicle (SV)-associated distribution similar to the vesicular transmembrane protein SPO. A newly developed “Flash and Freeze-fracture” method revealed the release of SPO-associated vesicles in both tonic and phasic modes and activity-dependent recruitment of CAPS2 to the AZ during phasic release, which lasted several minutes. Overall, these results indicate that GBR activation translocates CAPS2 to the AZ along with the fusion of CAPS2-associated SVs, contributing to a persistent RRP increase. Thus, we discovered structural and molecular mechanisms underlying tonic and phasic neurotransmitter release and their transition by GBR activation in MHb terminals. article_processing_charge: No author: - first_name: Ryuichi full_name: Shigemoto, Ryuichi id: 499F3ABC-F248-11E8-B48F-1D18A9856A87 last_name: Shigemoto orcid: 0000-0001-8761-9444 citation: ama: Shigemoto R. Transition from tonic to phasic neurotransmitter release by presynaptic GABAB receptor activation in medial habenula terminals. 2023. doi:10.15479/AT:ISTA:13173 apa: Shigemoto, R. (2023). Transition from tonic to phasic neurotransmitter release by presynaptic GABAB receptor activation in medial habenula terminals. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:13173 chicago: Shigemoto, Ryuichi. “Transition from Tonic to Phasic Neurotransmitter Release by Presynaptic GABAB Receptor Activation in Medial Habenula Terminals.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/AT:ISTA:13173. ieee: R. Shigemoto, “Transition from tonic to phasic neurotransmitter release by presynaptic GABAB receptor activation in medial habenula terminals.” Institute of Science and Technology Austria, 2023. ista: Shigemoto R. 2023. Transition from tonic to phasic neurotransmitter release by presynaptic GABAB receptor activation in medial habenula terminals, Institute of Science and Technology Austria, 10.15479/AT:ISTA:13173. mla: Shigemoto, Ryuichi. Transition from Tonic to Phasic Neurotransmitter Release by Presynaptic GABAB Receptor Activation in Medial Habenula Terminals. Institute of Science and Technology Austria, 2023, doi:10.15479/AT:ISTA:13173. short: R. Shigemoto, (2023). date_created: 2023-06-29T13:16:42Z date_published: 2023-07-29T00:00:00Z date_updated: 2024-03-12T13:44:18Z day: '29' ddc: - '571' department: - _id: RySh doi: 10.15479/AT:ISTA:13173 file: - access_level: closed checksum: ed59170869ba621f89f7c1894092192f content_type: application/x-zip-compressed creator: shigemot date_created: 2023-06-29T13:11:22Z date_updated: 2023-11-17T14:30:44Z description: After review an updated version of the data is provided file_id: '13174' file_name: Raw data for Koppensteiner et al.zip file_size: 542873672 relation: main_file title: Outdated Version - access_level: open_access checksum: c07860eb82b4d367245f1b589fe5c250 content_type: application/vnd.openxmlformats-officedocument.spreadsheetml.sheet creator: patrickd date_created: 2023-11-17T14:13:02Z date_updated: 2023-11-17T14:13:02Z file_id: '14550' file_name: 11-17-23 Updated Koppensteiner et al. raw data.xlsx file_size: 915079 relation: main_file success: 1 - access_level: open_access checksum: abf84b1699edac4349dc3a92d466fb7b content_type: application/x-zip-compressed creator: dernst date_created: 2024-02-06T07:21:43Z date_updated: 2024-02-06T07:21:43Z file_id: '14942' file_name: EM_Images.zip file_size: 544868924 relation: main_file success: 1 file_date_updated: 2024-02-06T07:21:43Z has_accepted_license: '1' keyword: - medial habenula - GABAB receptor - vesicle release - Flash and Freeze - Flash and Freeze-fracture month: '07' oa: 1 oa_version: Published Version publisher: Institute of Science and Technology Austria related_material: record: - id: '15084' relation: used_in_publication status: public status: public title: Transition from tonic to phasic neurotransmitter release by presynaptic GABAB receptor activation in medial habenula terminals 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: research_data user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2023' ... --- _id: '11686' abstract: - lang: eng text: Maternally inherited Wolbachia transinfections are being introduced into natural mosquito populations to reduce the transmission of dengue, Zika and other arboviruses. Wolbachia-induced cytoplasmic incompatibility provides a frequency-dependent reproductive advantage to infected females that can spread transinfections within and among populations. However, because transinfections generally reduce host fitness, they tend to spread within populations only after their frequency exceeds a critical threshold. This produces bistability with stable equilibrium frequencies at both 0 and 1, analogous to the bistability produced by underdominance between alleles or karyotypes and by population dynamics under Allee effects. Here, we analyze how stochastic frequency variation produced by finite population size can facilitate the local spread of variants with bistable dynamics into areas where invasion is unexpected from deterministic models. Our exemplar is the establishment of wMel Wolbachia in the Aedes aegypti population of Pyramid Estates (PE), a small community in far north Queensland, Australia. In 2011, wMel was stably introduced into Gordonvale, separated from PE by barriers to Ae. aegypti dispersal. After nearly six years during which wMel was observed only at low frequencies in PE, corresponding to an apparent equilibrium between immigration and selection, wMel rose to fixation by 2018. Using analytic approximations and statistical analyses, we demonstrate that the observed fixation of wMel at PE is consistent with both stochastic transition past an unstable threshold frequency and deterministic transformation produced by steady immigration at a rate just above the threshold required for deterministic invasion. The indeterminacy results from a delicate balance of parameters needed to produce the delayed transition observed. Our analyses suggest that once Wolbachia transinfections are established locally through systematic introductions, stochastic “threshold crossing” is likely to only minimally enhance spatial spread, providing a local ratchet that slightly – but systematically – aids area-wide transformation of disease-vector populations in heterogeneous landscapes. acknowledgement: 'Bill and Melinda Gates Foundation, Award: OPP1180815' article_processing_charge: No author: - first_name: Michael full_name: Turelli, Michael last_name: Turelli - first_name: Nicholas H full_name: Barton, Nicholas H id: 4880FE40-F248-11E8-B48F-1D18A9856A87 last_name: Barton orcid: 0000-0002-8548-5240 citation: ama: 'Turelli M, Barton NH. Wolbachia frequency data from: Why did the Wolbachia transinfection cross the road? Drift, deterministic dynamics and disease control. 2022. doi:10.25338/B81931' apa: 'Turelli, M., & Barton, N. H. (2022). Wolbachia frequency data from: Why did the Wolbachia transinfection cross the road? Drift, deterministic dynamics and disease control. Dryad. https://doi.org/10.25338/B81931' chicago: 'Turelli, Michael, and Nicholas H Barton. “Wolbachia Frequency Data from: Why Did the Wolbachia Transinfection Cross the Road? Drift, Deterministic Dynamics and Disease Control.” Dryad, 2022. https://doi.org/10.25338/B81931.' ieee: 'M. Turelli and N. H. Barton, “Wolbachia frequency data from: Why did the Wolbachia transinfection cross the road? Drift, deterministic dynamics and disease control.” Dryad, 2022.' ista: 'Turelli M, Barton NH. 2022. Wolbachia frequency data from: Why did the Wolbachia transinfection cross the road? Drift, deterministic dynamics and disease control, Dryad, 10.25338/B81931.' mla: 'Turelli, Michael, and Nicholas H. Barton. Wolbachia Frequency Data from: Why Did the Wolbachia Transinfection Cross the Road? Drift, Deterministic Dynamics and Disease Control. Dryad, 2022, doi:10.25338/B81931.' short: M. Turelli, N.H. Barton, (2022). date_created: 2022-07-29T06:45:41Z date_published: 2022-01-06T00:00:00Z date_updated: 2023-08-02T13:50:08Z day: '06' ddc: - '570' department: - _id: NiBa doi: 10.25338/B81931 keyword: - Biological sciences main_file_link: - open_access: '1' url: https://doi.org/10.25338/B81931 month: '01' oa: 1 oa_version: Published Version publisher: Dryad related_material: record: - id: '10604' relation: used_in_publication status: public status: public title: 'Wolbachia frequency data from: Why did the Wolbachia transinfection cross the road? Drift, deterministic dynamics and disease control' 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_reference user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf year: '2022' ... --- _id: '10833' abstract: - lang: eng text: Detailed information about the data set see "dataset description.txt" file. article_processing_charge: No author: - first_name: Roger full_name: Hasler, Roger last_name: Hasler - first_name: Ciril full_name: Reiner-Rozman, Ciril last_name: Reiner-Rozman - first_name: Stefan full_name: Fossati, Stefan last_name: Fossati - first_name: Patrik full_name: Aspermair, Patrik last_name: Aspermair - first_name: Jakub full_name: Dostalek, Jakub last_name: Dostalek - 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: Johannes full_name: Bintinger, Johannes last_name: Bintinger - first_name: Wolfgang full_name: Knoll, Wolfgang last_name: Knoll citation: ama: Hasler R, Reiner-Rozman C, Fossati S, et al. Field-effect transistor with a plasmonic fiber optic gate electrode as a multivariable biosensor device. 2022. doi:10.5281/ZENODO.5500360 apa: Hasler, R., Reiner-Rozman, C., Fossati, S., Aspermair, P., Dostalek, J., Lee, S., … Knoll, W. (2022). Field-effect transistor with a plasmonic fiber optic gate electrode as a multivariable biosensor device. Zenodo. https://doi.org/10.5281/ZENODO.5500360 chicago: Hasler, Roger, Ciril Reiner-Rozman, Stefan Fossati, Patrik Aspermair, Jakub Dostalek, Seungho Lee, Maria Ibáñez, Johannes Bintinger, and Wolfgang Knoll. “Field-Effect Transistor with a Plasmonic Fiber Optic Gate Electrode as a Multivariable Biosensor Device.” Zenodo, 2022. https://doi.org/10.5281/ZENODO.5500360. ieee: R. Hasler et al., “Field-effect transistor with a plasmonic fiber optic gate electrode as a multivariable biosensor device.” Zenodo, 2022. ista: Hasler R, Reiner-Rozman C, Fossati S, Aspermair P, Dostalek J, Lee S, Ibáñez M, Bintinger J, Knoll W. 2022. Field-effect transistor with a plasmonic fiber optic gate electrode as a multivariable biosensor device, Zenodo, 10.5281/ZENODO.5500360. mla: Hasler, Roger, et al. Field-Effect Transistor with a Plasmonic Fiber Optic Gate Electrode as a Multivariable Biosensor Device. Zenodo, 2022, doi:10.5281/ZENODO.5500360. short: R. Hasler, C. Reiner-Rozman, S. Fossati, P. Aspermair, J. Dostalek, S. Lee, M. Ibáñez, J. Bintinger, W. Knoll, (2022). date_created: 2022-03-07T08:19:11Z date_published: 2022-02-08T00:00:00Z date_updated: 2023-08-02T14:46:16Z day: '08' ddc: - '540' department: - _id: MaIb doi: 10.5281/ZENODO.5500360 main_file_link: - open_access: '1' url: https://doi.org/10.5281/zenodo.5500360 month: '02' oa: 1 oa_version: Published Version publisher: Zenodo related_material: record: - id: '10829' relation: used_in_publication status: public status: public title: Field-effect transistor with a plasmonic fiber optic gate electrode as a multivariable biosensor device type: research_data_reference user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf year: '2022' ... --- _id: '13076' abstract: - lang: eng text: "The source code for replicating experiments presented in the paper.\r\n\r\nThe implementation of the designed priority schedulers can be found in Galois-2.2.1/include/Galois/WorkList/:\r\nStealingMultiQueue.h is the StealingMultiQueue.\r\nMQOptimized/ contains MQ Optimized variants.\r\n\r\nWe provide images that contain all the dependencies and datasets. Images can be pulled from npostnikova/mq-based-schedulers repository, or downloaded from Zenodo. See readme for more detail." article_processing_charge: No author: - first_name: Anastasiia full_name: Postnikova, Anastasiia last_name: Postnikova - first_name: Nikita full_name: Koval, Nikita id: 2F4DB10C-F248-11E8-B48F-1D18A9856A87 last_name: Koval - first_name: Giorgi full_name: Nadiradze, Giorgi id: 3279A00C-F248-11E8-B48F-1D18A9856A87 last_name: Nadiradze - first_name: Dan-Adrian full_name: Alistarh, Dan-Adrian id: 4A899BFC-F248-11E8-B48F-1D18A9856A87 last_name: Alistarh orcid: 0000-0003-3650-940X citation: ama: Postnikova A, Koval N, Nadiradze G, Alistarh D-A. Multi-queues can be state-of-the-art priority schedulers. 2022. doi:10.5281/ZENODO.5733408 apa: Postnikova, A., Koval, N., Nadiradze, G., & Alistarh, D.-A. (2022). Multi-queues can be state-of-the-art priority schedulers. Zenodo. https://doi.org/10.5281/ZENODO.5733408 chicago: Postnikova, Anastasiia, Nikita Koval, Giorgi Nadiradze, and Dan-Adrian Alistarh. “Multi-Queues Can Be State-of-the-Art Priority Schedulers.” Zenodo, 2022. https://doi.org/10.5281/ZENODO.5733408. ieee: A. Postnikova, N. Koval, G. Nadiradze, and D.-A. Alistarh, “Multi-queues can be state-of-the-art priority schedulers.” Zenodo, 2022. ista: Postnikova A, Koval N, Nadiradze G, Alistarh D-A. 2022. Multi-queues can be state-of-the-art priority schedulers, Zenodo, 10.5281/ZENODO.5733408. mla: Postnikova, Anastasiia, et al. Multi-Queues Can Be State-of-the-Art Priority Schedulers. Zenodo, 2022, doi:10.5281/ZENODO.5733408. short: A. Postnikova, N. Koval, G. Nadiradze, D.-A. Alistarh, (2022). date_created: 2023-05-23T17:05:40Z date_published: 2022-01-03T00:00:00Z date_updated: 2023-08-03T06:48:34Z day: '03' ddc: - '510' department: - _id: DaAl doi: 10.5281/ZENODO.5733408 main_file_link: - open_access: '1' url: https://doi.org/10.5281/zenodo.5813846 month: '01' oa: 1 oa_version: Published Version publisher: Zenodo related_material: link: - relation: software url: https://github.com/npostnikova/mq-based-schedulers/tree/v1.1 record: - id: '11180' relation: used_in_publication status: public status: public title: Multi-queues can be state-of-the-art priority schedulers type: research_data_reference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2022' ... --- _id: '11695' abstract: - lang: eng text: 'Data underlying the figures in the publication "The chemistry of Cu3N and Cu3PdN nanocrystals" ' article_processing_charge: No author: - first_name: Mahsa full_name: Parvizian, Mahsa last_name: Parvizian - first_name: Alejandra full_name: Duran Balsa, Alejandra last_name: Duran Balsa - first_name: Rohan full_name: Pokratath, Rohan last_name: Pokratath - first_name: Curran full_name: Kalha, Curran last_name: Kalha - first_name: Seungho full_name: Lee, Seungho last_name: Lee - first_name: Dietger full_name: Van den Eynden, Dietger last_name: Van den Eynden - first_name: Maria full_name: Ibáñez, Maria id: 43C61214-F248-11E8-B48F-1D18A9856A87 last_name: Ibáñez orcid: 0000-0001-5013-2843 - first_name: Anna full_name: Regoutz, Anna last_name: Regoutz - first_name: Jonathan full_name: De Roo, Jonathan last_name: De Roo citation: ama: Parvizian M, Duran Balsa A, Pokratath R, et al. Data for “The chemistry of Cu3N and Cu3PdN nanocrystals.” 2022. doi:10.5281/ZENODO.6542908 apa: Parvizian, M., Duran Balsa, A., Pokratath, R., Kalha, C., Lee, S., Van den Eynden, D., … De Roo, J. (2022). Data for “The chemistry of Cu3N and Cu3PdN nanocrystals.” Zenodo. https://doi.org/10.5281/ZENODO.6542908 chicago: Parvizian, Mahsa, Alejandra Duran Balsa, Rohan Pokratath, Curran Kalha, Seungho Lee, Dietger Van den Eynden, Maria Ibáñez, Anna Regoutz, and Jonathan De Roo. “Data for ‘The Chemistry of Cu3N and Cu3PdN Nanocrystals.’” Zenodo, 2022. https://doi.org/10.5281/ZENODO.6542908. ieee: M. Parvizian et al., “Data for ‘The chemistry of Cu3N and Cu3PdN nanocrystals.’” Zenodo, 2022. ista: Parvizian M, Duran Balsa A, Pokratath R, Kalha C, Lee S, Van den Eynden D, Ibáñez M, Regoutz A, De Roo J. 2022. Data for ‘The chemistry of Cu3N and Cu3PdN nanocrystals’, Zenodo, 10.5281/ZENODO.6542908. mla: Parvizian, Mahsa, et al. Data for “The Chemistry of Cu3N and Cu3PdN Nanocrystals.” Zenodo, 2022, doi:10.5281/ZENODO.6542908. short: M. Parvizian, A. Duran Balsa, R. Pokratath, C. Kalha, S. Lee, D. Van den Eynden, M. Ibáñez, A. Regoutz, J. De Roo, (2022). date_created: 2022-07-29T09:31:13Z date_published: 2022-05-12T00:00:00Z date_updated: 2023-08-03T07:19:12Z day: '12' ddc: - '540' department: - _id: MaIb doi: 10.5281/ZENODO.6542908 main_file_link: - open_access: '1' url: https://doi.org/10.5281/ZENODO.6542908 month: '05' oa: 1 oa_version: Published Version publisher: Zenodo related_material: record: - id: '11451' relation: used_in_publication status: public status: public title: Data for "The chemistry of Cu3N and Cu3PdN nanocrystals" 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_reference user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf year: '2022' ... --- _id: '11711' abstract: - lang: eng text: Codes and data for reproducing the results of N. B. Budanur and B. Hof "An autonomous compartmental model for accelerating epidemics" article_processing_charge: No author: - first_name: Nazmi B full_name: Budanur, Nazmi B id: 3EA1010E-F248-11E8-B48F-1D18A9856A87 last_name: Budanur orcid: 0000-0003-0423-5010 citation: ama: Budanur NB. burakbudanur/autoacc-public. 2022. doi:10.5281/ZENODO.6802720 apa: Budanur, N. B. (2022). burakbudanur/autoacc-public. Zenodo. https://doi.org/10.5281/ZENODO.6802720 chicago: Budanur, Nazmi B. “Burakbudanur/Autoacc-Public.” Zenodo, 2022. https://doi.org/10.5281/ZENODO.6802720. ieee: N. B. Budanur, “burakbudanur/autoacc-public.” Zenodo, 2022. ista: Budanur NB. 2022. burakbudanur/autoacc-public, Zenodo, 10.5281/ZENODO.6802720. mla: Budanur, Nazmi B. Burakbudanur/Autoacc-Public. Zenodo, 2022, doi:10.5281/ZENODO.6802720. short: N.B. Budanur, (2022). date_created: 2022-08-01T08:06:33Z date_published: 2022-07-06T00:00:00Z date_updated: 2023-08-03T12:24:21Z day: '06' ddc: - '000' department: - _id: BjHo doi: 10.5281/ZENODO.6802720 has_accepted_license: '1' main_file_link: - open_access: '1' url: https://doi.org/10.5281/ZENODO.6802720 month: '07' oa: 1 oa_version: Published Version publisher: Zenodo related_material: record: - id: '11704' relation: used_in_publication status: public status: public title: burakbudanur/autoacc-public 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_reference user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf year: '2022' ... --- _id: '13064' abstract: - lang: eng text: Genetically informed, deep-phenotyped biobanks are an important research resource and it is imperative that the most powerful, versatile, and efficient analysis approaches are used. Here, we apply our recently developed Bayesian grouped mixture of regressions model (GMRM) in the UK and Estonian Biobanks and obtain the highest genomic prediction accuracy reported to date across 21 heritable traits. When compared to other approaches, GMRM accuracy was greater than annotation prediction models run in the LDAK or LDPred-funct software by 15% (SE 7%) and 14% (SE 2%), respectively, and was 18% (SE 3%) greater than a baseline BayesR model without single-nucleotide polymorphism (SNP) markers grouped into minor allele frequency–linkage disequilibrium (MAF-LD) annotation categories. For height, the prediction accuracy R 2 was 47% in a UK Biobank holdout sample, which was 76% of the estimated h SNP 2 . We then extend our GMRM prediction model to provide mixed-linear model association (MLMA) SNP marker estimates for genome-wide association (GWAS) discovery, which increased the independent loci detected to 16,162 in unrelated UK Biobank individuals, compared to 10,550 from BoltLMM and 10,095 from Regenie, a 62 and 65% increase, respectively. The average χ2 value of the leading markers increased by 15.24 (SE 0.41) for every 1% increase in prediction accuracy gained over a baseline BayesR model across the traits. Thus, we show that modeling genetic associations accounting for MAF and LD differences among SNP markers, and incorporating prior knowledge of genomic function, is important for both genomic prediction and discovery in large-scale individual-level studies. article_processing_charge: No author: - first_name: Etienne full_name: Orliac, Etienne last_name: Orliac - first_name: Daniel full_name: Trejo Banos, Daniel last_name: Trejo Banos - first_name: Sven full_name: Ojavee, Sven last_name: Ojavee - first_name: Kristi full_name: Läll, Kristi last_name: Läll - first_name: Reedik full_name: Mägi, Reedik last_name: Mägi - first_name: Peter full_name: Visscher, Peter last_name: Visscher - first_name: Matthew Richard full_name: Robinson, Matthew Richard id: E5D42276-F5DA-11E9-8E24-6303E6697425 last_name: Robinson orcid: 0000-0001-8982-8813 citation: ama: Orliac E, Trejo Banos D, Ojavee S, et al. Improving genome-wide association discovery and genomic prediction accuracy in biobank data. 2022. doi:10.5061/DRYAD.GTHT76HMZ apa: Orliac, E., Trejo Banos, D., Ojavee, S., Läll, K., Mägi, R., Visscher, P., & Robinson, M. R. (2022). Improving genome-wide association discovery and genomic prediction accuracy in biobank data. Dryad. https://doi.org/10.5061/DRYAD.GTHT76HMZ chicago: Orliac, Etienne, Daniel Trejo Banos, Sven Ojavee, Kristi Läll, Reedik Mägi, Peter Visscher, and Matthew Richard Robinson. “Improving Genome-Wide Association Discovery and Genomic Prediction Accuracy in Biobank Data.” Dryad, 2022. https://doi.org/10.5061/DRYAD.GTHT76HMZ. ieee: E. Orliac et al., “Improving genome-wide association discovery and genomic prediction accuracy in biobank data.” Dryad, 2022. ista: Orliac E, Trejo Banos D, Ojavee S, Läll K, Mägi R, Visscher P, Robinson MR. 2022. Improving genome-wide association discovery and genomic prediction accuracy in biobank data, Dryad, 10.5061/DRYAD.GTHT76HMZ. mla: Orliac, Etienne, et al. Improving Genome-Wide Association Discovery and Genomic Prediction Accuracy in Biobank Data. Dryad, 2022, doi:10.5061/DRYAD.GTHT76HMZ. short: E. Orliac, D. Trejo Banos, S. Ojavee, K. Läll, R. Mägi, P. Visscher, M.R. Robinson, (2022). date_created: 2023-05-23T16:28:13Z date_published: 2022-09-02T00:00:00Z date_updated: 2023-08-03T12:40:37Z day: '02' ddc: - '570' department: - _id: MaRo doi: 10.5061/DRYAD.GTHT76HMZ main_file_link: - open_access: '1' url: https://doi.org/10.5061/dryad.gtht76hmz month: '09' oa: 1 oa_version: Published Version publisher: Dryad related_material: record: - id: '11733' relation: used_in_publication status: public status: public title: Improving genome-wide association discovery and genomic prediction accuracy in biobank data 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_reference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2022' ... --- _id: '12339' abstract: - lang: eng text: 'Copy-number and point mutations form the basis for most evolutionary novelty through the process of gene duplication and divergence. While a plethora of genomic sequence data reveals the long-term fate of diverging coding sequences and their cis-regulatory elements, little is known about the early dynamics around the duplication event itself. In microorganisms, selection for increased gene expression often drives the expansion of gene copy-number mutations, which serves as a crude adaptation, prior to divergence through refining point mutations. Using a simple synthetic genetic system that allows us to distinguish copy-number and point mutations, we study their early and transient adaptive dynamics in real-time in Escherichia coli. We find two qualitatively different routes of adaptation depending on the level of functional improvement selected for: In conditions of high gene expression demand, the two types of mutations occur as a combination. Under low gene expression demand, negative epistasis between the two types of mutations renders them mutually exclusive. Thus, owing to their higher frequency, adaptation is dominated by copy-number mutations. Ultimately, due to high rates of reversal and pleiotropic cost, copy-number mutations may not only serve as a crude and transient adaptation but also constrain sequence divergence over evolutionary time scales.' article_processing_charge: No author: - first_name: Isabella full_name: Tomanek, Isabella id: 3981F020-F248-11E8-B48F-1D18A9856A87 last_name: Tomanek orcid: 0000-0001-6197-363X - first_name: Calin C full_name: Guet, Calin C id: 47F8433E-F248-11E8-B48F-1D18A9856A87 last_name: Guet orcid: 0000-0001-6220-2052 citation: ama: Tomanek I, Guet CC. Flow cytometry YFP and CFP data and deep sequencing data of populations evolving in galactose. 2022. doi:10.5061/dryad.rfj6q57ds apa: Tomanek, I., & Guet, C. C. (2022). Flow cytometry YFP and CFP data and deep sequencing data of populations evolving in galactose. Dryad. https://doi.org/10.5061/dryad.rfj6q57ds chicago: Tomanek, Isabella, and Calin C Guet. “Flow Cytometry YFP and CFP Data and Deep Sequencing Data of Populations Evolving in Galactose.” Dryad, 2022. https://doi.org/10.5061/dryad.rfj6q57ds. ieee: I. Tomanek and C. C. Guet, “Flow cytometry YFP and CFP data and deep sequencing data of populations evolving in galactose.” Dryad, 2022. ista: Tomanek I, Guet CC. 2022. Flow cytometry YFP and CFP data and deep sequencing data of populations evolving in galactose, Dryad, 10.5061/dryad.rfj6q57ds. mla: Tomanek, Isabella, and Calin C. Guet. Flow Cytometry YFP and CFP Data and Deep Sequencing Data of Populations Evolving in Galactose. Dryad, 2022, doi:10.5061/dryad.rfj6q57ds. short: I. Tomanek, C.C. Guet, (2022). date_created: 2023-01-23T09:00:37Z date_published: 2022-12-23T00:00:00Z date_updated: 2023-08-03T14:23:06Z day: '23' ddc: - '570' department: - _id: CaGu doi: 10.5061/dryad.rfj6q57ds main_file_link: - open_access: '1' url: https://doi.org/10.5061/dryad.rfj6q57ds month: '12' oa: 1 oa_version: Published Version publisher: Dryad related_material: record: - id: '12333' relation: used_in_publication status: public status: public title: Flow cytometry YFP and CFP data and deep sequencing data of populations evolving in galactose type: research_data_reference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2022' ... --- _id: '13066' abstract: - lang: eng text: Chromosomal inversions have been shown to play a major role in local adaptation by suppressing recombination between alternative arrangements and maintaining beneficial allele combinations. However, so far, their importance relative to the remaining genome remains largely unknown. Understanding the genetic architecture of adaptation requires better estimates of how loci of different effect sizes contribute to phenotypic variation. Here, we used three Swedish islands where the marine snail Littorina saxatilis has repeatedly evolved into two distinct ecotypes along a habitat transition. We estimated the contribution of inversion polymorphisms to phenotypic divergence while controlling for polygenic effects in the remaining genome using a quantitative genetics framework. We confirmed the importance of inversions but showed that contributions of loci outside inversions are of similar magnitude, with variable proportions dependent on the trait and the population. Some inversions showed consistent effects across all sites, whereas others exhibited site-specific effects, indicating that the genomic basis for replicated phenotypic divergence is only partly shared. The contributions of sexual dimorphism as well as environmental factors to phenotypic variation were significant but minor compared to inversions and polygenic background. Overall, this integrated approach provides insight into the multiple mechanisms contributing to parallel phenotypic divergence. article_processing_charge: No author: - first_name: Eva full_name: Koch, Eva last_name: Koch - first_name: Mark full_name: Ravinet, Mark last_name: Ravinet - first_name: Anja M full_name: Westram, Anja M id: 3C147470-F248-11E8-B48F-1D18A9856A87 last_name: Westram orcid: 0000-0003-1050-4969 - first_name: Kerstin full_name: Jonannesson, Kerstin last_name: Jonannesson - first_name: Roger full_name: Butlin, Roger last_name: Butlin citation: ama: 'Koch E, Ravinet M, Westram AM, Jonannesson K, Butlin R. Data from: Genetic architecture of repeated phenotypic divergence in Littorina saxatilis ecotype evolution. 2022. doi:10.5061/DRYAD.M905QFV4B' apa: 'Koch, E., Ravinet, M., Westram, A. M., Jonannesson, K., & Butlin, R. (2022). Data from: Genetic architecture of repeated phenotypic divergence in Littorina saxatilis ecotype evolution. Dryad. https://doi.org/10.5061/DRYAD.M905QFV4B' chicago: 'Koch, Eva, Mark Ravinet, Anja M Westram, Kerstin Jonannesson, and Roger Butlin. “Data from: Genetic Architecture of Repeated Phenotypic Divergence in Littorina Saxatilis Ecotype Evolution.” Dryad, 2022. https://doi.org/10.5061/DRYAD.M905QFV4B.' ieee: 'E. Koch, M. Ravinet, A. M. Westram, K. Jonannesson, and R. Butlin, “Data from: Genetic architecture of repeated phenotypic divergence in Littorina saxatilis ecotype evolution.” Dryad, 2022.' ista: 'Koch E, Ravinet M, Westram AM, Jonannesson K, Butlin R. 2022. Data from: Genetic architecture of repeated phenotypic divergence in Littorina saxatilis ecotype evolution, Dryad, 10.5061/DRYAD.M905QFV4B.' mla: 'Koch, Eva, et al. Data from: Genetic Architecture of Repeated Phenotypic Divergence in Littorina Saxatilis Ecotype Evolution. Dryad, 2022, doi:10.5061/DRYAD.M905QFV4B.' short: E. Koch, M. Ravinet, A.M. Westram, K. Jonannesson, R. Butlin, (2022). date_created: 2023-05-23T16:33:12Z date_published: 2022-07-28T00:00:00Z date_updated: 2023-08-04T09:42:10Z day: '28' ddc: - '570' department: - _id: NiBa doi: 10.5061/DRYAD.M905QFV4B main_file_link: - open_access: '1' url: https://doi.org/10.5061/dryad.m905qfv4b month: '07' oa: 1 oa_version: Published Version publisher: Dryad related_material: record: - id: '12247' relation: used_in_publication status: public status: public title: 'Data from: Genetic architecture of repeated phenotypic divergence in Littorina saxatilis ecotype evolution' 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_reference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2022' ... --- _id: '14520' abstract: - lang: eng text: 'This dataset comprises all data shown in the figures of the submitted article "Compact vacuum gap transmon qubits: Selective and sensitive probes for superconductor surface losses" at arxiv.org/abs/2206.14104. Additional raw data are available from the corresponding author on reasonable request.' article_processing_charge: No author: - first_name: Martin full_name: Zemlicka, Martin id: 2DCF8DE6-F248-11E8-B48F-1D18A9856A87 last_name: Zemlicka - first_name: Elena full_name: Redchenko, Elena id: 2C21D6E8-F248-11E8-B48F-1D18A9856A87 last_name: Redchenko - first_name: Matilda full_name: Peruzzo, Matilda id: 3F920B30-F248-11E8-B48F-1D18A9856A87 last_name: Peruzzo orcid: 0000-0002-3415-4628 - first_name: Farid full_name: Hassani, Farid id: 2AED110C-F248-11E8-B48F-1D18A9856A87 last_name: Hassani orcid: 0000-0001-6937-5773 - first_name: Andrea full_name: Trioni, Andrea id: 42F71B44-F248-11E8-B48F-1D18A9856A87 last_name: Trioni - first_name: Shabir full_name: Barzanjeh, Shabir id: 2D25E1F6-F248-11E8-B48F-1D18A9856A87 last_name: Barzanjeh orcid: 0000-0003-0415-1423 - first_name: Johannes M full_name: Fink, Johannes M id: 4B591CBA-F248-11E8-B48F-1D18A9856A87 last_name: Fink orcid: 0000-0001-8112-028X citation: ama: 'Zemlicka M, Redchenko E, Peruzzo M, et al. Compact vacuum gap transmon qubits: Selective and sensitive probes for superconductor surface losses. 2022. doi:10.5281/ZENODO.8408897' apa: 'Zemlicka, M., Redchenko, E., Peruzzo, M., Hassani, F., Trioni, A., Barzanjeh, S., & Fink, J. M. (2022). Compact vacuum gap transmon qubits: Selective and sensitive probes for superconductor surface losses. Zenodo. https://doi.org/10.5281/ZENODO.8408897' chicago: 'Zemlicka, Martin, Elena Redchenko, Matilda Peruzzo, Farid Hassani, Andrea Trioni, Shabir Barzanjeh, and Johannes M Fink. “Compact Vacuum Gap Transmon Qubits: Selective and Sensitive Probes for Superconductor Surface Losses.” Zenodo, 2022. https://doi.org/10.5281/ZENODO.8408897.' ieee: 'M. Zemlicka et al., “Compact vacuum gap transmon qubits: Selective and sensitive probes for superconductor surface losses.” Zenodo, 2022.' ista: 'Zemlicka M, Redchenko E, Peruzzo M, Hassani F, Trioni A, Barzanjeh S, Fink JM. 2022. Compact vacuum gap transmon qubits: Selective and sensitive probes for superconductor surface losses, Zenodo, 10.5281/ZENODO.8408897.' mla: 'Zemlicka, Martin, et al. Compact Vacuum Gap Transmon Qubits: Selective and Sensitive Probes for Superconductor Surface Losses. Zenodo, 2022, doi:10.5281/ZENODO.8408897.' short: M. Zemlicka, E. Redchenko, M. Peruzzo, F. Hassani, A. Trioni, S. Barzanjeh, J.M. Fink, (2022). date_created: 2023-11-13T08:09:10Z date_published: 2022-06-28T00:00:00Z date_updated: 2023-11-13T09:22:48Z day: '28' ddc: - '530' department: - _id: JoFi doi: 10.5281/ZENODO.8408897 has_accepted_license: '1' main_file_link: - open_access: '1' url: https://doi.org/10.5281/ZENODO.8408897 month: '06' oa: 1 oa_version: Published Version publisher: Zenodo related_material: record: - id: '14517' relation: used_in_publication status: public status: public title: 'Compact vacuum gap transmon qubits: Selective and sensitive probes for superconductor surface losses' 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_reference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2022' ... --- _id: '10934' abstract: - lang: eng text: 'FtsA is crucial for assembly of the E. coli divisome, as it dynamically links cytoplasmic FtsZ filaments with transmembrane cell division proteins. FtsA allegedly initiates cell division by switching from an inactive polymeric to an active monomeric confirmation, which recruits downstream proteins and stabilizes FtsZ filaments. Here, we use biochemical reconstitution experiments combined with quantitative fluorescence microscopy to study divisome activation in vitro. We compare wildtype-FtsA with FtsA-R286W, a constantly active gain-of-function mutant and find that R286W outperforms the wildtype protein in replicating FtsZ treadmilling dynamics, stabilizing FtsZ filaments and recruiting FtsN. We attribute these differences to a faster membrane exchange of FtsA-R286W and its higher packing density below FtsZ filaments. Using FRET microscopy, we find that FtsN binding does not compete with, but promotes FtsA self-interaction. Our findings suggest a model where FtsA always forms dynamic polymers on the membrane, which re-organize during assembly and activation of the divisome. ' acknowledged_ssus: - _id: Bio - _id: LifeSc acknowledgement: We acknowledge members of the Loose laboratory at IST Austria for helpful discussions—in particular L. Lindorfer for his assistance with cloning and purifications. We thank J. Löwe and T. Nierhaus (MRC-LMB Cambridge, UK) for sharing unpublished work and helpful discussions, as well as D. Vavylonis and D. Rutkowski (Lehigh University, Bethlehem, PA, USA) as well as S. Martin (University of Lausanne, Switzerland) for sharing their code for FRAP analysis. We are also thankful for the support by the Scientific Service Units (SSU) of IST Austria through resources provided by the Imaging and Optics Facility (IOF) and the Lab Support Facility (LSF). This work was supported by the European Research Council through grant ERC 2015-StG-679239 and by the Austrian Science Fund (FWF) StandAlone P34607 to M.L. and HFSP LT 000824/2016-L4 to N.B. For the purpose of open access, we have applied a CC BY public copyright licence to any Author Accepted Manuscript version arising from this submission. article_processing_charge: No author: - first_name: Philipp full_name: Radler, Philipp id: 40136C2A-F248-11E8-B48F-1D18A9856A87 last_name: Radler orcid: ' 0000-0001-9198-2182 ' citation: ama: Radler P. In vitro reconstitution of Escherichia coli divisome activation. 2022. doi:10.15479/AT:ISTA:10934 apa: Radler, P. (2022). In vitro reconstitution of Escherichia coli divisome activation. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:10934 chicago: Radler, Philipp. “In Vitro Reconstitution of Escherichia Coli Divisome Activation.” Institute of Science and Technology Austria, 2022. https://doi.org/10.15479/AT:ISTA:10934. ieee: P. Radler, “In vitro reconstitution of Escherichia coli divisome activation.” Institute of Science and Technology Austria, 2022. ista: Radler P. 2022. In vitro reconstitution of Escherichia coli divisome activation, Institute of Science and Technology Austria, 10.15479/AT:ISTA:10934. mla: Radler, Philipp. In Vitro Reconstitution of Escherichia Coli Divisome Activation. Institute of Science and Technology Austria, 2022, doi:10.15479/AT:ISTA:10934. short: P. Radler, (2022). contributor: - contributor_type: supervisor first_name: Martin id: 462D4284-F248-11E8-B48F-1D18A9856A87 last_name: Loose orcid: 0000-0001-7309-9724 - contributor_type: researcher first_name: Christoph M id: 4DF26D8C-F248-11E8-B48F-1D18A9856A87 last_name: Sommer - contributor_type: researcher first_name: Paulo last_name: Caldas - contributor_type: researcher first_name: David id: B9577E20-AA38-11E9-AC9A-0930E6697425 last_name: Michalik - contributor_type: researcher first_name: Natalia last_name: Baranova date_created: 2022-03-31T11:32:32Z date_published: 2022-04-05T00:00:00Z date_updated: 2024-02-21T12:35:18Z day: '05' ddc: - '572' department: - _id: GradSch - _id: MaLo doi: 10.15479/AT:ISTA:10934 ec_funded: 1 file: - access_level: open_access checksum: 52d50202e04e9daa618a58e686d8ab58 content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document creator: pradler date_created: 2022-04-22T10:15:19Z date_updated: 2022-04-22T10:15:19Z file_id: '11328' file_name: Inventory for Data repository.docx file_size: 13469 relation: main_file success: 1 - 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access_level: open_access checksum: 3f4928a36e1b1f295054668060df3079 content_type: application/octet-stream creator: pradler date_created: 2022-04-05T08:51:55Z date_updated: 2022-04-05T08:51:55Z file_id: '10953' file_name: Raw Microscopy_FRET FtsA His6 + FtsN & FtsZ_01.z01 file_size: 4294960000 relation: main_file success: 1 file_date_updated: 2022-04-22T10:15:19Z has_accepted_license: '1' keyword: - Bacterial cell division - in vitro reconstitution - FtsZ - FtsN - FtsA month: '04' oa: 1 oa_version: Submitted Version project: - _id: 2595697A-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '679239' name: Self-Organization of the Bacterial Cell - _id: fc38323b-9c52-11eb-aca3-ff8afb4a011d grant_number: P34607 name: "Understanding bacterial cell division by in vitro\r\nreconstitution" publisher: Institute of Science and Technology Austria related_material: link: - description: A custom written code (FRAPdiff) to quantify the Off binding rate and Diffusion coefficient of membrane bound proteins. Written by Christoph Sommer. relation: software url: https://doi.org/10.5281/zenodo.6400639 record: - id: '11373' relation: used_in_publication status: public - id: '14280' relation: used_in_publication status: public status: public title: In vitro reconstitution of Escherichia coli divisome activation tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: research_data user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2022' ... --- _id: '11542' article_processing_charge: No author: - first_name: Rouven full_name: Schulz, Rouven id: 4C5E7B96-F248-11E8-B48F-1D18A9856A87 last_name: Schulz orcid: 0000-0001-5297-733X citation: ama: Schulz R. Source Data (Chimeric GPCRs mimic distinct signaling pathways and modulate microglia responses). 2022. doi:10.15479/AT:ISTA:11542 apa: Schulz, R. (2022). Source Data (Chimeric GPCRs mimic distinct signaling pathways and modulate microglia responses). Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:11542 chicago: Schulz, Rouven. “Source Data (Chimeric GPCRs Mimic Distinct Signaling Pathways and Modulate Microglia Responses).” Institute of Science and Technology Austria, 2022. https://doi.org/10.15479/AT:ISTA:11542. ieee: R. Schulz, “Source Data (Chimeric GPCRs mimic distinct signaling pathways and modulate microglia responses).” Institute of Science and Technology Austria, 2022. ista: Schulz R. 2022. Source Data (Chimeric GPCRs mimic distinct signaling pathways and modulate microglia responses), Institute of Science and Technology Austria, 10.15479/AT:ISTA:11542. mla: Schulz, Rouven. Source Data (Chimeric GPCRs Mimic Distinct Signaling Pathways and Modulate Microglia Responses). Institute of Science and Technology Austria, 2022, doi:10.15479/AT:ISTA:11542. short: R. Schulz, (2022). contributor: - contributor_type: contact_person first_name: Sandra id: 36ACD32E-F248-11E8-B48F-1D18A9856A87 last_name: Siegert orcid: 0000-0001-8635-0877 date_created: 2022-07-08T11:03:02Z date_published: 2022-01-01T00:00:00Z date_updated: 2024-02-21T12:34:51Z department: - _id: GradSch - _id: SaSi doi: 10.15479/AT:ISTA:11542 file: - access_level: open_access checksum: 71e8186583f3adbb6c69a88ac9e6e49b content_type: application/vnd.openxmlformats-officedocument.spreadsheetml.sheet creator: rschulz date_created: 2022-07-08T10:56:52Z date_updated: 2022-07-08T10:56:52Z file_id: '11543' file_name: Source Data.xlsx file_size: 135784571 relation: main_file success: 1 file_date_updated: 2022-07-08T10:56:52Z has_accepted_license: '1' oa: 1 oa_version: None publisher: Institute of Science and Technology Austria related_material: link: - relation: contains url: https://www.biorxiv.org/content/10.1101/2021.06.21.449162v1 record: - id: '11995' relation: used_in_publication status: public status: public title: Source Data (Chimeric GPCRs mimic distinct signaling pathways and modulate microglia responses) 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: '2022' ... --- _id: '12522' abstract: - lang: eng text: This .zip File contains the transport data, the codes for the data analysis, the microscopy analysis and the codes for the theoretical simulations for "Majorana-like Coulomb spectroscopy in the absence of zero bias peaks" by M. Valentini, et. al. The transport data are saved with hdf5 file format. The files can be open with the log browser of Labber. article_processing_charge: No author: - first_name: Marco full_name: Valentini, Marco id: C0BB2FAC-D767-11E9-B658-BC13E6697425 last_name: Valentini - first_name: Pablo full_name: San-Jose, Pablo last_name: San-Jose - first_name: Jordi full_name: Arbiol, Jordi last_name: Arbiol - first_name: Sara full_name: Marti-Sanchez, Sara last_name: Marti-Sanchez - first_name: Marc full_name: Botifoll, Marc last_name: Botifoll citation: ama: Valentini M, San-Jose P, Arbiol J, Marti-Sanchez S, Botifoll M. Data for “Majorana-like Coulomb spectroscopy in the absence of zero bias peaks.” 2022. doi:10.15479/AT:ISTA:12102 apa: Valentini, M., San-Jose, P., Arbiol, J., Marti-Sanchez, S., & Botifoll, M. (2022). Data for “Majorana-like Coulomb spectroscopy in the absence of zero bias peaks.” Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:12102 chicago: Valentini, Marco, Pablo San-Jose, Jordi Arbiol, Sara Marti-Sanchez, and Marc Botifoll. “Data for ‘Majorana-like Coulomb Spectroscopy in the Absence of Zero Bias Peaks.’” Institute of Science and Technology Austria, 2022. https://doi.org/10.15479/AT:ISTA:12102. ieee: M. Valentini, P. San-Jose, J. Arbiol, S. Marti-Sanchez, and M. Botifoll, “Data for ‘Majorana-like Coulomb spectroscopy in the absence of zero bias peaks.’” Institute of Science and Technology Austria, 2022. ista: Valentini M, San-Jose P, Arbiol J, Marti-Sanchez S, Botifoll M. 2022. Data for ‘Majorana-like Coulomb spectroscopy in the absence of zero bias peaks’, Institute of Science and Technology Austria, 10.15479/AT:ISTA:12102. mla: Valentini, Marco, et al. Data for “Majorana-like Coulomb Spectroscopy in the Absence of Zero Bias Peaks.” Institute of Science and Technology Austria, 2022, doi:10.15479/AT:ISTA:12102. short: M. Valentini, P. San-Jose, J. Arbiol, S. Marti-Sanchez, M. Botifoll, (2022). contributor: - contributor_type: contact_person first_name: Marco id: C0BB2FAC-D767-11E9-B658-BC13E6697425 last_name: Valentini date_created: 2023-02-07T08:13:39Z date_published: 2022-09-25T00:00:00Z date_updated: 2024-02-21T12:35:34Z day: '25' ddc: - '530' department: - _id: GeKa doi: 10.15479/AT:ISTA:12102 file: - access_level: open_access checksum: 0dbd6327bf84c7e81b295c4bc9d12826 content_type: application/x-zip-compressed creator: dernst date_created: 2023-02-07T08:18:24Z date_updated: 2023-02-07T08:18:24Z file_id: '12523' file_name: Majorana_like.zip file_size: 3609122411 relation: main_file success: 1 file_date_updated: 2023-02-07T08:18:24Z has_accepted_license: '1' month: '09' oa: 1 oa_version: Published Version publisher: Institute of Science and Technology Austria related_material: record: - id: '12118' relation: used_in_publication status: public - id: '13286' relation: used_in_publication status: public status: public title: Data for "Majorana-like Coulomb spectroscopy in the absence of zero bias peaks" 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: '2022' ... --- _id: '11321' abstract: - lang: eng text: 'Here are the research data underlying the publication "Effects of fine-scale population structure on the distribution of heterozygosity in a long-term study of Antirrhinum majus" Further information are summed up in the README document. ' article_processing_charge: No author: - first_name: Parvathy full_name: Surendranadh, Parvathy id: 455235B8-F248-11E8-B48F-1D18A9856A87 last_name: Surendranadh - first_name: Louise S full_name: Arathoon, Louise S id: 2CFCFF98-F248-11E8-B48F-1D18A9856A87 last_name: Arathoon orcid: 0000-0003-1771-714X - first_name: Carina full_name: Baskett, Carina id: 3B4A7CE2-F248-11E8-B48F-1D18A9856A87 last_name: Baskett orcid: 0000-0002-7354-8574 - first_name: David full_name: Field, David id: 419049E2-F248-11E8-B48F-1D18A9856A87 last_name: Field orcid: 0000-0002-4014-8478 - first_name: Melinda full_name: Pickup, Melinda id: 2C78037E-F248-11E8-B48F-1D18A9856A87 last_name: Pickup orcid: 0000-0001-6118-0541 - first_name: Nicholas H full_name: Barton, Nicholas H id: 4880FE40-F248-11E8-B48F-1D18A9856A87 last_name: Barton orcid: 0000-0002-8548-5240 citation: ama: Surendranadh P, Arathoon LS, Baskett C, Field D, Pickup M, Barton NH. Effects of fine-scale population structure on the distribution of heterozygosity in a long-term study of Antirrhinum majus. 2022. doi:10.15479/at:ista:11321 apa: Surendranadh, P., Arathoon, L. S., Baskett, C., Field, D., Pickup, M., & Barton, N. H. (2022). Effects of fine-scale population structure on the distribution of heterozygosity in a long-term study of Antirrhinum majus. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:11321 chicago: Surendranadh, Parvathy, Louise S Arathoon, Carina Baskett, David Field, Melinda Pickup, and Nicholas H Barton. “Effects of Fine-Scale Population Structure on the Distribution of Heterozygosity in a Long-Term Study of Antirrhinum Majus.” Institute of Science and Technology Austria, 2022. https://doi.org/10.15479/at:ista:11321. ieee: P. Surendranadh, L. S. Arathoon, C. Baskett, D. Field, M. Pickup, and N. H. Barton, “Effects of fine-scale population structure on the distribution of heterozygosity in a long-term study of Antirrhinum majus.” Institute of Science and Technology Austria, 2022. ista: Surendranadh P, Arathoon LS, Baskett C, Field D, Pickup M, Barton NH. 2022. Effects of fine-scale population structure on the distribution of heterozygosity in a long-term study of Antirrhinum majus, Institute of Science and Technology Austria, 10.15479/at:ista:11321. mla: Surendranadh, Parvathy, et al. Effects of Fine-Scale Population Structure on the Distribution of Heterozygosity in a Long-Term Study of Antirrhinum Majus. Institute of Science and Technology Austria, 2022, doi:10.15479/at:ista:11321. short: P. Surendranadh, L.S. Arathoon, C. Baskett, D. Field, M. Pickup, N.H. Barton, (2022). contributor: - contributor_type: project_member first_name: Louise S id: 2CFCFF98-F248-11E8-B48F-1D18A9856A87 last_name: Arathoon - contributor_type: project_member first_name: Carina id: 3B4A7CE2-F248-11E8-B48F-1D18A9856A87 last_name: Baskett orcid: 0000-0002-7354-8574 - contributor_type: project_member first_name: David id: 419049E2-F248-11E8-B48F-1D18A9856A87 last_name: Field orcid: 0000-0002-4014-8478 - contributor_type: project_member first_name: Melinda id: 2C78037E-F248-11E8-B48F-1D18A9856A87 last_name: Pickup orcid: 0000-0001-6118-0541 - contributor_type: project_member first_name: Nicholas H id: 4880FE40-F248-11E8-B48F-1D18A9856A87 last_name: Barton orcid: 0000-0002-8548-5240 date_created: 2022-04-22T09:42:24Z date_published: 2022-04-28T00:00:00Z date_updated: 2024-02-21T12:41:09Z day: '28' ddc: - '570' department: - _id: GradSch - _id: NiBa doi: 10.15479/at:ista:11321 file: - access_level: open_access checksum: 96c1b86cdf25481f2a52972fcc45ca7f content_type: application/x-zip-compressed creator: larathoo date_created: 2022-04-22T09:39:03Z date_updated: 2022-04-22T09:39:03Z file_id: '11326' file_name: Data_Code.zip file_size: 13260571 relation: main_file success: 1 file_date_updated: 2022-04-22T09:39:03Z has_accepted_license: '1' month: '04' oa: 1 oa_version: Published Version publisher: Institute of Science and Technology Austria related_material: record: - id: '11411' relation: used_in_publication status: public - id: '9192' relation: earlier_version status: public - id: '8254' relation: earlier_version status: public status: public title: Effects of fine-scale population structure on the distribution of heterozygosity in a long-term study of Antirrhinum majus 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: '2022' ... --- _id: '11653' abstract: - lang: eng text: Eurasian brine shrimp (genus Artemia) have closely related sexual and asexual lineages of parthenogenetic females, which produce rare males at low frequencies. Although they are known to have ZW chromosomes, these are not well characterized, and it is unclear whether they are shared across the clade. Furthermore, the underlying genetic architecture of the transmission of asexuality, which can occur when rare males mate with closely related sexual females, is not well understood. We produced a chromosome-level assembly for the sexual Eurasian species A. sinica and characterized in detail the pair of sex chromosomes of this species. We combined this new assembly with short-read genomic data for the sexual species A. sp. Kazakhstan and several asexual lineages of A. parthenogenetica, allowing us to perform an in-depth characterization of sex-chromosome evolution across the genus. We identified a small differentiated region of the ZW pair that is shared by all sexual and asexual lineages, supporting the shared ancestry of the sex chromosomes. We also inferred that recombination suppression has spread to larger sections of the chromosome independently in the American and Eurasian lineages. Finally, we took advantage of a rare male, which we backcrossed to sexual females, to explore the genetic basis of asexuality. Our results suggest that parthenogenesis is likely partly controlled by a locus on the Z chromosome, highlighting the interplay between sex determination and asexuality. article_processing_charge: No author: - first_name: Marwan N full_name: Elkrewi, Marwan N id: 0B46FACA-A8E1-11E9-9BD3-79D1E5697425 last_name: Elkrewi orcid: 0000-0002-5328-7231 citation: ama: Elkrewi MN. Data from Elkrewi, Khauratovich, Toups et al. 2022, “ZW sex-chromosome evolution and contagious parthenogenesis in Artemia brine shrimp.” 2022. doi:10.15479/AT:ISTA:11653 apa: Elkrewi, M. N. (2022). Data from Elkrewi, Khauratovich, Toups et al. 2022, “ZW sex-chromosome evolution and contagious parthenogenesis in Artemia brine shrimp.” Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:11653 chicago: Elkrewi, Marwan N. “Data from Elkrewi, Khauratovich, Toups et Al. 2022, ‘ZW Sex-Chromosome Evolution and Contagious Parthenogenesis in Artemia Brine Shrimp.’” Institute of Science and Technology Austria, 2022. https://doi.org/10.15479/AT:ISTA:11653. ieee: M. N. Elkrewi, “Data from Elkrewi, Khauratovich, Toups et al. 2022, ‘ZW sex-chromosome evolution and contagious parthenogenesis in Artemia brine shrimp.’” Institute of Science and Technology Austria, 2022. ista: Elkrewi MN. 2022. Data from Elkrewi, Khauratovich, Toups et al. 2022, ‘ZW sex-chromosome evolution and contagious parthenogenesis in Artemia brine shrimp’, Institute of Science and Technology Austria, 10.15479/AT:ISTA:11653. mla: Elkrewi, Marwan N. Data from Elkrewi, Khauratovich, Toups et Al. 2022, “ZW Sex-Chromosome Evolution and Contagious Parthenogenesis in Artemia Brine Shrimp.” Institute of Science and Technology Austria, 2022, doi:10.15479/AT:ISTA:11653. short: M.N. Elkrewi, (2022). contributor: - first_name: Marwan N id: 0B46FACA-A8E1-11E9-9BD3-79D1E5697425 last_name: Elkrewi orcid: 0000-0002-5328-7231 - first_name: Uladzislava last_name: Khauratovich - first_name: Melissa A id: 4E099E4E-F248-11E8-B48F-1D18A9856A87 last_name: Toups - first_name: Vincent K id: 57854184-AAE0-11E9-8D04-98D6E5697425 last_name: Bett - first_name: Andrea id: 353FAC84-AE61-11E9-8BFC-00D3E5697425 last_name: Mrnjavac - first_name: Ariana id: 2A0848E2-F248-11E8-B48F-1D18A9856A87 last_name: Macon - first_name: Christelle id: 32DF5794-F248-11E8-B48F-1D18A9856A87 last_name: Fraisse orcid: 0000-0001-8441-5075 - first_name: Luca last_name: Sax - first_name: Ann K id: 4C0A3874-F248-11E8-B48F-1D18A9856A87 last_name: Huylmans - first_name: Francisco last_name: 'Hontoria ' - first_name: Beatriz id: 49E1C5C6-F248-11E8-B48F-1D18A9856A87 last_name: Vicoso orcid: 0000-0002-4579-8306 date_created: 2022-07-26T11:01:47Z date_published: 2022-08-05T00:00:00Z date_updated: 2024-02-21T12:35:53Z day: '05' ddc: - '570' department: - _id: GradSch - _id: BeVi doi: 10.15479/AT:ISTA:11653 file: - access_level: open_access checksum: 5f1d7c6d7ab5375ed2564521432bed0c content_type: application/x-zip-compressed creator: melkrewi date_created: 2022-07-26T12:37:52Z date_updated: 2022-08-08T22:30:04Z description: | The folder contains the following datasets (fasta files, and text files): Sup. Dataset 1: Genome assemblies: A. sinica male high quality assembly, A. sp. Kazakhstan male draft assembly Sup. Dataset 2: Male transcriptome assemblies for A. sinica and A. franciscana Sup. Dataset 3: Male and female coverage for A. sinica, A. sp. Kazakhstan, A. urmiana, and A. parthenogenetica females and rare male. Sup. Dataset 4: Artemia sinica Male:female FST per 1Kb window Sup. Dataset 5: FASTA file with candidate W scaffolds Sup. Dataset 6: Candidate W-derived transcripts and alignments Sup. Dataset 7: Gene expression with genomic location Sup. Dataset 8: VCF for asexual female and rare male Sup. Dataset 9: FST between backcrossed asexual and control females (pooled analysis) Sup. Dataset 10: VCF of backcrossed asexual and control females (individual analysis using A. sp. Kazakhstan as the reference), and inferred ancestry Sup. Dataset 11: GO and DE annotations of all the Artemia sinica transcripts and their locations in the Artemia sinica male genome. embargo: 2022-08-07 file_id: '11655' file_name: Data.zip file_size: 2209382998 relation: main_file title: Supplementary Datasets file_date_updated: 2022-08-08T22:30:04Z has_accepted_license: '1' month: '08' oa: 1 oa_version: Published Version publisher: Institute of Science and Technology Austria related_material: record: - id: '12248' relation: used_in_publication status: public status: public title: Data from Elkrewi, Khauratovich, Toups et al. 2022, "ZW sex-chromosome evolution and contagious parthenogenesis in Artemia brine shrimp" 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: '2022' ... --- _id: '13072' abstract: - lang: eng text: CpGs and corresponding mean weights for DNAm-based prediction of cognitive abilities (6 traits) article_processing_charge: No author: - first_name: Daniel L full_name: McCartney, Daniel L last_name: McCartney - first_name: Robert F full_name: Hillary, Robert F last_name: Hillary - first_name: Eleanor LS full_name: Conole, Eleanor LS last_name: Conole - first_name: Daniel full_name: Trejo Banos, Daniel last_name: Trejo Banos - first_name: Danni A full_name: Gadd, Danni A last_name: Gadd - first_name: Rosie M full_name: Walker, Rosie M last_name: Walker - first_name: Cliff full_name: Nangle, Cliff last_name: Nangle - first_name: Robin full_name: Flaig, Robin last_name: Flaig - first_name: Archie full_name: Campbell, Archie last_name: Campbell - first_name: Alison D full_name: Murray, Alison D last_name: Murray - first_name: Susana full_name: Munoz Maniega, Susana last_name: Munoz Maniega - first_name: Maria full_name: del C Valdes-Hernandez, Maria last_name: del C Valdes-Hernandez - first_name: Mathew A full_name: Harris, Mathew A last_name: Harris - first_name: Mark E full_name: Bastin, Mark E last_name: Bastin - first_name: Joanna M full_name: Wardlaw, Joanna M last_name: Wardlaw - first_name: Sarah E full_name: Harris, Sarah E last_name: Harris - first_name: David J full_name: Porteous, David J last_name: Porteous - first_name: Elliot M full_name: Tucker-Drob, Elliot M last_name: Tucker-Drob - first_name: Andrew M full_name: McIntosh, Andrew M last_name: McIntosh - first_name: Kathryn L full_name: Evans, Kathryn L last_name: Evans - first_name: Ian J full_name: Deary, Ian J last_name: Deary - first_name: Simon R full_name: Cox, Simon R last_name: Cox - first_name: Matthew Richard full_name: Robinson, Matthew Richard id: E5D42276-F5DA-11E9-8E24-6303E6697425 last_name: Robinson orcid: 0000-0001-8982-8813 - first_name: Riccardo E full_name: Marioni, Riccardo E last_name: Marioni citation: ama: McCartney DL, Hillary RF, Conole EL, et al. Blood-based epigenome-wide analyses of cognitive abilities. 2021. doi:10.5281/ZENODO.5794028 apa: McCartney, D. L., Hillary, R. F., Conole, E. L., Trejo Banos, D., Gadd, D. A., Walker, R. M., … Marioni, R. E. (2021). Blood-based epigenome-wide analyses of cognitive abilities. Zenodo. https://doi.org/10.5281/ZENODO.5794028 chicago: McCartney, Daniel L, Robert F Hillary, Eleanor LS Conole, Daniel Trejo Banos, Danni A Gadd, Rosie M Walker, Cliff Nangle, et al. “Blood-Based Epigenome-Wide Analyses of Cognitive Abilities.” Zenodo, 2021. https://doi.org/10.5281/ZENODO.5794028. ieee: D. L. McCartney et al., “Blood-based epigenome-wide analyses of cognitive abilities.” Zenodo, 2021. ista: McCartney DL, Hillary RF, Conole EL, Trejo Banos D, Gadd DA, Walker RM, Nangle C, Flaig R, Campbell A, Murray AD, Munoz Maniega S, del C Valdes-Hernandez M, Harris MA, Bastin ME, Wardlaw JM, Harris SE, Porteous DJ, Tucker-Drob EM, McIntosh AM, Evans KL, Deary IJ, Cox SR, Robinson MR, Marioni RE. 2021. Blood-based epigenome-wide analyses of cognitive abilities, Zenodo, 10.5281/ZENODO.5794028. mla: McCartney, Daniel L., et al. Blood-Based Epigenome-Wide Analyses of Cognitive Abilities. Zenodo, 2021, doi:10.5281/ZENODO.5794028. short: D.L. McCartney, R.F. Hillary, E.L. Conole, D. Trejo Banos, D.A. Gadd, R.M. Walker, C. Nangle, R. Flaig, A. Campbell, A.D. Murray, S. Munoz Maniega, M. del C Valdes-Hernandez, M.A. Harris, M.E. Bastin, J.M. Wardlaw, S.E. Harris, D.J. Porteous, E.M. Tucker-Drob, A.M. McIntosh, K.L. Evans, I.J. Deary, S.R. Cox, M.R. Robinson, R.E. Marioni, (2021). date_created: 2023-05-23T16:46:20Z date_published: 2021-12-20T00:00:00Z date_updated: 2023-08-02T14:05:12Z day: '20' ddc: - '570' department: - _id: MaRo doi: 10.5281/ZENODO.5794028 main_file_link: - open_access: '1' url: https://doi.org/10.5281/zenodo.5794029 month: '12' oa: 1 oa_version: Published Version publisher: Zenodo related_material: record: - id: '10702' relation: used_in_publication status: public status: public title: Blood-based epigenome-wide analyses of cognitive abilities 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_reference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2021' ... --- _id: '13068' abstract: - lang: eng text: Source data and source code for the graphs in "Spatiotemporal dynamics of self-organized branching pancreatic cancer-derived organoids". article_processing_charge: No author: - first_name: Samuel full_name: Randriamanantsoa, Samuel last_name: Randriamanantsoa - first_name: Aristeidis full_name: Papargyriou, Aristeidis last_name: Papargyriou - first_name: Carlo full_name: Maurer, Carlo last_name: Maurer - first_name: Katja full_name: Peschke, Katja last_name: Peschke - first_name: Maximilian full_name: Schuster, Maximilian last_name: Schuster - first_name: Giulia full_name: Zecchin, Giulia last_name: Zecchin - first_name: Katja full_name: Steiger, Katja last_name: Steiger - first_name: Rupert full_name: Öllinger, Rupert last_name: Öllinger - first_name: Dieter full_name: Saur, Dieter last_name: Saur - first_name: Christina full_name: Scheel, Christina last_name: Scheel - first_name: Roland full_name: Rad, Roland last_name: Rad - first_name: Edouard B full_name: Hannezo, Edouard B id: 3A9DB764-F248-11E8-B48F-1D18A9856A87 last_name: Hannezo orcid: 0000-0001-6005-1561 - first_name: Maximilian full_name: Reichert, Maximilian last_name: Reichert - first_name: Andreas R. full_name: Bausch, Andreas R. last_name: Bausch citation: ama: Randriamanantsoa S, Papargyriou A, Maurer C, et al. Spatiotemporal dynamics of self-organized branching in pancreas-derived organoids. 2021. doi:10.5281/ZENODO.5148117 apa: Randriamanantsoa, S., Papargyriou, A., Maurer, C., Peschke, K., Schuster, M., Zecchin, G., … Bausch, A. R. (2021). Spatiotemporal dynamics of self-organized branching in pancreas-derived organoids. Zenodo. https://doi.org/10.5281/ZENODO.5148117 chicago: Randriamanantsoa, Samuel, Aristeidis Papargyriou, Carlo Maurer, Katja Peschke, Maximilian Schuster, Giulia Zecchin, Katja Steiger, et al. “Spatiotemporal Dynamics of Self-Organized Branching in Pancreas-Derived Organoids.” Zenodo, 2021. https://doi.org/10.5281/ZENODO.5148117. ieee: S. Randriamanantsoa et al., “Spatiotemporal dynamics of self-organized branching in pancreas-derived organoids.” Zenodo, 2021. ista: Randriamanantsoa S, Papargyriou A, Maurer C, Peschke K, Schuster M, Zecchin G, Steiger K, Öllinger R, Saur D, Scheel C, Rad R, Hannezo EB, Reichert M, Bausch AR. 2021. Spatiotemporal dynamics of self-organized branching in pancreas-derived organoids, Zenodo, 10.5281/ZENODO.5148117. mla: Randriamanantsoa, Samuel, et al. Spatiotemporal Dynamics of Self-Organized Branching in Pancreas-Derived Organoids. Zenodo, 2021, doi:10.5281/ZENODO.5148117. short: S. Randriamanantsoa, A. Papargyriou, C. Maurer, K. Peschke, M. Schuster, G. Zecchin, K. Steiger, R. Öllinger, D. Saur, C. Scheel, R. Rad, E.B. Hannezo, M. Reichert, A.R. Bausch, (2021). date_created: 2023-05-23T16:39:24Z date_published: 2021-07-30T00:00:00Z date_updated: 2023-08-04T09:25:23Z day: '30' ddc: - '570' department: - _id: EdHa doi: 10.5281/ZENODO.5148117 main_file_link: - open_access: '1' url: https://doi.org/10.5281/zenodo.6577226 month: '07' oa: 1 oa_version: Published Version publisher: Zenodo related_material: record: - id: '12217' relation: used_in_publication status: public status: public title: Spatiotemporal dynamics of self-organized branching in pancreas-derived organoids 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_reference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2021' ... --- _id: '12987' abstract: - lang: eng text: Chromosomal inversion polymorphisms, segments of chromosomes that are flipped in orientation and occur in reversed order in some individuals, have long been recognized to play an important role in local adaptation. They can reduce recombination in heterozygous individuals and thus help to maintain sets of locally adapted alleles. In a wide range of organisms, populations adapted to different habitats differ in frequency of inversion arrangements. However, getting a full understanding of the importance of inversions for adaptation requires confirmation of their influence on traits under divergent selection. Here, we studied a marine snail, Littorina saxatilis, that has evolved ecotypes adapted to wave exposure or crab predation. These two types occur in close proximity on different parts of the shore. Gene flow between them exists in contact zones. However, they exhibit strong phenotypic divergence in several traits under habitat-specific selection, including size, shape and behaviour. We used crosses between these ecotypes to identify genomic regions that explain variation in these traits by using QTL analysis and variance partitioning across linkage groups. We could show that previously detected inversion regions contribute to adaptive divergence. Some inversions influenced multiple traits suggesting that they contain sets of locally adaptive alleles. Our study also identified regions without known inversions that are important for phenotypic divergence. Thus, we provide a more complete overview of the importance of inversions in relation to the remaining genome. article_processing_charge: No author: - first_name: Eva full_name: Koch, Eva last_name: Koch - first_name: Hernán E. full_name: Morales, Hernán E. last_name: Morales - first_name: Jenny full_name: Larsson, Jenny last_name: Larsson - first_name: Anja M full_name: Westram, Anja M id: 3C147470-F248-11E8-B48F-1D18A9856A87 last_name: Westram orcid: 0000-0003-1050-4969 - first_name: Rui full_name: Faria, Rui last_name: Faria - first_name: Alan R. full_name: Lemmon, Alan R. last_name: Lemmon - first_name: E. Moriarty full_name: Lemmon, E. Moriarty last_name: Lemmon - first_name: Kerstin full_name: Johannesson, Kerstin last_name: Johannesson - first_name: Roger K. full_name: Butlin, Roger K. last_name: Butlin citation: ama: 'Koch E, Morales HE, Larsson J, et al. Data from: Genetic variation for adaptive traits is associated with polymorphic inversions in Littorina saxatilis. 2021. doi:10.5061/DRYAD.ZGMSBCCB4' apa: 'Koch, E., Morales, H. E., Larsson, J., Westram, A. M., Faria, R., Lemmon, A. R., … Butlin, R. K. (2021). Data from: Genetic variation for adaptive traits is associated with polymorphic inversions in Littorina saxatilis. Dryad. https://doi.org/10.5061/DRYAD.ZGMSBCCB4' chicago: 'Koch, Eva, Hernán E. Morales, Jenny Larsson, Anja M Westram, Rui Faria, Alan R. Lemmon, E. Moriarty Lemmon, Kerstin Johannesson, and Roger K. Butlin. “Data from: Genetic Variation for Adaptive Traits Is Associated with Polymorphic Inversions in Littorina Saxatilis.” Dryad, 2021. https://doi.org/10.5061/DRYAD.ZGMSBCCB4.' ieee: 'E. Koch et al., “Data from: Genetic variation for adaptive traits is associated with polymorphic inversions in Littorina saxatilis.” Dryad, 2021.' ista: 'Koch E, Morales HE, Larsson J, Westram AM, Faria R, Lemmon AR, Lemmon EM, Johannesson K, Butlin RK. 2021. Data from: Genetic variation for adaptive traits is associated with polymorphic inversions in Littorina saxatilis, Dryad, 10.5061/DRYAD.ZGMSBCCB4.' mla: 'Koch, Eva, et al. Data from: Genetic Variation for Adaptive Traits Is Associated with Polymorphic Inversions in Littorina Saxatilis. Dryad, 2021, doi:10.5061/DRYAD.ZGMSBCCB4.' short: E. Koch, H.E. Morales, J. Larsson, A.M. Westram, R. Faria, A.R. Lemmon, E.M. Lemmon, K. Johannesson, R.K. Butlin, (2021). date_created: 2023-05-16T12:34:09Z date_published: 2021-04-10T00:00:00Z date_updated: 2023-08-08T13:34:07Z day: '10' ddc: - '570' department: - _id: NiBa doi: 10.5061/DRYAD.ZGMSBCCB4 has_accepted_license: '1' main_file_link: - open_access: '1' url: https://doi.org/10.5061/dryad.zgmsbccb4 month: '04' oa: 1 oa_version: Published Version publisher: Dryad related_material: record: - id: '9394' relation: used_in_publication status: public status: public title: 'Data from: Genetic variation for adaptive traits is associated with polymorphic inversions in Littorina saxatilis' 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_reference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2021' ... --- _id: '13080' abstract: - lang: eng text: "Data for the manuscript 'Closing of the Induced Gap in a Hybrid Superconductor-Semiconductor Nanowire' ([2006.01275] Closing of the Induced Gap in a Hybrid Superconductor-Semiconductor Nanowire (arxiv.org))\r\n\r\nWe upload a pdf with extended data sets, and the raw data for these extended datasets as well." article_processing_charge: No author: - first_name: Denise full_name: Puglia, Denise id: 4D495994-AE37-11E9-AC72-31CAE5697425 last_name: Puglia - first_name: Esteban full_name: Martinez, Esteban last_name: Martinez - first_name: Gerbold full_name: Menard, Gerbold last_name: Menard - first_name: Andreas full_name: Pöschl, Andreas last_name: Pöschl - first_name: Sergei full_name: Gronin, Sergei last_name: Gronin - first_name: Geoffrey full_name: Gardner, Geoffrey last_name: Gardner - first_name: Ray full_name: Kallaher, Ray last_name: Kallaher - first_name: Michael full_name: Manfra, Michael last_name: Manfra - first_name: Charles full_name: Marcus, Charles last_name: Marcus - first_name: Andrew P full_name: Higginbotham, Andrew P id: 4AD6785A-F248-11E8-B48F-1D18A9856A87 last_name: Higginbotham orcid: 0000-0003-2607-2363 - first_name: Lucas full_name: Casparis, Lucas last_name: Casparis citation: ama: Puglia D, Martinez E, Menard G, et al. Data for ’Closing of the Induced Gap in a Hybrid Superconductor-Semiconductor Nanowire. 2021. doi:10.5281/ZENODO.4592435 apa: Puglia, D., Martinez, E., Menard, G., Pöschl, A., Gronin, S., Gardner, G., … Casparis, L. (2021). Data for ’Closing of the Induced Gap in a Hybrid Superconductor-Semiconductor Nanowire. Zenodo. https://doi.org/10.5281/ZENODO.4592435 chicago: Puglia, Denise, Esteban Martinez, Gerbold Menard, Andreas Pöschl, Sergei Gronin, Geoffrey Gardner, Ray Kallaher, et al. “Data for ’Closing of the Induced Gap in a Hybrid Superconductor-Semiconductor Nanowire.” Zenodo, 2021. https://doi.org/10.5281/ZENODO.4592435. ieee: D. Puglia et al., “Data for ’Closing of the Induced Gap in a Hybrid Superconductor-Semiconductor Nanowire.” Zenodo, 2021. ista: Puglia D, Martinez E, Menard G, Pöschl A, Gronin S, Gardner G, Kallaher R, Manfra M, Marcus C, Higginbotham AP, Casparis L. 2021. Data for ’Closing of the Induced Gap in a Hybrid Superconductor-Semiconductor Nanowire, Zenodo, 10.5281/ZENODO.4592435. mla: Puglia, Denise, et al. Data for ’Closing of the Induced Gap in a Hybrid Superconductor-Semiconductor Nanowire. Zenodo, 2021, doi:10.5281/ZENODO.4592435. short: D. Puglia, E. Martinez, G. Menard, A. Pöschl, S. Gronin, G. Gardner, R. Kallaher, M. Manfra, C. Marcus, A.P. Higginbotham, L. Casparis, (2021). date_created: 2023-05-23T17:11:28Z date_published: 2021-03-09T00:00:00Z date_updated: 2023-08-08T14:08:07Z day: '09' ddc: - '530' department: - _id: AnHi doi: 10.5281/ZENODO.4592435 main_file_link: - open_access: '1' url: https://doi.org/10.5281/zenodo.4592460 month: '03' oa: 1 oa_version: Published Version publisher: Zenodo related_material: link: - relation: software url: https://github.com/caslu85/Induced-Gap-Closing-Shared/tree/1.1.3 record: - id: '9570' relation: used_in_publication status: public status: public title: Data for 'Closing of the Induced Gap in a Hybrid Superconductor-Semiconductor Nanowire type: research_data_reference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2021' ... --- _id: '13057' abstract: - lang: eng text: 'This dataset comprises all data shown in the figures of the submitted article "Geometric superinductance qubits: Controlling phase delocalization across a single Josephson junction". Additional raw data are available from the corresponding author on reasonable request.' article_processing_charge: No author: - first_name: Matilda full_name: Peruzzo, Matilda id: 3F920B30-F248-11E8-B48F-1D18A9856A87 last_name: Peruzzo orcid: 0000-0002-3415-4628 - first_name: Farid full_name: Hassani, Farid id: 2AED110C-F248-11E8-B48F-1D18A9856A87 last_name: Hassani orcid: 0000-0001-6937-5773 - first_name: Grisha full_name: Szep, Grisha last_name: Szep - first_name: Andrea full_name: Trioni, Andrea id: 42F71B44-F248-11E8-B48F-1D18A9856A87 last_name: Trioni - first_name: Elena full_name: Redchenko, Elena id: 2C21D6E8-F248-11E8-B48F-1D18A9856A87 last_name: Redchenko - first_name: Martin full_name: Zemlicka, Martin id: 2DCF8DE6-F248-11E8-B48F-1D18A9856A87 last_name: Zemlicka - first_name: Johannes M full_name: Fink, Johannes M id: 4B591CBA-F248-11E8-B48F-1D18A9856A87 last_name: Fink orcid: 0000-0001-8112-028X citation: ama: 'Peruzzo M, Hassani F, Szep G, et al. Geometric superinductance qubits: Controlling phase delocalization across a single Josephson junction. 2021. doi:10.5281/ZENODO.5592103' apa: 'Peruzzo, M., Hassani, F., Szep, G., Trioni, A., Redchenko, E., Zemlicka, M., & Fink, J. M. (2021). Geometric superinductance qubits: Controlling phase delocalization across a single Josephson junction. Zenodo. https://doi.org/10.5281/ZENODO.5592103' chicago: 'Peruzzo, Matilda, Farid Hassani, Grisha Szep, Andrea Trioni, Elena Redchenko, Martin Zemlicka, and Johannes M Fink. “Geometric Superinductance Qubits: Controlling Phase Delocalization across a Single Josephson Junction.” Zenodo, 2021. https://doi.org/10.5281/ZENODO.5592103.' ieee: 'M. Peruzzo et al., “Geometric superinductance qubits: Controlling phase delocalization across a single Josephson junction.” Zenodo, 2021.' ista: 'Peruzzo M, Hassani F, Szep G, Trioni A, Redchenko E, Zemlicka M, Fink JM. 2021. Geometric superinductance qubits: Controlling phase delocalization across a single Josephson junction, Zenodo, 10.5281/ZENODO.5592103.' mla: 'Peruzzo, Matilda, et al. Geometric Superinductance Qubits: Controlling Phase Delocalization across a Single Josephson Junction. Zenodo, 2021, doi:10.5281/ZENODO.5592103.' short: M. Peruzzo, F. Hassani, G. Szep, A. Trioni, E. Redchenko, M. Zemlicka, J.M. Fink, (2021). date_created: 2023-05-23T13:42:27Z date_published: 2021-10-22T00:00:00Z date_updated: 2023-08-11T10:44:21Z day: '22' ddc: - '530' department: - _id: JoFi doi: 10.5281/ZENODO.5592103 main_file_link: - open_access: '1' url: https://doi.org/10.5281/zenodo.5592104 month: '10' oa: 1 oa_version: Published Version publisher: Zenodo related_material: record: - id: '9928' relation: used_in_publication status: public status: public title: 'Geometric superinductance qubits: Controlling phase delocalization across a single Josephson 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: research_data_reference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2021' ... --- _id: '13061' abstract: - lang: eng text: Infections early in life can have enduring effects on an organism’s development and immunity. In this study, we show that this equally applies to developing “superorganisms” – incipient social insect colonies. When we exposed newly mated Lasius niger ant queens to a low pathogen dose, their colonies grew more slowly than controls before winter, but reached similar sizes afterwards. Independent of exposure, queen hibernation survival improved when the ratio of pupae to workers was small. Queens that reared fewer pupae before worker emergence exhibited lower pathogen levels, indicating that high brood rearing efforts interfere with the ability of the queen’s immune system to suppress pathogen proliferation. Early-life queen pathogen-exposure also improved the immunocompetence of her worker offspring, as demonstrated by challenging the workers to the same pathogen a year later. Transgenerational transfer of the queen’s pathogen experience to her workforce can hence durably reduce the disease susceptibility of the whole superorganism. article_processing_charge: No author: - first_name: Barbara E full_name: Casillas Perez, Barbara E id: 351ED2AA-F248-11E8-B48F-1D18A9856A87 last_name: Casillas Perez - first_name: Christopher full_name: Pull, Christopher id: 3C7F4840-F248-11E8-B48F-1D18A9856A87 last_name: Pull orcid: 0000-0003-1122-3982 - first_name: Filip full_name: Naiser, Filip last_name: Naiser - first_name: Elisabeth full_name: Naderlinger, Elisabeth last_name: Naderlinger - first_name: Jiri full_name: Matas, Jiri last_name: Matas - first_name: Sylvia full_name: Cremer, Sylvia id: 2F64EC8C-F248-11E8-B48F-1D18A9856A87 last_name: Cremer orcid: 0000-0002-2193-3868 citation: ama: Casillas Perez BE, Pull C, Naiser F, Naderlinger E, Matas J, Cremer S. Early queen infection shapes developmental dynamics and induces long-term disease protection in incipient ant colonies. 2021. doi:10.5061/DRYAD.7PVMCVDTJ apa: Casillas Perez, B. E., Pull, C., Naiser, F., Naderlinger, E., Matas, J., & Cremer, S. (2021). Early queen infection shapes developmental dynamics and induces long-term disease protection in incipient ant colonies. Dryad. https://doi.org/10.5061/DRYAD.7PVMCVDTJ chicago: Casillas Perez, Barbara E, Christopher Pull, Filip Naiser, Elisabeth Naderlinger, Jiri Matas, and Sylvia Cremer. “Early Queen Infection Shapes Developmental Dynamics and Induces Long-Term Disease Protection in Incipient Ant Colonies.” Dryad, 2021. https://doi.org/10.5061/DRYAD.7PVMCVDTJ. ieee: B. E. Casillas Perez, C. Pull, F. Naiser, E. Naderlinger, J. Matas, and S. Cremer, “Early queen infection shapes developmental dynamics and induces long-term disease protection in incipient ant colonies.” Dryad, 2021. ista: Casillas Perez BE, Pull C, Naiser F, Naderlinger E, Matas J, Cremer S. 2021. Early queen infection shapes developmental dynamics and induces long-term disease protection in incipient ant colonies, Dryad, 10.5061/DRYAD.7PVMCVDTJ. mla: Casillas Perez, Barbara E., et al. Early Queen Infection Shapes Developmental Dynamics and Induces Long-Term Disease Protection in Incipient Ant Colonies. Dryad, 2021, doi:10.5061/DRYAD.7PVMCVDTJ. short: B.E. Casillas Perez, C. Pull, F. Naiser, E. Naderlinger, J. Matas, S. Cremer, (2021). date_created: 2023-05-23T16:14:35Z date_published: 2021-10-29T00:00:00Z date_updated: 2023-08-14T11:45:28Z day: '29' ddc: - '570' department: - _id: SyCr doi: 10.5061/DRYAD.7PVMCVDTJ ec_funded: 1 main_file_link: - open_access: '1' url: https://doi.org/10.5061/dryad.7pvmcvdtj month: '10' oa: 1 oa_version: Published Version project: - _id: 2649B4DE-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '771402' name: Epidemics in ant societies on a chip publisher: Dryad related_material: record: - id: '10284' relation: used_in_publication status: public status: public title: Early queen infection shapes developmental dynamics and induces long-term disease protection in incipient ant colonies 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_reference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2021' ... --- _id: '13069' abstract: - lang: eng text: To survive elevated temperatures, ectotherms adjust the fluidity of membranes by fine-tuning lipid desaturation levels in a process previously described to be cell-autonomous. We have discovered that, in Caenorhabditis elegans, neuronal Heat shock Factor 1 (HSF-1), the conserved master regulator of the heat shock response (HSR)- causes extensive fat remodelling in peripheral tissues. These changes include a decrease in fat desaturase and acid lipase expression in the intestine, and a global shift in the saturation levels of plasma membrane’s phospholipids. The observed remodelling of plasma membrane is in line with ectothermic adaptive responses and gives worms a cumulative advantage to warm temperatures. We have determined that at least six TAX-2/TAX-4 cGMP gated channel expressing sensory neurons and TGF-β/BMP are required for signalling across tissues to modulate fat desaturation. We also find neuronal hsf-1 is not only sufficient but also partially necessary to control the fat remodelling response and for survival at warm temperatures. This is the first study to show that a thermostat-based mechanism can cell non-autonomously coordinate membrane saturation and composition across tissues in a multicellular animal. article_processing_charge: No author: - first_name: Laetitia full_name: Chauve, Laetitia last_name: Chauve - first_name: Francesca full_name: Hodge, Francesca last_name: Hodge - first_name: Sharlene full_name: Murdoch, Sharlene last_name: Murdoch - first_name: Fatemah full_name: Masoudzadeh, Fatemah last_name: Masoudzadeh - first_name: Harry-Jack full_name: Mann, Harry-Jack last_name: Mann - first_name: Andrea full_name: Lopez-Clavijo, Andrea last_name: Lopez-Clavijo - first_name: Hanneke full_name: Okkenhaug, Hanneke last_name: Okkenhaug - first_name: Greg full_name: West, Greg last_name: West - first_name: Bebiana C. full_name: Sousa, Bebiana C. last_name: Sousa - first_name: Anne full_name: Segonds-Pichon, Anne last_name: Segonds-Pichon - first_name: Cheryl full_name: Li, Cheryl last_name: Li - first_name: Steven full_name: Wingett, Steven last_name: Wingett - first_name: Hermine full_name: Kienberger, Hermine last_name: Kienberger - first_name: Karin full_name: Kleigrewe, Karin last_name: Kleigrewe - first_name: Mario full_name: de Bono, Mario id: 4E3FF80E-F248-11E8-B48F-1D18A9856A87 last_name: de Bono orcid: 0000-0001-8347-0443 - first_name: Michael full_name: Wakelam, Michael last_name: Wakelam - first_name: Olivia full_name: Casanueva, Olivia last_name: Casanueva citation: ama: Chauve L, Hodge F, Murdoch S, et al. Neuronal HSF-1 coordinates the propagation of fat desaturation across tissues to enable adaptation to high temperatures in C. elegans. 2021. doi:10.5281/ZENODO.5519410 apa: Chauve, L., Hodge, F., Murdoch, S., Masoudzadeh, F., Mann, H.-J., Lopez-Clavijo, A., … Casanueva, O. (2021). Neuronal HSF-1 coordinates the propagation of fat desaturation across tissues to enable adaptation to high temperatures in C. elegans. Zenodo. https://doi.org/10.5281/ZENODO.5519410 chicago: Chauve, Laetitia, Francesca Hodge, Sharlene Murdoch, Fatemah Masoudzadeh, Harry-Jack Mann, Andrea Lopez-Clavijo, Hanneke Okkenhaug, et al. “Neuronal HSF-1 Coordinates the Propagation of Fat Desaturation across Tissues to Enable Adaptation to High Temperatures in C. Elegans.” Zenodo, 2021. https://doi.org/10.5281/ZENODO.5519410. ieee: L. Chauve et al., “Neuronal HSF-1 coordinates the propagation of fat desaturation across tissues to enable adaptation to high temperatures in C. elegans.” Zenodo, 2021. ista: Chauve L, Hodge F, Murdoch S, Masoudzadeh F, Mann H-J, Lopez-Clavijo A, Okkenhaug H, West G, Sousa BC, Segonds-Pichon A, Li C, Wingett S, Kienberger H, Kleigrewe K, de Bono M, Wakelam M, Casanueva O. 2021. Neuronal HSF-1 coordinates the propagation of fat desaturation across tissues to enable adaptation to high temperatures in C. elegans, Zenodo, 10.5281/ZENODO.5519410. mla: Chauve, Laetitia, et al. Neuronal HSF-1 Coordinates the Propagation of Fat Desaturation across Tissues to Enable Adaptation to High Temperatures in C. Elegans. Zenodo, 2021, doi:10.5281/ZENODO.5519410. short: L. Chauve, F. Hodge, S. Murdoch, F. Masoudzadeh, H.-J. Mann, A. Lopez-Clavijo, H. Okkenhaug, G. West, B.C. Sousa, A. Segonds-Pichon, C. Li, S. Wingett, H. Kienberger, K. Kleigrewe, M. de Bono, M. Wakelam, O. Casanueva, (2021). date_created: 2023-05-23T16:40:56Z date_published: 2021-12-25T00:00:00Z date_updated: 2023-08-14T11:53:26Z day: '25' ddc: - '570' department: - _id: MaDe doi: 10.5281/ZENODO.5519410 main_file_link: - open_access: '1' url: https://doi.org/10.5281/zenodo.5547464 month: '12' oa: 1 oa_version: Published Version publisher: Zenodo related_material: record: - id: '10322' relation: used_in_publication status: public status: public title: Neuronal HSF-1 coordinates the propagation of fat desaturation across tissues to enable adaptation to high temperatures in C. elegans 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_reference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2021' ... --- _id: '13058' abstract: - lang: eng text: The zip file includes source data used in the main text of the manuscript "Theory of branching morphogenesis by local interactions and global guidance", as well as a representative Jupyter notebook to reproduce the main figures. A sample script for the simulations of branching and annihilating random walks is also included (Sample_script_for_simulations_of_BARWs.ipynb) to generate exemplary branched networks under external guidance. A detailed description of the simulation setup is provided in the supplementary information of the manuscipt. article_processing_charge: No author: - first_name: Mehmet C full_name: Ucar, Mehmet C id: 50B2A802-6007-11E9-A42B-EB23E6697425 last_name: Ucar orcid: 0000-0003-0506-4217 citation: ama: Ucar MC. Source data for the manuscript “Theory of branching morphogenesis by local interactions and global guidance.” 2021. doi:10.5281/ZENODO.5257160 apa: Ucar, M. C. (2021). Source data for the manuscript “Theory of branching morphogenesis by local interactions and global guidance.” Zenodo. https://doi.org/10.5281/ZENODO.5257160 chicago: Ucar, Mehmet C. “Source Data for the Manuscript ‘Theory of Branching Morphogenesis by Local Interactions and Global Guidance.’” Zenodo, 2021. https://doi.org/10.5281/ZENODO.5257160. ieee: M. C. Ucar, “Source data for the manuscript ‘Theory of branching morphogenesis by local interactions and global guidance.’” Zenodo, 2021. ista: Ucar MC. 2021. Source data for the manuscript ‘Theory of branching morphogenesis by local interactions and global guidance’, Zenodo, 10.5281/ZENODO.5257160. mla: Ucar, Mehmet C. Source Data for the Manuscript “Theory of Branching Morphogenesis by Local Interactions and Global Guidance.” Zenodo, 2021, doi:10.5281/ZENODO.5257160. short: M.C. Ucar, (2021). date_created: 2023-05-23T13:46:34Z date_published: 2021-08-25T00:00:00Z date_updated: 2023-08-14T13:18:46Z day: '25' ddc: - '570' department: - _id: EdHa doi: 10.5281/ZENODO.5257160 main_file_link: - open_access: '1' url: https://doi.org/10.5281/zenodo.5257161 month: '08' oa: 1 oa_version: Published Version publisher: Zenodo related_material: record: - id: '10402' relation: used_in_publication status: public status: public title: Source data for the manuscript "Theory of branching morphogenesis by local interactions and global guidance" 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_reference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2021' ... --- _id: '13062' abstract: - lang: eng text: 'This paper analyzes the conditions for local adaptation in a metapopulation with infinitely many islands under a model of hard selection, where population size depends on local fitness. Each island belongs to one of two distinct ecological niches or habitats. Fitness is influenced by an additive trait which is under habitat-dependent directional selection. Our analysis is based on the diffusion approximation and accounts for both genetic drift and demographic stochasticity. By neglecting linkage disequilibria, it yields the joint distribution of allele frequencies and population size on each island. We find that under hard selection, the conditions for local adaptation in a rare habitat are more restrictive for more polygenic traits: even moderate migration load per locus at very many loci is sufficient for population sizes to decline. This further reduces the efficacy of selection at individual loci due to increased drift and because smaller populations are more prone to swamping due to migration, causing a positive feedback between increasing maladaptation and declining population sizes. Our analysis also highlights the importance of demographic stochasticity, which exacerbates the decline in numbers of maladapted populations, leading to population collapse in the rare habitat at significantly lower migration than predicted by deterministic arguments.' article_processing_charge: No author: - first_name: Eniko full_name: Szep, Eniko id: 485BB5A4-F248-11E8-B48F-1D18A9856A87 last_name: Szep - first_name: Himani full_name: Sachdeva, Himani id: 42377A0A-F248-11E8-B48F-1D18A9856A87 last_name: Sachdeva - first_name: Nicholas H full_name: Barton, Nicholas H id: 4880FE40-F248-11E8-B48F-1D18A9856A87 last_name: Barton orcid: 0000-0002-8548-5240 citation: ama: 'Szep E, Sachdeva H, Barton NH. Supplementary code for: Polygenic local adaptation in metapopulations: A stochastic eco-evolutionary model. 2021. doi:10.5061/DRYAD.8GTHT76P1' apa: 'Szep, E., Sachdeva, H., & Barton, N. H. (2021). Supplementary code for: Polygenic local adaptation in metapopulations: A stochastic eco-evolutionary model. Dryad. https://doi.org/10.5061/DRYAD.8GTHT76P1' chicago: 'Szep, Eniko, Himani Sachdeva, and Nicholas H Barton. “Supplementary Code for: Polygenic Local Adaptation in Metapopulations: A Stochastic Eco-Evolutionary Model.” Dryad, 2021. https://doi.org/10.5061/DRYAD.8GTHT76P1.' ieee: 'E. Szep, H. Sachdeva, and N. H. Barton, “Supplementary code for: Polygenic local adaptation in metapopulations: A stochastic eco-evolutionary model.” Dryad, 2021.' ista: 'Szep E, Sachdeva H, Barton NH. 2021. Supplementary code for: Polygenic local adaptation in metapopulations: A stochastic eco-evolutionary model, Dryad, 10.5061/DRYAD.8GTHT76P1.' mla: 'Szep, Eniko, et al. Supplementary Code for: Polygenic Local Adaptation in Metapopulations: A Stochastic Eco-Evolutionary Model. Dryad, 2021, doi:10.5061/DRYAD.8GTHT76P1.' short: E. Szep, H. Sachdeva, N.H. Barton, (2021). date_created: 2023-05-23T16:17:02Z date_published: 2021-03-02T00:00:00Z date_updated: 2023-09-05T15:44:05Z day: '02' ddc: - '570' department: - _id: NiBa doi: 10.5061/DRYAD.8GTHT76P1 main_file_link: - open_access: '1' url: https://doi.org/10.5061/dryad.8gtht76p1 month: '03' oa: 1 oa_version: Published Version publisher: Dryad related_material: record: - id: '9252' relation: used_in_publication status: public status: public title: 'Supplementary code for: Polygenic local adaptation in metapopulations: A stochastic eco-evolutionary model' 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_reference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2021' ... --- _id: '13063' abstract: - lang: eng text: We develop a Bayesian model (BayesRR-RC) that provides robust SNP-heritability estimation, an alternative to marker discovery, and accurate genomic prediction, taking 22 seconds per iteration to estimate 8.4 million SNP-effects and 78 SNP-heritability parameters in the UK Biobank. We find that only $\leq$ 10\% of the genetic variation captured for height, body mass index, cardiovascular disease, and type 2 diabetes is attributable to proximal regulatory regions within 10kb upstream of genes, while 12-25% is attributed to coding regions, 32-44% to introns, and 22-28% to distal 10-500kb upstream regions. Up to 24% of all cis and coding regions of each chromosome are associated with each trait, with over 3,100 independent exonic and intronic regions and over 5,400 independent regulatory regions having >95% probability of contributing >0.001% to the genetic variance of these four traits. Our open-source software (GMRM) provides a scalable alternative to current approaches for biobank data. article_processing_charge: No author: - first_name: Matthew Richard full_name: Robinson, Matthew Richard id: E5D42276-F5DA-11E9-8E24-6303E6697425 last_name: Robinson orcid: 0000-0001-8982-8813 citation: ama: Robinson MR. Probabilistic inference of the genetic architecture of functional enrichment of complex traits. 2021. doi:10.5061/dryad.sqv9s4n51 apa: Robinson, M. R. (2021). Probabilistic inference of the genetic architecture of functional enrichment of complex traits. Dryad. https://doi.org/10.5061/dryad.sqv9s4n51 chicago: Robinson, Matthew Richard. “Probabilistic Inference of the Genetic Architecture of Functional Enrichment of Complex Traits.” Dryad, 2021. https://doi.org/10.5061/dryad.sqv9s4n51. ieee: M. R. Robinson, “Probabilistic inference of the genetic architecture of functional enrichment of complex traits.” Dryad, 2021. ista: Robinson MR. 2021. Probabilistic inference of the genetic architecture of functional enrichment of complex traits, Dryad, 10.5061/dryad.sqv9s4n51. mla: Robinson, Matthew Richard. Probabilistic Inference of the Genetic Architecture of Functional Enrichment of Complex Traits. Dryad, 2021, doi:10.5061/dryad.sqv9s4n51. short: M.R. Robinson, (2021). date_created: 2023-05-23T16:20:16Z date_published: 2021-11-04T00:00:00Z date_updated: 2023-09-26T10:36:15Z day: '04' ddc: - '570' department: - _id: MaRo doi: 10.5061/dryad.sqv9s4n51 main_file_link: - open_access: '1' url: https://doi.org/10.5061/dryad.sqv9s4n51 month: '11' oa: 1 oa_version: Published Version publisher: Dryad related_material: link: - relation: software url: https://github.com/medical-genomics-group/gmrm record: - id: '8429' relation: used_in_publication status: public status: public title: Probabilistic inference of the genetic architecture of functional enrichment of complex traits 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_reference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2021' ... --- _id: '14988' abstract: - lang: eng text: Raw data generated from the publication - The TPLATE complex mediates membrane bending during plant clathrin-mediated endocytosis by Johnson et al., 2021 In PNAS article_processing_charge: No author: - first_name: Alexander J full_name: Johnson, Alexander J id: 46A62C3A-F248-11E8-B48F-1D18A9856A87 last_name: Johnson orcid: 0000-0002-2739-8843 citation: ama: Johnson AJ. Raw data from Johnson et al, PNAS, 2021. 2021. doi:10.5281/ZENODO.5747100 apa: Johnson, A. J. (2021). Raw data from Johnson et al, PNAS, 2021. Zenodo. https://doi.org/10.5281/ZENODO.5747100 chicago: Johnson, Alexander J. “Raw Data from Johnson et Al, PNAS, 2021.” Zenodo, 2021. https://doi.org/10.5281/ZENODO.5747100. ieee: A. J. Johnson, “Raw data from Johnson et al, PNAS, 2021.” Zenodo, 2021. ista: Johnson AJ. 2021. Raw data from Johnson et al, PNAS, 2021, Zenodo, 10.5281/ZENODO.5747100. mla: Johnson, Alexander J. Raw Data from Johnson et Al, PNAS, 2021. Zenodo, 2021, doi:10.5281/ZENODO.5747100. short: A.J. Johnson, (2021). date_created: 2024-02-14T14:13:48Z date_published: 2021-12-01T00:00:00Z date_updated: 2024-02-19T11:06:09Z day: '01' ddc: - '580' department: - _id: JiFr doi: 10.5281/ZENODO.5747100 has_accepted_license: '1' main_file_link: - open_access: '1' url: https://doi.org/10.5281/zenodo.5747100 month: '12' oa: 1 oa_version: Published Version publisher: Zenodo related_material: record: - id: '9887' relation: used_in_publication status: public status: public title: Raw data from Johnson et al, PNAS, 2021 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_reference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2021' ... --- _id: '9291' abstract: - lang: eng text: "This .zip File contains the transport data for figures presented in the main text and 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)." 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. Raw transport data for: Enhancement of proximity induced superconductivity in planar germanium. 2021. doi:10.15479/AT:ISTA:9291' apa: 'Katsaros, G. (2021). Raw transport data for: Enhancement of proximity induced superconductivity in planar germanium. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:9291' chicago: 'Katsaros, Georgios. “Raw Transport Data for: Enhancement of Proximity Induced Superconductivity in Planar Germanium.” Institute of Science and Technology Austria, 2021. https://doi.org/10.15479/AT:ISTA:9291.' ieee: 'G. Katsaros, “Raw transport data for: Enhancement of proximity induced superconductivity in planar germanium.” Institute of Science and Technology Austria, 2021.' ista: 'Katsaros G. 2021. Raw transport data for: Enhancement of proximity induced superconductivity in planar germanium, Institute of Science and Technology Austria, 10.15479/AT:ISTA:9291.' mla: 'Katsaros, Georgios. Raw Transport Data for: Enhancement of Proximity Induced Superconductivity in Planar Germanium. Institute of Science and Technology Austria, 2021, doi:10.15479/AT:ISTA:9291.' short: G. Katsaros, (2021). date_created: 2021-03-27T13:47:49Z date_published: 2021-03-29T00:00:00Z date_updated: 2024-02-21T12:37:14Z day: '29' ddc: - '530' department: - _id: GeKa doi: 10.15479/AT:ISTA:9291 file: - access_level: open_access checksum: 635df3c08fc13c3dac008cd421aefbe4 content_type: application/x-zip-compressed creator: gkatsaro date_created: 2021-03-27T13:46:17Z date_updated: 2021-03-27T13:46:17Z file_id: '9292' file_name: Raw Data- Enhancement of Superconductivity in a Planar Ge hole gas.zip file_size: 10616071 relation: main_file success: 1 - access_level: open_access checksum: 12b3ca69ae7509a346711baae0b02a75 content_type: text/plain creator: dernst date_created: 2021-04-01T07:52:56Z date_updated: 2021-04-01T07:52:56Z file_id: '9302' file_name: README.txt file_size: 470 relation: main_file success: 1 file_date_updated: 2021-04-01T07:52:56Z has_accepted_license: '1' month: '03' oa: 1 oa_version: Published Version publisher: Institute of Science and Technology Austria status: public title: 'Raw transport data for: 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: '2021' ... --- _id: '9636' article_processing_charge: No author: - first_name: Andrew P full_name: Higginbotham, Andrew P id: 4AD6785A-F248-11E8-B48F-1D18A9856A87 last_name: Higginbotham orcid: 0000-0003-2607-2363 citation: ama: Higginbotham AP. Data for “Breakdown of induced p ± ip pairing in a superconductor-semiconductor hybrid.” 2021. apa: Higginbotham, A. P. (2021). Data for “Breakdown of induced p ± ip pairing in a superconductor-semiconductor hybrid.” Institute of Science and Technology Austria. chicago: Higginbotham, Andrew P. “Data for ‘Breakdown of Induced p ± Ip Pairing in a Superconductor-Semiconductor Hybrid.’” Institute of Science and Technology Austria, 2021. ieee: A. P. Higginbotham, “Data for ‘Breakdown of induced p ± ip pairing in a superconductor-semiconductor hybrid.’” Institute of Science and Technology Austria, 2021. ista: Higginbotham AP. 2021. Data for ‘Breakdown of induced p ± ip pairing in a superconductor-semiconductor hybrid’, Institute of Science and Technology Austria. mla: Higginbotham, Andrew P. Data for “Breakdown of Induced p ± Ip Pairing in a Superconductor-Semiconductor Hybrid.” Institute of Science and Technology Austria, 2021. short: A.P. Higginbotham, (2021). date_created: 2021-07-07T20:43:10Z date_published: 2021-01-01T00:00:00Z date_updated: 2024-02-21T12:36:52Z department: - _id: AnHi file: - access_level: open_access checksum: 18e90687ec7bbd75f8bfea4d8293fb30 content_type: application/zip creator: ahigginb date_created: 2021-07-07T20:37:28Z date_updated: 2021-07-07T20:37:28Z file_id: '9637' file_name: figures_data.zip file_size: 3345244 relation: main_file success: 1 file_date_updated: 2021-07-07T20:37:28Z has_accepted_license: '1' oa: 1 oa_version: Submitted Version publisher: Institute of Science and Technology Austria related_material: record: - id: '10029' relation: used_in_publication status: public status: public title: Data for "Breakdown of induced p ± ip pairing in a superconductor-semiconductor hybrid" 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: research_data user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2021' ... --- _id: '9323' abstract: - lang: eng text: This .zip File contains the data for figures presented in the main text and supplementary material of "A singlet triplet hole spin qubit in planar Ge" by D. Jirovec, et. al. The 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). A single file is acquired with QCodes and features the corresponding data type. XRD data are in .dat format and a code to open the data is provided. The code for simulations is as well provided in Python. article_processing_charge: No author: - first_name: Daniel full_name: Jirovec, Daniel id: 4C473F58-F248-11E8-B48F-1D18A9856A87 last_name: Jirovec orcid: 0000-0002-7197-4801 citation: ama: Jirovec D. Research data for “A singlet-triplet hole spin qubit planar Ge.” 2021. doi:10.15479/AT:ISTA:9323 apa: Jirovec, D. (2021). Research data for “A singlet-triplet hole spin qubit planar Ge.” Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:9323 chicago: Jirovec, Daniel. “Research Data for ‘A Singlet-Triplet Hole Spin Qubit Planar Ge.’” Institute of Science and Technology Austria, 2021. https://doi.org/10.15479/AT:ISTA:9323. ieee: D. Jirovec, “Research data for ‘A singlet-triplet hole spin qubit planar Ge.’” Institute of Science and Technology Austria, 2021. ista: Jirovec D. 2021. Research data for ‘A singlet-triplet hole spin qubit planar Ge’, Institute of Science and Technology Austria, 10.15479/AT:ISTA:9323. mla: Jirovec, Daniel. Research Data for “A Singlet-Triplet Hole Spin Qubit Planar Ge.” Institute of Science and Technology Austria, 2021, doi:10.15479/AT:ISTA:9323. short: D. Jirovec, (2021). contributor: - contributor_type: project_member first_name: Daniel id: 4C473F58-F248-11E8-B48F-1D18A9856A87 last_name: Jirovec date_created: 2021-04-14T09:50:22Z date_published: 2021-04-14T00:00:00Z date_updated: 2024-02-21T12:39:15Z day: '14' ddc: - '530' department: - _id: GradSch - _id: GeKa doi: 10.15479/AT:ISTA:9323 file: - access_level: open_access checksum: c569d2a2ce1694445cdbca19cf8ae023 content_type: application/x-zip-compressed creator: djirovec date_created: 2021-04-14T09:48:47Z date_updated: 2021-04-14T09:48:47Z file_id: '9324' file_name: DataRepositorySTqubit.zip file_size: 221832287 relation: main_file success: 1 - access_level: open_access checksum: 845bdf87430718ad6aff47eda7b5fc92 content_type: application/octet-stream creator: djirovec date_created: 2021-04-14T09:49:30Z date_updated: 2021-04-14T09:49:30Z file_id: '9325' file_name: ReadMe file_size: 4323 relation: main_file success: 1 file_date_updated: 2021-04-14T09:49:30Z has_accepted_license: '1' month: '04' oa: 1 oa_version: Published Version publisher: Institute of Science and Technology Austria related_material: record: - id: '8909' relation: used_in_publication status: public status: public title: Research data for "A singlet-triplet hole spin qubit planar Ge" 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: '2021' ... --- _id: '9389' abstract: - lang: eng text: "This .zip File contains the transport data for \"Non-topological zero bias peaks in full-shell nanowires induced by flux tunable Andreev states\" by M. Valentini, et. al. \r\nThe measurements were done using Labber Software and the data is stored in the hdf5 file format.\r\nInstructions of how to read the data are in \"Notebook_Valentini.pdf\"." acknowledged_ssus: - _id: NanoFab article_processing_charge: No author: - first_name: Marco full_name: Valentini, Marco id: C0BB2FAC-D767-11E9-B658-BC13E6697425 last_name: Valentini citation: ama: Valentini M. Research data for “Non-topological zero bias peaks in full-shell nanowires induced by flux tunable Andreev states.” 2021. doi:10.15479/AT:ISTA:9389 apa: Valentini, M. (2021). Research data for “Non-topological zero bias peaks in full-shell nanowires induced by flux tunable Andreev states.” Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:9389 chicago: Valentini, Marco. “Research Data for ‘Non-Topological Zero Bias Peaks in Full-Shell Nanowires Induced by Flux Tunable Andreev States.’” Institute of Science and Technology Austria, 2021. https://doi.org/10.15479/AT:ISTA:9389. ieee: M. Valentini, “Research data for ‘Non-topological zero bias peaks in full-shell nanowires induced by flux tunable Andreev states.’” Institute of Science and Technology Austria, 2021. ista: Valentini M. 2021. Research data for ‘Non-topological zero bias peaks in full-shell nanowires induced by flux tunable Andreev states’, Institute of Science and Technology Austria, 10.15479/AT:ISTA:9389. mla: Valentini, Marco. Research Data for “Non-Topological Zero Bias Peaks in Full-Shell Nanowires Induced by Flux Tunable Andreev States.” Institute of Science and Technology Austria, 2021, doi:10.15479/AT:ISTA:9389. short: M. Valentini, (2021). contributor: - contributor_type: contact_person first_name: Marco id: C0BB2FAC-D767-11E9-B658-BC13E6697425 last_name: Valentini date_created: 2021-05-14T12:07:53Z date_published: 2021-01-01T00:00:00Z date_updated: 2024-02-21T12:40:09Z ddc: - '530' department: - _id: GradSch - _id: GeKa doi: 10.15479/AT:ISTA:9389 file: - access_level: open_access checksum: 80a905c4eef24dab6fb247e81a3d67f5 content_type: application/pdf creator: mvalenti date_created: 2021-05-14T11:42:23Z date_updated: 2021-05-14T11:42:23Z file_id: '9390' file_name: Notebook_Valentini.pdf file_size: 10572981 relation: main_file - access_level: open_access checksum: 1e61a7e63949448a8db0091cdac23570 content_type: application/x-zip-compressed creator: mvalenti date_created: 2021-05-14T11:56:48Z date_updated: 2021-05-14T11:56:48Z file_id: '9391' file_name: Experimental_data.zip file_size: 99076111 relation: main_file file_date_updated: 2021-05-14T11:56:48Z has_accepted_license: '1' oa: 1 oa_version: Published Version publisher: Institute of Science and Technology Austria related_material: record: - id: '8910' relation: used_in_publication status: public status: public title: Research data for "Non-topological zero bias peaks in full-shell nanowires induced by flux tunable Andreev states" 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: '2021' ... --- _id: '9192' abstract: - lang: eng text: Here are the research data underlying the publication " Effects of fine-scale population structure on inbreeding in a long-term study of snapdragons (Antirrhinum majus)." Further information are summed up in the README document. article_processing_charge: No author: - first_name: Parvathy full_name: Surendranadh, Parvathy id: 455235B8-F248-11E8-B48F-1D18A9856A87 last_name: Surendranadh - first_name: Louise S full_name: Arathoon, Louise S id: 2CFCFF98-F248-11E8-B48F-1D18A9856A87 last_name: Arathoon orcid: 0000-0003-1771-714X - first_name: Carina full_name: Baskett, Carina id: 3B4A7CE2-F248-11E8-B48F-1D18A9856A87 last_name: Baskett orcid: 0000-0002-7354-8574 - first_name: David full_name: Field, David id: 419049E2-F248-11E8-B48F-1D18A9856A87 last_name: Field orcid: 0000-0002-4014-8478 - first_name: Melinda full_name: Pickup, Melinda id: 2C78037E-F248-11E8-B48F-1D18A9856A87 last_name: Pickup orcid: 0000-0001-6118-0541 - first_name: Nicholas H full_name: Barton, Nicholas H id: 4880FE40-F248-11E8-B48F-1D18A9856A87 last_name: Barton orcid: 0000-0002-8548-5240 citation: ama: Surendranadh P, Arathoon LS, Baskett C, Field D, Pickup M, Barton NH. Effects of fine-scale population structure on the distribution of heterozygosity in a long-term study of Antirrhinum majus. 2021. doi:10.15479/AT:ISTA:9192 apa: Surendranadh, P., Arathoon, L. S., Baskett, C., Field, D., Pickup, M., & Barton, N. H. (2021). Effects of fine-scale population structure on the distribution of heterozygosity in a long-term study of Antirrhinum majus. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:9192 chicago: Surendranadh, Parvathy, Louise S Arathoon, Carina Baskett, David Field, Melinda Pickup, and Nicholas H Barton. “Effects of Fine-Scale Population Structure on the Distribution of Heterozygosity in a Long-Term Study of Antirrhinum Majus.” Institute of Science and Technology Austria, 2021. https://doi.org/10.15479/AT:ISTA:9192. ieee: P. Surendranadh, L. S. Arathoon, C. Baskett, D. Field, M. Pickup, and N. H. Barton, “Effects of fine-scale population structure on the distribution of heterozygosity in a long-term study of Antirrhinum majus.” Institute of Science and Technology Austria, 2021. ista: Surendranadh P, Arathoon LS, Baskett C, Field D, Pickup M, Barton NH. 2021. Effects of fine-scale population structure on the distribution of heterozygosity in a long-term study of Antirrhinum majus, Institute of Science and Technology Austria, 10.15479/AT:ISTA:9192. mla: Surendranadh, Parvathy, et al. Effects of Fine-Scale Population Structure on the Distribution of Heterozygosity in a Long-Term Study of Antirrhinum Majus. Institute of Science and Technology Austria, 2021, doi:10.15479/AT:ISTA:9192. short: P. Surendranadh, L.S. Arathoon, C. Baskett, D. Field, M. Pickup, N.H. Barton, (2021). contributor: - contributor_type: project_member first_name: Parvathy id: 455235B8-F248-11E8-B48F-1D18A9856A87 last_name: Surendranadh - contributor_type: project_member first_name: Louise S id: 2CFCFF98-F248-11E8-B48F-1D18A9856A87 last_name: Arathoon - contributor_type: project_member first_name: Carina id: 3B4A7CE2-F248-11E8-B48F-1D18A9856A87 last_name: Baskett - contributor_type: project_member first_name: David id: 419049E2-F248-11E8-B48F-1D18A9856A87 last_name: Field orcid: 0000-0002-4014-8478 - contributor_type: project_member first_name: Melinda id: 2C78037E-F248-11E8-B48F-1D18A9856A87 last_name: Pickup orcid: 0000-0001-6118-0541 - contributor_type: project_leader first_name: Nicholas H id: 4880FE40-F248-11E8-B48F-1D18A9856A87 last_name: Barton orcid: 0000-0002-8548-5240 date_created: 2021-02-24T17:49:21Z date_published: 2021-02-26T00:00:00Z date_updated: 2024-02-21T12:41:09Z day: '26' ddc: - '576' department: - _id: GradSch - _id: NiBa doi: 10.15479/AT:ISTA:9192 file: - access_level: open_access checksum: f85537815809a8a4b7da9d01163f88c0 content_type: application/x-zip-compressed creator: larathoo date_created: 2021-02-24T17:45:13Z date_updated: 2021-02-24T17:45:13Z file_id: '9193' file_name: Data_Code.zip file_size: 5934452 relation: main_file success: 1 file_date_updated: 2021-02-24T17:45:13Z has_accepted_license: '1' month: '02' oa: 1 oa_version: Published Version publisher: Institute of Science and Technology Austria related_material: record: - id: '11411' relation: used_in_publication status: public - id: '11321' relation: later_version status: public - id: '8254' relation: earlier_version status: public status: public title: Effects of fine-scale population structure on the distribution of heterozygosity in a long-term study of Antirrhinum majus 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: '2021' ... --- _id: '9949' article_processing_charge: No author: - first_name: Beatriz full_name: Vicoso, Beatriz id: 49E1C5C6-F248-11E8-B48F-1D18A9856A87 last_name: Vicoso orcid: 0000-0002-4579-8306 citation: ama: Vicoso B. Data from Hyulmans et al 2021, “Transitions to asexuality and evolution of gene expression in Artemia brine shrimp.” 2021. doi:10.15479/AT:ISTA:9949 apa: Vicoso, B. (2021). Data from Hyulmans et al 2021, “Transitions to asexuality and evolution of gene expression in Artemia brine shrimp.” Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:9949 chicago: Vicoso, Beatriz. “Data from Hyulmans et Al 2021, ‘Transitions to Asexuality and Evolution of Gene Expression in Artemia Brine Shrimp.’” Institute of Science and Technology Austria, 2021. https://doi.org/10.15479/AT:ISTA:9949. ieee: B. Vicoso, “Data from Hyulmans et al 2021, ‘Transitions to asexuality and evolution of gene expression in Artemia brine shrimp.’” Institute of Science and Technology Austria, 2021. ista: Vicoso B. 2021. Data from Hyulmans et al 2021, ‘Transitions to asexuality and evolution of gene expression in Artemia brine shrimp’, Institute of Science and Technology Austria, 10.15479/AT:ISTA:9949. mla: Vicoso, Beatriz. Data from Hyulmans et Al 2021, “Transitions to Asexuality and Evolution of Gene Expression in Artemia Brine Shrimp.” Institute of Science and Technology Austria, 2021, doi:10.15479/AT:ISTA:9949. short: B. Vicoso, (2021). date_created: 2021-08-21T13:44:22Z date_published: 2021-08-24T00:00:00Z date_updated: 2024-02-21T12:40:30Z day: '24' department: - _id: BeVi doi: 10.15479/AT:ISTA:9949 file: - access_level: open_access checksum: 90461837eed66beac6fa302993cf0ca9 content_type: application/zip creator: bvicoso date_created: 2021-08-21T13:43:59Z date_updated: 2021-08-21T13:43:59Z file_id: '9950' file_name: Data.zip file_size: 139188306 relation: main_file success: 1 file_date_updated: 2021-08-21T13:43:59Z has_accepted_license: '1' month: '08' oa: 1 oa_version: None publisher: Institute of Science and Technology Austria related_material: record: - id: '10166' relation: used_in_publication status: public status: public title: Data from Hyulmans et al 2021, "Transitions to asexuality and evolution of gene expression in Artemia brine shrimp" 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: '2021' ... --- _id: '13073' abstract: - lang: eng text: The Mytilus complex of marine mussel species forms a mosaic of hybrid zones, found across temperate regions of the globe. This allows us to study "replicated" instances of secondary contact between closely-related species. Previous work on this complex has shown that local introgression is both widespread and highly heterogeneous, and has identified SNPs that are outliers of differentiation between lineages. Here, we developed an ancestry-informative panel of such SNPs. We then compared their frequencies in newly-sampled populations, including samples from within the hybrid zones, and parental populations at different distances from the contact. Results show that close to the hybrid zones, some outlier loci are near to fixation for the heterospecific allele, suggesting enhanced local introgression, or the local sweep of a shared ancestral allele. Conversely, genomic cline analyses, treating local parental populations as the reference, reveal a globally high concordance among loci, albeit with a few signals of asymmetric introgression. Enhanced local introgression at specific loci is consistent with the early transfer of adaptive variants after contact, possibly including asymmetric bi-stable variants (Dobzhansky-Muller incompatibilities), or haplotypes loaded with fewer deleterious mutations. Having escaped one barrier, however, these variants can be trapped or delayed at the next barrier, confining the introgression locally. These results shed light on the decay of species barriers during phases of contact. article_processing_charge: No author: - first_name: Alexis full_name: Simon, Alexis last_name: Simon - first_name: Christelle full_name: Fraisse, Christelle id: 32DF5794-F248-11E8-B48F-1D18A9856A87 last_name: Fraisse orcid: 0000-0001-8441-5075 - first_name: Tahani full_name: El Ayari, Tahani last_name: El Ayari - first_name: Cathy full_name: Liautard-Haag, Cathy last_name: Liautard-Haag - first_name: Petr full_name: Strelkov, Petr last_name: Strelkov - first_name: John full_name: Welch, John last_name: Welch - first_name: Nicolas full_name: Bierne, Nicolas last_name: Bierne citation: ama: Simon A, Fraisse C, El Ayari T, et al. How do species barriers decay? concordance and local introgression in mosaic hybrid zones of mussels. 2020. doi:10.5061/DRYAD.R4XGXD29N apa: Simon, A., Fraisse, C., El Ayari, T., Liautard-Haag, C., Strelkov, P., Welch, J., & Bierne, N. (2020). How do species barriers decay? concordance and local introgression in mosaic hybrid zones of mussels. Dryad. https://doi.org/10.5061/DRYAD.R4XGXD29N chicago: Simon, Alexis, Christelle Fraisse, Tahani El Ayari, Cathy Liautard-Haag, Petr Strelkov, John Welch, and Nicolas Bierne. “How Do Species Barriers Decay? Concordance and Local Introgression in Mosaic Hybrid Zones of Mussels.” Dryad, 2020. https://doi.org/10.5061/DRYAD.R4XGXD29N. ieee: A. Simon et al., “How do species barriers decay? concordance and local introgression in mosaic hybrid zones of mussels.” Dryad, 2020. ista: Simon A, Fraisse C, El Ayari T, Liautard-Haag C, Strelkov P, Welch J, Bierne N. 2020. How do species barriers decay? concordance and local introgression in mosaic hybrid zones of mussels, Dryad, 10.5061/DRYAD.R4XGXD29N. mla: Simon, Alexis, et al. How Do Species Barriers Decay? Concordance and Local Introgression in Mosaic Hybrid Zones of Mussels. Dryad, 2020, doi:10.5061/DRYAD.R4XGXD29N. short: A. Simon, C. Fraisse, T. El Ayari, C. Liautard-Haag, P. Strelkov, J. Welch, N. Bierne, (2020). date_created: 2023-05-23T16:48:27Z date_published: 2020-09-22T00:00:00Z date_updated: 2023-08-04T11:04:11Z day: '22' ddc: - '570' department: - _id: NiBa doi: 10.5061/DRYAD.R4XGXD29N main_file_link: - open_access: '1' url: https://doi.org/10.5061/dryad.r4xgxd29n month: '09' oa: 1 oa_version: Published Version publisher: Dryad related_material: record: - id: '8708' relation: used_in_publication status: public status: public title: How do species barriers decay? concordance and local introgression in mosaic hybrid zones of mussels 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_reference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2020' ... --- _id: '13065' abstract: - lang: eng text: Domestication is a human-induced selection process that imprints the genomes of domesticated populations over a short evolutionary time scale, and that occurs in a given demographic context. Reconstructing historical gene flow, effective population size changes and their timing is therefore of fundamental interest to understand how plant demography and human selection jointly shape genomic divergence during domestication. Yet, the comparison under a single statistical framework of independent domestication histories across different crop species has been little evaluated so far. Thus, it is unclear whether domestication leads to convergent demographic changes that similarly affect crop genomes. To address this question, we used existing and new transcriptome data on three crop species of Solanaceae (eggplant, pepper and tomato), together with their close wild relatives. We fitted twelve demographic models of increasing complexity on the unfolded joint allele frequency spectrum for each wild/crop pair, and we found evidence for both shared and species-specific demographic processes between species. A convergent history of domestication with gene-flow was inferred for all three species, along with evidence of strong reduction in the effective population size during the cultivation stage of tomato and pepper. The absence of any reduction in size of the crop in eggplant stands out from the classical view of the domestication process; as does the existence of a “protracted period” of management before cultivation. Our results also suggest divergent management strategies of modern cultivars among species as their current demography substantially differs. Finally, the timing of domestication is species-specific and supported by the few historical records available. article_processing_charge: No author: - first_name: Stephanie full_name: Arnoux, Stephanie last_name: Arnoux - first_name: Christelle full_name: Fraisse, Christelle id: 32DF5794-F248-11E8-B48F-1D18A9856A87 last_name: Fraisse orcid: 0000-0001-8441-5075 - first_name: Christopher full_name: Sauvage, Christopher last_name: Sauvage citation: ama: 'Arnoux S, Fraisse C, Sauvage C. VCF files of synonymous SNPs related to: Genomic inference of complex domestication histories in three Solanaceae species. 2020. doi:10.5061/DRYAD.Q2BVQ83HD' apa: 'Arnoux, S., Fraisse, C., & Sauvage, C. (2020). VCF files of synonymous SNPs related to: Genomic inference of complex domestication histories in three Solanaceae species. Dryad. https://doi.org/10.5061/DRYAD.Q2BVQ83HD' chicago: 'Arnoux, Stephanie, Christelle Fraisse, and Christopher Sauvage. “VCF Files of Synonymous SNPs Related to: Genomic Inference of Complex Domestication Histories in Three Solanaceae Species.” Dryad, 2020. https://doi.org/10.5061/DRYAD.Q2BVQ83HD.' ieee: 'S. Arnoux, C. Fraisse, and C. Sauvage, “VCF files of synonymous SNPs related to: Genomic inference of complex domestication histories in three Solanaceae species.” Dryad, 2020.' ista: 'Arnoux S, Fraisse C, Sauvage C. 2020. VCF files of synonymous SNPs related to: Genomic inference of complex domestication histories in three Solanaceae species, Dryad, 10.5061/DRYAD.Q2BVQ83HD.' mla: 'Arnoux, Stephanie, et al. VCF Files of Synonymous SNPs Related to: Genomic Inference of Complex Domestication Histories in Three Solanaceae Species. Dryad, 2020, doi:10.5061/DRYAD.Q2BVQ83HD.' short: S. Arnoux, C. Fraisse, C. Sauvage, (2020). date_created: 2023-05-23T16:30:20Z date_published: 2020-10-19T00:00:00Z date_updated: 2023-08-04T11:19:26Z day: '19' ddc: - '570' department: - _id: NiBa doi: 10.5061/DRYAD.Q2BVQ83HD main_file_link: - open_access: '1' url: https://doi.org/10.5061/dryad.q2bvq83hd month: '10' oa: 1 oa_version: Published Version publisher: Dryad related_material: link: - relation: software url: https://github.com/starnoux/arnoux_et_al_2019 record: - id: '8928' relation: used_in_publication status: public status: public title: 'VCF files of synonymous SNPs related to: Genomic inference of complex domestication histories in three Solanaceae species' 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_reference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2020' ... --- _id: '9885' abstract: - lang: eng text: Data obtained from the fine-grained simulations used in Figures 2-5, data obtained from the coarse-grained numerical calculations used in Figure 6, and a sample script for the fine-grained simulation as a Jupyter notebook (ZIP) article_processing_charge: No author: - first_name: Mehmet C full_name: Ucar, Mehmet C id: 50B2A802-6007-11E9-A42B-EB23E6697425 last_name: Ucar orcid: 0000-0003-0506-4217 - first_name: Reinhard full_name: Lipowsky, Reinhard last_name: Lipowsky citation: ama: Ucar MC, Lipowsky R. MURL_Dataz. 2020. doi:10.1021/acs.nanolett.9b04445.s002 apa: Ucar, M. C., & Lipowsky, R. (2020). MURL_Dataz. American Chemical Society . https://doi.org/10.1021/acs.nanolett.9b04445.s002 chicago: Ucar, Mehmet C, and Reinhard Lipowsky. “MURL_Dataz.” American Chemical Society , 2020. https://doi.org/10.1021/acs.nanolett.9b04445.s002. ieee: M. C. Ucar and R. Lipowsky, “MURL_Dataz.” American Chemical Society , 2020. ista: Ucar MC, Lipowsky R. 2020. MURL_Dataz, American Chemical Society , 10.1021/acs.nanolett.9b04445.s002. mla: Ucar, Mehmet C., and Reinhard Lipowsky. MURL_Dataz. American Chemical Society , 2020, doi:10.1021/acs.nanolett.9b04445.s002. short: M.C. Ucar, R. Lipowsky, (2020). date_created: 2021-08-11T13:16:03Z date_published: 2020-01-08T00:00:00Z date_updated: 2023-08-17T14:07:52Z day: '08' department: - _id: EdHa doi: 10.1021/acs.nanolett.9b04445.s002 month: '01' oa_version: Published Version publisher: 'American Chemical Society ' related_material: record: - id: '7166' relation: used_in_publication status: public status: public title: MURL_Dataz type: research_data_reference user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf year: '2020' ... --- _id: '9779' article_processing_charge: No author: - first_name: Rok full_name: Grah, Rok id: 483E70DE-F248-11E8-B48F-1D18A9856A87 last_name: Grah orcid: 0000-0003-2539-3560 - first_name: Tamar full_name: Friedlander, Tamar last_name: Friedlander citation: ama: Grah R, Friedlander T. Distribution of crosstalk values. 2020. doi:10.1371/journal.pcbi.1007642.s003 apa: Grah, R., & Friedlander, T. (2020). Distribution of crosstalk values. Public Library of Science. https://doi.org/10.1371/journal.pcbi.1007642.s003 chicago: Grah, Rok, and Tamar Friedlander. “Distribution of Crosstalk Values.” Public Library of Science, 2020. https://doi.org/10.1371/journal.pcbi.1007642.s003. ieee: R. Grah and T. Friedlander, “Distribution of crosstalk values.” Public Library of Science, 2020. ista: Grah R, Friedlander T. 2020. Distribution of crosstalk values, Public Library of Science, 10.1371/journal.pcbi.1007642.s003. mla: Grah, Rok, and Tamar Friedlander. Distribution of Crosstalk Values. Public Library of Science, 2020, doi:10.1371/journal.pcbi.1007642.s003. short: R. Grah, T. Friedlander, (2020). date_created: 2021-08-06T07:24:37Z date_published: 2020-02-25T00:00:00Z date_updated: 2023-08-18T06:47:47Z day: '25' department: - _id: GaTk doi: 10.1371/journal.pcbi.1007642.s003 month: '02' oa_version: Published Version publisher: Public Library of Science related_material: record: - id: '7569' relation: research_data status: public status: public title: Distribution of crosstalk values type: research_data_reference user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf year: '2020' ... --- _id: '9776' article_processing_charge: No author: - first_name: Rok full_name: Grah, Rok id: 483E70DE-F248-11E8-B48F-1D18A9856A87 last_name: Grah orcid: 0000-0003-2539-3560 - first_name: Tamar full_name: Friedlander, Tamar last_name: Friedlander citation: ama: Grah R, Friedlander T. Supporting information. 2020. doi:10.1371/journal.pcbi.1007642.s001 apa: Grah, R., & Friedlander, T. (2020). Supporting information. Public Library of Science. https://doi.org/10.1371/journal.pcbi.1007642.s001 chicago: Grah, Rok, and Tamar Friedlander. “Supporting Information.” Public Library of Science, 2020. https://doi.org/10.1371/journal.pcbi.1007642.s001. ieee: R. Grah and T. Friedlander, “Supporting information.” Public Library of Science, 2020. ista: Grah R, Friedlander T. 2020. Supporting information, Public Library of Science, 10.1371/journal.pcbi.1007642.s001. mla: Grah, Rok, and Tamar Friedlander. Supporting Information. Public Library of Science, 2020, doi:10.1371/journal.pcbi.1007642.s001. short: R. Grah, T. Friedlander, (2020). date_created: 2021-08-06T07:15:04Z date_published: 2020-02-25T00:00:00Z date_updated: 2023-08-18T06:47:47Z day: '25' department: - _id: GaTk doi: 10.1371/journal.pcbi.1007642.s001 month: '02' oa_version: Published Version publisher: Public Library of Science related_material: record: - id: '7569' relation: used_in_publication status: public status: public title: Supporting information type: research_data_reference user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf year: '2020' ... --- _id: '9708' abstract: - lang: eng text: This research data supports 'Hard antinodal gap revealed by quantum oscillations in the pseudogap regime of underdoped high-Tc superconductors'. A Readme file for plotting each figure is provided. article_processing_charge: No author: - first_name: Mate full_name: Hartstein, Mate last_name: Hartstein - first_name: Yu-Te full_name: Hsu, Yu-Te last_name: Hsu - first_name: Kimberly A full_name: Modic, Kimberly A id: 13C26AC0-EB69-11E9-87C6-5F3BE6697425 last_name: Modic orcid: 0000-0001-9760-3147 - first_name: Juan full_name: Porras, Juan last_name: Porras - first_name: Toshinao full_name: Loew, Toshinao last_name: Loew - first_name: Matthieu full_name: Le Tacon, Matthieu last_name: Le Tacon - first_name: Huakun full_name: Zuo, Huakun last_name: Zuo - first_name: Jinhua full_name: Wang, Jinhua last_name: Wang - first_name: Zengwei full_name: Zhu, Zengwei last_name: Zhu - first_name: Mun full_name: Chan, Mun last_name: Chan - first_name: Ross full_name: McDonald, Ross last_name: McDonald - first_name: Gilbert full_name: Lonzarich, Gilbert last_name: Lonzarich - first_name: Bernhard full_name: Keimer, Bernhard last_name: Keimer - first_name: Suchitra full_name: Sebastian, Suchitra last_name: Sebastian - first_name: Neil full_name: Harrison, Neil last_name: Harrison citation: ama: Hartstein M, Hsu Y-T, Modic KA, et al. Accompanying dataset for “Hard antinodal gap revealed by quantum oscillations in the pseudogap regime of underdoped high-Tc superconductors.” 2020. doi:10.17863/cam.50169 apa: Hartstein, M., Hsu, Y.-T., Modic, K. A., Porras, J., Loew, T., Le Tacon, M., … Harrison, N. (2020). Accompanying dataset for “Hard antinodal gap revealed by quantum oscillations in the pseudogap regime of underdoped high-Tc superconductors.” Apollo - University of Cambridge. https://doi.org/10.17863/cam.50169 chicago: Hartstein, Mate, Yu-Te Hsu, Kimberly A Modic, Juan Porras, Toshinao Loew, Matthieu Le Tacon, Huakun Zuo, et al. “Accompanying Dataset for ‘Hard Antinodal Gap Revealed by Quantum Oscillations in the Pseudogap Regime of Underdoped High-Tc Superconductors.’” Apollo - University of Cambridge, 2020. https://doi.org/10.17863/cam.50169. ieee: M. Hartstein et al., “Accompanying dataset for ‘Hard antinodal gap revealed by quantum oscillations in the pseudogap regime of underdoped high-Tc superconductors.’” Apollo - University of Cambridge, 2020. ista: Hartstein M, Hsu Y-T, Modic KA, Porras J, Loew T, Le Tacon M, Zuo H, Wang J, Zhu Z, Chan M, McDonald R, Lonzarich G, Keimer B, Sebastian S, Harrison N. 2020. Accompanying dataset for ‘Hard antinodal gap revealed by quantum oscillations in the pseudogap regime of underdoped high-Tc superconductors’, Apollo - University of Cambridge, 10.17863/cam.50169. mla: Hartstein, Mate, et al. Accompanying Dataset for “Hard Antinodal Gap Revealed by Quantum Oscillations in the Pseudogap Regime of Underdoped High-Tc Superconductors.” Apollo - University of Cambridge, 2020, doi:10.17863/cam.50169. short: M. Hartstein, Y.-T. Hsu, K.A. Modic, J. Porras, T. Loew, M. Le Tacon, H. Zuo, J. Wang, Z. Zhu, M. Chan, R. McDonald, G. Lonzarich, B. Keimer, S. Sebastian, N. Harrison, (2020). date_created: 2021-07-23T10:00:35Z date_published: 2020-05-29T00:00:00Z date_updated: 2023-08-21T07:06:48Z day: '29' department: - _id: KiMo doi: 10.17863/cam.50169 has_accepted_license: '1' main_file_link: - open_access: '1' url: https://doi.org/10.17863/CAM.50169 month: '05' oa: 1 oa_version: Published Version publisher: Apollo - University of Cambridge related_material: record: - id: '7942' relation: used_in_publication status: public status: public title: Accompanying dataset for 'Hard antinodal gap revealed by quantum oscillations in the pseudogap regime of underdoped high-Tc superconductors' 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_reference user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf year: '2020' ... --- _id: '8809' abstract: - lang: eng text: When divergent populations are connected by gene flow, the establishment of complete reproductive isolation usually requires the joint action of multiple barrier effects. One example where multiple barrier effects are coupled consists of a single trait that is under divergent natural selection and also mediates assortative mating. Such multiple-effect traits can strongly reduce gene flow. However, there are few cases where patterns of assortative mating have been described quantitatively and their impact on gene flow has been determined. Two ecotypes of the coastal marine snail, Littorina saxatilis, occur in North Atlantic rocky-shore habitats dominated by either crab predation or wave action. There is evidence for divergent natural selection acting on size, and size-assortative mating has previously been documented. Here, we analyze the mating pattern in L. saxatilis with respect to size in intensively-sampled transects across boundaries between the habitats. We show that the mating pattern is mostly conserved between ecotypes and that it generates both assortment and directional sexual selection for small male size. Using simulations, we show that the mating pattern can contribute to reproductive isolation between ecotypes but the barrier to gene flow is likely strengthened more by sexual selection than by assortment. article_processing_charge: No author: - first_name: Samuel full_name: Perini, Samuel last_name: Perini - first_name: Marina full_name: Rafajlovic, Marina last_name: Rafajlovic - first_name: Anja M full_name: Westram, Anja M id: 3C147470-F248-11E8-B48F-1D18A9856A87 last_name: Westram orcid: 0000-0003-1050-4969 - first_name: Kerstin full_name: Johannesson, Kerstin last_name: Johannesson - first_name: Roger full_name: Butlin, Roger last_name: Butlin citation: ama: 'Perini S, Rafajlovic M, Westram AM, Johannesson K, Butlin R. Data from: Assortative mating, sexual selection and their consequences for gene flow in Littorina. 2020. doi:10.5061/dryad.qrfj6q5cn' apa: 'Perini, S., Rafajlovic, M., Westram, A. M., Johannesson, K., & Butlin, R. (2020). Data from: Assortative mating, sexual selection and their consequences for gene flow in Littorina. Dryad. https://doi.org/10.5061/dryad.qrfj6q5cn' chicago: 'Perini, Samuel, Marina Rafajlovic, Anja M Westram, Kerstin Johannesson, and Roger Butlin. “Data from: Assortative Mating, Sexual Selection and Their Consequences for Gene Flow in Littorina.” Dryad, 2020. https://doi.org/10.5061/dryad.qrfj6q5cn.' ieee: 'S. Perini, M. Rafajlovic, A. M. Westram, K. Johannesson, and R. Butlin, “Data from: Assortative mating, sexual selection and their consequences for gene flow in Littorina.” Dryad, 2020.' ista: 'Perini S, Rafajlovic M, Westram AM, Johannesson K, Butlin R. 2020. Data from: Assortative mating, sexual selection and their consequences for gene flow in Littorina, Dryad, 10.5061/dryad.qrfj6q5cn.' mla: 'Perini, Samuel, et al. Data from: Assortative Mating, Sexual Selection and Their Consequences for Gene Flow in Littorina. Dryad, 2020, doi:10.5061/dryad.qrfj6q5cn.' short: S. Perini, M. Rafajlovic, A.M. Westram, K. Johannesson, R. Butlin, (2020). date_created: 2020-11-25T11:07:25Z date_published: 2020-07-01T00:00:00Z date_updated: 2023-08-22T07:13:37Z day: '01' department: - _id: NiBa doi: 10.5061/dryad.qrfj6q5cn has_accepted_license: '1' main_file_link: - open_access: '1' url: https://doi.org/10.5061/dryad.qrfj6q5cn month: '07' oa: 1 oa_version: Published Version publisher: Dryad related_material: record: - id: '7995' relation: used_in_publication status: public status: public title: 'Data from: Assortative mating, sexual selection and their consequences for gene flow in Littorina' 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_reference user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf year: '2020' ... --- _id: '9326' abstract: - lang: eng text: The mitochondrial respiratory chain, formed by five protein complexes, utilizes energy from catabolic processes to synthesize ATP. Complex I, the first and the largest protein complex of the chain, harvests electrons from NADH to reduce quinone, while pumping protons across the mitochondrial membrane. Detailed knowledge of the working principle of such coupled charge-transfer processes remains, however, fragmentary due to bottlenecks in understanding redox-driven conformational transitions and their interplay with the hydrated proton pathways. Complex I from Thermus thermophilus encases 16 subunits with nine iron–sulfur clusters, reduced by electrons from NADH. Here, employing the latest crystal structure of T. thermophilus complex I, we have used microsecond-scale molecular dynamics simulations to study the chemo-mechanical coupling between redox changes of the iron–sulfur clusters and conformational transitions across complex I. First, we identify the redox switches within complex I, which allosterically couple the dynamics of the quinone binding pocket to the site of NADH reduction. Second, our free-energy calculations reveal that the affinity of the quinone, specifically menaquinone, for the binding-site is higher than that of its reduced, menaquinol forma design essential for menaquinol release. Remarkably, the barriers to diffusive menaquinone dynamics are lesser than that of the more ubiquitous ubiquinone, and the naphthoquinone headgroup of the former furnishes stronger binding interactions with the pocket, favoring menaquinone for charge transport in T. thermophilus. Our computations are consistent with experimentally validated mutations and hierarchize the key residues into three functional classes, identifying new mutation targets. Third, long-range hydrogen-bond networks connecting the quinone-binding site to the transmembrane subunits are found to be responsible for proton pumping. Put together, the simulations reveal the molecular design principles linking redox reactions to quinone turnover to proton translocation in complex I. article_processing_charge: No author: - first_name: Chitrak full_name: Gupta, Chitrak last_name: Gupta - first_name: Umesh full_name: Khaniya, Umesh last_name: Khaniya - first_name: Chun full_name: Chan, Chun last_name: Chan - first_name: Francois full_name: Dehez, Francois last_name: Dehez - first_name: Mrinal full_name: Shekhar, Mrinal last_name: Shekhar - first_name: M. R. full_name: Gunner, M. R. last_name: Gunner - first_name: Leonid A full_name: Sazanov, Leonid A id: 338D39FE-F248-11E8-B48F-1D18A9856A87 last_name: Sazanov orcid: 0000-0002-0977-7989 - first_name: Christophe full_name: Chipot, Christophe last_name: Chipot - first_name: Abhishek full_name: Singharoy, Abhishek last_name: Singharoy citation: ama: Gupta C, Khaniya U, Chan C, et al. Charge transfer and chemo-mechanical coupling in respiratory complex I. 2020. doi:10.1021/jacs.9b13450.s002 apa: Gupta, C., Khaniya, U., Chan, C., Dehez, F., Shekhar, M., Gunner, M. R., … Singharoy, A. (2020). Charge transfer and chemo-mechanical coupling in respiratory complex I. American Chemical Society. https://doi.org/10.1021/jacs.9b13450.s002 chicago: Gupta, Chitrak, Umesh Khaniya, Chun Chan, Francois Dehez, Mrinal Shekhar, M. R. Gunner, Leonid A Sazanov, Christophe Chipot, and Abhishek Singharoy. “Charge Transfer and Chemo-Mechanical Coupling in Respiratory Complex I.” American Chemical Society, 2020. https://doi.org/10.1021/jacs.9b13450.s002. ieee: C. Gupta et al., “Charge transfer and chemo-mechanical coupling in respiratory complex I.” American Chemical Society, 2020. ista: Gupta C, Khaniya U, Chan C, Dehez F, Shekhar M, Gunner MR, Sazanov LA, Chipot C, Singharoy A. 2020. Charge transfer and chemo-mechanical coupling in respiratory complex I, American Chemical Society, 10.1021/jacs.9b13450.s002. mla: Gupta, Chitrak, et al. Charge Transfer and Chemo-Mechanical Coupling in Respiratory Complex I. American Chemical Society, 2020, doi:10.1021/jacs.9b13450.s002. short: C. Gupta, U. Khaniya, C. Chan, F. Dehez, M. Shekhar, M.R. Gunner, L.A. Sazanov, C. Chipot, A. Singharoy, (2020). date_created: 2021-04-14T12:05:20Z date_published: 2020-05-20T00:00:00Z date_updated: 2023-08-22T07:49:37Z day: '20' department: - _id: LeSa doi: 10.1021/jacs.9b13450.s002 main_file_link: - open_access: '1' month: '05' oa: 1 oa_version: Published Version publisher: American Chemical Society related_material: record: - id: '8040' relation: used_in_publication status: public status: public title: Charge transfer and chemo-mechanical coupling in respiratory complex I 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: research_data_reference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2020' ... --- _id: '9713' abstract: - lang: eng text: Additional analyses of the trajectories article_processing_charge: No author: - first_name: Chitrak full_name: Gupta, Chitrak last_name: Gupta - first_name: Umesh full_name: Khaniya, Umesh last_name: Khaniya - first_name: Chun Kit full_name: Chan, Chun Kit last_name: Chan - first_name: Francois full_name: Dehez, Francois last_name: Dehez - first_name: Mrinal full_name: Shekhar, Mrinal last_name: Shekhar - first_name: M.R. full_name: Gunner, M.R. last_name: Gunner - first_name: Leonid A full_name: Sazanov, Leonid A id: 338D39FE-F248-11E8-B48F-1D18A9856A87 last_name: Sazanov orcid: 0000-0002-0977-7989 - first_name: Christophe full_name: Chipot, Christophe last_name: Chipot - first_name: Abhishek full_name: Singharoy, Abhishek last_name: Singharoy citation: ama: Gupta C, Khaniya U, Chan CK, et al. Supporting information. 2020. doi:10.1021/jacs.9b13450.s001 apa: Gupta, C., Khaniya, U., Chan, C. K., Dehez, F., Shekhar, M., Gunner, M. R., … Singharoy, A. (2020). Supporting information. American Chemical Society . https://doi.org/10.1021/jacs.9b13450.s001 chicago: Gupta, Chitrak, Umesh Khaniya, Chun Kit Chan, Francois Dehez, Mrinal Shekhar, M.R. Gunner, Leonid A Sazanov, Christophe Chipot, and Abhishek Singharoy. “Supporting Information.” American Chemical Society , 2020. https://doi.org/10.1021/jacs.9b13450.s001. ieee: C. Gupta et al., “Supporting information.” American Chemical Society , 2020. ista: Gupta C, Khaniya U, Chan CK, Dehez F, Shekhar M, Gunner MR, Sazanov LA, Chipot C, Singharoy A. 2020. Supporting information, American Chemical Society , 10.1021/jacs.9b13450.s001. mla: Gupta, Chitrak, et al. Supporting Information. American Chemical Society , 2020, doi:10.1021/jacs.9b13450.s001. short: C. Gupta, U. Khaniya, C.K. Chan, F. Dehez, M. Shekhar, M.R. Gunner, L.A. Sazanov, C. Chipot, A. Singharoy, (2020). date_created: 2021-07-23T12:02:39Z date_published: 2020-05-20T00:00:00Z date_updated: 2023-08-22T07:49:38Z day: '20' department: - _id: LeSa doi: 10.1021/jacs.9b13450.s001 month: '05' oa_version: Published Version publisher: 'American Chemical Society ' related_material: record: - id: '8040' relation: used_in_publication status: public status: public title: Supporting information type: research_data_reference user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf year: '2020' ... --- _id: '9878' article_processing_charge: No author: - first_name: Chitrak full_name: Gupta, Chitrak last_name: Gupta - first_name: Umesh full_name: Khaniya, Umesh last_name: Khaniya - first_name: Chun Kit full_name: Chan, Chun Kit last_name: Chan - first_name: Francois full_name: Dehez, Francois last_name: Dehez - first_name: Mrinal full_name: Shekhar, Mrinal last_name: Shekhar - first_name: M.R. full_name: Gunner, M.R. last_name: Gunner - first_name: Leonid A full_name: Sazanov, Leonid A id: 338D39FE-F248-11E8-B48F-1D18A9856A87 last_name: Sazanov orcid: 0000-0002-0977-7989 - first_name: Christophe full_name: Chipot, Christophe last_name: Chipot - first_name: Abhishek full_name: Singharoy, Abhishek last_name: Singharoy citation: ama: Gupta C, Khaniya U, Chan CK, et al. Movies. 2020. doi:10.1021/jacs.9b13450.s002 apa: Gupta, C., Khaniya, U., Chan, C. K., Dehez, F., Shekhar, M., Gunner, M. R., … Singharoy, A. (2020). Movies. American Chemical Society. https://doi.org/10.1021/jacs.9b13450.s002 chicago: Gupta, Chitrak, Umesh Khaniya, Chun Kit Chan, Francois Dehez, Mrinal Shekhar, M.R. Gunner, Leonid A Sazanov, Christophe Chipot, and Abhishek Singharoy. “Movies.” American Chemical Society, 2020. https://doi.org/10.1021/jacs.9b13450.s002. ieee: C. Gupta et al., “Movies.” American Chemical Society, 2020. ista: Gupta C, Khaniya U, Chan CK, Dehez F, Shekhar M, Gunner MR, Sazanov LA, Chipot C, Singharoy A. 2020. Movies, American Chemical Society, 10.1021/jacs.9b13450.s002. mla: Gupta, Chitrak, et al. Movies. American Chemical Society, 2020, doi:10.1021/jacs.9b13450.s002. short: C. Gupta, U. Khaniya, C.K. Chan, F. Dehez, M. Shekhar, M.R. Gunner, L.A. Sazanov, C. Chipot, A. Singharoy, (2020). date_created: 2021-08-11T09:18:54Z date_published: 2020-05-20T00:00:00Z date_updated: 2023-08-22T07:49:38Z day: '20' department: - _id: LeSa doi: 10.1021/jacs.9b13450.s002 month: '05' oa_version: Published Version publisher: American Chemical Society related_material: record: - id: '8040' relation: used_in_publication status: public status: public title: Movies type: research_data_reference user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf year: '2020' ... --- _id: '9706' abstract: - lang: eng text: 'Additional file 2: Supplementary Tables. The association of pre-adjusted protein levels with biological and technical covariates. Protein levels were adjusted for age, sex, array plate and four genetic principal components (population structure) prior to analyses. Significant associations are emboldened. (Table S1). pQTLs associated with inflammatory biomarker levels from Bayesian penalised regression model (Posterior Inclusion Probability > 95%). (Table S2). All pQTLs associated with inflammatory biomarker levels from ordinary least squares regression model (P < 7.14 × 10− 10). (Table S3). Summary of lambda values relating to ordinary least squares GWAS and EWAS performed on inflammatory protein levels (n = 70) in Lothian Birth Cohort 1936 study. (Table S4). Conditionally significant pQTLs associated with inflammatory biomarker levels from ordinary least squares regression model (P < 7.14 × 10− 10). (Table S5). Comparison of variance explained by ordinary least squares and Bayesian penalised regression models for concordantly identified SNPs. (Table S6). Estimate of heritability for blood protein levels as well as proportion of variance explained attributable to different prior mixtures. (Table S7). Comparison of heritability estimates from Ahsan et al. (maximum likelihood) and Hillary et al. (Bayesian penalised regression). (Table S8). List of concordant SNPs identified by linear model and Bayesian penalised regression and whether they have been previously identified as eQTLs. (Table S9). Bayesian tests of colocalisation for cis pQTLs and cis eQTLs. (Table S10). Sherlock algorithm: Genes whose expression are putatively associated with circulating inflammatory proteins that harbour pQTLs. (Table S11). CpGs associated with inflammatory protein biomarkers as identified by Bayesian model (Bayesian model; Posterior Inclusion Probability > 95%). (Table S12). CpGs associated with inflammatory protein biomarkers as identified by linear model (limma) at P < 5.14 × 10− 10. (Table S13). CpGs associated with inflammatory protein biomarkers as identified by mixed linear model (OSCA) at P < 5.14 × 10− 10. (Table S14). Estimate of variance explained for blood protein levels by DNA methylation as well as proportion of explained attributable to different prior mixtures - BayesR+. (Table S15). Comparison of variance in protein levels explained by genome-wide DNA methylation data by mixed linear model (OSCA) and Bayesian penalised regression model (BayesR+). (Table S16). Variance in circulating inflammatory protein biomarker levels explained by common genetic and methylation data (joint and conditional estimates from BayesR+). Ordered by combined variance explained by genetic and epigenetic data - smallest to largest. Significant results from t-tests comparing distributions for variance explained by methylation or genetics alone versus combined estimate are emboldened. (Table S17). Genetic and epigenetic factors identified by BayesR+ when conditioning on all SNPs and CpGs together. (Table S18). Mendelian Randomisation analyses to assess whether proteins with concordantly identified genetic signals are causally associated with Alzheimer’s disease risk. (Table S19).' article_processing_charge: No author: - first_name: Robert F. full_name: Hillary, Robert F. last_name: Hillary - first_name: Daniel full_name: Trejo-Banos, Daniel last_name: Trejo-Banos - first_name: Athanasios full_name: Kousathanas, Athanasios last_name: Kousathanas - first_name: Daniel L. full_name: McCartney, Daniel L. last_name: McCartney - first_name: Sarah E. full_name: Harris, Sarah E. last_name: Harris - first_name: Anna J. full_name: Stevenson, Anna J. last_name: Stevenson - first_name: Marion full_name: Patxot, Marion last_name: Patxot - first_name: Sven Erik full_name: Ojavee, Sven Erik last_name: Ojavee - first_name: Qian full_name: Zhang, Qian last_name: Zhang - first_name: David C. full_name: Liewald, David C. last_name: Liewald - first_name: Craig W. full_name: Ritchie, Craig W. last_name: Ritchie - first_name: Kathryn L. full_name: Evans, Kathryn L. last_name: Evans - first_name: Elliot M. full_name: Tucker-Drob, Elliot M. last_name: Tucker-Drob - first_name: Naomi R. full_name: Wray, Naomi R. last_name: Wray - first_name: 'Allan F. ' full_name: 'McRae, Allan F. ' last_name: McRae - first_name: Peter M. full_name: Visscher, Peter M. last_name: Visscher - first_name: Ian J. full_name: Deary, Ian J. last_name: Deary - first_name: Matthew Richard full_name: Robinson, Matthew Richard id: E5D42276-F5DA-11E9-8E24-6303E6697425 last_name: Robinson orcid: 0000-0001-8982-8813 - first_name: 'Riccardo E. ' full_name: 'Marioni, Riccardo E. ' last_name: Marioni citation: ama: Hillary RF, Trejo-Banos D, Kousathanas A, et al. Additional file 2 of multi-method genome- and epigenome-wide studies of inflammatory protein levels in healthy older adults. 2020. doi:10.6084/m9.figshare.12629697.v1 apa: Hillary, R. F., Trejo-Banos, D., Kousathanas, A., McCartney, D. L., Harris, S. E., Stevenson, A. J., … Marioni, R. E. (2020). Additional file 2 of multi-method genome- and epigenome-wide studies of inflammatory protein levels in healthy older adults. Springer Nature. https://doi.org/10.6084/m9.figshare.12629697.v1 chicago: Hillary, Robert F., Daniel Trejo-Banos, Athanasios Kousathanas, Daniel L. McCartney, Sarah E. Harris, Anna J. Stevenson, Marion Patxot, et al. “Additional File 2 of Multi-Method Genome- and Epigenome-Wide Studies of Inflammatory Protein Levels in Healthy Older Adults.” Springer Nature, 2020. https://doi.org/10.6084/m9.figshare.12629697.v1. ieee: R. F. Hillary et al., “Additional file 2 of multi-method genome- and epigenome-wide studies of inflammatory protein levels in healthy older adults.” Springer Nature, 2020. ista: Hillary RF, Trejo-Banos D, Kousathanas A, McCartney DL, Harris SE, Stevenson AJ, Patxot M, Ojavee SE, Zhang Q, Liewald DC, Ritchie CW, Evans KL, Tucker-Drob EM, Wray NR, McRae AF, Visscher PM, Deary IJ, Robinson MR, Marioni RE. 2020. Additional file 2 of multi-method genome- and epigenome-wide studies of inflammatory protein levels in healthy older adults, Springer Nature, 10.6084/m9.figshare.12629697.v1. mla: Hillary, Robert F., et al. Additional File 2 of Multi-Method Genome- and Epigenome-Wide Studies of Inflammatory Protein Levels in Healthy Older Adults. Springer Nature, 2020, doi:10.6084/m9.figshare.12629697.v1. short: R.F. Hillary, D. Trejo-Banos, A. Kousathanas, D.L. McCartney, S.E. Harris, A.J. Stevenson, M. Patxot, S.E. Ojavee, Q. Zhang, D.C. Liewald, C.W. Ritchie, K.L. Evans, E.M. Tucker-Drob, N.R. Wray, A.F. McRae, P.M. Visscher, I.J. Deary, M.R. Robinson, R.E. Marioni, (2020). date_created: 2021-07-23T08:59:15Z date_published: 2020-07-09T00:00:00Z date_updated: 2023-08-22T07:55:36Z day: '09' department: - _id: MaRo doi: 10.6084/m9.figshare.12629697.v1 has_accepted_license: '1' main_file_link: - open_access: '1' url: https://doi.org/10.6084/m9.figshare.12629697.v1 month: '07' oa: 1 oa_version: Published Version other_data_license: CC0 + CC BY (4.0) publisher: Springer Nature related_material: record: - id: '8133' relation: used_in_publication status: public status: public title: Additional file 2 of multi-method genome- and epigenome-wide studies of inflammatory protein levels in healthy older adults 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_reference user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf year: '2020' ... --- _id: '13056' abstract: - lang: eng text: This datasets comprises all data shown in plots of the submitted article "Converting microwave and telecom photons with a silicon photonic nanomechanical interface". Additional raw data are available from the corresponding author on reasonable request. article_processing_charge: No author: - first_name: Georg M full_name: Arnold, Georg M id: 3770C838-F248-11E8-B48F-1D18A9856A87 last_name: Arnold orcid: 0000-0003-1397-7876 - first_name: Matthias full_name: Wulf, Matthias id: 45598606-F248-11E8-B48F-1D18A9856A87 last_name: Wulf orcid: 0000-0001-6613-1378 - first_name: Shabir full_name: Barzanjeh, Shabir id: 2D25E1F6-F248-11E8-B48F-1D18A9856A87 last_name: Barzanjeh orcid: 0000-0003-0415-1423 - first_name: Elena full_name: Redchenko, Elena id: 2C21D6E8-F248-11E8-B48F-1D18A9856A87 last_name: Redchenko - first_name: Alfredo R full_name: Rueda Sanchez, Alfredo R id: 3B82B0F8-F248-11E8-B48F-1D18A9856A87 last_name: Rueda Sanchez orcid: 0000-0001-6249-5860 - first_name: William J full_name: Hease, William J id: 29705398-F248-11E8-B48F-1D18A9856A87 last_name: Hease orcid: 0000-0001-9868-2166 - first_name: Farid full_name: Hassani, Farid id: 2AED110C-F248-11E8-B48F-1D18A9856A87 last_name: Hassani orcid: 0000-0001-6937-5773 - first_name: Johannes M full_name: Fink, Johannes M id: 4B591CBA-F248-11E8-B48F-1D18A9856A87 last_name: Fink orcid: 0000-0001-8112-028X citation: ama: Arnold GM, Wulf M, Barzanjeh S, et al. Converting microwave and telecom photons with a silicon photonic nanomechanical interface. 2020. doi:10.5281/ZENODO.3961561 apa: Arnold, G. M., Wulf, M., Barzanjeh, S., Redchenko, E., Rueda Sanchez, A. R., Hease, W. J., … Fink, J. M. (2020). Converting microwave and telecom photons with a silicon photonic nanomechanical interface. Zenodo. https://doi.org/10.5281/ZENODO.3961561 chicago: Arnold, Georg M, Matthias Wulf, Shabir Barzanjeh, Elena Redchenko, Alfredo R Rueda Sanchez, William J Hease, Farid Hassani, and Johannes M Fink. “Converting Microwave and Telecom Photons with a Silicon Photonic Nanomechanical Interface.” Zenodo, 2020. https://doi.org/10.5281/ZENODO.3961561. ieee: G. M. Arnold et al., “Converting microwave and telecom photons with a silicon photonic nanomechanical interface.” Zenodo, 2020. ista: Arnold GM, Wulf M, Barzanjeh S, Redchenko E, Rueda Sanchez AR, Hease WJ, Hassani F, Fink JM. 2020. Converting microwave and telecom photons with a silicon photonic nanomechanical interface, Zenodo, 10.5281/ZENODO.3961561. mla: Arnold, Georg M., et al. Converting Microwave and Telecom Photons with a Silicon Photonic Nanomechanical Interface. Zenodo, 2020, doi:10.5281/ZENODO.3961561. short: G.M. Arnold, M. Wulf, S. Barzanjeh, E. Redchenko, A.R. Rueda Sanchez, W.J. Hease, F. Hassani, J.M. Fink, (2020). date_created: 2023-05-23T13:37:41Z date_published: 2020-07-27T00:00:00Z date_updated: 2023-08-22T09:27:11Z day: '27' ddc: - '530' department: - _id: JoFi doi: 10.5281/ZENODO.3961561 main_file_link: - open_access: '1' url: https://doi.org/10.5281/zenodo.3961562 month: '07' oa: 1 oa_version: Published Version publisher: Zenodo related_material: record: - id: '8529' relation: used_in_publication status: public status: public title: Converting microwave and telecom photons with a silicon photonic nanomechanical interface 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_reference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2020' ... --- _id: '13070' abstract: - lang: eng text: This dataset comprises all data shown in the figures of the submitted article "Surpassing the resistance quantum with a geometric superinductor". Additional raw data are available from the corresponding author on reasonable request. article_processing_charge: No author: - first_name: Matilda full_name: Peruzzo, Matilda id: 3F920B30-F248-11E8-B48F-1D18A9856A87 last_name: Peruzzo orcid: 0000-0002-3415-4628 - first_name: Andrea full_name: Trioni, Andrea id: 42F71B44-F248-11E8-B48F-1D18A9856A87 last_name: Trioni - first_name: Farid full_name: Hassani, Farid id: 2AED110C-F248-11E8-B48F-1D18A9856A87 last_name: Hassani orcid: 0000-0001-6937-5773 - first_name: Martin full_name: Zemlicka, Martin id: 2DCF8DE6-F248-11E8-B48F-1D18A9856A87 last_name: Zemlicka - first_name: Johannes M full_name: Fink, Johannes M id: 4B591CBA-F248-11E8-B48F-1D18A9856A87 last_name: Fink orcid: 0000-0001-8112-028X citation: ama: Peruzzo M, Trioni A, Hassani F, Zemlicka M, Fink JM. Surpassing the resistance quantum with a geometric superinductor. 2020. doi:10.5281/ZENODO.4052882 apa: Peruzzo, M., Trioni, A., Hassani, F., Zemlicka, M., & Fink, J. M. (2020). Surpassing the resistance quantum with a geometric superinductor. Zenodo. https://doi.org/10.5281/ZENODO.4052882 chicago: Peruzzo, Matilda, Andrea Trioni, Farid Hassani, Martin Zemlicka, and Johannes M Fink. “Surpassing the Resistance Quantum with a Geometric Superinductor.” Zenodo, 2020. https://doi.org/10.5281/ZENODO.4052882. ieee: M. Peruzzo, A. Trioni, F. Hassani, M. Zemlicka, and J. M. Fink, “Surpassing the resistance quantum with a geometric superinductor.” Zenodo, 2020. ista: Peruzzo M, Trioni A, Hassani F, Zemlicka M, Fink JM. 2020. Surpassing the resistance quantum with a geometric superinductor, Zenodo, 10.5281/ZENODO.4052882. mla: Peruzzo, Matilda, et al. Surpassing the Resistance Quantum with a Geometric Superinductor. Zenodo, 2020, doi:10.5281/ZENODO.4052882. short: M. Peruzzo, A. Trioni, F. Hassani, M. Zemlicka, J.M. Fink, (2020). date_created: 2023-05-23T16:42:30Z date_published: 2020-09-27T00:00:00Z date_updated: 2023-08-22T13:23:57Z day: '27' ddc: - '530' department: - _id: JoFi doi: 10.5281/ZENODO.4052882 main_file_link: - open_access: '1' url: https://doi.org/10.5281/zenodo.4052883 month: '09' oa: 1 oa_version: Published Version publisher: Zenodo related_material: record: - id: '8755' relation: used_in_publication status: public status: public title: Surpassing the resistance quantum with a geometric superinductor 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_reference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2020' ... --- _id: '13071' abstract: - lang: eng text: This dataset comprises all data shown in the plots of the main part of the submitted article "Bidirectional Electro-Optic Wavelength Conversion in the Quantum Ground State". Additional raw data are available from the corresponding author on reasonable request. article_processing_charge: No author: - first_name: William J full_name: Hease, William J id: 29705398-F248-11E8-B48F-1D18A9856A87 last_name: Hease orcid: 0000-0001-9868-2166 - first_name: Alfredo R full_name: Rueda Sanchez, Alfredo R id: 3B82B0F8-F248-11E8-B48F-1D18A9856A87 last_name: Rueda Sanchez orcid: 0000-0001-6249-5860 - first_name: Rishabh full_name: Sahu, Rishabh id: 47D26E34-F248-11E8-B48F-1D18A9856A87 last_name: Sahu orcid: 0000-0001-6264-2162 - first_name: Matthias full_name: Wulf, Matthias id: 45598606-F248-11E8-B48F-1D18A9856A87 last_name: Wulf orcid: 0000-0001-6613-1378 - first_name: Georg M full_name: Arnold, Georg M id: 3770C838-F248-11E8-B48F-1D18A9856A87 last_name: Arnold orcid: 0000-0003-1397-7876 - first_name: Harald full_name: Schwefel, Harald last_name: Schwefel - first_name: Johannes M full_name: Fink, Johannes M id: 4B591CBA-F248-11E8-B48F-1D18A9856A87 last_name: Fink orcid: 0000-0001-8112-028X citation: ama: Hease WJ, Rueda Sanchez AR, Sahu R, et al. Bidirectional electro-optic wavelength conversion in the quantum ground state. 2020. doi:10.5281/ZENODO.4266025 apa: Hease, W. J., Rueda Sanchez, A. R., Sahu, R., Wulf, M., Arnold, G. M., Schwefel, H., & Fink, J. M. (2020). Bidirectional electro-optic wavelength conversion in the quantum ground state. Zenodo. https://doi.org/10.5281/ZENODO.4266025 chicago: Hease, William J, Alfredo R Rueda Sanchez, Rishabh Sahu, Matthias Wulf, Georg M Arnold, Harald Schwefel, and Johannes M Fink. “Bidirectional Electro-Optic Wavelength Conversion in the Quantum Ground State.” Zenodo, 2020. https://doi.org/10.5281/ZENODO.4266025. ieee: W. J. Hease et al., “Bidirectional electro-optic wavelength conversion in the quantum ground state.” Zenodo, 2020. ista: Hease WJ, Rueda Sanchez AR, Sahu R, Wulf M, Arnold GM, Schwefel H, Fink JM. 2020. Bidirectional electro-optic wavelength conversion in the quantum ground state, Zenodo, 10.5281/ZENODO.4266025. mla: Hease, William J., et al. Bidirectional Electro-Optic Wavelength Conversion in the Quantum Ground State. Zenodo, 2020, doi:10.5281/ZENODO.4266025. short: W.J. Hease, A.R. Rueda Sanchez, R. Sahu, M. Wulf, G.M. Arnold, H. Schwefel, J.M. Fink, (2020). date_created: 2023-05-23T16:44:11Z date_published: 2020-11-10T00:00:00Z date_updated: 2023-08-24T11:16:35Z day: '10' ddc: - '530' department: - _id: JoFi doi: 10.5281/ZENODO.4266025 main_file_link: - open_access: '1' url: https://doi.org/10.5281/zenodo.4266026 month: '11' oa: 1 oa_version: Published Version publisher: Zenodo related_material: record: - id: '9114' relation: used_in_publication status: public status: public title: Bidirectional electro-optic wavelength conversion in the quantum ground state 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_reference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2020' ... --- _id: '9799' abstract: - lang: eng text: Fitness interactions between mutations can influence a population’s evolution in many different ways. While epistatic effects are difficult to measure precisely, important information is captured by the mean and variance of log fitnesses for individuals carrying different numbers of mutations. We derive predictions for these quantities from a class of simple fitness landscapes, based on models of optimizing selection on quantitative traits. We also explore extensions to the models, including modular pleiotropy, variable effect sizes, mutational bias and maladaptation of the wild type. We illustrate our approach by reanalysing a large dataset of mutant effects in a yeast snoRNA. Though characterized by some large epistatic effects, these data give a good overall fit to the non-epistatic null model, suggesting that epistasis might have limited influence on the evolutionary dynamics in this system. We also show how the amount of epistasis depends on both the underlying fitness landscape and the distribution of mutations, and so is expected to vary in consistent ways between new mutations, standing variation and fixed mutations. article_processing_charge: No author: - first_name: Christelle full_name: Fraisse, Christelle id: 32DF5794-F248-11E8-B48F-1D18A9856A87 last_name: Fraisse orcid: 0000-0001-8441-5075 - first_name: John J. full_name: Welch, John J. last_name: Welch citation: ama: Fraisse C, Welch JJ. Simulation code for Fig S1 from the distribution of epistasis on simple fitness landscapes. 2020. doi:10.6084/m9.figshare.7957469.v1 apa: Fraisse, C., & Welch, J. J. (2020). Simulation code for Fig S1 from the distribution of epistasis on simple fitness landscapes. Royal Society of London. https://doi.org/10.6084/m9.figshare.7957469.v1 chicago: Fraisse, Christelle, and John J. Welch. “Simulation Code for Fig S1 from the Distribution of Epistasis on Simple Fitness Landscapes.” Royal Society of London, 2020. https://doi.org/10.6084/m9.figshare.7957469.v1. ieee: C. Fraisse and J. J. Welch, “Simulation code for Fig S1 from the distribution of epistasis on simple fitness landscapes.” Royal Society of London, 2020. ista: Fraisse C, Welch JJ. 2020. Simulation code for Fig S1 from the distribution of epistasis on simple fitness landscapes, Royal Society of London, 10.6084/m9.figshare.7957469.v1. mla: Fraisse, Christelle, and John J. Welch. Simulation Code for Fig S1 from the Distribution of Epistasis on Simple Fitness Landscapes. Royal Society of London, 2020, doi:10.6084/m9.figshare.7957469.v1. short: C. Fraisse, J.J. Welch, (2020). date_created: 2021-08-06T11:26:57Z date_published: 2020-10-15T00:00:00Z date_updated: 2023-08-25T10:34:41Z day: '15' department: - _id: BeVi - _id: NiBa doi: 10.6084/m9.figshare.7957469.v1 main_file_link: - open_access: '1' url: https://doi.org/10.6084/m9.figshare.7957469.v1 month: '10' oa: 1 oa_version: Published Version publisher: Royal Society of London related_material: record: - id: '6467' relation: used_in_publication status: public status: public title: Simulation code for Fig S1 from the distribution of epistasis on simple fitness landscapes type: research_data_reference user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf year: '2020' ... --- _id: '9798' abstract: - lang: eng text: Fitness interactions between mutations can influence a population’s evolution in many different ways. While epistatic effects are difficult to measure precisely, important information is captured by the mean and variance of log fitnesses for individuals carrying different numbers of mutations. We derive predictions for these quantities from a class of simple fitness landscapes, based on models of optimizing selection on quantitative traits. We also explore extensions to the models, including modular pleiotropy, variable effect sizes, mutational bias and maladaptation of the wild type. We illustrate our approach by reanalysing a large dataset of mutant effects in a yeast snoRNA. Though characterized by some large epistatic effects, these data give a good overall fit to the non-epistatic null model, suggesting that epistasis might have limited influence on the evolutionary dynamics in this system. We also show how the amount of epistasis depends on both the underlying fitness landscape and the distribution of mutations, and so is expected to vary in consistent ways between new mutations, standing variation and fixed mutations. article_processing_charge: No author: - first_name: Christelle full_name: Fraisse, Christelle id: 32DF5794-F248-11E8-B48F-1D18A9856A87 last_name: Fraisse orcid: 0000-0001-8441-5075 - first_name: John J. full_name: Welch, John J. last_name: Welch citation: ama: Fraisse C, Welch JJ. Simulation code for Fig S2 from the distribution of epistasis on simple fitness landscapes. 2020. doi:10.6084/m9.figshare.7957472.v1 apa: Fraisse, C., & Welch, J. J. (2020). Simulation code for Fig S2 from the distribution of epistasis on simple fitness landscapes. Royal Society of London. https://doi.org/10.6084/m9.figshare.7957472.v1 chicago: Fraisse, Christelle, and John J. Welch. “Simulation Code for Fig S2 from the Distribution of Epistasis on Simple Fitness Landscapes.” Royal Society of London, 2020. https://doi.org/10.6084/m9.figshare.7957472.v1. ieee: C. Fraisse and J. J. Welch, “Simulation code for Fig S2 from the distribution of epistasis on simple fitness landscapes.” Royal Society of London, 2020. ista: Fraisse C, Welch JJ. 2020. Simulation code for Fig S2 from the distribution of epistasis on simple fitness landscapes, Royal Society of London, 10.6084/m9.figshare.7957472.v1. mla: Fraisse, Christelle, and John J. Welch. Simulation Code for Fig S2 from the Distribution of Epistasis on Simple Fitness Landscapes. Royal Society of London, 2020, doi:10.6084/m9.figshare.7957472.v1. short: C. Fraisse, J.J. Welch, (2020). date_created: 2021-08-06T11:18:15Z date_published: 2020-10-15T00:00:00Z date_updated: 2023-08-25T10:34:41Z day: '15' department: - _id: BeVi - _id: NiBa doi: 10.6084/m9.figshare.7957472.v1 main_file_link: - open_access: '1' url: https://doi.org/10.6084/m9.figshare.7957472.v1 month: '10' oa: 1 oa_version: Published Version publisher: Royal Society of London related_material: record: - id: '6467' relation: used_in_publication status: public status: public title: Simulation code for Fig S2 from the distribution of epistasis on simple fitness landscapes type: research_data_reference user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf year: '2020' ... --- _id: '13060' abstract: - lang: eng text: Coinfections with multiple pathogens can result in complex within-host dynamics affecting virulence and transmission. Whilst multiple infections are intensively studied in solitary hosts, it is so far unresolved how social host interactions interfere with pathogen competition, and if this depends on coinfection diversity. We studied how the collective disease defenses of ants – their social immunity ­– influence pathogen competition in coinfections of same or different fungal pathogen species. Social immunity reduced virulence for all pathogen combinations, but interfered with spore production only in different-species coinfections. Here, it decreased overall pathogen sporulation success, whilst simultaneously increasing co-sporulation on individual cadavers and maintaining a higher pathogen diversity at the community-level. Mathematical modeling revealed that host sanitary care alone can modulate competitive outcomes between pathogens, giving advantage to fast-germinating, thus less grooming-sensitive ones. Host social interactions can hence modulate infection dynamics in coinfected group members, thereby altering pathogen communities at the host- and population-level. article_processing_charge: No author: - first_name: Barbara full_name: Milutinovic, Barbara id: 2CDC32B8-F248-11E8-B48F-1D18A9856A87 last_name: Milutinovic orcid: 0000-0002-8214-4758 - first_name: Miriam full_name: Stock, Miriam id: 42462816-F248-11E8-B48F-1D18A9856A87 last_name: Stock - first_name: Anna V full_name: Grasse, Anna V id: 406F989C-F248-11E8-B48F-1D18A9856A87 last_name: Grasse - first_name: Elisabeth full_name: Naderlinger, Elisabeth id: 31757262-F248-11E8-B48F-1D18A9856A87 last_name: Naderlinger - first_name: Christian full_name: Hilbe, Christian id: 2FDF8F3C-F248-11E8-B48F-1D18A9856A87 last_name: Hilbe orcid: 0000-0001-5116-955X - first_name: Sylvia full_name: Cremer, Sylvia id: 2F64EC8C-F248-11E8-B48F-1D18A9856A87 last_name: Cremer orcid: 0000-0002-2193-3868 citation: ama: Milutinovic B, Stock M, Grasse AV, Naderlinger E, Hilbe C, Cremer S. Social immunity modulates competition between coinfecting pathogens. 2020. doi:10.5061/DRYAD.CRJDFN318 apa: Milutinovic, B., Stock, M., Grasse, A. V., Naderlinger, E., Hilbe, C., & Cremer, S. (2020). Social immunity modulates competition between coinfecting pathogens. Dryad. https://doi.org/10.5061/DRYAD.CRJDFN318 chicago: Milutinovic, Barbara, Miriam Stock, Anna V Grasse, Elisabeth Naderlinger, Christian Hilbe, and Sylvia Cremer. “Social Immunity Modulates Competition between Coinfecting Pathogens.” Dryad, 2020. https://doi.org/10.5061/DRYAD.CRJDFN318. ieee: B. Milutinovic, M. Stock, A. V. Grasse, E. Naderlinger, C. Hilbe, and S. Cremer, “Social immunity modulates competition between coinfecting pathogens.” Dryad, 2020. ista: Milutinovic B, Stock M, Grasse AV, Naderlinger E, Hilbe C, Cremer S. 2020. Social immunity modulates competition between coinfecting pathogens, Dryad, 10.5061/DRYAD.CRJDFN318. mla: Milutinovic, Barbara, et al. Social Immunity Modulates Competition between Coinfecting Pathogens. Dryad, 2020, doi:10.5061/DRYAD.CRJDFN318. short: B. Milutinovic, M. Stock, A.V. Grasse, E. Naderlinger, C. Hilbe, S. Cremer, (2020). date_created: 2023-05-23T16:11:22Z date_published: 2020-12-19T00:00:00Z date_updated: 2023-09-05T16:04:48Z day: '19' ddc: - '570' department: - _id: SyCr - _id: KrCh doi: 10.5061/DRYAD.CRJDFN318 main_file_link: - open_access: '1' url: https://doi.org/10.5061/dryad.crjdfn318 month: '12' oa: 1 oa_version: Published Version publisher: Dryad related_material: record: - id: '7343' relation: used_in_publication status: public status: public title: Social immunity modulates competition between coinfecting pathogens 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_reference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2020' ... --- _id: '9780' abstract: - lang: eng text: "PADREV : 4,4'-dimethoxy[1,1'-biphenyl]-2,2',5,5'-tetrol\r\nSpace Group: C 2 (5), Cell: a 24.488(16)Å b 5.981(4)Å c 3.911(3)Å, α 90° β 91.47(3)° γ 90°" article_processing_charge: No author: - first_name: Werner full_name: Schlemmer, Werner last_name: Schlemmer - first_name: Philipp full_name: Nothdurft, Philipp last_name: Nothdurft - first_name: Alina full_name: Petzold, Alina last_name: Petzold - first_name: Gisbert full_name: Riess, Gisbert last_name: Riess - first_name: Philipp full_name: Frühwirt, Philipp last_name: Frühwirt - first_name: Max full_name: Schmallegger, Max last_name: Schmallegger - first_name: Georg full_name: Gescheidt-Demner, Georg last_name: Gescheidt-Demner - first_name: Roland full_name: Fischer, Roland last_name: Fischer - first_name: Stefan Alexander full_name: Freunberger, Stefan Alexander id: A8CA28E6-CE23-11E9-AD2D-EC27E6697425 last_name: Freunberger orcid: 0000-0003-2902-5319 - first_name: Wolfgang full_name: Kern, Wolfgang last_name: Kern - first_name: Stefan full_name: Spirk, Stefan last_name: Spirk citation: ama: 'Schlemmer W, Nothdurft P, Petzold A, et al. CCDC 1991959: Experimental Crystal Structure Determination. 2020. doi:10.5517/ccdc.csd.cc24vsrk' apa: 'Schlemmer, W., Nothdurft, P., Petzold, A., Riess, G., Frühwirt, P., Schmallegger, M., … Spirk, S. (2020). CCDC 1991959: Experimental Crystal Structure Determination. CCDC. https://doi.org/10.5517/ccdc.csd.cc24vsrk' chicago: 'Schlemmer, Werner, Philipp Nothdurft, Alina Petzold, Gisbert Riess, Philipp Frühwirt, Max Schmallegger, Georg Gescheidt-Demner, et al. “CCDC 1991959: Experimental Crystal Structure Determination.” CCDC, 2020. https://doi.org/10.5517/ccdc.csd.cc24vsrk.' ieee: 'W. Schlemmer et al., “CCDC 1991959: Experimental Crystal Structure Determination.” CCDC, 2020.' ista: 'Schlemmer W, Nothdurft P, Petzold A, Riess G, Frühwirt P, Schmallegger M, Gescheidt-Demner G, Fischer R, Freunberger SA, Kern W, Spirk S. 2020. CCDC 1991959: Experimental Crystal Structure Determination, CCDC, 10.5517/ccdc.csd.cc24vsrk.' mla: 'Schlemmer, Werner, et al. CCDC 1991959: Experimental Crystal Structure Determination. CCDC, 2020, doi:10.5517/ccdc.csd.cc24vsrk.' short: W. Schlemmer, P. Nothdurft, A. Petzold, G. Riess, P. Frühwirt, M. Schmallegger, G. Gescheidt-Demner, R. Fischer, S.A. Freunberger, W. Kern, S. Spirk, (2020). date_created: 2021-08-06T07:41:07Z date_published: 2020-03-22T00:00:00Z date_updated: 2023-09-05T16:03:47Z day: '22' department: - _id: StFr doi: 10.5517/ccdc.csd.cc24vsrk main_file_link: - open_access: '1' url: https://dx.doi.org/10.5517/ccdc.csd.cc24vsrk month: '03' oa: 1 oa_version: Published Version publisher: CCDC related_material: record: - id: '8329' relation: used_in_publication status: public status: public title: 'CCDC 1991959: Experimental Crystal Structure Determination' type: research_data_reference user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf year: '2020' ... --- _id: '9777' article_processing_charge: No author: - first_name: Rok full_name: Grah, Rok id: 483E70DE-F248-11E8-B48F-1D18A9856A87 last_name: Grah orcid: 0000-0003-2539-3560 - first_name: Tamar full_name: Friedlander, Tamar last_name: Friedlander citation: ama: Grah R, Friedlander T. Maximizing crosstalk. 2020. doi:10.1371/journal.pcbi.1007642.s002 apa: Grah, R., & Friedlander, T. (2020). Maximizing crosstalk. Public Library of Science. https://doi.org/10.1371/journal.pcbi.1007642.s002 chicago: Grah, Rok, and Tamar Friedlander. “Maximizing Crosstalk.” Public Library of Science, 2020. https://doi.org/10.1371/journal.pcbi.1007642.s002. ieee: R. Grah and T. Friedlander, “Maximizing crosstalk.” Public Library of Science, 2020. ista: Grah R, Friedlander T. 2020. Maximizing crosstalk, Public Library of Science, 10.1371/journal.pcbi.1007642.s002. mla: Grah, Rok, and Tamar Friedlander. Maximizing Crosstalk. Public Library of Science, 2020, doi:10.1371/journal.pcbi.1007642.s002. short: R. Grah, T. Friedlander, (2020). date_created: 2021-08-06T07:21:51Z date_published: 2020-02-25T00:00:00Z date_updated: 2023-09-12T11:02:25Z day: '25' department: - _id: GaTk doi: 10.1371/journal.pcbi.1007642.s002 main_file_link: - open_access: '1' url: https://doi.org/10.1371/journal.pcbi.1007642.s002 month: '02' oa: 1 oa_version: None publisher: Public Library of Science related_material: record: - id: '7569' relation: used_in_publication status: public status: public title: Maximizing crosstalk type: research_data_reference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2020' ... --- _id: '9814' abstract: - lang: eng text: Data and mathematica notebooks for plotting figures from Language learning with communication between learners article_processing_charge: No author: - first_name: Rasmus full_name: Ibsen-Jensen, Rasmus id: 3B699956-F248-11E8-B48F-1D18A9856A87 last_name: Ibsen-Jensen orcid: 0000-0003-4783-0389 - first_name: Josef full_name: Tkadlec, Josef id: 3F24CCC8-F248-11E8-B48F-1D18A9856A87 last_name: Tkadlec orcid: 0000-0002-1097-9684 - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Martin full_name: Nowak, Martin last_name: Nowak citation: ama: Ibsen-Jensen R, Tkadlec J, Chatterjee K, Nowak M. Data and mathematica notebooks for plotting figures from language learning with communication between learners from language acquisition with communication between learners. 2020. doi:10.6084/m9.figshare.5973013.v1 apa: Ibsen-Jensen, R., Tkadlec, J., Chatterjee, K., & Nowak, M. (2020). Data and mathematica notebooks for plotting figures from language learning with communication between learners from language acquisition with communication between learners. Royal Society. https://doi.org/10.6084/m9.figshare.5973013.v1 chicago: Ibsen-Jensen, Rasmus, Josef Tkadlec, Krishnendu Chatterjee, and Martin Nowak. “Data and Mathematica Notebooks for Plotting Figures from Language Learning with Communication between Learners from Language Acquisition with Communication between Learners.” Royal Society, 2020. https://doi.org/10.6084/m9.figshare.5973013.v1. ieee: R. Ibsen-Jensen, J. Tkadlec, K. Chatterjee, and M. Nowak, “Data and mathematica notebooks for plotting figures from language learning with communication between learners from language acquisition with communication between learners.” Royal Society, 2020. ista: Ibsen-Jensen R, Tkadlec J, Chatterjee K, Nowak M. 2020. Data and mathematica notebooks for plotting figures from language learning with communication between learners from language acquisition with communication between learners, Royal Society, 10.6084/m9.figshare.5973013.v1. mla: Ibsen-Jensen, Rasmus, et al. Data and Mathematica Notebooks for Plotting Figures from Language Learning with Communication between Learners from Language Acquisition with Communication between Learners. Royal Society, 2020, doi:10.6084/m9.figshare.5973013.v1. short: R. Ibsen-Jensen, J. Tkadlec, K. Chatterjee, M. Nowak, (2020). date_created: 2021-08-06T13:09:57Z date_published: 2020-10-15T00:00:00Z date_updated: 2023-10-18T06:36:00Z day: '15' department: - _id: KrCh doi: 10.6084/m9.figshare.5973013.v1 main_file_link: - open_access: '1' url: https://doi.org/10.6084/m9.figshare.5973013.v1 month: '10' oa: 1 oa_version: Published Version publisher: Royal Society related_material: record: - id: '198' relation: used_in_publication status: public status: public title: Data and mathematica notebooks for plotting figures from language learning with communication between learners from language acquisition with communication between learners type: research_data_reference user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf year: '2020' ... --- _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: - '530' department: - _id: GeKa doi: 10.15479/AT:ISTA:8834 file: - access_level: open_access checksum: 898607ac9d7cfbd5c7dd84bcb6d8a924 content_type: application/octet-stream creator: gkatsaro date_created: 2020-12-02T10:46:21Z date_updated: 2020-12-02T10:46:21Z file_id: '8836' file_name: Figure1-ICvsVG.hdf5 file_size: 898039 relation: main_file success: 1 - access_level: open_access checksum: f6f5888f8425e82b4dcd5ec3db9162a6 content_type: application/octet-stream creator: gkatsaro date_created: 2020-12-02T10:46:21Z date_updated: 2020-12-02T10:46:21Z file_id: '8837' file_name: Figure1-RNvsVG.hdf5 file_size: 184971 relation: main_file success: 1 - access_level: open_access checksum: 63a26c4b0299538610ec58c48c0ab1e3 content_type: application/octet-stream creator: gkatsaro date_created: 2020-12-02T10:46:22Z date_updated: 2020-12-02T10:46:22Z file_id: '8838' file_name: Figure2-MAR.hdf5 file_size: 2097740 relation: main_file success: 1 - access_level: open_access checksum: 4c6795b64b05088606ab7881f801acd7 content_type: application/octet-stream creator: gkatsaro date_created: 2020-12-02T10:46:22Z date_updated: 2020-12-02T10:46:22Z file_id: '8839' file_name: Figure3-Fraunhofer.hdf5 file_size: 911501 relation: main_file success: 1 - 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lang: eng text: 'Antibiotics that interfere with translation, when combined, interact in diverse and difficult-to-predict ways. Here, we explain these interactions by "translation bottlenecks": points in the translation cycle where antibiotics block ribosomal progression. To elucidate the underlying mechanisms of drug interactions between translation inhibitors, we generate translation bottlenecks genetically using inducible control of translation factors that regulate well-defined translation cycle steps. These perturbations accurately mimic antibiotic action and drug interactions, supporting that the interplay of different translation bottlenecks causes these interactions. We further show that growth laws, combined with drug uptake and binding kinetics, enable the direct prediction of a large fraction of observed interactions, yet fail to predict suppression. However, varying two translation bottlenecks simultaneously supports that dense traffic of ribosomes and competition for translation factors account for the previously unexplained suppression. These results highlight the importance of "continuous epistasis" in bacterial physiology.' acknowledged_ssus: - _id: LifeSc 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 “Mechanisms of drug interactions between translation-inhibiting antibiotics.” 2020. doi:10.15479/AT:ISTA:8097 apa: Kavcic, B. (2020). Analysis scripts and research data for the paper “Mechanisms of drug interactions between translation-inhibiting antibiotics.” Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:8097 chicago: Kavcic, Bor. “Analysis Scripts and Research Data for the Paper ‘Mechanisms of Drug Interactions between Translation-Inhibiting Antibiotics.’” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:8097. ieee: B. Kavcic, “Analysis scripts and research data for the paper ‘Mechanisms of drug interactions between translation-inhibiting antibiotics.’” Institute of Science and Technology Austria, 2020. ista: Kavcic B. 2020. Analysis scripts and research data for the paper ‘Mechanisms of drug interactions between translation-inhibiting antibiotics’, Institute of Science and Technology Austria, 10.15479/AT:ISTA:8097. mla: Kavcic, Bor. Analysis Scripts and Research Data for the Paper “Mechanisms of Drug Interactions between Translation-Inhibiting Antibiotics.” Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:8097. short: B. Kavcic, (2020). contributor: - contributor_type: research_group first_name: Gašper id: 3D494DCA-F248-11E8-B48F-1D18A9856A87 last_name: Tkačik orcid: 0000-0002-6699-1455 - contributor_type: research_group first_name: Tobias id: 3E6DB97A-F248-11E8-B48F-1D18A9856A87 last_name: Bollenbach date_created: 2020-07-06T20:40:19Z date_published: 2020-07-15T00:00:00Z date_updated: 2024-02-21T12:40:51Z day: '15' department: - _id: GaTk doi: 10.15479/AT:ISTA:8097 file: - access_level: open_access checksum: 5c321dbbb6d4b3c85da786fd3ebbdc98 content_type: application/zip creator: bkavcic date_created: 2020-07-06T20:38:27Z date_updated: 2020-07-14T12:48:09Z file_id: '8098' file_name: natComm_2020_scripts.zip file_size: 255770756 relation: main_file file_date_updated: 2020-07-14T12:48:09Z has_accepted_license: '1' keyword: - Escherichia coli - antibiotic combinations - translation - growth laws - drug interactions - bacterial physiology - translation inhibitors month: '07' oa: 1 oa_version: Published Version publisher: Institute of Science and Technology Austria status: public title: Analysis scripts and research data for the paper "Mechanisms of drug interactions between translation-inhibiting antibiotics" 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: '8254' abstract: - lang: eng text: "Here are the research data underlying the publication \"Estimating inbreeding and its effects in a long-term study of snapdragons (Antirrhinum majus)\". Further information are summed up in the README document.\r\nThe files for this record have been updated and are now found in the linked DOI https://doi.org/10.15479/AT:ISTA:9192." article_processing_charge: No author: - first_name: Louise S full_name: Arathoon, Louise S id: 2CFCFF98-F248-11E8-B48F-1D18A9856A87 last_name: Arathoon orcid: 0000-0003-1771-714X citation: ama: Arathoon LS. Estimating inbreeding and its effects in a long-term study of snapdragons (Antirrhinum majus). 2020. doi:10.15479/AT:ISTA:8254 apa: Arathoon, L. S. (2020). Estimating inbreeding and its effects in a long-term study of snapdragons (Antirrhinum majus). Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:8254 chicago: Arathoon, Louise S. “Estimating Inbreeding and Its Effects in a Long-Term Study of Snapdragons (Antirrhinum Majus).” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:8254. ieee: L. S. Arathoon, “Estimating inbreeding and its effects in a long-term study of snapdragons (Antirrhinum majus).” Institute of Science and Technology Austria, 2020. ista: Arathoon LS. 2020. Estimating inbreeding and its effects in a long-term study of snapdragons (Antirrhinum majus), Institute of Science and Technology Austria, 10.15479/AT:ISTA:8254. mla: Arathoon, Louise S. Estimating Inbreeding and Its Effects in a Long-Term Study of Snapdragons (Antirrhinum Majus). Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:8254. short: L.S. Arathoon, (2020). contributor: - contributor_type: data_collector first_name: Louise S id: 2CFCFF98-F248-11E8-B48F-1D18A9856A87 last_name: Arathoon - contributor_type: project_member first_name: Parvathy id: 455235B8-F248-11E8-B48F-1D18A9856A87 last_name: Surendranadh - contributor_type: project_member first_name: Nicholas H id: 4880FE40-F248-11E8-B48F-1D18A9856A87 last_name: Barton orcid: 0000-0002-8548-5240 - contributor_type: project_member first_name: David id: 419049E2-F248-11E8-B48F-1D18A9856A87 last_name: Field orcid: 0000-0002-4014-8478 - contributor_type: project_member first_name: Melinda id: 2C78037E-F248-11E8-B48F-1D18A9856A87 last_name: Pickup orcid: 0000-0001-6118-0541 - contributor_type: project_member first_name: Carina id: 3B4A7CE2-F248-11E8-B48F-1D18A9856A87 last_name: Baskett date_created: 2020-08-12T12:49:23Z date_published: 2020-08-18T00:00:00Z date_updated: 2024-02-21T12:41:09Z day: '18' ddc: - '576' department: - _id: NiBa doi: 10.15479/AT:ISTA:8254 file: - access_level: open_access checksum: 4f1382ed4384751b6013398c11557bf6 content_type: application/x-zip-compressed creator: dernst date_created: 2020-08-18T08:03:23Z date_updated: 2020-08-18T08:03:23Z file_id: '8280' file_name: Data_Rcode_MathematicaNB.zip file_size: 5778420 relation: main_file success: 1 file_date_updated: 2020-08-18T08:03:23Z has_accepted_license: '1' month: '08' oa: 1 oa_version: Published Version publisher: Institute of Science and Technology Austria related_material: record: - id: '11321' relation: later_version status: public - id: '9192' relation: later_version status: public status: public title: Estimating inbreeding and its effects in a long-term study of snapdragons (Antirrhinum majus) 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: '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: '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: '7383' abstract: - lang: eng text: Organisms cope with change by employing transcriptional regulators. However, when faced with rare environments, the evolution of transcriptional regulators and their promoters may be too slow. We ask whether the intrinsic instability of gene duplication and amplification provides a generic alternative to canonical gene regulation. By real-time monitoring of gene copy number mutations in E. coli, we show that gene duplications and amplifications enable adaptation to fluctuating environments by rapidly generating copy number, and hence expression level, polymorphism. This ‘amplification-mediated gene expression tuning’ occurs on timescales similar to canonical gene regulation and can deal with rapid environmental changes. Mathematical modeling shows that amplifications also tune gene expression in stochastic environments where transcription factor-based schemes are hard to evolve or maintain. The fleeting nature of gene amplifications gives rise to a generic population-level mechanism that relies on genetic heterogeneity to rapidly tune expression of any gene, without leaving any genomic signature. article_processing_charge: No author: - first_name: Rok full_name: Grah, Rok id: 483E70DE-F248-11E8-B48F-1D18A9856A87 last_name: Grah orcid: 0000-0003-2539-3560 citation: ama: 'Grah R. Matlab scripts for the Paper: Gene Amplification as a Form of Population-Level Gene Expression regulation. 2020. doi:10.15479/AT:ISTA:7383' apa: 'Grah, R. (2020). Matlab scripts for the Paper: Gene Amplification as a Form of Population-Level Gene Expression regulation. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:7383' chicago: 'Grah, Rok. “Matlab Scripts for the Paper: Gene Amplification as a Form of Population-Level Gene Expression Regulation.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:7383.' ieee: 'R. Grah, “Matlab scripts for the Paper: Gene Amplification as a Form of Population-Level Gene Expression regulation.” Institute of Science and Technology Austria, 2020.' ista: 'Grah R. 2020. Matlab scripts for the Paper: Gene Amplification as a Form of Population-Level Gene Expression regulation, Institute of Science and Technology Austria, 10.15479/AT:ISTA:7383.' mla: 'Grah, Rok. Matlab Scripts for the Paper: Gene Amplification as a Form of Population-Level Gene Expression Regulation. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:7383.' short: R. Grah, (2020). contributor: - contributor_type: project_leader first_name: Calin C id: 47F8433E-F248-11E8-B48F-1D18A9856A87 last_name: Guet orcid: 0000-0001-6220-2052 date_created: 2020-01-28T10:41:49Z date_published: 2020-01-28T00:00:00Z date_updated: 2024-02-21T12:42:31Z day: '28' department: - _id: CaGu - _id: GaTk doi: 10.15479/AT:ISTA:7383 file: - access_level: open_access checksum: 9d292cf5207b3829225f44c044cdb3fd content_type: application/zip creator: rgrah date_created: 2020-01-28T10:39:40Z date_updated: 2020-07-14T12:47:57Z file_id: '7384' file_name: Scripts.zip file_size: 73363365 relation: main_file - access_level: open_access checksum: 4076ceab32ef588cc233802bab24c1ab content_type: text/plain creator: rgrah date_created: 2020-01-28T10:39:30Z date_updated: 2020-07-14T12:47:57Z file_id: '7385' file_name: READ_ME_MAIN.txt file_size: 962 relation: main_file file_date_updated: 2020-07-14T12:47:57Z has_accepted_license: '1' keyword: - Matlab scripts - analysis of microfluidics - mathematical model month: '01' oa: 1 oa_version: Published Version publisher: Institute of Science and Technology Austria related_material: record: - id: '7652' relation: used_in_publication status: public status: public title: 'Matlab scripts for the Paper: Gene Amplification as a Form of Population-Level Gene Expression regulation' type: research_data user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2020' ... --- _id: '9222' 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. Transport data for: Site‐controlled uniform Ge/Si Hut wires with electrically tunable spin–orbit coupling. 2020. doi:10.15479/AT:ISTA:9222' apa: 'Katsaros, G. (2020). Transport data for: Site‐controlled uniform Ge/Si Hut wires with electrically tunable spin–orbit coupling. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:9222' chicago: 'Katsaros, Georgios. “Transport Data for: Site‐controlled Uniform Ge/Si Hut Wires with Electrically Tunable Spin–Orbit Coupling.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:9222.' ieee: 'G. Katsaros, “Transport data for: Site‐controlled uniform Ge/Si Hut wires with electrically tunable spin–orbit coupling.” Institute of Science and Technology Austria, 2020.' ista: 'Katsaros G. 2020. Transport data for: Site‐controlled uniform Ge/Si Hut wires with electrically tunable spin–orbit coupling, Institute of Science and Technology Austria, 10.15479/AT:ISTA:9222.' mla: 'Katsaros, Georgios. Transport Data for: Site‐controlled Uniform Ge/Si Hut Wires with Electrically Tunable Spin–Orbit Coupling. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:9222.' short: G. Katsaros, (2020). contributor: - contributor_type: research_group first_name: Georgios id: 38DB5788-F248-11E8-B48F-1D18A9856A87 last_name: Katsaros date_created: 2021-03-05T18:00:47Z date_published: 2020-03-16T00:00:00Z date_updated: 2024-02-21T12:42:13Z day: '16' ddc: - '530' department: - _id: GeKa doi: 10.15479/AT:ISTA:9222 file: - access_level: open_access checksum: 41b66e195ed3dbd73077feee77b05652 content_type: application/x-zip-compressed creator: gkatsaro date_created: 2021-03-05T17:50:45Z date_updated: 2021-03-05T17:50:45Z file_id: '9223' file_name: DOI_SiteControlledHWs.zip file_size: 13317557 relation: main_file - access_level: open_access checksum: a1dc5f710ba4b3bb7f248195ba754ab2 content_type: text/plain creator: dernst date_created: 2021-03-10T07:31:50Z date_updated: 2021-03-10T07:31:50Z file_id: '9233' file_name: Readme.txt file_size: 3515 relation: main_file success: 1 file_date_updated: 2021-03-10T07:31:50Z has_accepted_license: '1' month: '03' oa: 1 oa_version: Published Version publisher: Institute of Science and Technology Austria related_material: record: - id: '7541' relation: used_in_publication status: public status: public title: 'Transport data for: Site‐controlled uniform Ge/Si Hut wires with electrically tunable spin–orbit coupling' 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: '8375' abstract: - lang: eng text: 'Supplementary movies showing the following sequences for spatio-temporarily programmed shells: input geometry and actuation time landscape; comparison of morphing processes from a camera recording and a simulation; final actuated shape.' article_processing_charge: No author: - first_name: Ruslan full_name: Guseinov, Ruslan id: 3AB45EE2-F248-11E8-B48F-1D18A9856A87 last_name: Guseinov orcid: 0000-0001-9819-5077 citation: ama: 'Guseinov R. Supplementary data for “Computational design of curved thin shells: from glass façades to programmable matter.” 2020. doi:10.15479/AT:ISTA:8375' apa: 'Guseinov, R. (2020). Supplementary data for “Computational design of curved thin shells: from glass façades to programmable matter.” Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:8375' chicago: 'Guseinov, Ruslan. “Supplementary Data for ‘Computational Design of Curved Thin Shells: From Glass Façades to Programmable Matter.’” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:8375.' ieee: 'R. Guseinov, “Supplementary data for ‘Computational design of curved thin shells: from glass façades to programmable matter.’” Institute of Science and Technology Austria, 2020.' ista: 'Guseinov R. 2020. Supplementary data for ‘Computational design of curved thin shells: from glass façades to programmable matter’, Institute of Science and Technology Austria, 10.15479/AT:ISTA:8375.' mla: 'Guseinov, Ruslan. Supplementary Data for “Computational Design of Curved Thin Shells: From Glass Façades to Programmable Matter.” Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:8375.' short: R. Guseinov, (2020). contributor: - contributor_type: researcher first_name: Ruslan id: 3AB45EE2-F248-11E8-B48F-1D18A9856A87 last_name: Guseinov orcid: 0000-0001-9819-5077 - contributor_type: researcher first_name: Connor last_name: McMahan - contributor_type: researcher first_name: Jesus id: 2DC83906-F248-11E8-B48F-1D18A9856A87 last_name: Perez Rodriguez - contributor_type: researcher first_name: Chiara last_name: Daraio - contributor_type: researcher first_name: Bernd id: 49876194-F248-11E8-B48F-1D18A9856A87 last_name: Bickel orcid: 0000-0001-6511-9385 date_created: 2020-09-11T09:52:54Z date_published: 2020-09-21T00:00:00Z date_updated: 2024-02-21T12:44:29Z day: '21' ddc: - '000' department: - _id: BeBi doi: 10.15479/AT:ISTA:8375 ec_funded: 1 file: - access_level: open_access checksum: 4029ffd65fb82ef2366b2fc2a4908e16 content_type: video/mp4 creator: rguseino date_created: 2020-09-11T09:45:21Z date_updated: 2020-09-11T09:45:21Z file_id: '8376' file_name: supplementary_movie_1.mp4 file_size: 29214988 relation: main_file success: 1 - access_level: open_access checksum: 8ed03b04d80f1a4e622cb22e6100afd8 content_type: video/mp4 creator: rguseino date_created: 2020-09-11T09:45:25Z date_updated: 2020-09-11T09:45:25Z file_id: '8377' file_name: supplementary_movie_2.mp4 file_size: 28449475 relation: main_file success: 1 - access_level: open_access checksum: ad6864afb5e694e5c52a88fba4e02eea content_type: video/mp4 creator: rguseino date_created: 2020-09-11T09:45:28Z date_updated: 2020-09-11T09:45:28Z file_id: '8378' file_name: supplementary_movie_3.mp4 file_size: 26315853 relation: main_file success: 1 - access_level: open_access checksum: b079cef7871fe1afb69af0e2b099f3b1 content_type: video/mp4 creator: rguseino date_created: 2020-09-11T09:45:33Z date_updated: 2020-09-11T09:45:33Z file_id: '8379' file_name: supplementary_movie_4.mp4 file_size: 25198755 relation: main_file success: 1 - access_level: open_access checksum: 9d1d48a8ed5c109a999c51b044ee523d content_type: video/mp4 creator: rguseino date_created: 2020-09-11T09:45:36Z date_updated: 2020-09-11T09:45:36Z file_id: '8380' file_name: supplementary_movie_5.mp4 file_size: 29011354 relation: main_file success: 1 - access_level: open_access checksum: d414d0059e982d752d218756b3c3ce05 content_type: text/plain creator: rguseino date_created: 2020-09-11T09:52:36Z date_updated: 2020-09-11T09:52:36Z file_id: '8381' file_name: readme.txt file_size: 586 relation: main_file success: 1 file_date_updated: 2020-09-11T09:52:36Z has_accepted_license: '1' month: '09' oa: 1 oa_version: Published Version project: - _id: 24F9549A-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '715767' name: 'MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and Modeling' publisher: Institute of Science and Technology Austria related_material: record: - id: '8366' relation: used_in_publication status: public status: public title: 'Supplementary data for "Computational design of curved thin shells: from glass façades to programmable matter"' 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: '7689' abstract: - lang: eng text: "These are the supplementary research data to the publication \"Zero field splitting of heavy-hole states in quantum dots\". All matrix files have the same format. Within each column the bias voltage is changed. Each column corresponds to either a different gate voltage or magnetic field. The voltage values are given in mV, the current values in pA. Find a specific description in the included Readme file.\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. Supplementary data for “Zero field splitting of heavy-hole states in quantum dots.” 2020. doi:10.15479/AT:ISTA:7689 apa: Katsaros, G. (2020). Supplementary data for “Zero field splitting of heavy-hole states in quantum dots.” Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:7689 chicago: Katsaros, Georgios. “Supplementary Data for ‘Zero Field Splitting of Heavy-Hole States in Quantum Dots.’” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:7689. ieee: G. Katsaros, “Supplementary data for ‘Zero field splitting of heavy-hole states in quantum dots.’” Institute of Science and Technology Austria, 2020. ista: Katsaros G. 2020. Supplementary data for ‘Zero field splitting of heavy-hole states in quantum dots’, Institute of Science and Technology Austria, 10.15479/AT:ISTA:7689. mla: Katsaros, Georgios. Supplementary Data for “Zero Field Splitting of Heavy-Hole States in Quantum Dots.” Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:7689. short: G. Katsaros, (2020). contributor: - contributor_type: contact_person first_name: Georgios id: 38DB5788-F248-11E8-B48F-1D18A9856A87 last_name: Katsaros date_created: 2020-05-01T15:14:46Z date_published: 2020-05-01T00:00:00Z date_updated: 2024-02-21T12:44:02Z day: '01' ddc: - '530' department: - _id: GeKa doi: 10.15479/AT:ISTA:7689 ec_funded: 1 file: - access_level: open_access checksum: d23c0cb9e2d19e14e2f902b88b97c05d content_type: application/x-zip-compressed creator: gkatsaro date_created: 2020-05-01T15:13:28Z date_updated: 2020-07-14T12:48:02Z file_id: '7786' file_name: DOI_ZeroFieldSplitting.zip file_size: 5514403 relation: main_file file_date_updated: 2020-07-14T12:48:02Z has_accepted_license: '1' month: '05' oa: 1 oa_version: Published Version project: - _id: 237E5020-32DE-11EA-91FC-C7463DDC885E call_identifier: H2020 grant_number: '862046' name: TOPOLOGICALLY PROTECTED AND SCALABLE QUANTUM BITS - _id: 237B3DA4-32DE-11EA-91FC-C7463DDC885E call_identifier: FWF grant_number: P32235 name: Towards scalable hut wire quantum devices publisher: Institute of Science and Technology Austria related_material: record: - id: '8203' relation: used_in_publication status: public status: public title: Supplementary data for "Zero field splitting of heavy-hole states in quantum dots" 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: '8761' acknowledged_ssus: - _id: ScienComp article_processing_charge: No author: - first_name: Ruslan full_name: Guseinov, Ruslan id: 3AB45EE2-F248-11E8-B48F-1D18A9856A87 last_name: Guseinov orcid: 0000-0001-9819-5077 citation: ama: Guseinov R. Supplementary data for “Computational design of cold bent glass façades.” 2020. doi:10.15479/AT:ISTA:8761 apa: Guseinov, R. (2020). Supplementary data for “Computational design of cold bent glass façades.” Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:8761 chicago: Guseinov, Ruslan. “Supplementary Data for ‘Computational Design of Cold Bent Glass Façades.’” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:8761. ieee: R. Guseinov, “Supplementary data for ‘Computational design of cold bent glass façades.’” Institute of Science and Technology Austria, 2020. ista: Guseinov R. 2020. Supplementary data for ‘Computational design of cold bent glass façades’, Institute of Science and Technology Austria, 10.15479/AT:ISTA:8761. mla: Guseinov, Ruslan. Supplementary Data for “Computational Design of Cold Bent Glass Façades.” Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:8761. short: R. Guseinov, (2020). contributor: - contributor_type: researcher first_name: Konstantinos last_name: Gavriil - contributor_type: researcher first_name: Ruslan id: 3AB45EE2-F248-11E8-B48F-1D18A9856A87 last_name: Guseinov orcid: 0000-0001-9819-5077 - contributor_type: researcher first_name: Jesus id: 2DC83906-F248-11E8-B48F-1D18A9856A87 last_name: Perez Rodriguez - contributor_type: researcher first_name: Davide last_name: Pellis - contributor_type: researcher first_name: Paul M id: 13C09E74-18D9-11E9-8878-32CFE5697425 last_name: Henderson orcid: 0000-0002-5198-7445 - contributor_type: researcher first_name: Florian last_name: Rist - contributor_type: researcher first_name: Helmut last_name: Pottmann - contributor_type: researcher first_name: Bernd id: 49876194-F248-11E8-B48F-1D18A9856A87 last_name: Bickel orcid: 0000-0001-6511-9385 date_created: 2020-11-16T10:47:18Z date_published: 2020-11-23T00:00:00Z date_updated: 2024-02-21T12:43:22Z day: '23' ddc: - '000' department: - _id: BeBi doi: 10.15479/AT:ISTA:8761 ec_funded: 1 file: - access_level: open_access checksum: f5ae57b97017b9f61081032703361233 content_type: application/x-gzip creator: rguseino date_created: 2020-11-16T10:31:29Z date_updated: 2020-11-16T10:31:29Z file_id: '8762' file_name: mdn_model.tar.gz file_size: 15378270 relation: main_file success: 1 - access_level: open_access checksum: b0d25e04060ee78c585ee2f23542c744 content_type: application/x-gzip creator: rguseino date_created: 2020-11-16T10:43:23Z date_updated: 2020-11-16T10:43:23Z file_id: '8763' file_name: optimal_panels_data.tar.gz file_size: 615387734 relation: main_file success: 1 - access_level: open_access checksum: 69c1dde3434ada86d125e0c2588caf1e content_type: text/plain creator: rguseino date_created: 2020-11-18T10:04:59Z date_updated: 2020-11-18T10:04:59Z file_id: '8770' file_name: readme.txt file_size: 1228 relation: main_file success: 1 file_date_updated: 2020-11-18T10:04:59Z has_accepted_license: '1' month: '11' oa: 1 oa_version: Published Version project: - _id: 24F9549A-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '715767' name: 'MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and Modeling' publisher: Institute of Science and Technology Austria related_material: link: - relation: software url: https://github.com/russelmann/cold-glass-acm record: - id: '8562' relation: used_in_publication status: public status: public title: Supplementary data for "Computational design of cold bent glass façades" 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: '8563' abstract: - lang: eng text: "Supplementary data provided for the provided for the publication:\r\nIgor Gridchyn , Philipp Schoenenberger , Joseph O'Neill , Jozsef Csicsvari (2020) Optogenetic inhibition-mediated activity-dependent modification of CA1 pyramidal-interneuron connections during behavior. Elife." article_processing_charge: No author: - first_name: Jozsef L full_name: Csicsvari, Jozsef L id: 3FA14672-F248-11E8-B48F-1D18A9856A87 last_name: Csicsvari orcid: 0000-0002-5193-4036 - first_name: Igor full_name: Gridchyn, Igor id: 4B60654C-F248-11E8-B48F-1D18A9856A87 last_name: Gridchyn orcid: 0000-0002-1807-1929 - first_name: Philipp full_name: Schönenberger, Philipp id: 3B9D816C-F248-11E8-B48F-1D18A9856A87 last_name: Schönenberger citation: ama: Csicsvari JL, Gridchyn I, Schönenberger P. Optogenetic alteration of hippocampal network activity. 2020. doi:10.15479/AT:ISTA:8563 apa: Csicsvari, J. L., Gridchyn, I., & Schönenberger, P. (2020). Optogenetic alteration of hippocampal network activity. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:8563 chicago: Csicsvari, Jozsef L, Igor Gridchyn, and Philipp Schönenberger. “Optogenetic Alteration of Hippocampal Network Activity.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:8563. ieee: J. L. Csicsvari, I. Gridchyn, and P. Schönenberger, “Optogenetic alteration of hippocampal network activity.” Institute of Science and Technology Austria, 2020. ista: Csicsvari JL, Gridchyn I, Schönenberger P. 2020. Optogenetic alteration of hippocampal network activity, Institute of Science and Technology Austria, 10.15479/AT:ISTA:8563. mla: Csicsvari, Jozsef L., et al. Optogenetic Alteration of Hippocampal Network Activity. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:8563. short: J.L. Csicsvari, I. Gridchyn, P. Schönenberger, (2020). contributor: - contributor_type: project_leader first_name: Jozsef L id: 3FA14672-F248-11E8-B48F-1D18A9856A87 last_name: Csicsvari orcid: 0000-0002-5193-4036 date_created: 2020-09-23T14:39:54Z date_published: 2020-10-19T00:00:00Z date_updated: 2024-02-21T12:43:41Z day: '19' ddc: - '570' department: - _id: JoCs doi: 10.15479/AT:ISTA:8563 file: - access_level: open_access checksum: a16098a6d172f9c42ab5af5f6991668c content_type: application/x-compressed creator: jozsef date_created: 2020-09-23T14:36:17Z date_updated: 2020-09-23T14:36:17Z file_id: '8564' file_name: upload.tgz file_size: 145243906 relation: main_file success: 1 - access_level: open_access checksum: 0bfc54b7e14c0694cd081617318ba606 content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document creator: jozsef date_created: 2020-10-19T10:12:29Z date_updated: 2020-10-19T10:12:29Z file_id: '8675' file_name: redme.docx file_size: 11648 relation: main_file success: 1 file_date_updated: 2020-10-19T10:12:29Z has_accepted_license: '1' month: '10' oa: 1 oa_version: Published Version publisher: Institute of Science and Technology Austria related_material: record: - id: '8740' relation: used_in_publication status: public status: public title: Optogenetic alteration of hippocampal network activity 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: research_data user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2020' ... --- _id: '14592' abstract: - lang: eng text: Cryo-electron microscopy (cryo-EM) of cellular specimens provides insights into biological processes and structures within a native context. However, a major challenge still lies in the efficient and reproducible preparation of adherent cells for subsequent cryo-EM analysis. This is due to the sensitivity of many cellular specimens to the varying seeding and culturing conditions required for EM experiments, the often limited amount of cellular material and also the fragility of EM grids and their substrate. Here, we present low-cost and reusable 3D printed grid holders, designed to improve specimen preparation when culturing challenging cellular samples directly on grids. The described grid holders increase cell culture reproducibility and throughput, and reduce the resources required for cell culturing. We show that grid holders can be integrated into various cryo-EM workflows, including micro-patterning approaches to control cell seeding on grids, and for generating samples for cryo-focused ion beam milling and cryo-electron tomography experiments. Their adaptable design allows for the generation of specialized grid holders customized to a large variety of applications. article_processing_charge: No author: - 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: Schur FK. STL-files for 3D-printed grid holders described in  Fäßler F, Zens B, et al.; 3D printed cell culture grid holders for improved cellular specimen preparation in cryo-electron microscopy. 2020. doi:10.15479/AT:ISTA:14592 apa: Schur, F. K. (2020). STL-files for 3D-printed grid holders described in  Fäßler F, Zens B, et al.; 3D printed cell culture grid holders for improved cellular specimen preparation in cryo-electron microscopy. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:14592 chicago: Schur, Florian KM. “STL-Files for 3D-Printed Grid Holders Described in  Fäßler F, Zens B, et Al.; 3D Printed Cell Culture Grid Holders for Improved Cellular Specimen Preparation in Cryo-Electron Microscopy.” Institute of Science and Technology Austria, 2020. https://doi.org/10.15479/AT:ISTA:14592. ieee: F. K. Schur, “STL-files for 3D-printed grid holders described in  Fäßler F, Zens B, et al.; 3D printed cell culture grid holders for improved cellular specimen preparation in cryo-electron microscopy.” Institute of Science and Technology Austria, 2020. ista: Schur FK. 2020. STL-files for 3D-printed grid holders described in  Fäßler F, Zens B, et al.; 3D printed cell culture grid holders for improved cellular specimen preparation in cryo-electron microscopy, Institute of Science and Technology Austria, 10.15479/AT:ISTA:14592. mla: Schur, Florian KM. STL-Files for 3D-Printed Grid Holders Described in  Fäßler F, Zens B, et Al.; 3D Printed Cell Culture Grid Holders for Improved Cellular Specimen Preparation in Cryo-Electron Microscopy. Institute of Science and Technology Austria, 2020, doi:10.15479/AT:ISTA:14592. short: F.K. Schur, (2020). contributor: - contributor_type: researcher first_name: Florian id: 404F5528-F248-11E8-B48F-1D18A9856A87 last_name: Fäßler orcid: 0000-0001-7149-769X - contributor_type: researcher first_name: Bettina id: 45FD126C-F248-11E8-B48F-1D18A9856A87 last_name: Zens - contributor_type: researcher first_name: Robert id: 4E01D6B4-F248-11E8-B48F-1D18A9856A87 last_name: Hauschild - contributor_type: researcher first_name: Florian KM id: 48AD8942-F248-11E8-B48F-1D18A9856A87 last_name: Schur orcid: 0000-0003-4790-8078 date_created: 2023-11-22T15:00:57Z date_published: 2020-12-01T00:00:00Z date_updated: 2024-02-21T12:44:48Z day: '01' ddc: - '570' department: - _id: FlSc doi: 10.15479/AT:ISTA:14592 file: - access_level: open_access checksum: 0108616e2a59e51879ea51299a29b091 content_type: application/zip creator: fschur date_created: 2023-11-22T14:58:44Z date_updated: 2023-11-22T14:58:44Z file_id: '14593' file_name: 3Dprint-files_download_v2.zip file_size: 49297 relation: main_file success: 1 - access_level: open_access checksum: 4c66ddedee4d01c1c4a7978208350cfc content_type: text/plain creator: cchlebak date_created: 2023-12-01T10:39:59Z date_updated: 2023-12-01T10:39:59Z file_id: '14637' file_name: readme.txt file_size: 641 relation: main_file success: 1 file_date_updated: 2023-12-01T10:39:59Z has_accepted_license: '1' 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 publisher: Institute of Science and Technology Austria related_material: record: - id: '8586' relation: research_data status: public status: public title: STL-files for 3D-printed grid holders described in Fäßler F, Zens B, et al.; 3D printed cell culture grid holders for improved cellular specimen preparation in cryo-electron microscopy tmp: image: /images/cc_by_nc_sa.png legal_code_url: https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode name: Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0) short: CC BY-NC-SA (4.0) type: research_data user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2020' ...