--- _id: '9946' abstract: - lang: eng text: We argue that the time is ripe to investigate differential monitoring, in which the specification of a program's behavior is implicitly given by a second program implementing the same informal specification. Similar ideas have been proposed before, and are currently implemented in restricted form for testing and specialized run-time analyses, aspects of which we combine. We discuss the challenges of implementing differential monitoring as a general-purpose, black-box run-time monitoring framework, and present promising results of a preliminary implementation, showing low monitoring overheads for diverse programs. acknowledgement: The authors would like to thank Borzoo Bonakdarpour, Derek Dreyer, Adrian Francalanza, Owolabi Legunsen, Matthew Milano, Manuel Rigger, Cesar Sanchez, and the members of the IST Verification Seminar for their helpful comments and insights on various stages of this work, as well as the reviewers of RV’21 for their helpful suggestions on the actual paper. alternative_title: - IST Austria Technical Report article_processing_charge: No author: - first_name: Fabian full_name: Mühlböck, Fabian id: 6395C5F6-89DF-11E9-9C97-6BDFE5697425 last_name: Mühlböck orcid: 0000-0003-1548-0177 - 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: Mühlböck F, Henzinger TA. Differential Monitoring. IST Austria; 2021. doi:10.15479/AT:ISTA:9946 apa: Mühlböck, F., & Henzinger, T. A. (2021). Differential monitoring. IST Austria. https://doi.org/10.15479/AT:ISTA:9946 chicago: Mühlböck, Fabian, and Thomas A Henzinger. Differential Monitoring. IST Austria, 2021. https://doi.org/10.15479/AT:ISTA:9946. ieee: F. Mühlböck and T. A. Henzinger, Differential monitoring. IST Austria, 2021. ista: Mühlböck F, Henzinger TA. 2021. Differential monitoring, IST Austria, 17p. mla: Mühlböck, Fabian, and Thomas A. Henzinger. Differential Monitoring. IST Austria, 2021, doi:10.15479/AT:ISTA:9946. short: F. Mühlböck, T.A. Henzinger, Differential Monitoring, IST Austria, 2021. date_created: 2021-08-20T20:00:37Z date_published: 2021-09-01T00:00:00Z date_updated: 2023-08-14T07:20:29Z day: '01' ddc: - '005' department: - _id: ToHe doi: 10.15479/AT:ISTA:9946 file: - access_level: open_access checksum: 0f9aafd59444cb6bdca6925d163ab946 content_type: application/pdf creator: fmuehlbo date_created: 2021-08-20T19:59:44Z date_updated: 2021-09-03T12:34:28Z file_id: '9948' file_name: differentialmonitoring-techreport.pdf file_size: '320453' relation: main_file file_date_updated: 2021-09-03T12:34:28Z has_accepted_license: '1' keyword: - run-time verification - software engineering - implicit specification language: - iso: eng month: '09' oa: 1 oa_version: Published Version page: '17' project: - _id: 25F42A32-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: Z211 name: The Wittgenstein Prize publication_identifier: issn: - 2664-1690 publication_status: published publisher: IST Austria related_material: record: - id: '9281' relation: other status: public - id: '10108' relation: shorter_version status: public status: public title: Differential monitoring type: technical_report user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 year: '2021' ... --- _id: '10073' abstract: - lang: eng text: Thermoelectric materials enable the direct conversion between heat and electricity. SnTe is a promising candidate due to its high charge transport performance. Here, we prepared SnTe nanocomposites by employing an aqueous method to synthetize SnTe nanoparticles (NP), followed by a unique surface treatment prior NP consolidation. This synthetic approach allowed optimizing the charge and phonon transport synergistically. The novelty of this strategy was the use of a soluble PbS molecular complex prepared using a thiol-amine solvent mixture that upon blending is adsorbed on the SnTe NP surface. Upon consolidation with spark plasma sintering, SnTe-PbS nanocomposite is formed. The presence of PbS complexes significantly compensates for the Sn vacancy and increases the average grain size of the nanocomposite, thus improving the carrier mobility. Moreover, lattice thermal conductivity is also reduced by the Pb and S-induced mass and strain fluctuation. As a result, an enhanced ZT of ca. 0.8 is reached at 873 K. Our finding provides a novel strategy to conduct rational surface treatment on NP-based thermoelectrics. acknowledged_ssus: - _id: EM-Fac acknowledgement: "The authors thank the EMF facility in IST Austria for providing SEM and EDX measurements.\r\n" article_number: '5416' article_processing_charge: Yes article_type: original author: - first_name: Cheng full_name: Chang, Cheng id: 9E331C2E-9F27-11E9-AE48-5033E6697425 last_name: Chang orcid: 0000-0002-9515-4277 - first_name: Maria full_name: Ibáñez, Maria id: 43C61214-F248-11E8-B48F-1D18A9856A87 last_name: Ibáñez orcid: 0000-0001-5013-2843 citation: ama: Chang C, Ibáñez M. Enhanced thermoelectric performance by surface engineering in SnTe-PbS nanocomposites. Materials. 2021;14(18). doi:10.3390/ma14185416 apa: Chang, C., & Ibáñez, M. (2021). Enhanced thermoelectric performance by surface engineering in SnTe-PbS nanocomposites. Materials. MDPI. https://doi.org/10.3390/ma14185416 chicago: Chang, Cheng, and Maria Ibáñez. “Enhanced Thermoelectric Performance by Surface Engineering in SnTe-PbS Nanocomposites.” Materials. MDPI, 2021. https://doi.org/10.3390/ma14185416. ieee: C. Chang and M. Ibáñez, “Enhanced thermoelectric performance by surface engineering in SnTe-PbS nanocomposites,” Materials, vol. 14, no. 18. MDPI, 2021. ista: Chang C, Ibáñez M. 2021. Enhanced thermoelectric performance by surface engineering in SnTe-PbS nanocomposites. Materials. 14(18), 5416. mla: Chang, Cheng, and Maria Ibáñez. “Enhanced Thermoelectric Performance by Surface Engineering in SnTe-PbS Nanocomposites.” Materials, vol. 14, no. 18, 5416, MDPI, 2021, doi:10.3390/ma14185416. short: C. Chang, M. Ibáñez, Materials 14 (2021). date_created: 2021-10-03T22:01:23Z date_published: 2021-09-19T00:00:00Z date_updated: 2023-08-14T08:00:01Z day: '19' ddc: - '540' department: - _id: MaIb doi: 10.3390/ma14185416 external_id: isi: - '000700689400001' pmid: - '34576640' file: - access_level: open_access checksum: 4929dfc673a3ae77c010b6174279cc1d content_type: application/pdf creator: cchlebak date_created: 2021-10-14T11:56:39Z date_updated: 2021-10-14T11:56:39Z file_id: '10140' file_name: 2021_Materials_Chang.pdf file_size: 4404141 relation: main_file success: 1 file_date_updated: 2021-10-14T11:56:39Z has_accepted_license: '1' intvolume: ' 14' isi: 1 issue: '18' language: - iso: eng license: https://creativecommons.org/licenses/by/4.0/ month: '09' oa: 1 oa_version: Published Version pmid: 1 project: - _id: 9B8804FC-BA93-11EA-9121-9846C619BF3A grant_number: M02889 name: Bottom-up Engineering for Thermoelectric Applications publication: Materials publication_identifier: eissn: - 1996-1944 publication_status: published publisher: MDPI quality_controlled: '1' scopus_import: '1' status: public title: Enhanced thermoelectric performance by surface engineering in SnTe-PbS nanocomposites tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 14 year: '2021' ... --- _id: '10167' abstract: - lang: eng text: Schistosomes, the human parasites responsible for snail fever, are female-heterogametic. Different parts of their ZW sex chromosomes have stopped recombining in distinct lineages, creating “evolutionary strata” of various ages. Although the Z-chromosome is well characterized at the genomic and molecular level, the W-chromosome has remained largely unstudied from an evolutionary perspective, as only a few W-linked genes have been detected outside of the model species Schistosoma mansoni. Here, we characterize the gene content and evolution of the W-chromosomes of S. mansoni and of the divergent species S. japonicum. We use a combined RNA/DNA k-mer based pipeline to assemble around 100 candidate W-specific transcripts in each of the species. About half of them map to known protein coding genes, the majority homologous to S. mansoni Z-linked genes. We perform an extended analysis of the evolutionary strata present in the two species (including characterizing a previously undetected young stratum in S. japonicum) to infer patterns of sequence and expression evolution of W-linked genes at different time points after recombination was lost. W-linked genes show evidence of degeneration, including high rates of protein evolution and reduced expression. Most are found in young lineage-specific strata, with only a few high expression ancestral W-genes remaining, consistent with the progressive erosion of nonrecombining regions. Among these, the splicing factor u2af2 stands out as a promising candidate for primary sex determination, opening new avenues for understanding the molecular basis of the reproductive biology of this group. acknowledged_ssus: - _id: ScienComp acknowledgement: The authors thank IT support at IST Austria for providing an optimal environment for bioinformatic analyses. This work was supported by an Austrian Science Foundation FWF grant (Project P28842) to B.V. article_processing_charge: No article_type: original author: - first_name: Marwan N full_name: Elkrewi, Marwan N id: 0B46FACA-A8E1-11E9-9BD3-79D1E5697425 last_name: Elkrewi orcid: 0000-0002-5328-7231 - first_name: Mikhail A. full_name: Moldovan, Mikhail A. id: c8bb7f32-3315-11ec-b58b-e5950e6c14a0 last_name: Moldovan orcid: 0000-0002-8876-6494 - first_name: Marion A L full_name: Picard, Marion A L id: 2C921A7A-F248-11E8-B48F-1D18A9856A87 last_name: Picard orcid: 0000-0002-8101-2518 - first_name: Beatriz full_name: Vicoso, Beatriz id: 49E1C5C6-F248-11E8-B48F-1D18A9856A87 last_name: Vicoso orcid: 0000-0002-4579-8306 citation: ama: Elkrewi MN, Moldovan MA, Picard MAL, Vicoso B. Schistosome W-Linked genes inform temporal dynamics of sex chromosome evolution and suggest candidate for sex determination. Molecular Biology and Evolution. 2021. doi:10.1093/molbev/msab178 apa: Elkrewi, M. N., Moldovan, M. A., Picard, M. A. L., & Vicoso, B. (2021). Schistosome W-Linked genes inform temporal dynamics of sex chromosome evolution and suggest candidate for sex determination. Molecular Biology and Evolution. Oxford University Press . https://doi.org/10.1093/molbev/msab178 chicago: Elkrewi, Marwan N, Mikhail A. Moldovan, Marion A L Picard, and Beatriz Vicoso. “Schistosome W-Linked Genes Inform Temporal Dynamics of Sex Chromosome Evolution and Suggest Candidate for Sex Determination.” Molecular Biology and Evolution. Oxford University Press , 2021. https://doi.org/10.1093/molbev/msab178. ieee: M. N. Elkrewi, M. A. Moldovan, M. A. L. Picard, and B. Vicoso, “Schistosome W-Linked genes inform temporal dynamics of sex chromosome evolution and suggest candidate for sex determination,” Molecular Biology and Evolution. Oxford University Press , 2021. ista: Elkrewi MN, Moldovan MA, Picard MAL, Vicoso B. 2021. Schistosome W-Linked genes inform temporal dynamics of sex chromosome evolution and suggest candidate for sex determination. Molecular Biology and Evolution. mla: Elkrewi, Marwan N., et al. “Schistosome W-Linked Genes Inform Temporal Dynamics of Sex Chromosome Evolution and Suggest Candidate for Sex Determination.” Molecular Biology and Evolution, Oxford University Press , 2021, doi:10.1093/molbev/msab178. short: M.N. Elkrewi, M.A. Moldovan, M.A.L. Picard, B. Vicoso, Molecular Biology and Evolution (2021). date_created: 2021-10-21T07:49:12Z date_published: 2021-06-19T00:00:00Z date_updated: 2023-08-14T08:03:06Z day: '19' ddc: - '610' department: - _id: BeVi doi: 10.1093/molbev/msab178 external_id: isi: - '000741368600009' pmid: - '34146097' file: - access_level: open_access checksum: 1b096702fb356d9c0eb88e1b3fcff5f8 content_type: application/pdf creator: dernst date_created: 2022-05-06T09:47:18Z date_updated: 2022-05-06T09:47:18Z file_id: '11352' file_name: 2021_MolecularBiolEvolution_Elkrewi.pdf file_size: 1008594 relation: main_file success: 1 file_date_updated: 2022-05-06T09:47:18Z has_accepted_license: '1' isi: 1 keyword: - sex chromosomes - evolutionary strata - W-linked gene - sex determining gene - schistosome parasites language: - iso: eng month: '06' oa: 1 oa_version: Published Version pmid: 1 project: - _id: 250ED89C-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P28842-B22 name: Sex chromosome evolution under male- and female- heterogamety publication: Molecular Biology and Evolution publication_identifier: eissn: - 1537-1719 issn: - 0737-4038 publication_status: published publisher: 'Oxford University Press ' quality_controlled: '1' scopus_import: '1' status: public title: Schistosome W-Linked genes inform temporal dynamics of sex chromosome evolution and suggest candidate for sex determination tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 year: '2021' ... --- _id: '10163' abstract: - lang: eng text: The C-terminal domain (CTD) of the largest subunit of RNA polymerase II (Pol II) is a regulatory hub for transcription and RNA processing. Here, we identify PHD-finger protein 3 (PHF3) as a regulator of transcription and mRNA stability that docks onto Pol II CTD through its SPOC domain. We characterize SPOC as a CTD reader domain that preferentially binds two phosphorylated Serine-2 marks in adjacent CTD repeats. PHF3 drives liquid-liquid phase separation of phosphorylated Pol II, colocalizes with Pol II clusters and tracks with Pol II across the length of genes. PHF3 knock-out or SPOC deletion in human cells results in increased Pol II stalling, reduced elongation rate and an increase in mRNA stability, with marked derepression of neuronal genes. Key neuronal genes are aberrantly expressed in Phf3 knock-out mouse embryonic stem cells, resulting in impaired neuronal differentiation. Our data suggest that PHF3 acts as a prominent effector of neuronal gene regulation by bridging transcription with mRNA decay. acknowledgement: 'D.S. thanks Claudine Kraft, Renée Schroeder, Verena Jantsch, Franz Klein and Peter Schlögelhofer for support. We thank Anita Testa Salmazo for help with purifying Pol II; Matthias Geyer and Robert Düster for sharing DYRK1A kinase; Felix Hartmann and Clemens Plaschka for help with mass photometry; Goran Kokic for design of the arrest assay sequences; Petra van der Lelij for help with generating mESC KO; Maximilian Freilinger for help with the purification of mEGFP-CTD; Stefan Ameres, Nina Fasching and Brian Reichholf for advice on SLAM-seq and for sharing reagents; Laura Gallego Valle for advice regarding LLPS assays; Krzysztof Chylinski for advice regarding CRISPR/Cas9 methodology; VBCF Protein Technologies facility for purifying PHF3 and providing gRNAs and Cas9; VBCF NGS facility for sequencing; Monoclonal antibody facility at the Helmholtz center for Pol II antibodies; Friedrich Propst and Elzbieta Kowalska for advice and for sharing materials; Egon Ogris for sharing materials; Martin Eilers for recommending a ChIP-grade TFIIS antibody; Susanne Opravil, Otto Hudecz, Markus Hartl and Natascha Hartl for mass spectrometry analysis; staff of the X-ray beamlines at the ESRF in Grenoble for their excellent support; Christa Bücker, Anton Meinhart, Clemens Plaschka and members of the Slade lab for critical comments on the manuscript; Life Science Editors for editing assistance. M.B. and D.S. acknowledge support by the FWF-funded DK ‘Chromosome Dynamics’. T.K. is a recipient of the DOC fellowship from the Austrian Academy of Sciences. U.S. is supported by the L’Oreal for Women in Science Austria Fellowship and the Austrian Science Fund (FWF T 795-B30). M.L is supported by the Vienna Science and Technology Fund (WWTF, VRG14-006). R.S. is supported by the Czech Science Foundation (15-17670 S and 21-24460 S), Ministry of Education, Youths and Sports of the Czech Republic (CEITEC 2020 project (LQ1601)), and the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (Grant agreement no. 649030); this publication reflects only the author’s view and the Research Executive Agency is not responsible for any use that may be made of the information it contains. M.S. is supported by the Czech Science Foundation (GJ20-21581Y). K.D.C. research is supported by the Austrian Science Fund (FWF) Projects I525 and I1593, P22276, P19060, and W1221, Federal Ministry of Economy, Family and Youth through the initiative ‘Laura Bassi Centres of Expertise’, funding from the Centre of Optimized Structural Studies No. 253275, the Wellcome Trust Collaborative Award (201543/Z/16), COST action BM1405 Non-globular proteins - from sequence to structure, function and application in molecular physiopathology (NGP-NET), the Vienna Science and Technology Fund (WWTF LS17-008), and by the University of Vienna. This project was funded by the MFPL start-up grant, the Vienna Science and Technology Fund (WWTF LS14-001), and the Austrian Science Fund (P31546-B28 and W1258 “DK: Integrative Structural Biology”) to D.S.' article_number: '6078' article_processing_charge: No article_type: original author: - first_name: Lisa-Marie full_name: Appel, Lisa-Marie last_name: Appel - first_name: Vedran full_name: Franke, Vedran last_name: Franke - first_name: Melania full_name: Bruno, Melania last_name: Bruno - first_name: Irina full_name: Grishkovskaya, Irina last_name: Grishkovskaya - first_name: Aiste full_name: Kasiliauskaite, Aiste last_name: Kasiliauskaite - first_name: Tanja full_name: Kaufmann, Tanja last_name: Kaufmann - first_name: Ursula E. full_name: Schoeberl, Ursula E. last_name: Schoeberl - first_name: Martin G. full_name: Puchinger, Martin G. last_name: Puchinger - first_name: Sebastian full_name: Kostrhon, Sebastian last_name: Kostrhon - first_name: Carmen full_name: Ebenwaldner, Carmen last_name: Ebenwaldner - first_name: Marek full_name: Sebesta, Marek last_name: Sebesta - first_name: Etienne full_name: Beltzung, Etienne last_name: Beltzung - first_name: Karl full_name: Mechtler, Karl last_name: Mechtler - first_name: Gen full_name: Lin, Gen last_name: Lin - first_name: Anna full_name: Vlasova, Anna last_name: Vlasova - first_name: Martin full_name: Leeb, Martin last_name: Leeb - first_name: Rushad full_name: Pavri, Rushad last_name: Pavri - first_name: Alexander full_name: Stark, Alexander last_name: Stark - first_name: Altuna full_name: Akalin, Altuna last_name: Akalin - first_name: Richard full_name: Stefl, Richard last_name: Stefl - first_name: Carrie A full_name: Bernecky, Carrie A id: 2CB9DFE2-F248-11E8-B48F-1D18A9856A87 last_name: Bernecky orcid: 0000-0003-0893-7036 - first_name: Kristina full_name: Djinovic-Carugo, Kristina last_name: Djinovic-Carugo - first_name: Dea full_name: Slade, Dea last_name: Slade citation: ama: Appel L-M, Franke V, Bruno M, et al. PHF3 regulates neuronal gene expression through the Pol II CTD reader domain SPOC. Nature Communications. 2021;12(1). doi:10.1038/s41467-021-26360-2 apa: Appel, L.-M., Franke, V., Bruno, M., Grishkovskaya, I., Kasiliauskaite, A., Kaufmann, T., … Slade, D. (2021). PHF3 regulates neuronal gene expression through the Pol II CTD reader domain SPOC. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-021-26360-2 chicago: Appel, Lisa-Marie, Vedran Franke, Melania Bruno, Irina Grishkovskaya, Aiste Kasiliauskaite, Tanja Kaufmann, Ursula E. Schoeberl, et al. “PHF3 Regulates Neuronal Gene Expression through the Pol II CTD Reader Domain SPOC.” Nature Communications. Springer Nature, 2021. https://doi.org/10.1038/s41467-021-26360-2. ieee: L.-M. Appel et al., “PHF3 regulates neuronal gene expression through the Pol II CTD reader domain SPOC,” Nature Communications, vol. 12, no. 1. Springer Nature, 2021. ista: Appel L-M, Franke V, Bruno M, Grishkovskaya I, Kasiliauskaite A, Kaufmann T, Schoeberl UE, Puchinger MG, Kostrhon S, Ebenwaldner C, Sebesta M, Beltzung E, Mechtler K, Lin G, Vlasova A, Leeb M, Pavri R, Stark A, Akalin A, Stefl R, Bernecky C, Djinovic-Carugo K, Slade D. 2021. PHF3 regulates neuronal gene expression through the Pol II CTD reader domain SPOC. Nature Communications. 12(1), 6078. mla: Appel, Lisa-Marie, et al. “PHF3 Regulates Neuronal Gene Expression through the Pol II CTD Reader Domain SPOC.” Nature Communications, vol. 12, no. 1, 6078, Springer Nature, 2021, doi:10.1038/s41467-021-26360-2. short: L.-M. Appel, V. Franke, M. Bruno, I. Grishkovskaya, A. Kasiliauskaite, T. Kaufmann, U.E. Schoeberl, M.G. Puchinger, S. Kostrhon, C. Ebenwaldner, M. Sebesta, E. Beltzung, K. Mechtler, G. Lin, A. Vlasova, M. Leeb, R. Pavri, A. Stark, A. Akalin, R. Stefl, C. Bernecky, K. Djinovic-Carugo, D. Slade, Nature Communications 12 (2021). date_created: 2021-10-20T14:40:32Z date_published: 2021-10-19T00:00:00Z date_updated: 2023-08-14T08:02:31Z day: '19' ddc: - '610' department: - _id: CaBe doi: 10.1038/s41467-021-26360-2 external_id: isi: - '000709050300001' file: - access_level: open_access checksum: d99fcd51aebde19c21314e3de0148007 content_type: application/pdf creator: cchlebak date_created: 2021-10-21T13:51:49Z date_updated: 2021-10-21T13:51:49Z file_id: '10169' file_name: 2021_NatComm_Appel.pdf file_size: 5111706 relation: main_file success: 1 file_date_updated: 2021-10-21T13:51:49Z has_accepted_license: '1' intvolume: ' 12' isi: 1 issue: '1' keyword: - general physics and astronomy - general biochemistry - genetics and molecular biology - general chemistry language: - iso: eng month: '10' oa: 1 oa_version: Published Version publication: Nature Communications publication_identifier: eissn: - 2041-1723 publication_status: published publisher: Springer Nature quality_controlled: '1' related_material: link: - description: 'Preprint ' relation: earlier_version url: https://www.biorxiv.org/content/10.1101/2020.02.11.943159 status: public title: PHF3 regulates neuronal gene expression through the Pol II CTD reader domain SPOC tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 12 year: '2021' ... --- _id: '9547' abstract: - lang: eng text: With the wider availability of full-color 3D printers, color-accurate 3D-print preparation has received increased attention. A key challenge lies in the inherent translucency of commonly used print materials that blurs out details of the color texture. Previous work tries to compensate for these scattering effects through strategic assignment of colored primary materials to printer voxels. To date, the highest-quality approach uses iterative optimization that relies on computationally expensive Monte Carlo light transport simulation to predict the surface appearance from subsurface scattering within a given print material distribution; that optimization, however, takes in the order of days on a single machine. In our work, we dramatically speed up the process by replacing the light transport simulation with a data-driven approach. Leveraging a deep neural network to predict the scattering within a highly heterogeneous medium, our method performs around two orders of magnitude faster than Monte Carlo rendering while yielding optimization results of similar quality level. The network is based on an established method from atmospheric cloud rendering, adapted to our domain and extended by a physically motivated weight sharing scheme that substantially reduces the network size. We analyze its performance in an end-to-end print preparation pipeline and compare quality and runtime to alternative approaches, and demonstrate its generalization to unseen geometry and material values. This for the first time enables full heterogenous material optimization for 3D-print preparation within time frames in the order of the actual printing time. acknowledgement: We thank Sebastian Cucerca for processing and capturing the phys-cal printouts. This work was supported by the Charles University grant SVV-260588 and Czech Science Foundation grant 19-07626S. This project has received funding from the European Union’s Horizon 2020 research and innovation programme, under the Marie Skłodowska Curie grant agreements No 642841 (DISTRO) and No765911 (RealVision), and under the European Research Council grant agreement No 715767 (MATERIALIZABLE). article_processing_charge: No article_type: original author: - first_name: Tobias full_name: Rittig, Tobias last_name: Rittig - first_name: Denis full_name: Sumin, Denis last_name: Sumin - first_name: Vahid full_name: Babaei, Vahid last_name: Babaei - first_name: Piotr full_name: Didyk, Piotr last_name: Didyk - first_name: Alexey full_name: Voloboy, Alexey last_name: Voloboy - first_name: Alexander full_name: Wilkie, Alexander last_name: Wilkie - first_name: Bernd full_name: Bickel, Bernd id: 49876194-F248-11E8-B48F-1D18A9856A87 last_name: Bickel orcid: 0000-0001-6511-9385 - first_name: Karol full_name: Myszkowski, Karol last_name: Myszkowski - first_name: Tim full_name: Weyrich, Tim last_name: Weyrich - first_name: Jaroslav full_name: Křivánek, Jaroslav last_name: Křivánek citation: ama: Rittig T, Sumin D, Babaei V, et al. Neural acceleration of scattering-aware color 3D printing. Computer Graphics Forum. 2021;40(2):205-219. doi:10.1111/cgf.142626 apa: Rittig, T., Sumin, D., Babaei, V., Didyk, P., Voloboy, A., Wilkie, A., … Křivánek, J. (2021). Neural acceleration of scattering-aware color 3D printing. Computer Graphics Forum. Wiley. https://doi.org/10.1111/cgf.142626 chicago: Rittig, Tobias, Denis Sumin, Vahid Babaei, Piotr Didyk, Alexey Voloboy, Alexander Wilkie, Bernd Bickel, Karol Myszkowski, Tim Weyrich, and Jaroslav Křivánek. “Neural Acceleration of Scattering-Aware Color 3D Printing.” Computer Graphics Forum. Wiley, 2021. https://doi.org/10.1111/cgf.142626. ieee: T. Rittig et al., “Neural acceleration of scattering-aware color 3D printing,” Computer Graphics Forum, vol. 40, no. 2. Wiley, pp. 205–219, 2021. ista: Rittig T, Sumin D, Babaei V, Didyk P, Voloboy A, Wilkie A, Bickel B, Myszkowski K, Weyrich T, Křivánek J. 2021. Neural acceleration of scattering-aware color 3D printing. Computer Graphics Forum. 40(2), 205–219. mla: Rittig, Tobias, et al. “Neural Acceleration of Scattering-Aware Color 3D Printing.” Computer Graphics Forum, vol. 40, no. 2, Wiley, 2021, pp. 205–19, doi:10.1111/cgf.142626. short: T. Rittig, D. Sumin, V. Babaei, P. Didyk, A. Voloboy, A. Wilkie, B. Bickel, K. Myszkowski, T. Weyrich, J. Křivánek, Computer Graphics Forum 40 (2021) 205–219. date_created: 2021-06-13T22:01:32Z date_published: 2021-05-01T00:00:00Z date_updated: 2023-08-14T08:01:50Z day: '01' ddc: - '004' department: - _id: BeBi doi: 10.1111/cgf.142626 ec_funded: 1 external_id: isi: - '000657959600017' file: - access_level: open_access checksum: 33271724215f54a75c39d2ed40f2c502 content_type: application/pdf creator: bbickel date_created: 2021-10-11T12:06:50Z date_updated: 2021-10-11T12:06:50Z file_id: '10120' file_name: ScatteringAwareColor3DPrinting_authorVersion.pdf file_size: 26026501 relation: main_file success: 1 file_date_updated: 2021-10-11T12:06:50Z has_accepted_license: '1' intvolume: ' 40' isi: 1 issue: '2' language: - iso: eng month: '05' oa: 1 oa_version: Submitted Version page: 205-219 project: - _id: 2508E324-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '642841' name: Distributed 3D Object Design - _id: 24F9549A-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '715767' name: 'MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and Modeling' publication: Computer Graphics Forum publication_identifier: eissn: - 1467-8659 issn: - 0167-7055 publication_status: published publisher: Wiley quality_controlled: '1' scopus_import: '1' status: public title: Neural acceleration of scattering-aware color 3D printing type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 40 year: '2021' ... --- _id: '10177' abstract: - lang: eng text: Phonon polaritons (PhPs)—light coupled to lattice vibrations—with in-plane hyperbolic dispersion exhibit ray-like propagation with large wave vectors and enhanced density of optical states along certain directions on a surface. As such, they have raised a surge of interest, promising unprecedented manipulation of infrared light at the nanoscale in a planar circuitry. Here, we demonstrate focusing of in-plane hyperbolic PhPs propagating along thin slabs of α-MoO3. To that end, we developed metallic nanoantennas of convex geometries for both efficient launching and focusing of the polaritons. The foci obtained exhibit enhanced near-field confinement and absorption compared to foci produced by in-plane isotropic PhPs. Foci sizes as small as λp/4.5 = λ0/50 were achieved (λp is the polariton wavelength and λ0 is the photon wavelength). Focusing of in-plane hyperbolic polaritons introduces a first and most basic building block developing planar polariton optics using in-plane anisotropic van der Waals materials. acknowledgement: J.M.-S. acknowledges financial support from the Ramón y Cajal Program of the Government of Spain and FSE (RYC2018-026196-I) and the Spanish Ministry of Science and Innovation (State Plan for Scientific and Technical Research and Innovation grant number PID2019-110308GA-I00). P.A.-G. acknowledges support from the European Research Council under starting grant no. 715496, 2DNANOPTICA, and the Spanish Ministry of Science and Innovation (State Plan for Scientific and Technical Research and Innovation grant number PID2019-111156GB-I00). J.T.-G. acknowledges support through the Severo Ochoa Program from the Government of the Principality of Asturias (PA-18-PF-BP17-126). G.A.-P. acknowledges support through the Severo Ochoa Program from the Government of the Principality of Asturias (PA-20-PF-BP19-053). K.V.V. and V.S.V. acknowledge the financial support from the Ministry of Science and Higher Education of the Russian Federation (agreement no. 075-15-2021-606). A.Y.N. acknowledges the Spanish Ministry of Science, Innovation, and Universities (national projects MAT2017-88358-C3-3-R and PID2020-115221GB-C42) and the Basque Department of Education (PIBA-2020-1-0014). R.H. acknowledges financial support from the Spanish Ministry of Science, Innovation, and Universities (national project number RTI2018-094830-B-100 and project number MDM-2016-0618 of the Marie de Maeztu Units of Excellence Program) and the Basque Government (grant number IT1164-19). article_number: abj0127 article_processing_charge: Yes article_type: original author: - first_name: Javier full_name: Martín-Sánchez, Javier last_name: Martín-Sánchez - first_name: Jiahua full_name: Duan, Jiahua last_name: Duan - first_name: Javier full_name: Taboada-Gutiérrez, Javier last_name: Taboada-Gutiérrez - first_name: Gonzalo full_name: Álvarez-Pérez, Gonzalo last_name: Álvarez-Pérez - first_name: Kirill V. full_name: Voronin, Kirill V. last_name: Voronin - first_name: Ivan full_name: Prieto Gonzalez, Ivan id: 2A307FE2-F248-11E8-B48F-1D18A9856A87 last_name: Prieto Gonzalez orcid: 0000-0002-7370-5357 - first_name: Weiliang full_name: Ma, Weiliang last_name: Ma - first_name: Qiaoliang full_name: Bao, Qiaoliang last_name: Bao - first_name: Valentyn S. full_name: Volkov, Valentyn S. last_name: Volkov - first_name: Rainer full_name: Hillenbrand, Rainer last_name: Hillenbrand - first_name: Alexey Y. full_name: Nikitin, Alexey Y. last_name: Nikitin - first_name: Pablo full_name: Alonso-González, Pablo last_name: Alonso-González citation: ama: Martín-Sánchez J, Duan J, Taboada-Gutiérrez J, et al. Focusing of in-plane hyperbolic polaritons in van der Waals crystals with tailored infrared nanoantennas. Science Advances. 2021;7(41). doi:10.1126/sciadv.abj0127 apa: Martín-Sánchez, J., Duan, J., Taboada-Gutiérrez, J., Álvarez-Pérez, G., Voronin, K. V., Prieto Gonzalez, I., … Alonso-González, P. (2021). Focusing of in-plane hyperbolic polaritons in van der Waals crystals with tailored infrared nanoantennas. Science Advances. American Association for the Advancement of Science. https://doi.org/10.1126/sciadv.abj0127 chicago: Martín-Sánchez, Javier, Jiahua Duan, Javier Taboada-Gutiérrez, Gonzalo Álvarez-Pérez, Kirill V. Voronin, Ivan Prieto Gonzalez, Weiliang Ma, et al. “Focusing of In-Plane Hyperbolic Polaritons in van Der Waals Crystals with Tailored Infrared Nanoantennas.” Science Advances. American Association for the Advancement of Science, 2021. https://doi.org/10.1126/sciadv.abj0127. ieee: J. Martín-Sánchez et al., “Focusing of in-plane hyperbolic polaritons in van der Waals crystals with tailored infrared nanoantennas,” Science Advances, vol. 7, no. 41. American Association for the Advancement of Science, 2021. ista: Martín-Sánchez J, Duan J, Taboada-Gutiérrez J, Álvarez-Pérez G, Voronin KV, Prieto Gonzalez I, Ma W, Bao Q, Volkov VS, Hillenbrand R, Nikitin AY, Alonso-González P. 2021. Focusing of in-plane hyperbolic polaritons in van der Waals crystals with tailored infrared nanoantennas. Science Advances. 7(41), abj0127. mla: Martín-Sánchez, Javier, et al. “Focusing of In-Plane Hyperbolic Polaritons in van Der Waals Crystals with Tailored Infrared Nanoantennas.” Science Advances, vol. 7, no. 41, abj0127, American Association for the Advancement of Science, 2021, doi:10.1126/sciadv.abj0127. short: J. Martín-Sánchez, J. Duan, J. Taboada-Gutiérrez, G. Álvarez-Pérez, K.V. Voronin, I. Prieto Gonzalez, W. Ma, Q. Bao, V.S. Volkov, R. Hillenbrand, A.Y. Nikitin, P. Alonso-González, Science Advances 7 (2021). date_created: 2021-10-24T22:01:33Z date_published: 2021-10-08T00:00:00Z date_updated: 2023-08-14T08:04:42Z day: '08' ddc: - '530' department: - _id: NanoFab doi: 10.1126/sciadv.abj0127 external_id: arxiv: - '2103.10852' isi: - '000704912700024' file: - access_level: open_access checksum: 0a470ef6a47d2b8a96ede4c4d28cfacd content_type: application/pdf creator: cziletti date_created: 2021-10-27T14:16:06Z date_updated: 2021-10-27T14:16:06Z file_id: '10189' file_name: 2021_ScienceAdv_Martin-Sanchez.pdf file_size: 2441163 relation: main_file success: 1 file_date_updated: 2021-10-27T14:16:06Z has_accepted_license: '1' intvolume: ' 7' isi: 1 issue: '41' language: - iso: eng license: https://creativecommons.org/licenses/by-nc/4.0/ month: '10' oa: 1 oa_version: Published Version publication: Science Advances publication_identifier: eissn: - '23752548' publication_status: published publisher: American Association for the Advancement of Science quality_controlled: '1' scopus_import: '1' status: public title: Focusing of in-plane hyperbolic polaritons in van der Waals crystals with tailored infrared nanoantennas tmp: image: /images/cc_by_nc.png legal_code_url: https://creativecommons.org/licenses/by-nc/4.0/legalcode name: Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0) short: CC BY-NC (4.0) type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 7 year: '2021' ... --- _id: '10146' abstract: - lang: eng text: The enzymes of the mitochondrial electron transport chain are key players of cell metabolism. Despite being active when isolated, in vivo they associate into supercomplexes1, whose precise role is debated. Supercomplexes CIII2CIV1-2 (refs. 2,3), CICIII2 (ref. 4) and CICIII2CIV (respirasome)5,6,7,8,9,10 exist in mammals, but in contrast to CICIII2 and the respirasome, to date the only known eukaryotic structures of CIII2CIV1-2 come from Saccharomyces cerevisiae11,12 and plants13, which have different organization. Here we present the first, to our knowledge, structures of mammalian (mouse and ovine) CIII2CIV and its assembly intermediates, in different conformations. We describe the assembly of CIII2CIV from the CIII2 precursor to the final CIII2CIV conformation, driven by the insertion of the N terminus of the assembly factor SCAF1 (ref. 14) deep into CIII2, while its C terminus is integrated into CIV. Our structures (which include CICIII2 and the respirasome) also confirm that SCAF1 is exclusively required for the assembly of CIII2CIV and has no role in the assembly of the respirasome. We show that CIII2 is asymmetric due to the presence of only one copy of subunit 9, which straddles both monomers and prevents the attachment of a second copy of SCAF1 to CIII2, explaining the presence of one copy of CIV in CIII2CIV in mammals. Finally, we show that CIII2 and CIV gain catalytic advantage when assembled into the supercomplex and propose a role for CIII2CIV in fine tuning the efficiency of electron transfer in the electron transport chain. acknowledged_ssus: - _id: PreCl - _id: EM-Fac - _id: ScienComp acknowledgement: We thank the pre-clinical facility of the IST Austria and A. Venturino for assistance with the animals; and V.-V. Hodirnau for assistance during the Titan Krios data collection, performed at the IST Austria. The data processing was performed at the IST high-performance computing cluster. This project has received funding from the European Union’s Horizon 2020 research and innovation program under the Marie Skłodowska-Curie grant agreement no. 754411. article_processing_charge: No article_type: original author: - first_name: Irene full_name: Vercellino, Irene id: 3ED6AF16-F248-11E8-B48F-1D18A9856A87 last_name: Vercellino orcid: 0000-0001-5618-3449 - first_name: Leonid A full_name: Sazanov, Leonid A id: 338D39FE-F248-11E8-B48F-1D18A9856A87 last_name: Sazanov orcid: 0000-0002-0977-7989 citation: ama: Vercellino I, Sazanov LA. Structure and assembly of the mammalian mitochondrial supercomplex CIII2CIV. Nature. 2021;598(7880):364-367. doi:10.1038/s41586-021-03927-z apa: Vercellino, I., & Sazanov, L. A. (2021). Structure and assembly of the mammalian mitochondrial supercomplex CIII2CIV. Nature. Springer Nature. https://doi.org/10.1038/s41586-021-03927-z chicago: Vercellino, Irene, and Leonid A Sazanov. “Structure and Assembly of the Mammalian Mitochondrial Supercomplex CIII2CIV.” Nature. Springer Nature, 2021. https://doi.org/10.1038/s41586-021-03927-z. ieee: I. Vercellino and L. A. Sazanov, “Structure and assembly of the mammalian mitochondrial supercomplex CIII2CIV,” Nature, vol. 598, no. 7880. Springer Nature, pp. 364–367, 2021. ista: Vercellino I, Sazanov LA. 2021. Structure and assembly of the mammalian mitochondrial supercomplex CIII2CIV. Nature. 598(7880), 364–367. mla: Vercellino, Irene, and Leonid A. Sazanov. “Structure and Assembly of the Mammalian Mitochondrial Supercomplex CIII2CIV.” Nature, vol. 598, no. 7880, Springer Nature, 2021, pp. 364–67, doi:10.1038/s41586-021-03927-z. short: I. Vercellino, L.A. Sazanov, Nature 598 (2021) 364–367. date_created: 2021-10-17T22:01:17Z date_published: 2021-10-14T00:00:00Z date_updated: 2023-08-14T08:01:21Z day: '14' department: - _id: LeSa doi: 10.1038/s41586-021-03927-z ec_funded: 1 external_id: isi: - '000704581600001' pmid: - '34616041' intvolume: ' 598' isi: 1 issue: '7880' language: - iso: eng month: '10' oa_version: None page: 364-367 pmid: 1 project: - _id: 260C2330-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '754411' name: ISTplus - Postdoctoral Fellowships publication: Nature publication_identifier: eissn: - 1476-4687 issn: - 0028-0836 publication_status: published publisher: Springer Nature quality_controlled: '1' related_material: link: - description: News on IST Webpage relation: press_release url: https://ist.ac.at/en/news/boosting-the-cells-power-house/ scopus_import: '1' status: public title: Structure and assembly of the mammalian mitochondrial supercomplex CIII2CIV type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 598 year: '2021' ... --- _id: '10176' abstract: - lang: eng text: "We give a combinatorial model for r-spin surfaces with parameterized boundary based on Novak (“Lattice topological field theories in two dimensions,” Ph.D. thesis, Universität Hamburg, 2015). The r-spin structure is encoded in terms of ℤ\U0001D45F-valued indices assigned to the edges of a polygonal decomposition. This combinatorial model is designed for our state-sum construction of two-dimensional topological field theories on r-spin surfaces. We show that an example of such a topological field theory computes the Arf-invariant of an r-spin surface as introduced by Randal-Williams [J. Topol. 7, 155 (2014)] and Geiges et al. [Osaka J. Math. 49, 449 (2012)]. This implies, in particular, that the r-spin Arf-invariant is constant on orbits of the mapping class group, providing an alternative proof of that fact." acknowledgement: We would like to thank Nils Carqueville, Tobias Dyckerhoff, Jan Hesse, Ehud Meir, Sebastian Novak, Louis-Hadrien Robert, Nick Salter, Walker Stern, and Lukas Woike for helpful discussions and comments. L.S. was supported by the DFG Research Training Group 1670 “Mathematics Inspired by String Theory and Quantum Field Theory.” article_number: '102302' article_processing_charge: No article_type: original author: - first_name: Ingo full_name: Runkel, Ingo last_name: Runkel - first_name: Lorant full_name: Szegedy, Lorant id: 7943226E-220E-11EA-94C7-D59F3DDC885E last_name: Szegedy orcid: 0000-0003-2834-5054 citation: ama: Runkel I, Szegedy L. Topological field theory on r-spin surfaces and the Arf-invariant. Journal of Mathematical Physics. 2021;62(10). doi:10.1063/5.0037826 apa: Runkel, I., & Szegedy, L. (2021). Topological field theory on r-spin surfaces and the Arf-invariant. Journal of Mathematical Physics. AIP Publishing. https://doi.org/10.1063/5.0037826 chicago: Runkel, Ingo, and Lorant Szegedy. “Topological Field Theory on R-Spin Surfaces and the Arf-Invariant.” Journal of Mathematical Physics. AIP Publishing, 2021. https://doi.org/10.1063/5.0037826. ieee: I. Runkel and L. Szegedy, “Topological field theory on r-spin surfaces and the Arf-invariant,” Journal of Mathematical Physics, vol. 62, no. 10. AIP Publishing, 2021. ista: Runkel I, Szegedy L. 2021. Topological field theory on r-spin surfaces and the Arf-invariant. Journal of Mathematical Physics. 62(10), 102302. mla: Runkel, Ingo, and Lorant Szegedy. “Topological Field Theory on R-Spin Surfaces and the Arf-Invariant.” Journal of Mathematical Physics, vol. 62, no. 10, 102302, AIP Publishing, 2021, doi:10.1063/5.0037826. short: I. Runkel, L. Szegedy, Journal of Mathematical Physics 62 (2021). date_created: 2021-10-24T22:01:32Z date_published: 2021-10-01T00:00:00Z date_updated: 2023-08-14T08:04:12Z day: '01' department: - _id: MiLe doi: 10.1063/5.0037826 external_id: arxiv: - '1802.09978' isi: - '000755638500010' intvolume: ' 62' isi: 1 issue: '10' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1802.09978 month: '10' oa: 1 oa_version: Preprint publication: Journal of Mathematical Physics publication_identifier: issn: - '00222488' publication_status: published publisher: AIP Publishing quality_controlled: '1' scopus_import: '1' status: public title: Topological field theory on r-spin surfaces and the Arf-invariant type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 62 year: '2021' ... --- _id: '10179' abstract: - lang: eng text: Inhibitory GABAergic interneurons migrate over long distances from their extracortical origin into the developing cortex. In humans, this process is uniquely slow and prolonged, and it is unclear whether guidance cues unique to humans govern the various phases of this complex developmental process. Here, we use fused cerebral organoids to identify key roles of neurotransmitter signaling pathways in guiding the migratory behavior of human cortical interneurons. We use scRNAseq to reveal expression of GABA, glutamate, glycine, and serotonin receptors along distinct maturation trajectories across interneuron migration. We develop an image analysis software package, TrackPal, to simultaneously assess 48 parameters for entire migration tracks of individual cells. By chemical screening, we show that different modes of interneuron migration depend on distinct neurotransmitter signaling pathways, linking transcriptional maturation of interneurons with their migratory behavior. Altogether, our study provides a comprehensive quantitative analysis of human interneuron migration and its functional modulation by neurotransmitter signaling. acknowledgement: We thank all Knoblich laboratory members for continued support and discussions. We thank the IMP/IMBA BioOptics facility, particularly Pawel Pasierbek, Alberto Moreno Cencerrado and Gerald Schmauss, the IMP/IMBA Molecular Biology Service, in particular Robert Heinen, the IMP Bioinformatics facility, in particular Thomas Burkard, the Vienna Biocenter Core Facilities (VBCF) Histopathology facility, in particular Tamara Engelmaier, and the VBCF Next Generation Sequencing Facility, notably Volodymyr Shubchynskyy and Carmen Czepe. We would also like to thank Simon Haendeler for advice on statistical analyses, Jose Guzman for discussions and assistance with slice culture setups, Oliver L. Eichmueller for discussions and assistance with microscopy, and E.H. Gustafson, S. Wolfinger, and D. Reumann for technical assistance regarding generation of cerebral organoids. This project received funding from the European Union’s Horizon 2020 research and innovation program under the Marie Skłodowska-Curie fellowship agreement Nr.707109 awarded to J.A.B. Work in J.A.K.'s laboratory is supported by the Austrian Federal Ministry of Education, Science and Research, the Austrian Academy of Sciences, the City of Vienna, a Research Program of the Austrian Science Fund FWF (SFBF78 Stem Cell, F 7803-B) and a European Research Council (ERC) Advanced Grant under the European 20 Union’s Horizon 2020 program (grant agreement no. 695642). article_number: e108714 article_processing_charge: Yes (in subscription journal) article_type: original author: - first_name: Sunanjay full_name: Bajaj, Sunanjay last_name: Bajaj - first_name: Joshua A. full_name: Bagley, Joshua A. last_name: Bagley - first_name: Christoph M full_name: Sommer, Christoph M id: 4DF26D8C-F248-11E8-B48F-1D18A9856A87 last_name: Sommer orcid: 0000-0003-1216-9105 - first_name: Abel full_name: Vertesy, Abel last_name: Vertesy - first_name: Sakurako full_name: Nagumo Wong, Sakurako last_name: Nagumo Wong - first_name: Veronica full_name: Krenn, Veronica last_name: Krenn - first_name: Julie full_name: Lévi-Strauss, Julie last_name: Lévi-Strauss - first_name: Juergen A. full_name: Knoblich, Juergen A. last_name: Knoblich citation: ama: Bajaj S, Bagley JA, Sommer CM, et al. Neurotransmitter signaling regulates distinct phases of multimodal human interneuron migration. EMBO Journal. 2021;40(23). doi:10.15252/embj.2021108714 apa: Bajaj, S., Bagley, J. A., Sommer, C. M., Vertesy, A., Nagumo Wong, S., Krenn, V., … Knoblich, J. A. (2021). Neurotransmitter signaling regulates distinct phases of multimodal human interneuron migration. EMBO Journal. Embo Press. https://doi.org/10.15252/embj.2021108714 chicago: Bajaj, Sunanjay, Joshua A. Bagley, Christoph M Sommer, Abel Vertesy, Sakurako Nagumo Wong, Veronica Krenn, Julie Lévi-Strauss, and Juergen A. Knoblich. “Neurotransmitter Signaling Regulates Distinct Phases of Multimodal Human Interneuron Migration.” EMBO Journal. Embo Press, 2021. https://doi.org/10.15252/embj.2021108714. ieee: S. Bajaj et al., “Neurotransmitter signaling regulates distinct phases of multimodal human interneuron migration,” EMBO Journal, vol. 40, no. 23. Embo Press, 2021. ista: Bajaj S, Bagley JA, Sommer CM, Vertesy A, Nagumo Wong S, Krenn V, Lévi-Strauss J, Knoblich JA. 2021. Neurotransmitter signaling regulates distinct phases of multimodal human interneuron migration. EMBO Journal. 40(23), e108714. mla: Bajaj, Sunanjay, et al. “Neurotransmitter Signaling Regulates Distinct Phases of Multimodal Human Interneuron Migration.” EMBO Journal, vol. 40, no. 23, e108714, Embo Press, 2021, doi:10.15252/embj.2021108714. short: S. Bajaj, J.A. Bagley, C.M. Sommer, A. Vertesy, S. Nagumo Wong, V. Krenn, J. Lévi-Strauss, J.A. Knoblich, EMBO Journal 40 (2021). date_created: 2021-10-24T22:01:34Z date_published: 2021-10-18T00:00:00Z date_updated: 2023-08-14T08:05:23Z day: '18' ddc: - '610' department: - _id: Bio doi: 10.15252/embj.2021108714 external_id: isi: - '000708012800001' pmid: - '34661293' file: - access_level: open_access checksum: 78d2d02e775322297e774f72810a41a4 content_type: application/pdf creator: alisjak date_created: 2021-12-13T14:54:14Z date_updated: 2021-12-13T14:54:14Z file_id: '10541' file_name: 2021_EMBO_Bajaj.pdf file_size: 7819881 relation: main_file success: 1 file_date_updated: 2021-12-13T14:54:14Z has_accepted_license: '1' intvolume: ' 40' isi: 1 issue: '23' language: - iso: eng month: '10' oa: 1 oa_version: Published Version pmid: 1 publication: EMBO Journal publication_identifier: eissn: - 1460-2075 issn: - 0261-4189 publication_status: published publisher: Embo Press quality_controlled: '1' scopus_import: '1' status: public title: Neurotransmitter signaling regulates distinct phases of multimodal human interneuron 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: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 40 year: '2021' ... --- _id: '10203' abstract: - lang: eng text: Single photon emitters in atomically-thin semiconductors can be deterministically positioned using strain induced by underlying nano-structures. Here, we couple monolayer WSe2 to high-refractive-index gallium phosphide dielectric nano-antennas providing both optical enhancement and monolayer deformation. For single photon emitters formed on such nano-antennas, we find very low (femto-Joule) saturation pulse energies and up to 104 times brighter photoluminescence than in WSe2 placed on low-refractive-index SiO2 pillars. We show that the key to these observations is the increase on average by a factor of 5 of the quantum efficiency of the emitters coupled to the nano-antennas. This further allows us to gain new insights into their photoluminescence dynamics, revealing the roles of the dark exciton reservoir and Auger processes. We also find that the coherence time of such emitters is limited by intrinsic dephasing processes. Our work establishes dielectric nano-antennas as a platform for high-efficiency quantum light generation in monolayer semiconductors. acknowledgement: L.S., P.G.Z., and A.I.T. thank the financial support of the European Graphene Flagship Project under grant agreements 881603 and EPSRC grant EP/S030751/1. L.S. and A.I.T. thank the European Union’s Horizon 2020 research and innovation programme under ITN Spin-NANO Marie Sklodowska-Curie grant agreement no. 676108. P.G.Z. and A.I.T. thank the European Union’s Horizon 2020 research and innovation programme under ITN 4PHOTON Marie Sklodowska-Curie grant agreement no. 721394. J.C., S.A.M., and R.S. acknowledge funding by EPSRC (EP/P033369 and EP/M013812). C.L.P., A.J.B., A.I.T., and A.M.F. acknowledge funding by EPSRC Programme Grant EP/N031776/1. S.A.M. acknowledges the Lee-Lucas Chair in Physics, the Solar Energies go Hybrid (SolTech) programme, and the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) under Germany’s Excellence Strategy - EXC 2089/1 - 390776260. article_number: '6063' article_processing_charge: No article_type: original author: - first_name: Luca full_name: Sortino, Luca last_name: Sortino - first_name: Panaiot G. full_name: Zotev, Panaiot G. last_name: Zotev - first_name: Catherine L. full_name: Phillips, Catherine L. last_name: Phillips - first_name: Alistair J. full_name: Brash, Alistair J. last_name: Brash - first_name: Javier full_name: Cambiasso, Javier last_name: Cambiasso - first_name: Elena full_name: Marensi, Elena id: 0BE7553A-1004-11EA-B805-18983DDC885E last_name: Marensi orcid: 0000-0001-7173-4923 - first_name: A. Mark full_name: Fox, A. Mark last_name: Fox - first_name: Stefan A. full_name: Maier, Stefan A. last_name: Maier - first_name: Riccardo full_name: Sapienza, Riccardo last_name: Sapienza - first_name: Alexander I. full_name: Tartakovskii, Alexander I. last_name: Tartakovskii citation: ama: Sortino L, Zotev PG, Phillips CL, et al. Bright single photon emitters with enhanced quantum efficiency in a two-dimensional semiconductor coupled with dielectric nano-antennas. Nature Communications. 2021;12. doi:10.1038/s41467-021-26262-3 apa: Sortino, L., Zotev, P. G., Phillips, C. L., Brash, A. J., Cambiasso, J., Marensi, E., … Tartakovskii, A. I. (2021). Bright single photon emitters with enhanced quantum efficiency in a two-dimensional semiconductor coupled with dielectric nano-antennas. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-021-26262-3 chicago: Sortino, Luca, Panaiot G. Zotev, Catherine L. Phillips, Alistair J. Brash, Javier Cambiasso, Elena Marensi, A. Mark Fox, Stefan A. Maier, Riccardo Sapienza, and Alexander I. Tartakovskii. “Bright Single Photon Emitters with Enhanced Quantum Efficiency in a Two-Dimensional Semiconductor Coupled with Dielectric Nano-Antennas.” Nature Communications. Springer Nature, 2021. https://doi.org/10.1038/s41467-021-26262-3. ieee: L. Sortino et al., “Bright single photon emitters with enhanced quantum efficiency in a two-dimensional semiconductor coupled with dielectric nano-antennas,” Nature Communications, vol. 12. Springer Nature, 2021. ista: Sortino L, Zotev PG, Phillips CL, Brash AJ, Cambiasso J, Marensi E, Fox AM, Maier SA, Sapienza R, Tartakovskii AI. 2021. Bright single photon emitters with enhanced quantum efficiency in a two-dimensional semiconductor coupled with dielectric nano-antennas. Nature Communications. 12, 6063. mla: Sortino, Luca, et al. “Bright Single Photon Emitters with Enhanced Quantum Efficiency in a Two-Dimensional Semiconductor Coupled with Dielectric Nano-Antennas.” Nature Communications, vol. 12, 6063, Springer Nature, 2021, doi:10.1038/s41467-021-26262-3. short: L. Sortino, P.G. Zotev, C.L. Phillips, A.J. Brash, J. Cambiasso, E. Marensi, A.M. Fox, S.A. Maier, R. Sapienza, A.I. Tartakovskii, Nature Communications 12 (2021). date_created: 2021-10-31T23:01:30Z date_published: 2021-10-18T00:00:00Z date_updated: 2023-08-14T08:12:12Z day: '18' ddc: - '530' department: - _id: BjHo doi: 10.1038/s41467-021-26262-3 external_id: arxiv: - '2103.16986' isi: - '000708601800015' file: - access_level: open_access checksum: 8580d128389860f732028c521cd5949e content_type: application/pdf creator: cchlebak date_created: 2021-11-03T11:31:24Z date_updated: 2021-11-03T11:31:24Z file_id: '10212' file_name: 2021_NatComm_Sortino.pdf file_size: 1434201 relation: main_file success: 1 file_date_updated: 2021-11-03T11:31:24Z has_accepted_license: '1' intvolume: ' 12' isi: 1 language: - iso: eng month: '10' oa: 1 oa_version: Published Version publication: Nature Communications publication_identifier: eissn: - 2041-1723 publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: Bright single photon emitters with enhanced quantum efficiency in a two-dimensional semiconductor coupled with dielectric nano-antennas tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 12 year: '2021' ... --- _id: '10178' abstract: - lang: eng text: In dense biological tissues, cell types performing different roles remain segregated by maintaining sharp interfaces. To better understand the mechanisms for such sharp compartmentalization, we study the effect of an imposed heterotypic tension at the interface between two distinct cell types in a fully 3D Voronoi model for confluent tissues. We find that cells rapidly sort and self-organize to generate a tissue-scale interface between cell types, and cells adjacent to this interface exhibit signature geometric features including nematic-like ordering, bimodal facet areas, and registration, or alignment, of cell centers on either side of the two-tissue interface. The magnitude of these features scales directly with the magnitude of the imposed tension, suggesting that biologists can estimate the magnitude of tissue surface tension between two tissue types simply by segmenting a 3D tissue. To uncover the underlying physical mechanisms driving these geometric features, we develop two minimal, ordered models using two different underlying lattices that identify an energetic competition between bulk cell shapes and tissue interface area. When the interface area dominates, changes to neighbor topology are costly and occur less frequently, which generates the observed geometric features. acknowledgement: "We thank Paula Sanematsu, Matthias Merkel, Daniel Sussman, Cristina Marchetti and Edouard Hannezo for helpful discussions, and M Merkel for developing and sharing the original version of the 3D Voronoi code. This work was primarily funded by NSF-PHY-1607416, NSF-PHY-2014192 , and are in the division of physics at the National Science Foundation. PS and MLM acknowledge additional support from Simons Grant No. 454947.\r\n" article_number: '093043' article_processing_charge: Yes article_type: original author: - first_name: Preeti full_name: Sahu, Preeti id: 55BA52EE-A185-11EA-88FD-18AD3DDC885E last_name: Sahu - first_name: J. M. full_name: Schwarz, J. M. last_name: Schwarz - first_name: M. Lisa full_name: Manning, M. Lisa last_name: Manning citation: ama: Sahu P, Schwarz JM, Manning ML. Geometric signatures of tissue surface tension in a three-dimensional model of confluent tissue. New Journal of Physics. 2021;23(9). doi:10.1088/1367-2630/ac23f1 apa: Sahu, P., Schwarz, J. M., & Manning, M. L. (2021). Geometric signatures of tissue surface tension in a three-dimensional model of confluent tissue. New Journal of Physics. IOP Publishing. https://doi.org/10.1088/1367-2630/ac23f1 chicago: Sahu, Preeti, J. M. Schwarz, and M. Lisa Manning. “Geometric Signatures of Tissue Surface Tension in a Three-Dimensional Model of Confluent Tissue.” New Journal of Physics. IOP Publishing, 2021. https://doi.org/10.1088/1367-2630/ac23f1. ieee: P. Sahu, J. M. Schwarz, and M. L. Manning, “Geometric signatures of tissue surface tension in a three-dimensional model of confluent tissue,” New Journal of Physics, vol. 23, no. 9. IOP Publishing, 2021. ista: Sahu P, Schwarz JM, Manning ML. 2021. Geometric signatures of tissue surface tension in a three-dimensional model of confluent tissue. New Journal of Physics. 23(9), 093043. mla: Sahu, Preeti, et al. “Geometric Signatures of Tissue Surface Tension in a Three-Dimensional Model of Confluent Tissue.” New Journal of Physics, vol. 23, no. 9, 093043, IOP Publishing, 2021, doi:10.1088/1367-2630/ac23f1. short: P. Sahu, J.M. Schwarz, M.L. Manning, New Journal of Physics 23 (2021). date_created: 2021-10-24T22:01:34Z date_published: 2021-09-29T00:00:00Z date_updated: 2023-08-14T08:10:31Z day: '29' ddc: - '570' department: - _id: EdHa doi: 10.1088/1367-2630/ac23f1 external_id: arxiv: - '2102.05397' isi: - '000702042400001' file: - access_level: open_access checksum: ace603e8f0962b3ba55f23fa34f57764 content_type: application/pdf creator: cziletti date_created: 2021-10-28T12:06:01Z date_updated: 2021-10-28T12:06:01Z file_id: '10193' file_name: 2021_NewJPhys_Sahu.pdf file_size: 2215016 relation: main_file success: 1 file_date_updated: 2021-10-28T12:06:01Z has_accepted_license: '1' intvolume: ' 23' isi: 1 issue: '9' language: - iso: eng month: '09' oa: 1 oa_version: Published Version publication: New Journal of Physics publication_identifier: eissn: - '13672630' publication_status: published publisher: IOP Publishing quality_controlled: '1' scopus_import: '1' status: public title: Geometric signatures of tissue surface tension in a three-dimensional model of confluent tissue tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 23 year: '2021' ... --- _id: '10181' abstract: - lang: eng text: In this article we study some geometric properties of proximally smooth sets. First, we introduce a modification of the metric projection and prove its existence. Then we provide an algorithm for constructing a rectifiable curve between two sufficiently close points of a proximally smooth set in a uniformly convex and uniformly smooth Banach space, with the moduli of smoothness and convexity of power type. Our algorithm returns a reasonably short curve between two sufficiently close points of a proximally smooth set, is iterative and uses our modification of the metric projection. We estimate the length of the constructed curve and its deviation from the segment with the same endpoints. These estimates coincide up to a constant factor with those for the geodesics in a proximally smooth set in a Hilbert space. acknowledgement: Theorem 2 was obtained at Steklov Mathematical Institute RAS and supported by Russian Science Foundation, grant N 19-11-00087. article_processing_charge: No article_type: original author: - first_name: Grigory full_name: Ivanov, Grigory id: 87744F66-5C6F-11EA-AFE0-D16B3DDC885E last_name: Ivanov - first_name: Mariana S. full_name: Lopushanski, Mariana S. last_name: Lopushanski citation: ama: Ivanov G, Lopushanski MS. Rectifiable curves in proximally smooth sets. Set-Valued and Variational Analysis. 2021. doi:10.1007/s11228-021-00612-1 apa: Ivanov, G., & Lopushanski, M. S. (2021). Rectifiable curves in proximally smooth sets. Set-Valued and Variational Analysis. Springer Nature. https://doi.org/10.1007/s11228-021-00612-1 chicago: Ivanov, Grigory, and Mariana S. Lopushanski. “Rectifiable Curves in Proximally Smooth Sets.” Set-Valued and Variational Analysis. Springer Nature, 2021. https://doi.org/10.1007/s11228-021-00612-1. ieee: G. Ivanov and M. S. Lopushanski, “Rectifiable curves in proximally smooth sets,” Set-Valued and Variational Analysis. Springer Nature, 2021. ista: Ivanov G, Lopushanski MS. 2021. Rectifiable curves in proximally smooth sets. Set-Valued and Variational Analysis. mla: Ivanov, Grigory, and Mariana S. Lopushanski. “Rectifiable Curves in Proximally Smooth Sets.” Set-Valued and Variational Analysis, Springer Nature, 2021, doi:10.1007/s11228-021-00612-1. short: G. Ivanov, M.S. Lopushanski, Set-Valued and Variational Analysis (2021). date_created: 2021-10-24T22:01:35Z date_published: 2021-10-09T00:00:00Z date_updated: 2023-08-14T08:11:38Z day: '09' department: - _id: UlWa doi: 10.1007/s11228-021-00612-1 external_id: arxiv: - '2012.10691' isi: - '000705774800001' isi: 1 language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/2012.10691 month: '10' oa: 1 oa_version: Published Version publication: Set-Valued and Variational Analysis publication_identifier: eissn: - 1877-0541 issn: - 0927-6947 publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: Rectifiable curves in proximally smooth sets type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 year: '2021' ... --- _id: '10202' abstract: - lang: eng text: Zygotic genome activation (ZGA) initiates regionalized transcription underlying distinct cellular identities. ZGA is dependent upon dynamic chromatin architecture sculpted by conserved DNA-binding proteins. However, the direct mechanistic link between the onset of ZGA and the tissue-specific transcription remains unclear. Here, we have addressed the involvement of chromatin organizer Satb2 in orchestrating both processes during zebrafish embryogenesis. Integrative analysis of transcriptome, genome-wide occupancy and chromatin accessibility reveals contrasting molecular activities of maternally deposited and zygotically synthesized Satb2. Maternal Satb2 prevents premature transcription of zygotic genes by influencing the interplay between the pluripotency factors. By contrast, zygotic Satb2 activates transcription of the same group of genes during neural crest development and organogenesis. Thus, our comparative analysis of maternal versus zygotic function of Satb2 underscores how these antithetical activities are temporally coordinated and functionally implemented highlighting the evolutionary implications of the biphasic and bimodal regulation of landmark developmental transitions by a single determinant. acknowledgement: 'We are grateful to the members of C.-P.H. and SG lab for discussions. Authors thank Shubha Tole for providing embryonic mouse tissues. Authors are grateful to Alessandro Mongera and Chetana Sachidanandan for generous help with Tg: Sox10: GFP line. Authors would like to thank Satyajeet Khare, Vanessa Barone, Jyothish S., Shalini Mishra, Yoshita Bhide, and Keshav Jha for assistance in experiments. We would also like to thank Chaitanya Dingare for valuable suggestions. We thank Diana Pinhiero and Alexandra Schauer for critical reading of early versions of the manuscript. This work was supported by the Centre of Excellence in Epigenetics program of the Department of Biotechnology, Government of India Phase I (BT/01/COE/09/07) to S.G. and R.K.M., and Phase II (BT/COE/34/SP17426/2016) to S.G. and JC Bose Fellowship (JCB/2019/000013) from Science and Engineering Research Board, Government of India to S.G., DST-BMWF Indo-Austrian bilateral program grant to S.G. and C.-P.H. The work using animal models was partly supported by the infrastructure support grants from the Department of Biotechnology (National Facility for Laboratory Model Organisms: BT/INF/22/SP17358/2016 and Establishment of a Pune Biotech Cluster, Model Organism to Human Disease: B-2 Whole Animal Imaging & Tissue Processing FacilityBT/Pune-Biocluster/01/2015). S.J.P. was supported by Fellowship from the Council of Scientific and Industrial Research, India and travel fellowship from the Company of Biologists, UK. P.C.R. was supported by the Early Career Fellowship of the Wellcome Trust-DBT India Alliance (IA/E/16/1/503057). A.S. was supported by UGC and R.S. was supported by CSIR India. M.S. was supported by core funding from the Tata Institute of Fundamental Research (TIFR 12P-121).' article_number: '6094' article_processing_charge: Yes article_type: original author: - first_name: Saurabh J. full_name: Pradhan, Saurabh J. last_name: Pradhan - first_name: Puli Chandramouli full_name: Reddy, Puli Chandramouli last_name: Reddy - first_name: Michael full_name: Smutny, Michael id: 3FE6E4E8-F248-11E8-B48F-1D18A9856A87 last_name: Smutny orcid: 0000-0002-5920-9090 - first_name: Ankita full_name: Sharma, Ankita last_name: Sharma - first_name: Keisuke full_name: Sako, Keisuke id: 3BED66BE-F248-11E8-B48F-1D18A9856A87 last_name: Sako orcid: 0000-0002-6453-8075 - first_name: Meghana S. full_name: Oak, Meghana S. last_name: Oak - first_name: Rini full_name: Shah, Rini last_name: Shah - first_name: Mrinmoy full_name: Pal, Mrinmoy last_name: Pal - first_name: Ojas full_name: Deshpande, Ojas last_name: Deshpande - first_name: Greg full_name: Dsilva, Greg last_name: Dsilva - first_name: Yin full_name: Tang, Yin last_name: Tang - first_name: Rakesh full_name: Mishra, Rakesh last_name: Mishra - first_name: Girish full_name: Deshpande, Girish last_name: Deshpande - first_name: Antonio J. full_name: Giraldez, Antonio J. last_name: Giraldez - first_name: Mahendra full_name: Sonawane, Mahendra last_name: Sonawane - first_name: Carl-Philipp J full_name: Heisenberg, Carl-Philipp J id: 39427864-F248-11E8-B48F-1D18A9856A87 last_name: Heisenberg orcid: 0000-0002-0912-4566 - first_name: Sanjeev full_name: Galande, Sanjeev last_name: Galande citation: ama: Pradhan SJ, Reddy PC, Smutny M, et al. Satb2 acts as a gatekeeper for major developmental transitions during early vertebrate embryogenesis. Nature Communications. 2021;12(1). doi:10.1038/s41467-021-26234-7 apa: Pradhan, S. J., Reddy, P. C., Smutny, M., Sharma, A., Sako, K., Oak, M. S., … Galande, S. (2021). Satb2 acts as a gatekeeper for major developmental transitions during early vertebrate embryogenesis. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-021-26234-7 chicago: Pradhan, Saurabh J., Puli Chandramouli Reddy, Michael Smutny, Ankita Sharma, Keisuke Sako, Meghana S. Oak, Rini Shah, et al. “Satb2 Acts as a Gatekeeper for Major Developmental Transitions during Early Vertebrate Embryogenesis.” Nature Communications. Springer Nature, 2021. https://doi.org/10.1038/s41467-021-26234-7. ieee: S. J. Pradhan et al., “Satb2 acts as a gatekeeper for major developmental transitions during early vertebrate embryogenesis,” Nature Communications, vol. 12, no. 1. Springer Nature, 2021. ista: Pradhan SJ, Reddy PC, Smutny M, Sharma A, Sako K, Oak MS, Shah R, Pal M, Deshpande O, Dsilva G, Tang Y, Mishra R, Deshpande G, Giraldez AJ, Sonawane M, Heisenberg C-PJ, Galande S. 2021. Satb2 acts as a gatekeeper for major developmental transitions during early vertebrate embryogenesis. Nature Communications. 12(1), 6094. mla: Pradhan, Saurabh J., et al. “Satb2 Acts as a Gatekeeper for Major Developmental Transitions during Early Vertebrate Embryogenesis.” Nature Communications, vol. 12, no. 1, 6094, Springer Nature, 2021, doi:10.1038/s41467-021-26234-7. short: S.J. Pradhan, P.C. Reddy, M. Smutny, A. Sharma, K. Sako, M.S. Oak, R. Shah, M. Pal, O. Deshpande, G. Dsilva, Y. Tang, R. Mishra, G. Deshpande, A.J. Giraldez, M. Sonawane, C.-P.J. Heisenberg, S. Galande, Nature Communications 12 (2021). date_created: 2021-10-31T23:01:29Z date_published: 2021-10-19T00:00:00Z date_updated: 2023-08-14T10:32:48Z day: '19' ddc: - '570' department: - _id: CaHe doi: 10.1038/s41467-021-26234-7 external_id: isi: - '000709050300016' pmid: - '34667153' file: - access_level: open_access checksum: c40a69ae94435ecd3a30c9874a11ef2b content_type: application/pdf creator: cziletti date_created: 2021-11-09T13:59:26Z date_updated: 2021-11-09T13:59:26Z file_id: '10262' file_name: 2021_NatureComm_Pradhan.pdf file_size: 7144437 relation: main_file success: 1 file_date_updated: 2021-11-09T13:59:26Z has_accepted_license: '1' intvolume: ' 12' isi: 1 issue: '1' language: - iso: eng month: '10' oa: 1 oa_version: Published Version pmid: 1 publication: Nature Communications publication_identifier: eissn: - '20411723' publication_status: published publisher: Springer Nature quality_controlled: '1' related_material: link: - description: Preprint relation: earlier_version url: 'https://doi.org/10.1101/2020.11.23.394171 ' scopus_import: '1' status: public title: Satb2 acts as a gatekeeper for major developmental transitions during early vertebrate embryogenesis tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 12 year: '2021' ... --- _id: '10271' abstract: - lang: eng text: Understanding interactions between antibiotics used in combination is an important theme in microbiology. Using the interactions between the antifolate drug trimethoprim and the ribosome-targeting antibiotic erythromycin in Escherichia coli as a model, we applied a transcriptomic approach for dissecting interactions between two antibiotics with different modes of action. When trimethoprim and erythromycin were combined, the transcriptional response of genes from the sulfate reduction pathway deviated from the dominant effect of trimethoprim on the transcriptome. We successfully altered the drug interaction from additivity to suppression by increasing the sulfate level in the growth environment and identified sulfate reduction as an important metabolic determinant that shapes the interaction between the two drugs. Our work highlights the potential of using prioritization of gene expression patterns as a tool for identifying key metabolic determinants that shape drug-drug interactions. We further demonstrated that the sigma factor-binding protein gene crl shapes the interactions between the two antibiotics, which provides a rare example of how naturally occurring variations between strains of the same bacterial species can sometimes generate very different drug interactions. acknowledgement: High-throughput sequencing data were generated by the Vienna BioCenter Core Facilities. The authors would like to thank Karin Mitosch, Bor Kavcic, and Nadine Kraupner for their constructive feedback. The authors would also like to thank Gertraud Stift, Julia Flor, Renate Srsek, Agnieszka Wiktor, and Booshini Fernando for technical support. article_number: '760017' article_processing_charge: No article_type: original author: - first_name: Qin full_name: Qi, Qin id: 3B22D412-F248-11E8-B48F-1D18A9856A87 last_name: Qi orcid: 0000-0002-6148-2416 - first_name: S. Andreas full_name: Angermayr, S. Andreas last_name: Angermayr - first_name: Mark Tobias full_name: Bollenbach, Mark Tobias id: 3E6DB97A-F248-11E8-B48F-1D18A9856A87 last_name: Bollenbach orcid: 0000-0003-4398-476X citation: ama: Qi Q, Angermayr SA, Bollenbach MT. Uncovering Key Metabolic Determinants of the Drug Interactions Between Trimethoprim and Erythromycin in Escherichia coli. Frontiers in Microbiology. 2021;12. doi:10.3389/fmicb.2021.760017 apa: Qi, Q., Angermayr, S. A., & Bollenbach, M. T. (2021). Uncovering Key Metabolic Determinants of the Drug Interactions Between Trimethoprim and Erythromycin in Escherichia coli. Frontiers in Microbiology. Frontiers. https://doi.org/10.3389/fmicb.2021.760017 chicago: Qi, Qin, S. Andreas Angermayr, and Mark Tobias Bollenbach. “Uncovering Key Metabolic Determinants of the Drug Interactions Between Trimethoprim and Erythromycin in Escherichia Coli.” Frontiers in Microbiology. Frontiers, 2021. https://doi.org/10.3389/fmicb.2021.760017. ieee: Q. Qi, S. A. Angermayr, and M. T. Bollenbach, “Uncovering Key Metabolic Determinants of the Drug Interactions Between Trimethoprim and Erythromycin in Escherichia coli,” Frontiers in Microbiology, vol. 12. Frontiers, 2021. ista: Qi Q, Angermayr SA, Bollenbach MT. 2021. Uncovering Key Metabolic Determinants of the Drug Interactions Between Trimethoprim and Erythromycin in Escherichia coli. Frontiers in Microbiology. 12, 760017. mla: Qi, Qin, et al. “Uncovering Key Metabolic Determinants of the Drug Interactions Between Trimethoprim and Erythromycin in Escherichia Coli.” Frontiers in Microbiology, vol. 12, 760017, Frontiers, 2021, doi:10.3389/fmicb.2021.760017. short: Q. Qi, S.A. Angermayr, M.T. Bollenbach, Frontiers in Microbiology 12 (2021). date_created: 2021-11-11T10:39:37Z date_published: 2021-10-20T00:00:00Z date_updated: 2023-08-14T11:43:23Z day: '20' ddc: - '610' doi: 10.3389/fmicb.2021.760017 ec_funded: 1 external_id: isi: - '000715997300001' pmid: - '34745067' file: - access_level: open_access checksum: d41321748e9588dd3cf03e9a7222127f content_type: application/pdf creator: cchlebak date_created: 2021-11-11T10:54:40Z date_updated: 2021-11-11T10:54:40Z file_id: '10272' file_name: 2021_FrontiersMicrob_Qi.pdf file_size: 2397203 relation: main_file success: 1 file_date_updated: 2021-11-11T10:54:40Z has_accepted_license: '1' intvolume: ' 12' isi: 1 keyword: - microbiology language: - iso: eng month: '10' oa: 1 oa_version: Published Version pmid: 1 project: - _id: 25E9AF9E-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P27201-B22 name: Revealing the mechanisms underlying drug interactions - _id: 25E83C2C-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '303507' name: Optimality principles in responses to antibiotics publication: Frontiers in Microbiology publication_identifier: eissn: - 1664-302X publication_status: published publisher: Frontiers quality_controlled: '1' scopus_import: '1' status: public title: Uncovering Key Metabolic Determinants of the Drug Interactions Between Trimethoprim and Erythromycin in Escherichia coli tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 12 year: '2021' ... --- _id: '10221' abstract: - lang: eng text: We prove that any deterministic matrix is approximately the identity in the eigenbasis of a large random Wigner matrix with very high probability and with an optimal error inversely proportional to the square root of the dimension. Our theorem thus rigorously verifies the Eigenstate Thermalisation Hypothesis by Deutsch (Phys Rev A 43:2046–2049, 1991) for the simplest chaotic quantum system, the Wigner ensemble. In mathematical terms, we prove the strong form of Quantum Unique Ergodicity (QUE) with an optimal convergence rate for all eigenvectors simultaneously, generalizing previous probabilistic QUE results in Bourgade and Yau (Commun Math Phys 350:231–278, 2017) and Bourgade et al. (Commun Pure Appl Math 73:1526–1596, 2020). acknowledgement: Open access funding provided by Institute of Science and Technology (IST Austria). article_processing_charge: Yes (via OA deal) article_type: original author: - first_name: Giorgio full_name: Cipolloni, Giorgio id: 42198EFA-F248-11E8-B48F-1D18A9856A87 last_name: Cipolloni orcid: 0000-0002-4901-7992 - first_name: László full_name: Erdös, László id: 4DBD5372-F248-11E8-B48F-1D18A9856A87 last_name: Erdös orcid: 0000-0001-5366-9603 - first_name: Dominik J full_name: Schröder, Dominik J id: 408ED176-F248-11E8-B48F-1D18A9856A87 last_name: Schröder orcid: 0000-0002-2904-1856 citation: ama: Cipolloni G, Erdös L, Schröder DJ. Eigenstate thermalization hypothesis for Wigner matrices. Communications in Mathematical Physics. 2021;388(2):1005–1048. doi:10.1007/s00220-021-04239-z apa: Cipolloni, G., Erdös, L., & Schröder, D. J. (2021). Eigenstate thermalization hypothesis for Wigner matrices. Communications in Mathematical Physics. Springer Nature. https://doi.org/10.1007/s00220-021-04239-z chicago: Cipolloni, Giorgio, László Erdös, and Dominik J Schröder. “Eigenstate Thermalization Hypothesis for Wigner Matrices.” Communications in Mathematical Physics. Springer Nature, 2021. https://doi.org/10.1007/s00220-021-04239-z. ieee: G. Cipolloni, L. Erdös, and D. J. Schröder, “Eigenstate thermalization hypothesis for Wigner matrices,” Communications in Mathematical Physics, vol. 388, no. 2. Springer Nature, pp. 1005–1048, 2021. ista: Cipolloni G, Erdös L, Schröder DJ. 2021. Eigenstate thermalization hypothesis for Wigner matrices. Communications in Mathematical Physics. 388(2), 1005–1048. mla: Cipolloni, Giorgio, et al. “Eigenstate Thermalization Hypothesis for Wigner Matrices.” Communications in Mathematical Physics, vol. 388, no. 2, Springer Nature, 2021, pp. 1005–1048, doi:10.1007/s00220-021-04239-z. short: G. Cipolloni, L. Erdös, D.J. Schröder, Communications in Mathematical Physics 388 (2021) 1005–1048. date_created: 2021-11-07T23:01:25Z date_published: 2021-10-29T00:00:00Z date_updated: 2023-08-14T10:29:49Z day: '29' ddc: - '510' department: - _id: LaEr doi: 10.1007/s00220-021-04239-z external_id: arxiv: - '2012.13215' isi: - '000712232700001' file: - access_level: open_access checksum: a2c7b6f5d23b5453cd70d1261272283b content_type: application/pdf creator: cchlebak date_created: 2022-02-02T10:19:55Z date_updated: 2022-02-02T10:19:55Z file_id: '10715' file_name: 2021_CommunMathPhys_Cipolloni.pdf file_size: 841426 relation: main_file success: 1 file_date_updated: 2022-02-02T10:19:55Z has_accepted_license: '1' intvolume: ' 388' isi: 1 issue: '2' language: - iso: eng month: '10' oa: 1 oa_version: Published Version page: 1005–1048 project: - _id: B67AFEDC-15C9-11EA-A837-991A96BB2854 name: IST Austria Open Access Fund publication: Communications in Mathematical Physics publication_identifier: eissn: - 1432-0916 issn: - 0010-3616 publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: Eigenstate thermalization hypothesis for Wigner matrices tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 388 year: '2021' ... --- _id: '10224' abstract: - lang: eng text: We investigate the Fröhlich polaron model on a three-dimensional torus, and give a proof of the second-order quantum corrections to its ground-state energy in the strong-coupling limit. Compared to previous work in the confined case, the translational symmetry (and its breaking in the Pekar approximation) makes the analysis substantially more challenging. acknowledgement: "Funding from the European Union’s Horizon 2020 research and innovation programme under the ERC grant agreement No 694227 is gratefully acknowledged. We would also like to thank Rupert Frank for many helpful discussions, especially related to the Gross coordinate transformation defined in Def. 4.7.\r\nOpen access funding provided by Institute of Science and Technology (IST Austria)." article_processing_charge: Yes (via OA deal) article_type: original author: - first_name: Dario full_name: Feliciangeli, Dario id: 41A639AA-F248-11E8-B48F-1D18A9856A87 last_name: Feliciangeli orcid: 0000-0003-0754-8530 - first_name: Robert full_name: Seiringer, Robert id: 4AFD0470-F248-11E8-B48F-1D18A9856A87 last_name: Seiringer orcid: 0000-0002-6781-0521 citation: ama: 'Feliciangeli D, Seiringer R. The strongly coupled polaron on the torus: Quantum corrections to the Pekar asymptotics. Archive for Rational Mechanics and Analysis. 2021;242(3):1835–1906. doi:10.1007/s00205-021-01715-7' apa: 'Feliciangeli, D., & Seiringer, R. (2021). The strongly coupled polaron on the torus: Quantum corrections to the Pekar asymptotics. Archive for Rational Mechanics and Analysis. Springer Nature. https://doi.org/10.1007/s00205-021-01715-7' chicago: 'Feliciangeli, Dario, and Robert Seiringer. “The Strongly Coupled Polaron on the Torus: Quantum Corrections to the Pekar Asymptotics.” Archive for Rational Mechanics and Analysis. Springer Nature, 2021. https://doi.org/10.1007/s00205-021-01715-7.' ieee: 'D. Feliciangeli and R. Seiringer, “The strongly coupled polaron on the torus: Quantum corrections to the Pekar asymptotics,” Archive for Rational Mechanics and Analysis, vol. 242, no. 3. Springer Nature, pp. 1835–1906, 2021.' ista: 'Feliciangeli D, Seiringer R. 2021. The strongly coupled polaron on the torus: Quantum corrections to the Pekar asymptotics. Archive for Rational Mechanics and Analysis. 242(3), 1835–1906.' mla: 'Feliciangeli, Dario, and Robert Seiringer. “The Strongly Coupled Polaron on the Torus: Quantum Corrections to the Pekar Asymptotics.” Archive for Rational Mechanics and Analysis, vol. 242, no. 3, Springer Nature, 2021, pp. 1835–1906, doi:10.1007/s00205-021-01715-7.' short: D. Feliciangeli, R. Seiringer, Archive for Rational Mechanics and Analysis 242 (2021) 1835–1906. date_created: 2021-11-07T23:01:26Z date_published: 2021-10-25T00:00:00Z date_updated: 2023-08-14T10:32:19Z day: '25' ddc: - '530' department: - _id: RoSe doi: 10.1007/s00205-021-01715-7 ec_funded: 1 external_id: arxiv: - '2101.12566' isi: - '000710850600001' file: - access_level: open_access checksum: 672e9c21b20f1a50854b7c821edbb92f content_type: application/pdf creator: alisjak date_created: 2021-12-14T08:35:42Z date_updated: 2021-12-14T08:35:42Z file_id: '10544' file_name: 2021_Springer_Feliciangeli.pdf file_size: 990529 relation: main_file success: 1 file_date_updated: 2021-12-14T08:35:42Z has_accepted_license: '1' intvolume: ' 242' isi: 1 issue: '3' language: - iso: eng month: '10' oa: 1 oa_version: Published Version page: 1835–1906 project: - _id: 25C6DC12-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '694227' name: Analysis of quantum many-body systems publication: Archive for Rational Mechanics and Analysis publication_identifier: eissn: - 1432-0673 issn: - 0003-9527 publication_status: published publisher: Springer Nature quality_controlled: '1' related_material: record: - id: '9787' relation: earlier_version status: public scopus_import: '1' status: public title: 'The strongly coupled polaron on the torus: Quantum corrections to the Pekar asymptotics' tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 242 year: '2021' ... --- _id: '10281' abstract: - lang: eng text: Mutations affecting mTOR or RAS signaling underlie defined syndromes (the so-called mTORopathies and RASopathies) with high risk for Autism Spectrum Disorder (ASD). These syndromes show a broad variety of somatic phenotypes including cancers, skin abnormalities, heart disease and facial dysmorphisms. Less well studied are the neuropsychiatric symptoms such as ASD. Here, we assess the relevance of these signalopathies in ASD reviewing genetic, human cell model, rodent studies and clinical trials. We conclude that signalopathies have an increased liability for ASD and that, in particular, ASD individuals with dysmorphic features and intellectual disability (ID) have a higher chance for disruptive mutations in RAS- and mTOR-related genes. Studies on rodent and human cell models confirm aberrant neuronal development as the underlying pathology. Human studies further suggest that multiple hits are necessary to induce the respective phenotypes. Recent clinical trials do only report improvements for comorbid conditions such as epilepsy or cancer but not for behavioral aspects. Animal models show that treatment during early development can rescue behavioral phenotypes. Taken together, we suggest investigating the differential roles of mTOR and RAS signaling in both human and rodent models, and to test drug treatment both during and after neuronal development in the available model systems acknowledgement: 'This review was funded by the IMI2 Initiative under the grant AIMS-2-TRIALS No 777394, by the Hessian Ministry for Science and Arts; State of Hesse Ministry for Science and Arts: LOEWE-Grant to the CePTER-Consortium (www.uni-frankfurt.de/67689811); Research (BMBF) under the grant RAISE-genic No 779282 all to AGC. This work was also supported by the European Union’s Horizon 2020 research and innovation program (ERC) grant 715508 (REVERSEAUTISM) and by the Austrian Science Fund (FWF) (DK W1232-B24) both to G.N. and both BMBF GeNeRARe 01GM1519A and CRC 1080, project B10, of the German Research Foundation (DFG) to M.J.S, respectively. We want to thank R. Waltes for her support in preparing this manuscript.' alternative_title: - Special Issue "From Genes to Therapy in Autism Spectrum Disorder" article_number: '1746' article_processing_charge: No article_type: original author: - first_name: Verica full_name: Vasic, Verica last_name: Vasic - first_name: Mattson S.O. full_name: Jones, Mattson S.O. last_name: Jones - first_name: Denise full_name: Haslinger, Denise id: 76922BDA-3D3B-11EA-90BD-A44F3DDC885E last_name: Haslinger - first_name: Lisa full_name: Knaus, Lisa id: 3B2ABCF4-F248-11E8-B48F-1D18A9856A87 last_name: Knaus - first_name: Michael J. full_name: Schmeisser, Michael J. last_name: Schmeisser - first_name: Gaia full_name: Novarino, Gaia id: 3E57A680-F248-11E8-B48F-1D18A9856A87 last_name: Novarino orcid: 0000-0002-7673-7178 - first_name: Andreas G. full_name: Chiocchetti, Andreas G. last_name: Chiocchetti citation: ama: 'Vasic V, Jones MSO, Haslinger D, et al. Translating the role of mtor-and ras-associated signalopathies in autism spectrum disorder: Models, mechanisms and treatment. Genes. 2021;12(11). doi:10.3390/genes12111746' apa: 'Vasic, V., Jones, M. S. O., Haslinger, D., Knaus, L., Schmeisser, M. J., Novarino, G., & Chiocchetti, A. G. (2021). Translating the role of mtor-and ras-associated signalopathies in autism spectrum disorder: Models, mechanisms and treatment. Genes. MDPI. https://doi.org/10.3390/genes12111746' chicago: 'Vasic, Verica, Mattson S.O. Jones, Denise Haslinger, Lisa Knaus, Michael J. Schmeisser, Gaia Novarino, and Andreas G. Chiocchetti. “Translating the Role of Mtor-and Ras-Associated Signalopathies in Autism Spectrum Disorder: Models, Mechanisms and Treatment.” Genes. MDPI, 2021. https://doi.org/10.3390/genes12111746.' ieee: 'V. Vasic et al., “Translating the role of mtor-and ras-associated signalopathies in autism spectrum disorder: Models, mechanisms and treatment,” Genes, vol. 12, no. 11. MDPI, 2021.' ista: 'Vasic V, Jones MSO, Haslinger D, Knaus L, Schmeisser MJ, Novarino G, Chiocchetti AG. 2021. Translating the role of mtor-and ras-associated signalopathies in autism spectrum disorder: Models, mechanisms and treatment. Genes. 12(11), 1746.' mla: 'Vasic, Verica, et al. “Translating the Role of Mtor-and Ras-Associated Signalopathies in Autism Spectrum Disorder: Models, Mechanisms and Treatment.” Genes, vol. 12, no. 11, 1746, MDPI, 2021, doi:10.3390/genes12111746.' short: V. Vasic, M.S.O. Jones, D. Haslinger, L. Knaus, M.J. Schmeisser, G. Novarino, A.G. Chiocchetti, Genes 12 (2021). date_created: 2021-11-14T23:01:24Z date_published: 2021-10-30T00:00:00Z date_updated: 2023-08-14T11:46:12Z day: '30' ddc: - '570' department: - _id: GaNo doi: 10.3390/genes12111746 ec_funded: 1 external_id: isi: - '000834044200002' file: - access_level: open_access checksum: 256cb832a9c3051c7dc741f6423b8cbd content_type: application/pdf creator: dernst date_created: 2022-05-16T07:02:27Z date_updated: 2022-05-16T07:02:27Z file_id: '11380' file_name: 2021_Genes_Vasic.pdf file_size: 1335308 relation: main_file success: 1 file_date_updated: 2022-05-16T07:02:27Z has_accepted_license: '1' intvolume: ' 12' isi: 1 issue: '11' language: - iso: eng month: '10' oa: 1 oa_version: Published Version project: - _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: 2548AE96-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: W1232-B24 name: Molecular Drug Targets publication: Genes publication_identifier: eissn: - 2073-4425 publication_status: published publisher: MDPI quality_controlled: '1' scopus_import: '1' status: public title: 'Translating the role of mtor-and ras-associated signalopathies in autism spectrum disorder: Models, mechanisms and treatment' tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 12 year: '2021' ... --- _id: '10282' abstract: - lang: eng text: Advanced transcriptome sequencing has revealed that the majority of eukaryotic genes undergo alternative splicing (AS). Nonetheless, little effort has been dedicated to investigating the functional relevance of particular splicing events, even those in the key developmental and hormonal regulators. Combining approaches of genetics, biochemistry and advanced confocal microscopy, we describe the impact of alternative splicing on the PIN7 gene in the model plant Arabidopsis thaliana. PIN7 encodes a polarly localized transporter for the phytohormone auxin and produces two evolutionarily conserved transcripts, PIN7a and PIN7b. PIN7a and PIN7b, differing in a four amino acid stretch, exhibit almost identical expression patterns and subcellular localization. We reveal that they are closely associated and mutually influence each other's mobility within the plasma membrane. Phenotypic complementation tests indicate that the functional contribution of PIN7b per se is minor, but it markedly reduces the prominent PIN7a activity, which is required for correct seedling apical hook formation and auxin-mediated tropic responses. Our results establish alternative splicing of the PIN family as a conserved, functionally relevant mechanism, revealing an additional regulatory level of auxin-mediated plant development. acknowledgement: We thank Claus Schwechheimer for the pin34 and pin347 seeds, Yuliia Mironova for technical assistance, Ksenia Timofeyenko and Dmitry Konovalov for help with the evolutional analysis, Konstantin Kutashev and Siarhei Dabravolski for assistance with FRET-FLIM, Huibin Han for advice with hypocotyl imaging, Karel Müller for the initial qRT-PCR on the tobacco cell lines, Stano Pekár for suggestions regarding the statistical analysis of the morphodynamic measurements, and Jozef Mravec, Dolf Weijers and Lindy Abas for their comments on the manuscript. This work was supported by the Czech Science Foundation (projects 16-26428S and 19-23773S to IK, MH and KRůžička, 19-18917S to JHumpolíčková and 18-26981S to JF), and the Ministry of Education, Youth and Sports of the Czech Republic (MEYS, CZ.02.1.01/0.0/0.0/16_019/0000738) to KRůžička and JHejátko. The imaging facilities of the Institute of Experimental Botany and CEITEC are supported by MEYS (LM2018129 – Czech BioImaging and CZ.02.1.01/0.0/0.0/16_013/0001775). The authors declare no competing interests. article_processing_charge: No article_type: original author: - first_name: Ivan full_name: Kashkan, Ivan last_name: Kashkan - first_name: Mónika full_name: Hrtyan, Mónika id: 45A71A74-F248-11E8-B48F-1D18A9856A87 last_name: Hrtyan - first_name: Katarzyna full_name: Retzer, Katarzyna last_name: Retzer - first_name: Jana full_name: Humpolíčková, Jana last_name: Humpolíčková - first_name: Aswathy full_name: Jayasree, Aswathy last_name: Jayasree - first_name: Roberta full_name: Filepová, Roberta last_name: Filepová - first_name: Zuzana full_name: Vondráková, Zuzana last_name: Vondráková - first_name: Sibu full_name: Simon, Sibu id: 4542EF9A-F248-11E8-B48F-1D18A9856A87 last_name: Simon orcid: 0000-0002-1998-6741 - first_name: Debbie full_name: Rombaut, Debbie last_name: Rombaut - first_name: Thomas B. full_name: Jacobs, Thomas B. last_name: Jacobs - first_name: Mikko J. full_name: Frilander, Mikko J. last_name: Frilander - first_name: Jan full_name: Hejátko, Jan last_name: Hejátko - first_name: Jiří full_name: Friml, Jiří id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 - first_name: Jan full_name: Petrášek, Jan last_name: Petrášek - first_name: Kamil full_name: Růžička, Kamil last_name: Růžička citation: ama: Kashkan I, Hrtyan M, Retzer K, et al. Mutually opposing activity of PIN7 splicing isoforms is required for auxin-mediated tropic responses in Arabidopsis thaliana. New Phytologist. 2021;233:329-343. doi:10.1111/nph.17792 apa: Kashkan, I., Hrtyan, M., Retzer, K., Humpolíčková, J., Jayasree, A., Filepová, R., … Růžička, K. (2021). Mutually opposing activity of PIN7 splicing isoforms is required for auxin-mediated tropic responses in Arabidopsis thaliana. New Phytologist. Wiley. https://doi.org/10.1111/nph.17792 chicago: Kashkan, Ivan, Mónika Hrtyan, Katarzyna Retzer, Jana Humpolíčková, Aswathy Jayasree, Roberta Filepová, Zuzana Vondráková, et al. “Mutually Opposing Activity of PIN7 Splicing Isoforms Is Required for Auxin-Mediated Tropic Responses in Arabidopsis Thaliana.” New Phytologist. Wiley, 2021. https://doi.org/10.1111/nph.17792. ieee: I. Kashkan et al., “Mutually opposing activity of PIN7 splicing isoforms is required for auxin-mediated tropic responses in Arabidopsis thaliana,” New Phytologist, vol. 233. Wiley, pp. 329–343, 2021. ista: Kashkan I, Hrtyan M, Retzer K, Humpolíčková J, Jayasree A, Filepová R, Vondráková Z, Simon S, Rombaut D, Jacobs TB, Frilander MJ, Hejátko J, Friml J, Petrášek J, Růžička K. 2021. Mutually opposing activity of PIN7 splicing isoforms is required for auxin-mediated tropic responses in Arabidopsis thaliana. New Phytologist. 233, 329–343. mla: Kashkan, Ivan, et al. “Mutually Opposing Activity of PIN7 Splicing Isoforms Is Required for Auxin-Mediated Tropic Responses in Arabidopsis Thaliana.” New Phytologist, vol. 233, Wiley, 2021, pp. 329–43, doi:10.1111/nph.17792. short: I. Kashkan, M. Hrtyan, K. Retzer, J. Humpolíčková, A. Jayasree, R. Filepová, Z. Vondráková, S. Simon, D. Rombaut, T.B. Jacobs, M.J. Frilander, J. Hejátko, J. Friml, J. Petrášek, K. Růžička, New Phytologist 233 (2021) 329–343. date_created: 2021-11-14T23:01:24Z date_published: 2021-11-05T00:00:00Z date_updated: 2023-08-14T11:46:43Z day: '05' department: - _id: JiFr doi: 10.1111/nph.17792 external_id: isi: - '000714678100001' pmid: - '34637542' intvolume: ' 233' isi: 1 language: - iso: eng main_file_link: - open_access: '1' url: https://www.biorxiv.org/content/10.1101/2020.05.02.074070v2 month: '11' oa: 1 oa_version: Preprint page: 329-343 pmid: 1 publication: New Phytologist publication_identifier: eissn: - 1469-8137 issn: - 0028-646X publication_status: published publisher: Wiley quality_controlled: '1' scopus_import: '1' status: public title: Mutually opposing activity of PIN7 splicing isoforms is required for auxin-mediated tropic responses in Arabidopsis thaliana type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 233 year: '2021' ... --- _id: '10220' abstract: - lang: eng text: "We study conditions under which a finite simplicial complex K can be mapped to ℝd without higher-multiplicity intersections. An almost r-embedding is a map f: K → ℝd such that the images of any r pairwise disjoint simplices of K do not have a common point. We show that if r is not a prime power and d ≥ 2r + 1, then there is a counterexample to the topological Tverberg conjecture, i.e., there is an almost r-embedding of the (d +1)(r − 1)-simplex in ℝd. This improves on previous constructions of counterexamples (for d ≥ 3r) based on a series of papers by M. Özaydin, M. Gromov, P. Blagojević, F. Frick, G. Ziegler, and the second and fourth present authors.\r\n\r\nThe counterexamples are obtained by proving the following algebraic criterion in codimension 2: If r ≥ 3 and if K is a finite 2(r − 1)-complex, then there exists an almost r-embedding K → ℝ2r if and only if there exists a general position PL map f: K → ℝ2r such that the algebraic intersection number of the f-images of any r pairwise disjoint simplices of K is zero. This result can be restated in terms of a cohomological obstruction and extends an analogous codimension 3 criterion by the second and fourth authors. As another application, we classify ornaments f: S3 ⊔ S3 ⊔ S3 → ℝ5 up to ornament concordance.\r\n\r\nIt follows from work of M. Freedman, V. Krushkal and P. Teichner that the analogous criterion for r = 2 is false. We prove a lemma on singular higher-dimensional Borromean rings, yielding an elementary proof of the counterexample." acknowledgement: Research supported by the Swiss National Science Foundation (Project SNSF-PP00P2-138948), by the Austrian Science Fund (FWF Project P31312-N35), by the Russian Foundation for Basic Research (Grants No. 15-01-06302 and 19-01-00169), by a Simons-IUM Fellowship, and by the D. Zimin Dynasty Foundation Grant. We would like to thank E. Alkin, A. Klyachko, V. Krushkal, S. Melikhov, M. Tancer, P. Teichner and anonymous referees for helpful comments and discussions. article_processing_charge: No article_type: original author: - first_name: Sergey full_name: Avvakumov, Sergey id: 3827DAC8-F248-11E8-B48F-1D18A9856A87 last_name: Avvakumov - first_name: Isaac full_name: Mabillard, Isaac id: 32BF9DAA-F248-11E8-B48F-1D18A9856A87 last_name: Mabillard - first_name: Arkadiy B. full_name: Skopenkov, Arkadiy B. last_name: Skopenkov - first_name: Uli full_name: Wagner, Uli id: 36690CA2-F248-11E8-B48F-1D18A9856A87 last_name: Wagner orcid: 0000-0002-1494-0568 citation: ama: Avvakumov S, Mabillard I, Skopenkov AB, Wagner U. Eliminating higher-multiplicity intersections. III. Codimension 2. Israel Journal of Mathematics. 2021;245:501–534. doi:10.1007/s11856-021-2216-z apa: Avvakumov, S., Mabillard, I., Skopenkov, A. B., & Wagner, U. (2021). Eliminating higher-multiplicity intersections. III. Codimension 2. Israel Journal of Mathematics. Springer Nature. https://doi.org/10.1007/s11856-021-2216-z chicago: Avvakumov, Sergey, Isaac Mabillard, Arkadiy B. Skopenkov, and Uli Wagner. “Eliminating Higher-Multiplicity Intersections. III. Codimension 2.” Israel Journal of Mathematics. Springer Nature, 2021. https://doi.org/10.1007/s11856-021-2216-z. ieee: S. Avvakumov, I. Mabillard, A. B. Skopenkov, and U. Wagner, “Eliminating higher-multiplicity intersections. III. Codimension 2,” Israel Journal of Mathematics, vol. 245. Springer Nature, pp. 501–534, 2021. ista: Avvakumov S, Mabillard I, Skopenkov AB, Wagner U. 2021. Eliminating higher-multiplicity intersections. III. Codimension 2. Israel Journal of Mathematics. 245, 501–534. mla: Avvakumov, Sergey, et al. “Eliminating Higher-Multiplicity Intersections. III. Codimension 2.” Israel Journal of Mathematics, vol. 245, Springer Nature, 2021, pp. 501–534, doi:10.1007/s11856-021-2216-z. short: S. Avvakumov, I. Mabillard, A.B. Skopenkov, U. Wagner, Israel Journal of Mathematics 245 (2021) 501–534. date_created: 2021-11-07T23:01:24Z date_published: 2021-10-30T00:00:00Z date_updated: 2023-08-14T11:43:55Z day: '30' department: - _id: UlWa doi: 10.1007/s11856-021-2216-z external_id: arxiv: - '1511.03501' isi: - '000712942100013' intvolume: ' 245' isi: 1 language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1511.03501 month: '10' oa: 1 oa_version: Preprint page: '501–534 ' project: - _id: 26611F5C-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P31312 name: Algorithms for Embeddings and Homotopy Theory publication: Israel Journal of Mathematics publication_identifier: eissn: - 1565-8511 issn: - 0021-2172 publication_status: published publisher: Springer Nature quality_controlled: '1' related_material: record: - id: '8183' relation: earlier_version status: public - id: '9308' relation: earlier_version status: public scopus_import: '1' status: public title: Eliminating higher-multiplicity intersections. III. Codimension 2 type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 245 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 license: https://creativecommons.org/publicdomain/zero/1.0/ 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: '10301' abstract: - lang: eng text: De novo protein synthesis is required for synapse modifications underlying stable memory encoding. Yet neurons are highly compartmentalized cells and how protein synthesis can be regulated at the synapse level is unknown. Here, we characterize neuronal signaling complexes formed by the postsynaptic scaffold GIT1, the mechanistic target of rapamycin (mTOR) kinase, and Raptor that couple synaptic stimuli to mTOR-dependent protein synthesis; and identify NMDA receptors containing GluN3A subunits as key negative regulators of GIT1 binding to mTOR. Disruption of GIT1/mTOR complexes by enhancing GluN3A expression or silencing GIT1 inhibits synaptic mTOR activation and restricts the mTOR-dependent translation of specific activity-regulated mRNAs. Conversely, GluN3A removal enables complex formation, potentiates mTOR-dependent protein synthesis, and facilitates the consolidation of associative and spatial memories in mice. The memory enhancement becomes evident with light or spaced training, can be achieved by selectively deleting GluN3A from excitatory neurons during adulthood, and does not compromise other aspects of cognition such as memory flexibility or extinction. Our findings provide mechanistic insight into synaptic translational control and reveal a potentially selective target for cognitive enhancement. acknowledgement: We thank Stuart Lipton and Nobuki Nakanishi for providing the Grin3a knockout mice, Beverly Davidson for the AAV-caRheb, Jose Esteban for help with behavioral and biochemical experiments, and Noelia Campillo, Rebeca Martínez-Turrillas, and Ana Navarro for expert technical help. Work was funded by the UTE project CIMA; fellowships from the Fundación Tatiana Pérez de Guzmán el Bueno, FEBS, and IBRO (to M.J.C.D.), Generalitat Valenciana (to O.E.-Z.), Juan de la Cierva (to L.G.R.), FPI-MINECO (to E.R.V., to S.N.) and Intertalentum postdoctoral program (to V.B.); ANR (GluBrain3A) and ERC Advanced Grants (#693021) (to P.P.); Ramón y Cajal program RYC2014-15784, RETOS-MINECO SAF2016-76565-R, ERANET-Neuron JTC 2019 ISCIII AC19/00077 FEDER funds (to R.A.); RETOS-MINECO SAF2017-87928-R (to A.B.); an NIH grant (NS76637) and UTHSC College of Medicine funds (to S.J.T.); and NARSAD Independent Investigator Award and grants from the MINECO (CSD2008-00005, SAF2013-48983R, SAF2016-80895-R), Generalitat Valenciana (PROMETEO 2019/020)(to I.P.O.) and Severo-Ochoa Excellence Awards (SEV-2013-0317, SEV-2017-0723). article_number: e71575 article_processing_charge: No article_type: original author: - first_name: María J full_name: Conde-Dusman, María J last_name: Conde-Dusman - first_name: Partha N full_name: Dey, Partha N last_name: Dey - first_name: Óscar full_name: Elía-Zudaire, Óscar last_name: Elía-Zudaire - first_name: Luis E full_name: Garcia Rabaneda, Luis E id: 33D1B084-F248-11E8-B48F-1D18A9856A87 last_name: Garcia Rabaneda - first_name: Carmen full_name: García-Lira, Carmen last_name: García-Lira - first_name: Teddy full_name: Grand, Teddy last_name: Grand - first_name: Victor full_name: Briz, Victor last_name: Briz - first_name: Eric R full_name: Velasco, Eric R last_name: Velasco - first_name: Raül full_name: Andero Galí, Raül last_name: Andero Galí - first_name: Sergio full_name: Niñerola, Sergio last_name: Niñerola - first_name: Angel full_name: Barco, Angel last_name: Barco - first_name: Pierre full_name: Paoletti, Pierre last_name: Paoletti - first_name: John F full_name: Wesseling, John F last_name: Wesseling - first_name: Fabrizio full_name: Gardoni, Fabrizio last_name: Gardoni - first_name: Steven J full_name: Tavalin, Steven J last_name: Tavalin - first_name: Isabel full_name: Perez-Otaño, Isabel last_name: Perez-Otaño citation: ama: Conde-Dusman MJ, Dey PN, Elía-Zudaire Ó, et al. Control of protein synthesis and memory by GluN3A-NMDA receptors through inhibition of GIT1/mTORC1 assembly. eLife. 2021;10. doi:10.7554/elife.71575 apa: Conde-Dusman, M. J., Dey, P. N., Elía-Zudaire, Ó., Garcia Rabaneda, L. E., García-Lira, C., Grand, T., … Perez-Otaño, I. (2021). Control of protein synthesis and memory by GluN3A-NMDA receptors through inhibition of GIT1/mTORC1 assembly. ELife. eLife Sciences Publications. https://doi.org/10.7554/elife.71575 chicago: Conde-Dusman, María J, Partha N Dey, Óscar Elía-Zudaire, Luis E Garcia Rabaneda, Carmen García-Lira, Teddy Grand, Victor Briz, et al. “Control of Protein Synthesis and Memory by GluN3A-NMDA Receptors through Inhibition of GIT1/MTORC1 Assembly.” ELife. eLife Sciences Publications, 2021. https://doi.org/10.7554/elife.71575. ieee: M. J. Conde-Dusman et al., “Control of protein synthesis and memory by GluN3A-NMDA receptors through inhibition of GIT1/mTORC1 assembly,” eLife, vol. 10. eLife Sciences Publications, 2021. ista: Conde-Dusman MJ, Dey PN, Elía-Zudaire Ó, Garcia Rabaneda LE, García-Lira C, Grand T, Briz V, Velasco ER, Andero Galí R, Niñerola S, Barco A, Paoletti P, Wesseling JF, Gardoni F, Tavalin SJ, Perez-Otaño I. 2021. Control of protein synthesis and memory by GluN3A-NMDA receptors through inhibition of GIT1/mTORC1 assembly. eLife. 10, e71575. mla: Conde-Dusman, María J., et al. “Control of Protein Synthesis and Memory by GluN3A-NMDA Receptors through Inhibition of GIT1/MTORC1 Assembly.” ELife, vol. 10, e71575, eLife Sciences Publications, 2021, doi:10.7554/elife.71575. short: M.J. Conde-Dusman, P.N. Dey, Ó. Elía-Zudaire, L.E. Garcia Rabaneda, C. García-Lira, T. Grand, V. Briz, E.R. Velasco, R. Andero Galí, S. Niñerola, A. Barco, P. Paoletti, J.F. Wesseling, F. Gardoni, S.J. Tavalin, I. Perez-Otaño, ELife 10 (2021). date_created: 2021-11-18T06:59:45Z date_published: 2021-11-17T00:00:00Z date_updated: 2023-08-14T11:50:50Z day: '17' ddc: - '570' department: - _id: GaNo doi: 10.7554/elife.71575 external_id: isi: - '000720945900001' file: - access_level: open_access checksum: 59318e9e41507cec83c2f4070e6ad540 content_type: application/pdf creator: lgarciar date_created: 2021-11-18T07:02:02Z date_updated: 2021-11-18T07:02:02Z file_id: '10302' file_name: elife-71575-v1.pdf file_size: 2477302 relation: main_file success: 1 file_date_updated: 2021-11-18T07:02:02Z has_accepted_license: '1' intvolume: ' 10' isi: 1 keyword: - general immunology and microbiology - general biochemistry - genetics and molecular biology - general medicine - general neuroscience language: - iso: eng month: '11' oa: 1 oa_version: Published Version publication: eLife publication_identifier: issn: - 2050-084X publication_status: published publisher: eLife Sciences Publications quality_controlled: '1' status: public title: Control of protein synthesis and memory by GluN3A-NMDA receptors through inhibition of GIT1/mTORC1 assembly tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 10 year: '2021' ... --- _id: '10283' abstract: - lang: eng text: 'During the past decade, the scientific community and outside observers have noted a concerning lack of rigor and transparency in preclinical research that led to talk of a “reproducibility crisis” in the life sciences (Baker, 2016; Bespalov & Steckler, 2018; Heddleston et al, 2021). Various measures have been proposed to address the problem: from better training of scientists to more oversight to expanded publishing practices such as preregistration of studies. The recently published EQIPD (Enhancing Quality in Preclinical Data) System is, to date, the largest initiative that aims to establish a systematic approach for increasing the robustness and reliability of biomedical research (Bespalov et al, 2021). However, promoting a cultural change in research practices warrants a broad adoption of the Quality System and its underlying philosophy. It is here that academic Core Facilities (CF), research service providers at universities and research institutions, can make a difference. It is fair to assume that a significant fraction of published data originated from experiments that were designed, run, or analyzed in CFs. These academic services play an important role in the research ecosystem by offering access to cutting-edge equipment and by developing and testing novel techniques and methods that impact research in the academic and private sectors alike (Bikovski et al, 2020). Equipment and infrastructure are not the only value: CFs employ competent personnel with profound knowledge and practical experience of the specific field of interest: animal behavior, imaging, crystallography, genomics, and so on. Thus, CFs are optimally positioned to address concerns about the quality and robustness of preclinical research.' acknowledgement: This EQIPD project has received funding from the Innovative Medicines Initiative 2 Joint Undertaking under grant agreement no. 777364. This Joint Undertaking receives support from the European Union’s Horizon 2020 research and innovation program and EFPIA. LR was supported by the Faculty of Biology and Medicine, University of Lausanne. VV was supported by Biocenter Finland and the Jane and Aatos Erkko Foundation. CP and IKB received funding from the Federal Ministry of Education and Research (BMBF, grant 01PW18001). SB from the Vienna BioCenter Core Facilities (VBCF) Preclinical Phenotyping Facility acknowledges funding from the Austrian Federal Ministry of Education, Science & Research; and the City of Vienna. MT is an incumbent of the Carolito Stiftung Research Fellow Chair in Neurodegenerative Diseases. We thank Dr. Katja Kivinen (Helsinki Institute of Life Science) for discussions and feedback. article_number: e53824 article_processing_charge: Yes (in subscription journal) article_type: original author: - first_name: Leonardo full_name: Restivo, Leonardo last_name: Restivo - first_name: Björn full_name: Gerlach, Björn last_name: Gerlach - first_name: Michael full_name: Tsoory, Michael last_name: Tsoory - first_name: Lior full_name: Bikovski, Lior last_name: Bikovski - first_name: Sylvia full_name: Badurek, Sylvia last_name: Badurek - first_name: Claudia full_name: Pitzer, Claudia last_name: Pitzer - first_name: Isabelle C. full_name: Kos-Braun, Isabelle C. last_name: Kos-Braun - first_name: Anne Laure Mj full_name: Mausset-Bonnefont, Anne Laure Mj last_name: Mausset-Bonnefont - first_name: Jonathan full_name: Ward, Jonathan last_name: Ward - first_name: Michael full_name: Schunn, Michael id: 4272DB4A-F248-11E8-B48F-1D18A9856A87 last_name: Schunn orcid: 0000-0003-4326-5300 - first_name: Lucas P.J.J. full_name: Noldus, Lucas P.J.J. last_name: Noldus - first_name: Anton full_name: Bespalov, Anton last_name: Bespalov - first_name: Vootele full_name: Voikar, Vootele last_name: Voikar citation: ama: 'Restivo L, Gerlach B, Tsoory M, et al. Towards best practices in research: Role of academic core facilities. EMBO Reports. 2021;22. doi:10.15252/embr.202153824' apa: 'Restivo, L., Gerlach, B., Tsoory, M., Bikovski, L., Badurek, S., Pitzer, C., … Voikar, V. (2021). Towards best practices in research: Role of academic core facilities. EMBO Reports. EMBO Press. https://doi.org/10.15252/embr.202153824' chicago: 'Restivo, Leonardo, Björn Gerlach, Michael Tsoory, Lior Bikovski, Sylvia Badurek, Claudia Pitzer, Isabelle C. Kos-Braun, et al. “Towards Best Practices in Research: Role of Academic Core Facilities.” EMBO Reports. EMBO Press, 2021. https://doi.org/10.15252/embr.202153824.' ieee: 'L. Restivo et al., “Towards best practices in research: Role of academic core facilities,” EMBO Reports, vol. 22. EMBO Press, 2021.' ista: 'Restivo L, Gerlach B, Tsoory M, Bikovski L, Badurek S, Pitzer C, Kos-Braun IC, Mausset-Bonnefont ALM, Ward J, Schunn M, Noldus LPJJ, Bespalov A, Voikar V. 2021. Towards best practices in research: Role of academic core facilities. EMBO Reports. 22, e53824.' mla: 'Restivo, Leonardo, et al. “Towards Best Practices in Research: Role of Academic Core Facilities.” EMBO Reports, vol. 22, e53824, EMBO Press, 2021, doi:10.15252/embr.202153824.' short: L. Restivo, B. Gerlach, M. Tsoory, L. Bikovski, S. Badurek, C. Pitzer, I.C. Kos-Braun, A.L.M. Mausset-Bonnefont, J. Ward, M. Schunn, L.P.J.J. Noldus, A. Bespalov, V. Voikar, EMBO Reports 22 (2021). date_created: 2021-11-14T23:01:24Z date_published: 2021-11-04T00:00:00Z date_updated: 2023-08-14T11:47:35Z day: '04' ddc: - '570' department: - _id: PreCl doi: 10.15252/embr.202153824 external_id: isi: - '000714350000001' file: - access_level: open_access checksum: 74743baa6ef431ef60c3de3bc4da045a content_type: application/pdf creator: dernst date_created: 2022-05-16T07:07:41Z date_updated: 2022-05-16T07:07:41Z file_id: '11381' file_name: 2021_EmboReports_Restivo.pdf file_size: 488583 relation: main_file success: 1 file_date_updated: 2022-05-16T07:07:41Z has_accepted_license: '1' intvolume: ' 22' isi: 1 language: - iso: eng license: https://creativecommons.org/licenses/by-nc-nd/4.0/ month: '11' oa: 1 oa_version: Published Version publication: EMBO Reports publication_identifier: eissn: - 1469-3178 issn: - 1469-221X publication_status: published publisher: EMBO Press quality_controlled: '1' scopus_import: '1' status: public title: 'Towards best practices in research: Role of academic core facilities' tmp: image: /images/cc_by_nc_nd.png legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0) short: CC BY-NC-ND (4.0) type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 22 year: '2021' ... --- _id: '10310' abstract: - lang: eng text: A high-resolution structure of trimeric cyanobacterial Photosystem I (PSI) from Thermosynechococcus elongatus was reported as the first atomic model of PSI almost 20 years ago. However, the monomeric PSI structure has not yet been reported despite long-standing interest in its structure and extensive spectroscopic characterization of the loss of red chlorophylls upon monomerization. Here, we describe the structure of monomeric PSI from Thermosynechococcus elongatus BP-1. Comparison with the trimer structure gave detailed insights into monomerization-induced changes in both the central trimerization domain and the peripheral regions of the complex. Monomerization-induced loss of red chlorophylls is assigned to a cluster of chlorophylls adjacent to PsaX. Based on our findings, we propose a role of PsaX in the stabilization of red chlorophylls and that lipids of the surrounding membrane present a major source of thermal energy for uphill excitation energy transfer from red chlorophylls to P700. acknowledgement: We are grateful for additional support and valuable scientific input for this project by Yuko Misumi, Jiannan Li, Hisako Kubota-Kawai, Takeshi Kawabata, Mian Wu, Eiki Yamashita, Atsushi Nakagawa, Volker Hartmann, Melanie Völkel and Matthias Rögner. Parts of this research were funded by the German Research Council (DFG) within the framework of GRK 2341 (Microbial Substrate Conversion) to M.M.N., the Platform Project for Supporting Drug Discovery and Life Science Research [Basis for Supporting Innovative Drug Discovery and Life Science Research (BINDS)] from AMED under grant number JP20am0101117 (K.N.), JP16K07266 to Atsunori Oshima and C.G., a Grants-in-Aid for Scientific Research under grant number JP 25000013 (K.N.), 17H03647 (C.G.) and 16H06560 (G.K.) from MEXT-KAKENHI, the International Joint Research Promotion Program from Osaka University to M.M.N., C.G. and G.K., and the Cyclic Innovation for Clinical Empowerment (CiCLE) Grant Number JP17pc0101020 from AMED to K.N. and G.K. article_number: '304' article_processing_charge: No article_type: original author: - first_name: Mehmet Orkun full_name: Çoruh, Mehmet Orkun id: d25163e5-8d53-11eb-a251-e6dd8ea1b8ef last_name: Çoruh orcid: 0000-0002-3219-2022 - first_name: Anna full_name: Frank, Anna last_name: Frank - first_name: Hideaki full_name: Tanaka, Hideaki last_name: Tanaka - first_name: Akihiro full_name: Kawamoto, Akihiro last_name: Kawamoto - first_name: Eithar full_name: El-Mohsnawy, Eithar last_name: El-Mohsnawy - first_name: Takayuki full_name: Kato, Takayuki last_name: Kato - first_name: Keiichi full_name: Namba, Keiichi last_name: Namba - first_name: Christoph full_name: Gerle, Christoph last_name: Gerle - first_name: Marc M. full_name: Nowaczyk, Marc M. last_name: Nowaczyk - first_name: Genji full_name: Kurisu, Genji last_name: Kurisu citation: ama: Çoruh MO, Frank A, Tanaka H, et al. Cryo-EM structure of a functional monomeric Photosystem I from Thermosynechococcus elongatus reveals red chlorophyll cluster. Communications Biology. 2021;4(1). doi:10.1038/s42003-021-01808-9 apa: Çoruh, M. O., Frank, A., Tanaka, H., Kawamoto, A., El-Mohsnawy, E., Kato, T., … Kurisu, G. (2021). Cryo-EM structure of a functional monomeric Photosystem I from Thermosynechococcus elongatus reveals red chlorophyll cluster. Communications Biology. Springer . https://doi.org/10.1038/s42003-021-01808-9 chicago: Çoruh, Mehmet Orkun, Anna Frank, Hideaki Tanaka, Akihiro Kawamoto, Eithar El-Mohsnawy, Takayuki Kato, Keiichi Namba, Christoph Gerle, Marc M. Nowaczyk, and Genji Kurisu. “Cryo-EM Structure of a Functional Monomeric Photosystem I from Thermosynechococcus Elongatus Reveals Red Chlorophyll Cluster.” Communications Biology. Springer , 2021. https://doi.org/10.1038/s42003-021-01808-9. ieee: M. O. Çoruh et al., “Cryo-EM structure of a functional monomeric Photosystem I from Thermosynechococcus elongatus reveals red chlorophyll cluster,” Communications Biology, vol. 4, no. 1. Springer , 2021. ista: Çoruh MO, Frank A, Tanaka H, Kawamoto A, El-Mohsnawy E, Kato T, Namba K, Gerle C, Nowaczyk MM, Kurisu G. 2021. Cryo-EM structure of a functional monomeric Photosystem I from Thermosynechococcus elongatus reveals red chlorophyll cluster. Communications Biology. 4(1), 304. mla: Çoruh, Mehmet Orkun, et al. “Cryo-EM Structure of a Functional Monomeric Photosystem I from Thermosynechococcus Elongatus Reveals Red Chlorophyll Cluster.” Communications Biology, vol. 4, no. 1, 304, Springer , 2021, doi:10.1038/s42003-021-01808-9. short: M.O. Çoruh, A. Frank, H. Tanaka, A. Kawamoto, E. El-Mohsnawy, T. Kato, K. Namba, C. Gerle, M.M. Nowaczyk, G. Kurisu, Communications Biology 4 (2021). date_created: 2021-11-19T11:37:29Z date_published: 2021-03-08T00:00:00Z date_updated: 2023-08-14T11:51:19Z day: '08' ddc: - '570' department: - _id: LeSa doi: 10.1038/s42003-021-01808-9 external_id: isi: - '000627440700001' pmid: - '33686186' file: - access_level: open_access checksum: 8ffd39f2bba7152a2441802ff313bf0b content_type: application/pdf creator: cchlebak date_created: 2021-11-19T15:09:18Z date_updated: 2021-11-19T15:09:18Z file_id: '10318' file_name: 2021_CommBio_Çoruh.pdf file_size: 6030261 relation: main_file success: 1 file_date_updated: 2021-11-19T15:09:18Z has_accepted_license: '1' intvolume: ' 4' isi: 1 issue: '1' keyword: - general agricultural and biological Sciences - general biochemistry - genetics and molecular biology - medicine (miscellaneous) language: - iso: eng month: '03' oa: 1 oa_version: Published Version pmid: 1 publication: Communications Biology publication_identifier: issn: - 2399-3642 publication_status: published publisher: 'Springer ' quality_controlled: '1' scopus_import: '1' status: public title: Cryo-EM structure of a functional monomeric Photosystem I from Thermosynechococcus elongatus reveals red chlorophyll cluster tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 4 year: '2021' ... --- _id: '10270' abstract: - lang: eng text: Plants develop new organs to adjust their bodies to dynamic changes in the environment. How independent organs achieve anisotropic shapes and polarities is poorly understood. To address this question, we constructed a mechano-biochemical model for Arabidopsis root meristem growth that integrates biologically plausible principles. Computer model simulations demonstrate how differential growth of neighboring tissues results in the initial symmetry-breaking leading to anisotropic root growth. Furthermore, the root growth feeds back on a polar transport network of the growth regulator auxin. Model, predictions are in close agreement with in vivo patterns of anisotropic growth, auxin distribution, and cell polarity, as well as several root phenotypes caused by chemical, mechanical, or genetic perturbations. Our study demonstrates that the combination of tissue mechanics and polar auxin transport organizes anisotropic root growth and cell polarities during organ outgrowth. Therefore, a mobile auxin signal transported through immobile cells drives polarity and growth mechanics to coordinate complex organ development. acknowledgement: 'e are grateful Richard Smith, Anne-Lise Routier, Crisanto Gutierrez and Juergen Kleine-Vehn for providing critical comments on the manuscript. Funding: This work was supported by the Programa de Atraccion de Talento 2017 (Comunidad de Madrid, 2017-T1/BIO-5654 to KW), Severo Ochoa (SO) Programme for Centres of Excellence in R&D from the Agencia Estatal de Investigacion of Spain (grant SEV-2016–0672 (2017–2021) to KW via the CBGP). In the frame of SEV-2016–0672 funding MM is supported with a postdoctoral contract. KW was supported by Programa Estatal de Generacion del Conocimiento y Fortalecimiento Cientıfico y Tecnologico del Sistema de I + D + I 2019 (PGC2018-093387-A-I00) from MICIU (to KW). MG is recipient of an IST Interdisciplinary Project (IC1022IPC03).' article_number: '72132' article_processing_charge: Yes article_type: original author: - first_name: Marco full_name: Marconi, Marco last_name: Marconi - first_name: Marçal full_name: Gallemi, Marçal id: 460C6802-F248-11E8-B48F-1D18A9856A87 last_name: Gallemi orcid: 0000-0003-4675-6893 - first_name: Eva full_name: Benková, Eva id: 38F4F166-F248-11E8-B48F-1D18A9856A87 last_name: Benková orcid: 0000-0002-8510-9739 - first_name: Krzysztof full_name: Wabnik, Krzysztof last_name: Wabnik citation: ama: Marconi M, Gallemi M, Benková E, Wabnik K. A coupled mechano-biochemical model for cell polarity guided anisotropic root growth. eLife. 2021;10. doi:10.7554/elife.72132 apa: Marconi, M., Gallemi, M., Benková, E., & Wabnik, K. (2021). A coupled mechano-biochemical model for cell polarity guided anisotropic root growth. ELife. eLife Sciences Publications. https://doi.org/10.7554/elife.72132 chicago: Marconi, Marco, Marçal Gallemi, Eva Benková, and Krzysztof Wabnik. “A Coupled Mechano-Biochemical Model for Cell Polarity Guided Anisotropic Root Growth.” ELife. eLife Sciences Publications, 2021. https://doi.org/10.7554/elife.72132. ieee: M. Marconi, M. Gallemi, E. Benková, and K. Wabnik, “A coupled mechano-biochemical model for cell polarity guided anisotropic root growth,” eLife, vol. 10. eLife Sciences Publications, 2021. ista: Marconi M, Gallemi M, Benková E, Wabnik K. 2021. A coupled mechano-biochemical model for cell polarity guided anisotropic root growth. eLife. 10, 72132. mla: Marconi, Marco, et al. “A Coupled Mechano-Biochemical Model for Cell Polarity Guided Anisotropic Root Growth.” ELife, vol. 10, 72132, eLife Sciences Publications, 2021, doi:10.7554/elife.72132. short: M. Marconi, M. Gallemi, E. Benková, K. Wabnik, ELife 10 (2021). date_created: 2021-11-11T10:05:18Z date_published: 2021-11-01T00:00:00Z date_updated: 2023-08-14T11:49:23Z day: '01' ddc: - '570' department: - _id: EvBe doi: 10.7554/elife.72132 external_id: isi: - '000734671200001' pmid: - '34723798' file: - access_level: open_access checksum: fad13c509b53bb7a2bef9c946a7ca60a content_type: application/pdf creator: dernst date_created: 2022-05-13T09:00:29Z date_updated: 2022-05-13T09:00:29Z file_id: '11372' file_name: 2021_eLife_Marconi.pdf file_size: 14137503 relation: main_file success: 1 file_date_updated: 2022-05-13T09:00:29Z has_accepted_license: '1' intvolume: ' 10' isi: 1 language: - iso: eng month: '11' oa: 1 oa_version: Published Version pmid: 1 publication: eLife publication_identifier: issn: - 2050-084X publication_status: published publisher: eLife Sciences Publications quality_controlled: '1' scopus_import: '1' status: public title: A coupled mechano-biochemical model for cell polarity guided anisotropic root growth tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 10 year: '2021' ... --- _id: '10299' abstract: - lang: eng text: Turbulence generally arises in shear flows if velocities and hence, inertial forces are sufficiently large. In striking contrast, viscoelastic fluids can exhibit disordered motion even at vanishing inertia. Intermediate between these cases, a state of chaotic motion, “elastoinertial turbulence” (EIT), has been observed in a narrow Reynolds number interval. We here determine the origin of EIT in experiments and show that characteristic EIT structures can be detected across an unexpectedly wide range of parameters. Close to onset, a pattern of chevron-shaped streaks emerges in qualitative agreement with linear and weakly nonlinear theory. However, in experiments, the dynamics remain weakly chaotic, and the instability can be traced to far lower Reynolds numbers than permitted by theory. For increasing inertia, the flow undergoes a transformation to a wall mode composed of inclined near-wall streaks and shear layers. This mode persists to what is known as the “maximum drag reduction limit,” and overall EIT is found to dominate viscoelastic flows across more than three orders of magnitude in Reynolds number. acknowledgement: We thank Y. Dubief, R. Kerswell, E. Marensi, V. Shankar, V. Steinberg, and V. Terrapon for discussions and helpful comments. A.V. and B.H. acknowledge funding from the Austrian Science Fund, grant I4188-N30, within the Deutsche Forschungsgemeinschaft research unit FOR 2688. article_number: e2102350118 article_processing_charge: No article_type: original author: - first_name: George H full_name: Choueiri, George H id: 448BD5BC-F248-11E8-B48F-1D18A9856A87 last_name: Choueiri - first_name: Jose M full_name: Lopez Alonso, Jose M id: 40770848-F248-11E8-B48F-1D18A9856A87 last_name: Lopez Alonso orcid: 0000-0002-0384-2022 - first_name: Atul full_name: Varshney, Atul id: 2A2006B2-F248-11E8-B48F-1D18A9856A87 last_name: Varshney orcid: 0000-0002-3072-5999 - first_name: Sarath full_name: Sankar, Sarath last_name: Sankar - first_name: Björn full_name: Hof, Björn id: 3A374330-F248-11E8-B48F-1D18A9856A87 last_name: Hof orcid: 0000-0003-2057-2754 citation: ama: Choueiri GH, Lopez Alonso JM, Varshney A, Sankar S, Hof B. Experimental observation of the origin and structure of elastoinertial turbulence. Proceedings of the National Academy of Sciences. 2021;118(45). doi:10.1073/pnas.2102350118 apa: Choueiri, G. H., Lopez Alonso, J. M., Varshney, A., Sankar, S., & Hof, B. (2021). Experimental observation of the origin and structure of elastoinertial turbulence. Proceedings of the National Academy of Sciences. National Academy of Sciences. https://doi.org/10.1073/pnas.2102350118 chicago: Choueiri, George H, Jose M Lopez Alonso, Atul Varshney, Sarath Sankar, and Björn Hof. “Experimental Observation of the Origin and Structure of Elastoinertial Turbulence.” Proceedings of the National Academy of Sciences. National Academy of Sciences, 2021. https://doi.org/10.1073/pnas.2102350118. ieee: G. H. Choueiri, J. M. Lopez Alonso, A. Varshney, S. Sankar, and B. Hof, “Experimental observation of the origin and structure of elastoinertial turbulence,” Proceedings of the National Academy of Sciences, vol. 118, no. 45. National Academy of Sciences, 2021. ista: Choueiri GH, Lopez Alonso JM, Varshney A, Sankar S, Hof B. 2021. Experimental observation of the origin and structure of elastoinertial turbulence. Proceedings of the National Academy of Sciences. 118(45), e2102350118. mla: Choueiri, George H., et al. “Experimental Observation of the Origin and Structure of Elastoinertial Turbulence.” Proceedings of the National Academy of Sciences, vol. 118, no. 45, e2102350118, National Academy of Sciences, 2021, doi:10.1073/pnas.2102350118. short: G.H. Choueiri, J.M. Lopez Alonso, A. Varshney, S. Sankar, B. Hof, Proceedings of the National Academy of Sciences 118 (2021). date_created: 2021-11-17T13:24:24Z date_published: 2021-11-03T00:00:00Z date_updated: 2023-08-14T11:50:10Z day: '03' department: - _id: BjHo doi: 10.1073/pnas.2102350118 external_id: arxiv: - '2103.00023' isi: - '000720926900019' pmid: - ' 34732570' intvolume: ' 118' isi: 1 issue: '45' keyword: - multidisciplinary - elastoinertial turbulence - viscoelastic flows - elastic instability - drag reduction language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/2103.00023 month: '11' oa: 1 oa_version: Preprint pmid: 1 project: - _id: 238B8092-32DE-11EA-91FC-C7463DDC885E call_identifier: FWF grant_number: I04188 name: Instabilities in pulsating pipe flow of Newtonian and complex fluids publication: Proceedings of the National Academy of Sciences publication_identifier: eissn: - 1091-6490 issn: - 0027-8424 publication_status: published publisher: National Academy of Sciences quality_controlled: '1' scopus_import: '1' status: public title: Experimental observation of the origin and structure of elastoinertial turbulence type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 118 year: '2021' ... --- _id: '10280' abstract: - lang: eng text: 'Machines enabled the Industrial Revolution and are central to modern technological progress: A machine’s parts transmit forces, motion, and energy to one another in a predetermined manner. Today’s engineering frontier, building artificial micromachines that emulate the biological machinery of living organisms, requires faithful assembly and energy consumption at the microscale. Here, we demonstrate the programmable assembly of active particles into autonomous metamachines using optical templates. Metamachines, or machines made of machines, are stable, mobile and autonomous architectures, whose dynamics stems from the geometry. We use the interplay between anisotropic force generation of the active colloids with the control of their orientation by local geometry. This allows autonomous reprogramming of active particles of the metamachines to achieve multiple functions. It permits the modular assembly of metamachines by fusion, reconfiguration of metamachines and, we anticipate, a shift in focus of self-assembly towards active matter and reprogrammable materials.' acknowledgement: The authors thank R. Jazzar for useful advice regarding the synthesis of heterodimers. We thank S. Sacanna for critical reading. This material is based upon work supported by the National Science Foundation under Grant No. DMR-1554724 and Department of Army Research under grant W911NF-20-1-0112. article_number: '6398' article_processing_charge: Yes article_type: original author: - first_name: Antoine full_name: Aubret, Antoine last_name: Aubret - first_name: Quentin full_name: Martinet, Quentin id: b37485a8-d343-11eb-a0e9-df8c484ef8ab last_name: Martinet orcid: 0000-0002-2916-6632 - first_name: Jérémie A full_name: Palacci, Jérémie A id: 8fb92548-2b22-11eb-b7c1-a3f0d08d7c7d last_name: Palacci orcid: 0000-0002-7253-9465 citation: ama: Aubret A, Martinet Q, Palacci JA. Metamachines of pluripotent colloids. Nature Communications. 2021;12(1). doi:10.1038/s41467-021-26699-6 apa: Aubret, A., Martinet, Q., & Palacci, J. A. (2021). Metamachines of pluripotent colloids. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-021-26699-6 chicago: Aubret, Antoine, Quentin Martinet, and Jérémie A Palacci. “Metamachines of Pluripotent Colloids.” Nature Communications. Springer Nature, 2021. https://doi.org/10.1038/s41467-021-26699-6. ieee: A. Aubret, Q. Martinet, and J. A. Palacci, “Metamachines of pluripotent colloids,” Nature Communications, vol. 12, no. 1. Springer Nature, 2021. ista: Aubret A, Martinet Q, Palacci JA. 2021. Metamachines of pluripotent colloids. Nature Communications. 12(1), 6398. mla: Aubret, Antoine, et al. “Metamachines of Pluripotent Colloids.” Nature Communications, vol. 12, no. 1, 6398, Springer Nature, 2021, doi:10.1038/s41467-021-26699-6. short: A. Aubret, Q. Martinet, J.A. Palacci, Nature Communications 12 (2021). date_created: 2021-11-14T23:01:23Z date_published: 2021-11-04T00:00:00Z date_updated: 2023-08-14T11:48:37Z day: '04' ddc: - '530' department: - _id: JePa doi: 10.1038/s41467-021-26699-6 external_id: isi: - '000714754400010' pmid: - '34737315' file: - access_level: open_access checksum: 1c392b12b9b7b615d422d9fabe19cdb9 content_type: application/pdf creator: cchlebak date_created: 2021-11-15T13:25:52Z date_updated: 2021-11-15T13:25:52Z file_id: '10292' file_name: 2021_NatComm_Aubret.pdf file_size: 6282703 relation: main_file success: 1 file_date_updated: 2021-11-15T13:25:52Z has_accepted_license: '1' intvolume: ' 12' isi: 1 issue: '1' language: - iso: eng month: '11' oa: 1 oa_version: Published Version pmid: 1 publication: Nature Communications publication_identifier: eissn: - 2041-1723 publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: Metamachines of pluripotent colloids tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 12 year: '2021' ... --- _id: '10322' 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 remodeling 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 remodeling 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 6 TAX-2/TAX-4 cyclic guanosine monophosphate (cGMP) gated channel expressing sensory neurons, and transforming growth factor ß (TGF-β)/bone morphogenetic protein (BMP) are required for signaling across tissues to modulate fat desaturation. We also find neuronal hsf-1 is not only sufficient but also partially necessary to control the fat remodeling response and for survival at warm temperatures. This is the first study to show that a thermostat-based mechanism can cell nonautonomously coordinate membrane saturation and composition across tissues in a multicellular animal. acknowledgement: We dedicate this work to the memory of Michael J.O. Wakelam. We would like to acknowledge Michael Fasseas (Invermis, Magnitude Biosciences) for plasmid injections and Sunny Biotech for transgenics; Catalina Vallejos and John Marioni for statistical advice at the beginning of the work; Simon Walker, Imaging, Bioinformatics and Lipidomics Facilities at Babraham Institute for technical support; and Cindy Voisine, Michael Witting, Jon Houseley, Len Stephens, Carmen Nussbaum Krammer, Rebeca Aldunate, Patricija van Oosten-Hawle, Jean-Louis Bessereau, and Jane Alfred for feedback on the manuscript. We thank Andy Dillin, Atsushi Kuhara, Amy Walker, Andrew Leifer, Yun Zhang, and Michalis Barkoulas for reagents and Julie Ahringer, Anne Ferguson-Smith, and Anne Corcoran for support and helpful discussions. We also acknowledge Babraham Institute Facilities. article_number: e3001431 article_processing_charge: No article_type: original 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. PLoS Biology. 2021;19(11). doi:10.1371/journal.pbio.3001431 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. PLoS Biology. Public Library of Science. https://doi.org/10.1371/journal.pbio.3001431 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.” PLoS Biology. Public Library of Science, 2021. https://doi.org/10.1371/journal.pbio.3001431. 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,” PLoS Biology, vol. 19, no. 11. Public Library of Science, 2021. ista: Chauve L, Hodge F, Murdoch S, Masoudzadeh F, Mann HJ, 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. PLoS Biology. 19(11), e3001431. 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.” PLoS Biology, vol. 19, no. 11, e3001431, Public Library of Science, 2021, doi:10.1371/journal.pbio.3001431. 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, PLoS Biology 19 (2021). date_created: 2021-11-21T23:01:28Z date_published: 2021-11-01T00:00:00Z date_updated: 2023-08-14T11:53:27Z day: '01' ddc: - '570' department: - _id: MaDe doi: 10.1371/journal.pbio.3001431 external_id: isi: - '000715818400001' pmid: - '34723964' file: - access_level: open_access checksum: 0c61b667f814fd9435b3ac42036fc36d content_type: application/pdf creator: cchlebak date_created: 2021-11-22T09:34:03Z date_updated: 2021-11-22T09:34:03Z file_id: '10330' file_name: 2021_PLoSBio_Chauve.pdf file_size: 4069215 relation: main_file success: 1 file_date_updated: 2021-11-22T09:34:03Z has_accepted_license: '1' intvolume: ' 19' isi: 1 issue: '11' language: - iso: eng month: '11' oa: 1 oa_version: Published Version pmid: 1 publication: PLoS Biology publication_identifier: eissn: - 1545-7885 issn: - 1544-9173 publication_status: published publisher: Public Library of Science quality_controlled: '1' related_material: record: - id: '13069' relation: research_data status: public scopus_import: '1' 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: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 19 year: '2021' ... --- _id: '10222' abstract: - lang: eng text: Consider a random set of points on the unit sphere in ℝd, which can be either uniformly sampled or a Poisson point process. Its convex hull is a random inscribed polytope, whose boundary approximates the sphere. We focus on the case d = 3, for which there are elementary proofs and fascinating formulas for metric properties. In particular, we study the fraction of acute facets, the expected intrinsic volumes, the total edge length, and the distance to a fixed point. Finally we generalize the results to the ellipsoid with homeoid density. 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. 788183, from the Wittgenstein Prize, Austrian Science Fund (FWF), grant no. Z 342-N31, and from the DFG Collaborative Research Center TRR 109, ‘Discretization in Geometry and Dynamics’, Austrian Science Fund (FWF), grant no. I 02979-N35.\r\nWe are grateful to Dmitry Zaporozhets and Christoph Thäle for valuable comments and for directing us to relevant references. We also thank to Anton Mellit for a useful discussion on Bessel functions." article_processing_charge: Yes (via OA deal) article_type: original author: - first_name: Arseniy full_name: Akopyan, Arseniy id: 430D2C90-F248-11E8-B48F-1D18A9856A87 last_name: Akopyan orcid: 0000-0002-2548-617X - first_name: Herbert full_name: Edelsbrunner, Herbert id: 3FB178DA-F248-11E8-B48F-1D18A9856A87 last_name: Edelsbrunner orcid: 0000-0002-9823-6833 - first_name: Anton full_name: Nikitenko, Anton id: 3E4FF1BA-F248-11E8-B48F-1D18A9856A87 last_name: Nikitenko orcid: 0000-0002-0659-3201 citation: ama: Akopyan A, Edelsbrunner H, Nikitenko A. The beauty of random polytopes inscribed in the 2-sphere. Experimental Mathematics. 2021:1-15. doi:10.1080/10586458.2021.1980459 apa: Akopyan, A., Edelsbrunner, H., & Nikitenko, A. (2021). The beauty of random polytopes inscribed in the 2-sphere. Experimental Mathematics. Taylor and Francis. https://doi.org/10.1080/10586458.2021.1980459 chicago: Akopyan, Arseniy, Herbert Edelsbrunner, and Anton Nikitenko. “The Beauty of Random Polytopes Inscribed in the 2-Sphere.” Experimental Mathematics. Taylor and Francis, 2021. https://doi.org/10.1080/10586458.2021.1980459. ieee: A. Akopyan, H. Edelsbrunner, and A. Nikitenko, “The beauty of random polytopes inscribed in the 2-sphere,” Experimental Mathematics. Taylor and Francis, pp. 1–15, 2021. ista: Akopyan A, Edelsbrunner H, Nikitenko A. 2021. The beauty of random polytopes inscribed in the 2-sphere. Experimental Mathematics., 1–15. mla: Akopyan, Arseniy, et al. “The Beauty of Random Polytopes Inscribed in the 2-Sphere.” Experimental Mathematics, Taylor and Francis, 2021, pp. 1–15, doi:10.1080/10586458.2021.1980459. short: A. Akopyan, H. Edelsbrunner, A. Nikitenko, Experimental Mathematics (2021) 1–15. date_created: 2021-11-07T23:01:25Z date_published: 2021-10-25T00:00:00Z date_updated: 2023-08-14T11:57:07Z day: '25' ddc: - '510' department: - _id: HeEd doi: 10.1080/10586458.2021.1980459 ec_funded: 1 external_id: arxiv: - '2007.07783' isi: - '000710893500001' file: - access_level: open_access checksum: 3514382e3a1eb87fa6c61ad622874415 content_type: application/pdf creator: dernst date_created: 2023-08-14T11:55:10Z date_updated: 2023-08-14T11:55:10Z file_id: '14053' file_name: 2023_ExperimentalMath_Akopyan.pdf file_size: 1966019 relation: main_file success: 1 file_date_updated: 2023-08-14T11:55:10Z has_accepted_license: '1' isi: 1 language: - iso: eng month: '10' oa: 1 oa_version: Published Version page: 1-15 project: - _id: 266A2E9E-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '788183' name: Alpha Shape Theory Extended - _id: 268116B8-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: Z00342 name: The Wittgenstein Prize - _id: 0aa4bc98-070f-11eb-9043-e6fff9c6a316 grant_number: I4887 name: Discretization in Geometry and Dynamics - _id: 2561EBF4-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: I02979-N35 name: Persistence and stability of geometric complexes publication: Experimental Mathematics publication_identifier: eissn: - 1944-950X issn: - 1058-6458 publication_status: published publisher: Taylor and Francis quality_controlled: '1' scopus_import: '1' status: public title: The beauty of random polytopes inscribed in the 2-sphere tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2021' ... --- _id: '10323' abstract: - lang: eng text: Molecular chaperones are central to cellular protein homeostasis. Dynamic disorder is a key feature of the complexes of molecular chaperones and their client proteins, and it facilitates the client release towards a folded state or the handover to downstream components. The dynamic nature also implies that a given chaperone can interact with many different client proteins, based on physico-chemical sequence properties rather than on structural complementarity of their (folded) 3D structure. Yet, the balance between this promiscuity and some degree of client specificity is poorly understood. Here, we review recent atomic-level descriptions of chaperones with client proteins, including chaperones in complex with intrinsically disordered proteins, with membrane-protein precursors, or partially folded client proteins. We focus hereby on chaperone-client interactions that are independent of ATP. The picture emerging from these studies highlights the importance of dynamics in these complexes, whereby several interaction types, not only hydrophobic ones, contribute to the complex formation. We discuss these features of chaperone-client complexes and possible factors that may contribute to this balance of promiscuity and specificity. acknowledgement: We thank Juan C. Fontecilla-Camps for insightful discussions related to ATP-driven machineries, and Elif Karagöz for providing the structural model of the Hsp90-Tau complex. This study was supported by the European Research Council (StG-2012-311318-ProtDyn2Function) and the Agence Nationale de la Recherche (ANR-18-CE92-0032-MitoMemProtImp). article_number: '762005' article_processing_charge: Yes (via OA deal) article_type: original author: - first_name: Iva full_name: Sučec, Iva last_name: Sučec - first_name: Beate full_name: Bersch, Beate last_name: Bersch - first_name: Paul full_name: Schanda, Paul id: 7B541462-FAF6-11E9-A490-E8DFE5697425 last_name: Schanda orcid: 0000-0002-9350-7606 citation: ama: Sučec I, Bersch B, Schanda P. How do chaperones bind (partly) unfolded client proteins? Frontiers in Molecular Biosciences. 2021;8. doi:10.3389/fmolb.2021.762005 apa: Sučec, I., Bersch, B., & Schanda, P. (2021). How do chaperones bind (partly) unfolded client proteins? Frontiers in Molecular Biosciences. Frontiers. https://doi.org/10.3389/fmolb.2021.762005 chicago: Sučec, Iva, Beate Bersch, and Paul Schanda. “How Do Chaperones Bind (Partly) Unfolded Client Proteins?” Frontiers in Molecular Biosciences. Frontiers, 2021. https://doi.org/10.3389/fmolb.2021.762005. ieee: I. Sučec, B. Bersch, and P. Schanda, “How do chaperones bind (partly) unfolded client proteins?,” Frontiers in Molecular Biosciences, vol. 8. Frontiers, 2021. ista: Sučec I, Bersch B, Schanda P. 2021. How do chaperones bind (partly) unfolded client proteins? Frontiers in Molecular Biosciences. 8, 762005. mla: Sučec, Iva, et al. “How Do Chaperones Bind (Partly) Unfolded Client Proteins?” Frontiers in Molecular Biosciences, vol. 8, 762005, Frontiers, 2021, doi:10.3389/fmolb.2021.762005. short: I. Sučec, B. Bersch, P. Schanda, Frontiers in Molecular Biosciences 8 (2021). date_created: 2021-11-21T23:01:29Z date_published: 2021-10-25T00:00:00Z date_updated: 2023-08-14T11:55:04Z day: '25' ddc: - '547' department: - _id: PaSc doi: 10.3389/fmolb.2021.762005 external_id: isi: - '000717241700001' pmid: - '34760928' file: - access_level: open_access checksum: a5c9dbf80dc2c5aaa737f456c941d964 content_type: application/pdf creator: cchlebak date_created: 2021-11-23T15:06:58Z date_updated: 2021-11-23T15:06:58Z file_id: '10333' file_name: 2021_FrontiersMolBioSc_Sučec.pdf file_size: 4700798 relation: main_file success: 1 file_date_updated: 2021-11-23T15:06:58Z has_accepted_license: '1' intvolume: ' 8' isi: 1 language: - iso: eng month: '10' oa: 1 oa_version: Published Version pmid: 1 publication: Frontiers in Molecular Biosciences publication_identifier: eissn: - 2296-889X publication_status: published publisher: Frontiers quality_controlled: '1' scopus_import: '1' status: public title: How do chaperones bind (partly) unfolded client proteins? tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 8 year: '2021' ... --- _id: '10326' abstract: - lang: eng text: Strigolactones (SLs) are carotenoid-derived plant hormones that control shoot branching and communications between host plants and symbiotic fungi or root parasitic plants. Extensive studies have identified the key components participating in SL biosynthesis and signalling, whereas the catabolism or deactivation of endogenous SLs in planta remains largely unknown. Here, we report that the Arabidopsis carboxylesterase 15 (AtCXE15) and its orthologues function as efficient hydrolases of SLs. We show that overexpression of AtCXE15 promotes shoot branching by dampening SL-inhibited axillary bud outgrowth. We further demonstrate that AtCXE15 could bind and efficiently hydrolyse SLs both in vitro and in planta. We also provide evidence that AtCXE15 is capable of catalysing hydrolysis of diverse SL analogues and that such CXE15-dependent catabolism of SLs is evolutionarily conserved in seed plants. These results disclose a catalytic mechanism underlying homoeostatic regulation of SLs in plants, which also provides a rational approach to spatial-temporally manipulate the endogenous SLs and thus architecture of crops and ornamental plants. acknowledgement: We thank J. Li (Institute of Genetics and Developmental Biology, China) for providing the at14-1, atmax2-1, atmax3-9, atmax4-1, atmax1-1, kai2-2 (Col-0 background) mutants and B. Xu for providing the complementary DNA of P. patens. We are grateful to L. Wang for assistance with MST, B. Han for assistance with UPLC–MS, J. Li for assistance with confocal microscopy and B. Mikael and J. Zhang for their comments on the manuscript. This work was supported by grants from Strategic Priority Research Program of Chinese Academy of Sciences (Y.H., XDB27030102) and the National Natural Science Foundation of China (E.X., 31700253; Y.H., 31830055). article_processing_charge: No article_type: original author: - first_name: Enjun full_name: Xu, Enjun last_name: Xu - first_name: Liang full_name: Chai, Liang last_name: Chai - first_name: Shiqi full_name: Zhang, Shiqi last_name: Zhang - first_name: Ruixue full_name: Yu, Ruixue last_name: Yu - first_name: Xixi full_name: Zhang, Xixi id: 61A66458-47E9-11EA-85BA-8AEAAF14E49A last_name: Zhang orcid: 0000-0001-7048-4627 - first_name: Chongyi full_name: Xu, Chongyi last_name: Xu - first_name: Yuxin full_name: Hu, Yuxin last_name: Hu citation: ama: Xu E, Chai L, Zhang S, et al. Catabolism of strigolactones by a carboxylesterase. Nature Plants. 2021;7:1495–1504. doi:10.1038/s41477-021-01011-y apa: Xu, E., Chai, L., Zhang, S., Yu, R., Zhang, X., Xu, C., & Hu, Y. (2021). Catabolism of strigolactones by a carboxylesterase. Nature Plants. Springer Nature. https://doi.org/10.1038/s41477-021-01011-y chicago: Xu, Enjun, Liang Chai, Shiqi Zhang, Ruixue Yu, Xixi Zhang, Chongyi Xu, and Yuxin Hu. “Catabolism of Strigolactones by a Carboxylesterase.” Nature Plants. Springer Nature, 2021. https://doi.org/10.1038/s41477-021-01011-y. ieee: E. Xu et al., “Catabolism of strigolactones by a carboxylesterase,” Nature Plants, vol. 7. Springer Nature, pp. 1495–1504, 2021. ista: Xu E, Chai L, Zhang S, Yu R, Zhang X, Xu C, Hu Y. 2021. Catabolism of strigolactones by a carboxylesterase. Nature Plants. 7, 1495–1504. mla: Xu, Enjun, et al. “Catabolism of Strigolactones by a Carboxylesterase.” Nature Plants, vol. 7, Springer Nature, 2021, pp. 1495–1504, doi:10.1038/s41477-021-01011-y. short: E. Xu, L. Chai, S. Zhang, R. Yu, X. Zhang, C. Xu, Y. Hu, Nature Plants 7 (2021) 1495–1504. date_created: 2021-11-21T23:01:30Z date_published: 2021-11-11T00:00:00Z date_updated: 2023-08-14T11:54:02Z day: '11' department: - _id: JiFr doi: 10.1038/s41477-021-01011-y external_id: isi: - '000717408000002' pmid: - '34764442' intvolume: ' 7' isi: 1 language: - iso: eng month: '11' oa_version: None page: '1495–1504 ' pmid: 1 publication: Nature Plants publication_identifier: eissn: - 2055-0278 publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: Catabolism of strigolactones by a carboxylesterase type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 7 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: '10325' abstract: - lang: eng text: Since the inception of Bitcoin, a plethora of distributed ledgers differing in design and purpose has been created. While by design, blockchains provide no means to securely communicate with external systems, numerous attempts towards trustless cross-chain communication have been proposed over the years. Today, cross-chain communication (CCC) plays a fundamental role in cryptocurrency exchanges, scalability efforts via sharding, extension of existing systems through sidechains, and bootstrapping of new blockchains. Unfortunately, existing proposals are designed ad-hoc for specific use-cases, making it hard to gain confidence in their correctness and composability. We provide the first systematic exposition of cross-chain communication protocols. We formalize the underlying research problem and show that CCC is impossible without a trusted third party, contrary to common beliefs in the blockchain community. With this result in mind, we develop a framework to design new and evaluate existing CCC protocols, focusing on the inherent trust assumptions thereof, and derive a classification covering the field of cross-chain communication to date. We conclude by discussing open challenges for CCC research and the implications of interoperability on the security and privacy of blockchains. acknowledgement: 'We would like express our gratitude to Georgia Avarikioti, Daniel Perez and Dominik Harz for helpful comments and feedback on earlier versions of this manuscript. We also thank Nicholas Stifter, Aljosha Judmayer, Philipp Schindler, Edgar Weippl, and Alistair Stewart for insightful discussions during the early stages of this research. We also wish to thank the anonymous reviewers for their valuable comments that helped improve the presentation of our results. This research was funded by Bridge 1 858561 SESC; Bridge 1 864738 PR4DLT (all FFG); the Christian Doppler Laboratory for Security and Quality Improvement in the Production System Lifecycle (CDL-SQI); the competence center SBA-K1 funded by COMET; Chaincode Labs through the project SLN: Scalability for the Lightning Network; and by the Austrian Science Fund (FWF) through the Meitner program (project M-2608). Mustafa Al-Bassam is funded by a scholarship from the Alan Turing Institute. Alexei Zamyatin conducted the early stages of this work during his time at SBA Research, and was supported by a Binance Research Fellowship.' alternative_title: - LNCS article_processing_charge: No author: - first_name: Alexei full_name: Zamyatin, Alexei last_name: Zamyatin - first_name: Mustafa full_name: Al-Bassam, Mustafa last_name: Al-Bassam - first_name: Dionysis full_name: Zindros, Dionysis last_name: Zindros - first_name: Eleftherios full_name: Kokoris Kogias, Eleftherios id: f5983044-d7ef-11ea-ac6d-fd1430a26d30 last_name: Kokoris Kogias - first_name: Pedro full_name: Moreno-Sanchez, Pedro last_name: Moreno-Sanchez - first_name: Aggelos full_name: Kiayias, Aggelos last_name: Kiayias - first_name: William J. full_name: Knottenbelt, William J. last_name: Knottenbelt citation: ama: 'Zamyatin A, Al-Bassam M, Zindros D, et al. SoK: Communication across distributed ledgers. In: 25th International Conference on Financial Cryptography and Data Security. Vol 12675. Springer Nature; 2021:3-36. doi:10.1007/978-3-662-64331-0_1' apa: 'Zamyatin, A., Al-Bassam, M., Zindros, D., Kokoris Kogias, E., Moreno-Sanchez, P., Kiayias, A., & Knottenbelt, W. J. (2021). SoK: Communication across distributed ledgers. In 25th International Conference on Financial Cryptography and Data Security (Vol. 12675, pp. 3–36). Virtual: Springer Nature. https://doi.org/10.1007/978-3-662-64331-0_1' chicago: 'Zamyatin, Alexei, Mustafa Al-Bassam, Dionysis Zindros, Eleftherios Kokoris Kogias, Pedro Moreno-Sanchez, Aggelos Kiayias, and William J. Knottenbelt. “SoK: Communication across Distributed Ledgers.” In 25th International Conference on Financial Cryptography and Data Security, 12675:3–36. Springer Nature, 2021. https://doi.org/10.1007/978-3-662-64331-0_1.' ieee: 'A. Zamyatin et al., “SoK: Communication across distributed ledgers,” in 25th International Conference on Financial Cryptography and Data Security, Virtual, 2021, vol. 12675, pp. 3–36.' ista: 'Zamyatin A, Al-Bassam M, Zindros D, Kokoris Kogias E, Moreno-Sanchez P, Kiayias A, Knottenbelt WJ. 2021. SoK: Communication across distributed ledgers. 25th International Conference on Financial Cryptography and Data Security. FC: Financial Cryptography, LNCS, vol. 12675, 3–36.' mla: 'Zamyatin, Alexei, et al. “SoK: Communication across Distributed Ledgers.” 25th International Conference on Financial Cryptography and Data Security, vol. 12675, Springer Nature, 2021, pp. 3–36, doi:10.1007/978-3-662-64331-0_1.' short: A. Zamyatin, M. Al-Bassam, D. Zindros, E. Kokoris Kogias, P. Moreno-Sanchez, A. Kiayias, W.J. Knottenbelt, in:, 25th International Conference on Financial Cryptography and Data Security, Springer Nature, 2021, pp. 3–36. conference: end_date: 2021-03-05 location: Virtual name: 'FC: Financial Cryptography' start_date: 2021-03-01 date_created: 2021-11-21T23:01:29Z date_published: 2021-10-23T00:00:00Z date_updated: 2023-08-14T12:59:26Z day: '23' department: - _id: ElKo doi: 10.1007/978-3-662-64331-0_1 external_id: isi: - '000712016200001' isi: 1 language: - iso: eng main_file_link: - open_access: '1' url: https://eprint.iacr.org/2019/1128 month: '10' oa: 1 oa_version: Preprint page: 3-36 publication: 25th International Conference on Financial Cryptography and Data Security publication_identifier: eisbn: - 978-3-662-64331-0 eissn: - 1611-3349 isbn: - 9-783-6626-4330-3 issn: - 0302-9743 publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: 'SoK: Communication across distributed ledgers' type: conference user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: '12675 ' year: '2021' ... --- _id: '10324' abstract: - lang: eng text: Off-chain protocols (channels) are a promising solution to the scalability and privacy challenges of blockchain payments. Current proposals, however, require synchrony assumptions to preserve the safety of a channel, leaking to an adversary the exact amount of time needed to control the network for a successful attack. In this paper, we introduce Brick, the first payment channel that remains secure under network asynchrony and concurrently provides correct incentives. The core idea is to incorporate the conflict resolution process within the channel by introducing a rational committee of external parties, called wardens. Hence, if a party wants to close a channel unilaterally, it can only get the committee’s approval for the last valid state. Additionally, Brick provides sub-second latency because it does not employ heavy-weight consensus. Instead, Brick uses consistent broadcast to announce updates and close the channel, a light-weight abstraction that is powerful enough to preserve safety and liveness to any rational parties. We formally define and prove for Brick the properties a payment channel construction should fulfill. We also design incentives for Brick such that honest and rational behavior aligns. Finally, we provide a reference implementation of the smart contracts in Solidity. acknowledgement: We would like to thank Kaoutar Elkhiyaoui for her valuable feedback as well as Jakub Sliwinski for his impactful contribution to this work. alternative_title: - LNCS article_processing_charge: No author: - first_name: Zeta full_name: Avarikioti, Zeta last_name: Avarikioti - first_name: Eleftherios full_name: Kokoris Kogias, Eleftherios id: f5983044-d7ef-11ea-ac6d-fd1430a26d30 last_name: Kokoris Kogias - first_name: Roger full_name: Wattenhofer, Roger last_name: Wattenhofer - first_name: Dionysis full_name: Zindros, Dionysis last_name: Zindros citation: ama: 'Avarikioti Z, Kokoris Kogias E, Wattenhofer R, Zindros D. Brick: Asynchronous incentive-compatible payment channels. In: 25th International Conference on Financial Cryptography and Data Security. Vol 12675. Springer Nature; 2021:209-230. doi:10.1007/978-3-662-64331-0_11' apa: 'Avarikioti, Z., Kokoris Kogias, E., Wattenhofer, R., & Zindros, D. (2021). Brick: Asynchronous incentive-compatible payment channels. In 25th International Conference on Financial Cryptography and Data Security (Vol. 12675, pp. 209–230). Virtual: Springer Nature. https://doi.org/10.1007/978-3-662-64331-0_11' chicago: 'Avarikioti, Zeta, Eleftherios Kokoris Kogias, Roger Wattenhofer, and Dionysis Zindros. “Brick: Asynchronous Incentive-Compatible Payment Channels.” In 25th International Conference on Financial Cryptography and Data Security, 12675:209–30. Springer Nature, 2021. https://doi.org/10.1007/978-3-662-64331-0_11.' ieee: 'Z. Avarikioti, E. Kokoris Kogias, R. Wattenhofer, and D. Zindros, “Brick: Asynchronous incentive-compatible payment channels,” in 25th International Conference on Financial Cryptography and Data Security, Virtual, 2021, vol. 12675, pp. 209–230.' ista: 'Avarikioti Z, Kokoris Kogias E, Wattenhofer R, Zindros D. 2021. Brick: Asynchronous incentive-compatible payment channels. 25th International Conference on Financial Cryptography and Data Security. FC: Financial Cryptography, LNCS, vol. 12675, 209–230.' mla: 'Avarikioti, Zeta, et al. “Brick: Asynchronous Incentive-Compatible Payment Channels.” 25th International Conference on Financial Cryptography and Data Security, vol. 12675, Springer Nature, 2021, pp. 209–30, doi:10.1007/978-3-662-64331-0_11.' short: Z. Avarikioti, E. Kokoris Kogias, R. Wattenhofer, D. Zindros, in:, 25th International Conference on Financial Cryptography and Data Security, Springer Nature, 2021, pp. 209–230. conference: end_date: 2021-03-05 location: Virtual name: 'FC: Financial Cryptography' start_date: 2021-03-01 date_created: 2021-11-21T23:01:29Z date_published: 2021-10-23T00:00:00Z date_updated: 2023-08-14T12:59:58Z day: '23' department: - _id: ElKo doi: 10.1007/978-3-662-64331-0_11 external_id: arxiv: - '1905.11360' isi: - '000712016200011' isi: 1 language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1905.11360 month: '10' oa: 1 oa_version: Preprint page: 209-230 publication: 25th International Conference on Financial Cryptography and Data Security publication_identifier: eisbn: - 978-3-662-64331-0 eissn: - 1611-3349 isbn: - 9-783-6626-4330-3 issn: - 0302-9743 publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: 'Brick: Asynchronous incentive-compatible payment channels' type: conference user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: '12675 ' year: '2021' ... --- _id: '10363' abstract: - lang: eng text: Erythropoietin enhances oxygen delivery and reduces hypoxia-induced cell death, but its pro-thrombotic activity is problematic for use of erythropoietin in treating hypoxia. We constructed a fusion protein that stimulates red blood cell production and neuroprotection without triggering platelet production, a marker for thrombosis. The protein consists of an anti-glycophorin A nanobody and an erythropoietin mutant (L108A). The mutation reduces activation of erythropoietin receptor homodimers that induce erythropoiesis and thrombosis, but maintains the tissue-protective signaling. The binding of the nanobody element to glycophorin A rescues homodimeric erythropoietin receptor activation on red blood cell precursors. In a cell proliferation assay, the fusion protein is active at 10−14 M, allowing an estimate of the number of receptor–ligand complexes needed for signaling. This fusion protein stimulates erythroid cell proliferation in vitro and in mice, and shows neuroprotective activity in vitro. Our erythropoietin fusion protein presents a novel molecule for treating hypoxia. acknowledgement: This work was supported by funds from the Wyss Institute for Biologically Inspired Engineering and the Boston Biomedical Innovation Center (Pilot Award 112475; Drive Award U54HL119145). J.L., K.M.K., D.R.B., J.C.W. and P.A.S. were supported by the Harvard Medical School Department of Systems Biology. J.C.W. was further supported by the Harvard Medical School Laboratory of Systems Pharmacology. A.V., D.R.B. and P.A.S. were further supported by the Wyss Institute for Biologically Inspired Engineering. N.G.G. was sponsored by the Army Research Office under Grant Number W911NF-17-2-0092. The views and conclusions contained in this document are those of the authors and should not be interpreted as representing the official policies, either expressed or implied, of the Army Research Office or the U.S. Government. The U.S. Government is authorized to reproduce and distribute reprints for Government purposes notwithstanding any copyright notation herein. We sincerely thank Amanda Graveline and the Wyss Institute at Harvard for their scientific support. article_number: gzab025 article_processing_charge: No article_type: original author: - first_name: Jungmin full_name: Lee, Jungmin last_name: Lee - first_name: Andyna full_name: Vernet, Andyna last_name: Vernet - first_name: Nathalie full_name: Gruber, Nathalie id: 2C9C8316-AA17-11E9-B5C2-8BC2E5697425 last_name: Gruber - first_name: Kasia M. full_name: Kready, Kasia M. last_name: Kready - first_name: Devin R. full_name: Burrill, Devin R. last_name: Burrill - first_name: Jeffrey C. full_name: Way, Jeffrey C. last_name: Way - first_name: Pamela A. full_name: Silver, Pamela A. last_name: Silver citation: ama: Lee J, Vernet A, Gruber N, et al. Rational engineering of an erythropoietin fusion protein to treat hypoxia. Protein Engineering, Design and Selection. 2021;34. doi:10.1093/protein/gzab025 apa: Lee, J., Vernet, A., Gruber, N., Kready, K. M., Burrill, D. R., Way, J. C., & Silver, P. A. (2021). Rational engineering of an erythropoietin fusion protein to treat hypoxia. Protein Engineering, Design and Selection. Oxford University Press. https://doi.org/10.1093/protein/gzab025 chicago: Lee, Jungmin, Andyna Vernet, Nathalie Gruber, Kasia M. Kready, Devin R. Burrill, Jeffrey C. Way, and Pamela A. Silver. “Rational Engineering of an Erythropoietin Fusion Protein to Treat Hypoxia.” Protein Engineering, Design and Selection. Oxford University Press, 2021. https://doi.org/10.1093/protein/gzab025. ieee: J. Lee et al., “Rational engineering of an erythropoietin fusion protein to treat hypoxia,” Protein Engineering, Design and Selection, vol. 34. Oxford University Press, 2021. ista: Lee J, Vernet A, Gruber N, Kready KM, Burrill DR, Way JC, Silver PA. 2021. Rational engineering of an erythropoietin fusion protein to treat hypoxia. Protein Engineering, Design and Selection. 34, gzab025. mla: Lee, Jungmin, et al. “Rational Engineering of an Erythropoietin Fusion Protein to Treat Hypoxia.” Protein Engineering, Design and Selection, vol. 34, gzab025, Oxford University Press, 2021, doi:10.1093/protein/gzab025. short: J. Lee, A. Vernet, N. Gruber, K.M. Kready, D.R. Burrill, J.C. Way, P.A. Silver, Protein Engineering, Design and Selection 34 (2021). date_created: 2021-11-28T23:01:28Z date_published: 2021-11-01T00:00:00Z date_updated: 2023-08-14T13:01:38Z day: '01' department: - _id: CaGu doi: 10.1093/protein/gzab025 external_id: isi: - '000746596900001' pmid: - '34725710' intvolume: ' 34' isi: 1 language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1093/protein/gzab025 month: '11' oa: 1 oa_version: Published Version pmid: 1 publication: Protein Engineering, Design and Selection publication_identifier: eissn: - 1741-0134 issn: - 1741-0126 publication_status: published publisher: Oxford University Press quality_controlled: '1' scopus_import: '1' status: public title: Rational engineering of an erythropoietin fusion protein to treat hypoxia type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 34 year: '2021' ... --- _id: '10366' article_number: '203758' article_processing_charge: No article_type: letter_note author: - first_name: Carl-Philipp J full_name: Heisenberg, Carl-Philipp J id: 39427864-F248-11E8-B48F-1D18A9856A87 last_name: Heisenberg orcid: 0000-0002-0912-4566 - first_name: Ana Maria full_name: Lennon, Ana Maria last_name: Lennon - first_name: Roberto full_name: Mayor, Roberto last_name: Mayor - first_name: Guillaume full_name: Salbreux, Guillaume last_name: Salbreux citation: ama: 'Heisenberg C-PJ, Lennon AM, Mayor R, Salbreux G. Special rebranding issue: “Quantitative cell and developmental biology.” Cells and Development. 2021;168(12). doi:10.1016/j.cdev.2021.203758' apa: 'Heisenberg, C.-P. J., Lennon, A. M., Mayor, R., & Salbreux, G. (2021). Special rebranding issue: “Quantitative cell and developmental biology.” Cells and Development. Elsevier. https://doi.org/10.1016/j.cdev.2021.203758' chicago: 'Heisenberg, Carl-Philipp J, Ana Maria Lennon, Roberto Mayor, and Guillaume Salbreux. “Special Rebranding Issue: ‘Quantitative Cell and Developmental Biology.’” Cells and Development. Elsevier, 2021. https://doi.org/10.1016/j.cdev.2021.203758.' ieee: 'C.-P. J. Heisenberg, A. M. Lennon, R. Mayor, and G. Salbreux, “Special rebranding issue: ‘Quantitative cell and developmental biology,’” Cells and Development, vol. 168, no. 12. Elsevier, 2021.' ista: 'Heisenberg C-PJ, Lennon AM, Mayor R, Salbreux G. 2021. Special rebranding issue: “Quantitative cell and developmental biology”. Cells and Development. 168(12), 203758.' mla: 'Heisenberg, Carl-Philipp J., et al. “Special Rebranding Issue: ‘Quantitative Cell and Developmental Biology.’” Cells and Development, vol. 168, no. 12, 203758, Elsevier, 2021, doi:10.1016/j.cdev.2021.203758.' short: C.-P.J. Heisenberg, A.M. Lennon, R. Mayor, G. Salbreux, Cells and Development 168 (2021). date_created: 2021-11-28T23:01:30Z date_published: 2021-11-17T00:00:00Z date_updated: 2023-08-14T13:02:40Z day: '17' department: - _id: CaHe doi: 10.1016/j.cdev.2021.203758 external_id: isi: - '000974771600028' pmid: - '34800748' intvolume: ' 168' isi: 1 issue: '12' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1016/j.cdev.2021.203758 month: '11' oa: 1 oa_version: Published Version pmid: 1 publication: Cells and Development publication_identifier: issn: - 2667-2901 publication_status: published publisher: Elsevier quality_controlled: '1' scopus_import: '1' status: public title: 'Special rebranding issue: “Quantitative cell and developmental biology”' type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 168 year: '2021' ... --- _id: '10402' abstract: - lang: eng text: Branching morphogenesis governs the formation of many organs such as lung, kidney, and the neurovascular system. Many studies have explored system-specific molecular and cellular regulatory mechanisms, as well as self-organizing rules underlying branching morphogenesis. However, in addition to local cues, branched tissue growth can also be influenced by global guidance. Here, we develop a theoretical framework for a stochastic self-organized branching process in the presence of external cues. Combining analytical theory with numerical simulations, we predict differential signatures of global vs. local regulatory mechanisms on the branching pattern, such as angle distributions, domain size, and space-filling efficiency. We find that branch alignment follows a generic scaling law determined by the strength of global guidance, while local interactions influence the tissue density but not its overall territory. Finally, using zebrafish innervation as a model system, we test these key features of the model experimentally. Our work thus provides quantitative predictions to disentangle the role of different types of cues in shaping branched structures across scales. acknowledgement: We thank all members of our respective groups for helpful discussion on the paper. The authors are also grateful to Prof. Abdel El. Manira for support and sharing Tg(HUC:Gal4;UAS:Synaptohysin-GFP), to Haohao Wu for discussion, and thank Elena Zabalueva for the zebrafish schematic. The authors also acknowledge Zebrafish core facility, Genome Engineering Zebrafish and Biomedicum Imaging Core from the Karolinska Institutet for technical support. This work received funding from the ERC under the European Union’s Horizon 2020 research and innovation programme (grant agreement No. 851288 to E.H.) and under the Marie Skłodowska-Curie grant agreement No. 754411 (to M.C.U.); Swedish Research Council (to F.L., I.A. and S.H.); Knut and Alice Wallenberg Foundation (F.L. and I.A.); Swedish Brain Foundation (F.L. and S.H.); Ming Wai Lau Foundation (to F.L.); StratRegen (to F.L.); ERC Consolidator grant STEMMING-FROM-NERVE and ERC Synergy Grant KILL-OR-DIFFERENTIATE (to I.A.); Bertil Hallsten Research Foundation (to I.A.); Cancerfonden (to I.A.); the Paradifference Foundation (to I.A.); Austrian Science Fund (to I.A.); and StratNeuro (to S.H.). article_number: '6830' article_processing_charge: No article_type: original 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: Dmitrii full_name: Kamenev, Dmitrii last_name: Kamenev - first_name: Kazunori full_name: Sunadome, Kazunori last_name: Sunadome - first_name: Dominik C full_name: Fachet, Dominik C id: 14FDD550-AA41-11E9-A0E5-1ACCE5697425 last_name: Fachet - first_name: Francois full_name: Lallemend, Francois last_name: Lallemend - first_name: Igor full_name: Adameyko, Igor last_name: Adameyko - first_name: Saida full_name: Hadjab, Saida last_name: Hadjab - first_name: Edouard B full_name: Hannezo, Edouard B id: 3A9DB764-F248-11E8-B48F-1D18A9856A87 last_name: Hannezo orcid: 0000-0001-6005-1561 citation: ama: Ucar MC, Kamenev D, Sunadome K, et al. Theory of branching morphogenesis by local interactions and global guidance. Nature Communications. 2021;12. doi:10.1038/s41467-021-27135-5 apa: Ucar, M. C., Kamenev, D., Sunadome, K., Fachet, D. C., Lallemend, F., Adameyko, I., … Hannezo, E. B. (2021). Theory of branching morphogenesis by local interactions and global guidance. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-021-27135-5 chicago: Ucar, Mehmet C, Dmitrii Kamenev, Kazunori Sunadome, Dominik C Fachet, Francois Lallemend, Igor Adameyko, Saida Hadjab, and Edouard B Hannezo. “Theory of Branching Morphogenesis by Local Interactions and Global Guidance.” Nature Communications. Springer Nature, 2021. https://doi.org/10.1038/s41467-021-27135-5. ieee: M. C. Ucar et al., “Theory of branching morphogenesis by local interactions and global guidance,” Nature Communications, vol. 12. Springer Nature, 2021. ista: Ucar MC, Kamenev D, Sunadome K, Fachet DC, Lallemend F, Adameyko I, Hadjab S, Hannezo EB. 2021. Theory of branching morphogenesis by local interactions and global guidance. Nature Communications. 12, 6830. mla: Ucar, Mehmet C., et al. “Theory of Branching Morphogenesis by Local Interactions and Global Guidance.” Nature Communications, vol. 12, 6830, Springer Nature, 2021, doi:10.1038/s41467-021-27135-5. short: M.C. Ucar, D. Kamenev, K. Sunadome, D.C. Fachet, F. Lallemend, I. Adameyko, S. Hadjab, E.B. Hannezo, Nature Communications 12 (2021). date_created: 2021-12-05T23:01:40Z date_published: 2021-11-24T00:00:00Z date_updated: 2023-08-14T13:18:46Z day: '24' ddc: - '573' department: - _id: EdHa doi: 10.1038/s41467-021-27135-5 ec_funded: 1 external_id: isi: - '000722322900020' pmid: - '34819507' file: - access_level: open_access checksum: 63c56ec75314a71e63e7dd2920b3c5b5 content_type: application/pdf creator: cchlebak date_created: 2021-12-10T08:54:09Z date_updated: 2021-12-10T08:54:09Z file_id: '10529' file_name: 2021_NatComm_Ucar.pdf file_size: 2303405 relation: main_file success: 1 file_date_updated: 2021-12-10T08:54:09Z has_accepted_license: '1' intvolume: ' 12' isi: 1 language: - iso: eng month: '11' oa: 1 oa_version: Published Version pmid: 1 project: - _id: 05943252-7A3F-11EA-A408-12923DDC885E call_identifier: H2020 grant_number: '851288' name: Design Principles of Branching Morphogenesis - _id: 260C2330-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '754411' name: ISTplus - Postdoctoral Fellowships publication: Nature Communications publication_identifier: eissn: - 2041-1723 publication_status: published publisher: Springer Nature quality_controlled: '1' related_material: record: - id: '13058' relation: research_data status: public scopus_import: '1' status: public title: 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: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 12 year: '2021' ... --- _id: '10407' abstract: - lang: eng text: Digital hardware Trojans are integrated circuits whose implementation differ from the specification in an arbitrary and malicious way. For example, the circuit can differ from its specified input/output behavior after some fixed number of queries (known as “time bombs”) or on some particular input (known as “cheat codes”). To detect such Trojans, countermeasures using multiparty computation (MPC) or verifiable computation (VC) have been proposed. On a high level, to realize a circuit with specification F one has more sophisticated circuits F⋄ manufactured (where F⋄ specifies a MPC or VC of F ), and then embeds these F⋄ ’s into a master circuit which must be trusted but is relatively simple compared to F . Those solutions impose a significant overhead as F⋄ is much more complex than F , also the master circuits are not exactly trivial. In this work, we show that in restricted settings, where F has no evolving state and is queried on independent inputs, we can achieve a relaxed security notion using very simple constructions. In particular, we do not change the specification of the circuit at all (i.e., F=F⋄ ). Moreover the master circuit basically just queries a subset of its manufactured circuits and checks if they’re all the same. The security we achieve guarantees that, if the manufactured circuits are initially tested on up to T inputs, the master circuit will catch Trojans that try to deviate on significantly more than a 1/T fraction of the inputs. This bound is optimal for the type of construction considered, and we provably achieve it using a construction where 12 instantiations of F need to be embedded into the master. We also discuss an extremely simple construction with just 2 instantiations for which we conjecture that it already achieves the optimal bound. alternative_title: - LNCS article_processing_charge: No author: - first_name: Suvradip full_name: Chakraborty, Suvradip id: B9CD0494-D033-11E9-B219-A439E6697425 last_name: Chakraborty - first_name: Stefan full_name: Dziembowski, Stefan last_name: Dziembowski - first_name: Małgorzata full_name: Gałązka, Małgorzata last_name: Gałązka - first_name: Tomasz full_name: Lizurej, Tomasz last_name: Lizurej - first_name: Krzysztof Z full_name: Pietrzak, Krzysztof Z id: 3E04A7AA-F248-11E8-B48F-1D18A9856A87 last_name: Pietrzak orcid: 0000-0002-9139-1654 - first_name: Michelle X full_name: Yeo, Michelle X id: 2D82B818-F248-11E8-B48F-1D18A9856A87 last_name: Yeo citation: ama: 'Chakraborty S, Dziembowski S, Gałązka M, Lizurej T, Pietrzak KZ, Yeo MX. Trojan-resilience without cryptography. In: Vol 13043. Springer Nature; 2021:397-428. doi:10.1007/978-3-030-90453-1_14' apa: 'Chakraborty, S., Dziembowski, S., Gałązka, M., Lizurej, T., Pietrzak, K. Z., & Yeo, M. X. (2021). Trojan-resilience without cryptography (Vol. 13043, pp. 397–428). Presented at the TCC: Theory of Cryptography Conference, Raleigh, NC, United States: Springer Nature. https://doi.org/10.1007/978-3-030-90453-1_14' chicago: Chakraborty, Suvradip, Stefan Dziembowski, Małgorzata Gałązka, Tomasz Lizurej, Krzysztof Z Pietrzak, and Michelle X Yeo. “Trojan-Resilience without Cryptography,” 13043:397–428. Springer Nature, 2021. https://doi.org/10.1007/978-3-030-90453-1_14. ieee: 'S. Chakraborty, S. Dziembowski, M. Gałązka, T. Lizurej, K. Z. Pietrzak, and M. X. Yeo, “Trojan-resilience without cryptography,” presented at the TCC: Theory of Cryptography Conference, Raleigh, NC, United States, 2021, vol. 13043, pp. 397–428.' ista: 'Chakraborty S, Dziembowski S, Gałązka M, Lizurej T, Pietrzak KZ, Yeo MX. 2021. Trojan-resilience without cryptography. TCC: Theory of Cryptography Conference, LNCS, vol. 13043, 397–428.' mla: Chakraborty, Suvradip, et al. Trojan-Resilience without Cryptography. Vol. 13043, Springer Nature, 2021, pp. 397–428, doi:10.1007/978-3-030-90453-1_14. short: S. Chakraborty, S. Dziembowski, M. Gałązka, T. Lizurej, K.Z. Pietrzak, M.X. Yeo, in:, Springer Nature, 2021, pp. 397–428. conference: end_date: 2021-11-11 location: Raleigh, NC, United States name: 'TCC: Theory of Cryptography Conference' start_date: 2021-11-08 date_created: 2021-12-05T23:01:42Z date_published: 2021-11-04T00:00:00Z date_updated: 2023-08-14T13:07:46Z day: '04' department: - _id: KrPi doi: 10.1007/978-3-030-90453-1_14 ec_funded: 1 external_id: isi: - '000728364000014' intvolume: ' 13043' isi: 1 language: - iso: eng main_file_link: - open_access: '1' url: https://eprint.iacr.org/2021/1224 month: '11' oa: 1 oa_version: Preprint page: 397-428 project: - _id: 258AA5B2-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '682815' name: Teaching Old Crypto New Tricks publication_identifier: eissn: - 1611-3349 isbn: - 9-783-0309-0452-4 issn: - 0302-9743 publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: Trojan-resilience without cryptography type: conference user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 13043 year: '2021' ... --- _id: '10403' abstract: - lang: eng text: Synaptic transmission, connectivity, and dendritic morphology mature in parallel during brain development and are often disrupted in neurodevelopmental disorders. Yet how these changes influence the neuronal computations necessary for normal brain function are not well understood. To identify cellular mechanisms underlying the maturation of synaptic integration in interneurons, we combined patch-clamp recordings of excitatory inputs in mouse cerebellar stellate cells (SCs), three-dimensional reconstruction of SC morphology with excitatory synapse location, and biophysical modeling. We found that postnatal maturation of postsynaptic strength was homogeneously reduced along the somatodendritic axis, but dendritic integration was always sublinear. However, dendritic branching increased without changes in synapse density, leading to a substantial gain in distal inputs. Thus, changes in synapse distribution, rather than dendrite cable properties, are the dominant mechanism underlying the maturation of neuronal computation. These mechanisms favor the emergence of a spatially compartmentalized two-stage integration model promoting location-dependent integration within dendritic subunits. acknowledgement: This study was supported by the Centre National de la Recherche Scientifique and the Agence Nationale de la Recherche (ANR-13-BSV4-00166, to LC and DAD). TA was supported by fellowships from the Fondation pour la Recherche Medicale and the Swedish Research Council. We thank Dmitry Ershov from the Image Analysis Hub of the Institut Pasteur, Elodie Le Monnier, Elena Hollergschwandtner, Vanessa Zheden, and Corinne Nantet for technical support and Haining Zhong for providing the Venus-tagged PSD95 mouse line. We would like to thank Alberto Bacci, Ann Lohof, and Nelson Rebola for comments on the manuscript. article_number: e65954 article_processing_charge: No article_type: original author: - first_name: Celia full_name: Biane, Celia last_name: Biane - first_name: Florian full_name: Rückerl, Florian last_name: Rückerl - first_name: Therese full_name: Abrahamsson, Therese last_name: Abrahamsson - first_name: Cécile full_name: Saint-Cloment, Cécile last_name: Saint-Cloment - first_name: Jean full_name: Mariani, Jean last_name: Mariani - first_name: Ryuichi full_name: Shigemoto, Ryuichi id: 499F3ABC-F248-11E8-B48F-1D18A9856A87 last_name: Shigemoto orcid: 0000-0001-8761-9444 - first_name: David A. full_name: Digregorio, David A. last_name: Digregorio - first_name: Rachel M. full_name: Sherrard, Rachel M. last_name: Sherrard - first_name: Laurence full_name: Cathala, Laurence last_name: Cathala citation: ama: Biane C, Rückerl F, Abrahamsson T, et al. Developmental emergence of two-stage nonlinear synaptic integration in cerebellar interneurons. eLife. 2021;10. doi:10.7554/eLife.65954 apa: Biane, C., Rückerl, F., Abrahamsson, T., Saint-Cloment, C., Mariani, J., Shigemoto, R., … Cathala, L. (2021). Developmental emergence of two-stage nonlinear synaptic integration in cerebellar interneurons. ELife. eLife Sciences Publications. https://doi.org/10.7554/eLife.65954 chicago: Biane, Celia, Florian Rückerl, Therese Abrahamsson, Cécile Saint-Cloment, Jean Mariani, Ryuichi Shigemoto, David A. Digregorio, Rachel M. Sherrard, and Laurence Cathala. “Developmental Emergence of Two-Stage Nonlinear Synaptic Integration in Cerebellar Interneurons.” ELife. eLife Sciences Publications, 2021. https://doi.org/10.7554/eLife.65954. ieee: C. Biane et al., “Developmental emergence of two-stage nonlinear synaptic integration in cerebellar interneurons,” eLife, vol. 10. eLife Sciences Publications, 2021. ista: Biane C, Rückerl F, Abrahamsson T, Saint-Cloment C, Mariani J, Shigemoto R, Digregorio DA, Sherrard RM, Cathala L. 2021. Developmental emergence of two-stage nonlinear synaptic integration in cerebellar interneurons. eLife. 10, e65954. mla: Biane, Celia, et al. “Developmental Emergence of Two-Stage Nonlinear Synaptic Integration in Cerebellar Interneurons.” ELife, vol. 10, e65954, eLife Sciences Publications, 2021, doi:10.7554/eLife.65954. short: C. Biane, F. Rückerl, T. Abrahamsson, C. Saint-Cloment, J. Mariani, R. Shigemoto, D.A. Digregorio, R.M. Sherrard, L. Cathala, ELife 10 (2021). date_created: 2021-12-05T23:01:40Z date_published: 2021-11-03T00:00:00Z date_updated: 2023-08-14T13:12:07Z day: '03' ddc: - '570' department: - _id: RySh doi: 10.7554/eLife.65954 external_id: isi: - '000715789500001' file: - access_level: open_access checksum: c7c33c3319428d56e332e22349c50ed3 content_type: application/pdf creator: cchlebak date_created: 2021-12-10T08:31:41Z date_updated: 2021-12-10T08:31:41Z file_id: '10528' file_name: 2021_eLife_Biane.pdf file_size: 13131322 relation: main_file success: 1 file_date_updated: 2021-12-10T08:31:41Z has_accepted_license: '1' intvolume: ' 10' isi: 1 language: - iso: eng month: '11' oa: 1 oa_version: Published Version publication: eLife publication_identifier: eissn: - 2050-084X publication_status: published publisher: eLife Sciences Publications quality_controlled: '1' scopus_import: '1' status: public title: Developmental emergence of two-stage nonlinear synaptic integration in cerebellar interneurons tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 10 year: '2021' ... --- _id: '10401' abstract: - lang: eng text: Theoretical and experimental studies of the interaction between spins and temperature are vital for the development of spin caloritronics, as they dictate the design of future devices. In this work, we propose a two-terminal cold-atom simulator to study that interaction. The proposed quantum simulator consists of strongly interacting atoms that occupy two temperature reservoirs connected by a one-dimensional link. First, we argue that the dynamics in the link can be described using an inhomogeneous Heisenberg spin chain whose couplings are defined by the local temperature. Second, we show the existence of a spin current in a system with a temperature difference by studying the dynamics that follows the spin-flip of an atom in the link. A temperature gradient accelerates the impurity in one direction more than in the other, leading to an overall spin current similar to the spin Seebeck effect. acknowledgement: The authors acknowledge support from the European QuantERA ERA-NET Cofund in Quantum Technologies (Project QTFLAG Grant Agreement No. 731473) (R.E.B), CNPq (Conselho Nacional de Desenvolvimento Científico e Tecnológico) Brazil (A.F.), the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 754411 (A.G.V.), the Independent Research Fund Denmark, the Carlsberg Foundation, and Aarhus University Research Foundation under the Jens Christian Skou fellowship program (N.T.Z). article_number: '252' article_processing_charge: No article_type: original author: - first_name: Rafael E. full_name: Barfknecht, Rafael E. last_name: Barfknecht - first_name: Angela full_name: Foerster, Angela last_name: Foerster - first_name: Nikolaj T. full_name: Zinner, Nikolaj T. last_name: Zinner - first_name: Artem full_name: Volosniev, Artem id: 37D278BC-F248-11E8-B48F-1D18A9856A87 last_name: Volosniev orcid: 0000-0003-0393-5525 citation: ama: Barfknecht RE, Foerster A, Zinner NT, Volosniev A. Generation of spin currents by a temperature gradient in a two-terminal device. Communications Physics. 2021;4(1). doi:10.1038/s42005-021-00753-7 apa: Barfknecht, R. E., Foerster, A., Zinner, N. T., & Volosniev, A. (2021). Generation of spin currents by a temperature gradient in a two-terminal device. Communications Physics. Springer Nature. https://doi.org/10.1038/s42005-021-00753-7 chicago: Barfknecht, Rafael E., Angela Foerster, Nikolaj T. Zinner, and Artem Volosniev. “Generation of Spin Currents by a Temperature Gradient in a Two-Terminal Device.” Communications Physics. Springer Nature, 2021. https://doi.org/10.1038/s42005-021-00753-7. ieee: R. E. Barfknecht, A. Foerster, N. T. Zinner, and A. Volosniev, “Generation of spin currents by a temperature gradient in a two-terminal device,” Communications Physics, vol. 4, no. 1. Springer Nature, 2021. ista: Barfknecht RE, Foerster A, Zinner NT, Volosniev A. 2021. Generation of spin currents by a temperature gradient in a two-terminal device. Communications Physics. 4(1), 252. mla: Barfknecht, Rafael E., et al. “Generation of Spin Currents by a Temperature Gradient in a Two-Terminal Device.” Communications Physics, vol. 4, no. 1, 252, Springer Nature, 2021, doi:10.1038/s42005-021-00753-7. short: R.E. Barfknecht, A. Foerster, N.T. Zinner, A. Volosniev, Communications Physics 4 (2021). date_created: 2021-12-05T23:01:39Z date_published: 2021-11-26T00:00:00Z date_updated: 2023-08-14T13:04:34Z day: '26' ddc: - '530' department: - _id: MiLe doi: 10.1038/s42005-021-00753-7 ec_funded: 1 external_id: arxiv: - '2101.02020' isi: - 10.1038/s42005-021-00753-7 file: - access_level: open_access checksum: 9097319952cb9a3d96e7fd3aa9813a03 content_type: application/pdf creator: alisjak date_created: 2021-12-06T14:53:41Z date_updated: 2021-12-06T14:53:41Z file_id: '10420' file_name: 2021_NatComm_Barfknecht.pdf file_size: 1068984 relation: main_file success: 1 file_date_updated: 2021-12-06T14:53:41Z has_accepted_license: '1' intvolume: ' 4' issue: '1' language: - iso: eng month: '11' oa: 1 oa_version: Published Version project: - _id: 260C2330-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '754411' name: ISTplus - Postdoctoral Fellowships publication: Communications Physics publication_identifier: eissn: - '23993650' publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: Generation of spin currents by a temperature gradient in a two-terminal device tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 4 year: '2021' ... --- _id: '10404' abstract: - lang: eng text: While convolutional neural networks (CNNs) have found wide adoption as state-of-the-art models for image-related tasks, their predictions are often highly sensitive to small input perturbations, which the human vision is robust against. This paper presents Perturber, a web-based application that allows users to instantaneously explore how CNN activations and predictions evolve when a 3D input scene is interactively perturbed. Perturber offers a large variety of scene modifications, such as camera controls, lighting and shading effects, background modifications, object morphing, as well as adversarial attacks, to facilitate the discovery of potential vulnerabilities. Fine-tuned model versions can be directly compared for qualitative evaluation of their robustness. Case studies with machine learning experts have shown that Perturber helps users to quickly generate hypotheses about model vulnerabilities and to qualitatively compare model behavior. Using quantitative analyses, we could replicate users’ insights with other CNN architectures and input images, yielding new insights about the vulnerability of adversarially trained models. acknowledgement: "We thank Robert Geirhos and Roland Zimmermann for their participation in the case study and valuable feedback, Chris Olah and Nick Cammarata for valuable discussions in the early phase of the project, as well as the Distill Slack workspace as a platform for discussions. M.L. is supported in part by the Austrian Science Fund (FWF) under grant Z211-N23 (Wittgenstein Award). J.B. is supported by the German Federal Ministry of Education and Research\r\n(BMBF) through the Competence Center for Machine Learning (TUE.AI, FKZ 01IS18039A) and the International Max Planck Research School for Intelligent Systems (IMPRS-IS). R.H. is partially supported by Boeing and Horizon-2020 ECSEL (grant 783163, iDev40).\r\n" article_processing_charge: No article_type: original author: - first_name: Stefan full_name: Sietzen, Stefan last_name: Sietzen - first_name: Mathias full_name: Lechner, Mathias id: 3DC22916-F248-11E8-B48F-1D18A9856A87 last_name: Lechner - first_name: Judy full_name: Borowski, Judy last_name: Borowski - first_name: Ramin full_name: Hasani, Ramin last_name: Hasani - first_name: Manuela full_name: Waldner, Manuela last_name: Waldner citation: ama: Sietzen S, Lechner M, Borowski J, Hasani R, Waldner M. Interactive analysis of CNN robustness. Computer Graphics Forum. 2021;40(7):253-264. doi:10.1111/cgf.14418 apa: Sietzen, S., Lechner, M., Borowski, J., Hasani, R., & Waldner, M. (2021). Interactive analysis of CNN robustness. Computer Graphics Forum. Wiley. https://doi.org/10.1111/cgf.14418 chicago: Sietzen, Stefan, Mathias Lechner, Judy Borowski, Ramin Hasani, and Manuela Waldner. “Interactive Analysis of CNN Robustness.” Computer Graphics Forum. Wiley, 2021. https://doi.org/10.1111/cgf.14418. ieee: S. Sietzen, M. Lechner, J. Borowski, R. Hasani, and M. Waldner, “Interactive analysis of CNN robustness,” Computer Graphics Forum, vol. 40, no. 7. Wiley, pp. 253–264, 2021. ista: Sietzen S, Lechner M, Borowski J, Hasani R, Waldner M. 2021. Interactive analysis of CNN robustness. Computer Graphics Forum. 40(7), 253–264. mla: Sietzen, Stefan, et al. “Interactive Analysis of CNN Robustness.” Computer Graphics Forum, vol. 40, no. 7, Wiley, 2021, pp. 253–64, doi:10.1111/cgf.14418. short: S. Sietzen, M. Lechner, J. Borowski, R. Hasani, M. Waldner, Computer Graphics Forum 40 (2021) 253–264. date_created: 2021-12-05T23:01:40Z date_published: 2021-11-27T00:00:00Z date_updated: 2023-08-14T13:11:42Z day: '27' department: - _id: ToHe doi: 10.1111/cgf.14418 external_id: arxiv: - '2110.07667' isi: - '000722952000024' intvolume: ' 40' isi: 1 issue: '7' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/2110.07667 month: '11' oa: 1 oa_version: Preprint page: 253-264 project: - _id: 25F42A32-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: Z211 name: The Wittgenstein Prize publication: Computer Graphics Forum publication_identifier: eissn: - 1467-8659 issn: - 0167-7055 publication_status: published publisher: Wiley quality_controlled: '1' scopus_import: '1' status: public title: Interactive analysis of CNN robustness type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 40 year: '2021' ... --- _id: '10406' abstract: - lang: eng text: Multicellular organisms develop complex shapes from much simpler, single-celled zygotes through a process commonly called morphogenesis. Morphogenesis involves an interplay between several factors, ranging from the gene regulatory networks determining cell fate and differentiation to the mechanical processes underlying cell and tissue shape changes. Thus, the study of morphogenesis has historically been based on multidisciplinary approaches at the interface of biology with physics and mathematics. Recent technological advances have further improved our ability to study morphogenesis by bridging the gap between the genetic and biophysical factors through the development of new tools for visualizing, analyzing, and perturbing these factors and their biochemical intermediaries. Here, we review how a combination of genetic, microscopic, biophysical, and biochemical approaches has aided our attempts to understand morphogenesis and discuss potential approaches that may be beneficial to such an inquiry in the future. acknowledgement: The authors would like to thank Feyza Nur Arslan, Suyash Naik, Diana Pinheiro, Alexandra Schauer, and Shayan Shamipour for their comments on the draft. N.M. is supported by an ISTplus postdoctoral fellowship (H2020 Marie-Sklodowska-Curie COFUND Action). article_processing_charge: No article_type: original author: - first_name: Nikhil full_name: Mishra, Nikhil id: C4D70E82-1081-11EA-B3ED-9A4C3DDC885E last_name: Mishra orcid: 0000-0002-6425-5788 - first_name: Carl-Philipp J full_name: Heisenberg, Carl-Philipp J id: 39427864-F248-11E8-B48F-1D18A9856A87 last_name: Heisenberg orcid: 0000-0002-0912-4566 citation: ama: Mishra N, Heisenberg C-PJ. Dissecting organismal morphogenesis by bridging genetics and biophysics. Annual Review of Genetics. 2021;55:209-233. doi:10.1146/annurev-genet-071819-103748 apa: Mishra, N., & Heisenberg, C.-P. J. (2021). Dissecting organismal morphogenesis by bridging genetics and biophysics. Annual Review of Genetics. Annual Reviews. https://doi.org/10.1146/annurev-genet-071819-103748 chicago: Mishra, Nikhil, and Carl-Philipp J Heisenberg. “Dissecting Organismal Morphogenesis by Bridging Genetics and Biophysics.” Annual Review of Genetics. Annual Reviews, 2021. https://doi.org/10.1146/annurev-genet-071819-103748. ieee: N. Mishra and C.-P. J. Heisenberg, “Dissecting organismal morphogenesis by bridging genetics and biophysics,” Annual Review of Genetics, vol. 55. Annual Reviews, pp. 209–233, 2021. ista: Mishra N, Heisenberg C-PJ. 2021. Dissecting organismal morphogenesis by bridging genetics and biophysics. Annual Review of Genetics. 55, 209–233. mla: Mishra, Nikhil, and Carl-Philipp J. Heisenberg. “Dissecting Organismal Morphogenesis by Bridging Genetics and Biophysics.” Annual Review of Genetics, vol. 55, Annual Reviews, 2021, pp. 209–33, doi:10.1146/annurev-genet-071819-103748. short: N. Mishra, C.-P.J. Heisenberg, Annual Review of Genetics 55 (2021) 209–233. date_created: 2021-12-05T23:01:41Z date_published: 2021-08-30T00:00:00Z date_updated: 2023-08-14T13:05:13Z day: '30' department: - _id: CaHe doi: 10.1146/annurev-genet-071819-103748 ec_funded: 1 external_id: isi: - '000747220900010' pmid: - '34460295' intvolume: ' 55' isi: 1 keyword: - morphogenesis - forward genetics - high-resolution microscopy - biophysics - biochemistry - patterning language: - iso: eng month: '08' oa_version: None page: 209-233 pmid: 1 project: - _id: 260C2330-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '754411' name: ISTplus - Postdoctoral Fellowships publication: Annual Review of Genetics publication_identifier: eissn: - 1545-2948 issn: - 0066-4197 publication_status: published publisher: Annual Reviews quality_controlled: '1' scopus_import: '1' status: public title: Dissecting organismal morphogenesis by bridging genetics and biophysics type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 55 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: '10408' abstract: - lang: eng text: 'Key trees are often the best solution in terms of transmission cost and storage requirements for managing keys in a setting where a group needs to share a secret key, while being able to efficiently rotate the key material of users (in order to recover from a potential compromise, or to add or remove users). Applications include multicast encryption protocols like LKH (Logical Key Hierarchies) or group messaging like the current IETF proposal TreeKEM. A key tree is a (typically balanced) binary tree, where each node is identified with a key: leaf nodes hold users’ secret keys while the root is the shared group key. For a group of size N, each user just holds log(N) keys (the keys on the path from its leaf to the root) and its entire key material can be rotated by broadcasting 2log(N) ciphertexts (encrypting each fresh key on the path under the keys of its parents). In this work we consider the natural setting where we have many groups with partially overlapping sets of users, and ask if we can find solutions where the cost of rotating a key is better than in the trivial one where we have a separate key tree for each group. We show that in an asymptotic setting (where the number m of groups is fixed while the number N of users grows) there exist more general key graphs whose cost converges to the cost of a single group, thus saving a factor linear in the number of groups over the trivial solution. As our asymptotic “solution” converges very slowly and performs poorly on concrete examples, we propose an algorithm that uses a natural heuristic to compute a key graph for any given group structure. Our algorithm combines two greedy algorithms, and is thus very efficient: it first converts the group structure into a “lattice graph”, which is then turned into a key graph by repeatedly applying the algorithm for constructing a Huffman code. To better understand how far our proposal is from an optimal solution, we prove lower bounds on the update cost of continuous group-key agreement and multicast encryption in a symbolic model admitting (asymmetric) encryption, pseudorandom generators, and secret sharing as building blocks.' acknowledgement: B. Auerbach, M.A. Baig and K. Pietrzak—received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (682815 - TOCNeT); Karen Klein was supported in part by ERC CoG grant 724307 and conducted part of this work at IST Austria, funded by the ERC under the European Union’s Horizon 2020 research and innovation programme (682815 - TOCNeT); Guillermo Pascual-Perez was funded by the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 665385; Michael Walter conducted part of this work at IST Austria, funded by the ERC under the European Union’s Horizon 2020 research and innovation programme (682815 - TOCNeT). alternative_title: - LNCS article_processing_charge: No author: - first_name: Joel F full_name: Alwen, Joel F id: 2A8DFA8C-F248-11E8-B48F-1D18A9856A87 last_name: Alwen - first_name: Benedikt full_name: Auerbach, Benedikt id: D33D2B18-E445-11E9-ABB7-15F4E5697425 last_name: Auerbach orcid: 0000-0002-7553-6606 - first_name: Mirza Ahad full_name: Baig, Mirza Ahad id: 3EDE6DE4-AA5A-11E9-986D-341CE6697425 last_name: Baig - first_name: Miguel full_name: Cueto Noval, Miguel id: ffc563a3-f6e0-11ea-865d-e3cce03d17cc last_name: Cueto Noval - first_name: Karen full_name: Klein, Karen id: 3E83A2F8-F248-11E8-B48F-1D18A9856A87 last_name: Klein - first_name: Guillermo full_name: Pascual Perez, Guillermo id: 2D7ABD02-F248-11E8-B48F-1D18A9856A87 last_name: Pascual Perez orcid: 0000-0001-8630-415X - first_name: Krzysztof Z full_name: Pietrzak, Krzysztof Z id: 3E04A7AA-F248-11E8-B48F-1D18A9856A87 last_name: Pietrzak orcid: 0000-0002-9139-1654 - first_name: Michael full_name: Walter, Michael id: 488F98B0-F248-11E8-B48F-1D18A9856A87 last_name: Walter orcid: 0000-0003-3186-2482 citation: ama: 'Alwen JF, Auerbach B, Baig MA, et al. Grafting key trees: Efficient key management for overlapping groups. In: 19th International Conference. Vol 13044. Springer Nature; 2021:222-253. doi:10.1007/978-3-030-90456-2_8' apa: 'Alwen, J. F., Auerbach, B., Baig, M. A., Cueto Noval, M., Klein, K., Pascual Perez, G., … Walter, M. (2021). Grafting key trees: Efficient key management for overlapping groups. In 19th International Conference (Vol. 13044, pp. 222–253). Raleigh, NC, United States: Springer Nature. https://doi.org/10.1007/978-3-030-90456-2_8' chicago: 'Alwen, Joel F, Benedikt Auerbach, Mirza Ahad Baig, Miguel Cueto Noval, Karen Klein, Guillermo Pascual Perez, Krzysztof Z Pietrzak, and Michael Walter. “Grafting Key Trees: Efficient Key Management for Overlapping Groups.” In 19th International Conference, 13044:222–53. Springer Nature, 2021. https://doi.org/10.1007/978-3-030-90456-2_8.' ieee: 'J. F. Alwen et al., “Grafting key trees: Efficient key management for overlapping groups,” in 19th International Conference, Raleigh, NC, United States, 2021, vol. 13044, pp. 222–253.' ista: 'Alwen JF, Auerbach B, Baig MA, Cueto Noval M, Klein K, Pascual Perez G, Pietrzak KZ, Walter M. 2021. Grafting key trees: Efficient key management for overlapping groups. 19th International Conference. TCC: Theory of Cryptography, LNCS, vol. 13044, 222–253.' mla: 'Alwen, Joel F., et al. “Grafting Key Trees: Efficient Key Management for Overlapping Groups.” 19th International Conference, vol. 13044, Springer Nature, 2021, pp. 222–53, doi:10.1007/978-3-030-90456-2_8.' short: J.F. Alwen, B. Auerbach, M.A. Baig, M. Cueto Noval, K. Klein, G. Pascual Perez, K.Z. Pietrzak, M. Walter, in:, 19th International Conference, Springer Nature, 2021, pp. 222–253. conference: end_date: 2021-11-11 location: Raleigh, NC, United States name: 'TCC: Theory of Cryptography' start_date: 2021-11-08 date_created: 2021-12-05T23:01:42Z date_published: 2021-11-04T00:00:00Z date_updated: 2023-08-14T13:19:39Z day: '04' department: - _id: KrPi doi: 10.1007/978-3-030-90456-2_8 ec_funded: 1 external_id: isi: - '000728363700008' intvolume: ' 13044' isi: 1 language: - iso: eng main_file_link: - open_access: '1' url: https://eprint.iacr.org/2021/1158 month: '11' oa: 1 oa_version: Preprint page: 222-253 project: - _id: 258AA5B2-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '682815' name: Teaching Old Crypto New Tricks - _id: 2564DBCA-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '665385' name: International IST Doctoral Program publication: 19th International Conference publication_identifier: eisbn: - 978-3-030-90456-2 eissn: - 1611-3349 isbn: - 9-783-0309-0455-5 issn: - 0302-9743 publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: 'Grafting key trees: Efficient key management for overlapping groups' type: conference user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 13044 year: '2021' ... --- _id: '10527' abstract: - lang: eng text: We show that in a two-dimensional electron gas with an annular Fermi surface, long-range Coulomb interactions can lead to unconventional superconductivity by the Kohn-Luttinger mechanism. Superconductivity is strongly enhanced when the inner and outer Fermi surfaces are close to each other. The most prevalent state has chiral p-wave symmetry, but d-wave and extended s-wave pairing are also possible. We discuss these results in the context of rhombohedral trilayer graphene, where superconductivity was recently discovered in regimes where the normal state has an annular Fermi surface. Using realistic parameters, our mechanism can account for the order of magnitude of Tc, as well as its trends as a function of electron density and perpendicular displacement field. Moreover, it naturally explains some of the outstanding puzzles in this material, that include the weak temperature dependence of the resistivity above Tc, and the proximity of spin singlet superconductivity to the ferromagnetic phase. acknowledgement: We thank Yang-Zhi Chou, Andrey Chubukov, Johannes Hofmann, Steve Kivelson, Sri Raghu, and Sankar das Sarma, Jay Sau, Fengcheng Wu, and Andrea Young for many stimulating discussions and for their comments on the manuscript. E.B. thanks S. Chatterjee, T. Wang, and M. Zaletel for a collaboration on a related topic. A.G. acknowledges support by the European Unions Horizon 2020 research and innovation program under the Marie Sklodowska-Curie Grant Agreement No. 754411. E.B. and T.H. were supported by the European Research Council (ERC) under grant HQMAT (Grant Agreement No. 817799), by the Israel-USA Binational Science Foundation (BSF), and by a Research grant from Irving and Cherna Moskowitz. article_number: '247001' article_processing_charge: No article_type: original author: - first_name: Areg full_name: Ghazaryan, Areg id: 4AF46FD6-F248-11E8-B48F-1D18A9856A87 last_name: Ghazaryan orcid: 0000-0001-9666-3543 - first_name: Tobias full_name: Holder, Tobias last_name: Holder - first_name: Maksym full_name: Serbyn, Maksym id: 47809E7E-F248-11E8-B48F-1D18A9856A87 last_name: Serbyn orcid: 0000-0002-2399-5827 - first_name: Erez full_name: Berg, Erez last_name: Berg citation: ama: 'Ghazaryan A, Holder T, Serbyn M, Berg E. Unconventional superconductivity in systems with annular Fermi surfaces: Application to rhombohedral trilayer graphene. Physical Review Letters. 2021;127(24). doi:10.1103/physrevlett.127.247001' apa: 'Ghazaryan, A., Holder, T., Serbyn, M., & Berg, E. (2021). Unconventional superconductivity in systems with annular Fermi surfaces: Application to rhombohedral trilayer graphene. Physical Review Letters. American Physical Society. https://doi.org/10.1103/physrevlett.127.247001' chicago: 'Ghazaryan, Areg, Tobias Holder, Maksym Serbyn, and Erez Berg. “Unconventional Superconductivity in Systems with Annular Fermi Surfaces: Application to Rhombohedral Trilayer Graphene.” Physical Review Letters. American Physical Society, 2021. https://doi.org/10.1103/physrevlett.127.247001.' ieee: 'A. Ghazaryan, T. Holder, M. Serbyn, and E. Berg, “Unconventional superconductivity in systems with annular Fermi surfaces: Application to rhombohedral trilayer graphene,” Physical Review Letters, vol. 127, no. 24. American Physical Society, 2021.' ista: 'Ghazaryan A, Holder T, Serbyn M, Berg E. 2021. Unconventional superconductivity in systems with annular Fermi surfaces: Application to rhombohedral trilayer graphene. Physical Review Letters. 127(24), 247001.' mla: 'Ghazaryan, Areg, et al. “Unconventional Superconductivity in Systems with Annular Fermi Surfaces: Application to Rhombohedral Trilayer Graphene.” Physical Review Letters, vol. 127, no. 24, 247001, American Physical Society, 2021, doi:10.1103/physrevlett.127.247001.' short: A. Ghazaryan, T. Holder, M. Serbyn, E. Berg, Physical Review Letters 127 (2021). date_created: 2021-12-10T07:51:33Z date_published: 2021-12-09T00:00:00Z date_updated: 2023-08-14T13:19:13Z day: '09' department: - _id: MaSe doi: 10.1103/physrevlett.127.247001 ec_funded: 1 external_id: arxiv: - '2109.00011' isi: - '000923819400004' intvolume: ' 127' isi: 1 issue: '24' keyword: - general physics and astronomy language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/2109.00011 month: '12' oa: 1 oa_version: Preprint project: - _id: 260C2330-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '754411' name: ISTplus - Postdoctoral Fellowships publication: Physical Review Letters publication_identifier: eissn: - 1079-7114 issn: - 0031-9007 publication_status: published publisher: American Physical Society quality_controlled: '1' related_material: link: - description: News on IST Webpage relation: press_release url: https://ist.ac.at/en/news/resolving-the-puzzles-of-graphene-superconductivity/ scopus_import: '1' status: public title: 'Unconventional superconductivity in systems with annular Fermi surfaces: Application to rhombohedral trilayer graphene' type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 127 year: '2021' ... --- _id: '10534' abstract: - lang: eng text: For many years, fullerene derivatives have been the main n-type material of organic electronics and optoelectronics. Recently, fullerene derivatives functionalized with ethylene glycol (EG) side chains have been showing important properties such as enhanced dielectric constants, facile doping and enhanced self-assembly capabilities. Here, we have prepared field-effect transistors using a series of these fullerene derivatives equipped with EG side chains of different lengths. Transport data show the beneficial effect of increasing the EG side chain. In order to understand the material properties, full structural determination of these fullerene derivatives has been achieved by coupling the X-ray data with molecular dynamics (MD) simulations. The increase in transport properties is paired with the formation of extended layered structures, efficient molecular packing and an increase in the crystallite alignment. The layer-like structure is composed of conducting layers, containing of closely packed C60 balls approaching the inter-distance of 1 nm, that are separated by well-defined EG layers, where the EG chains are rather splayed with the chain direction almost perpendicular to the layer normal. Such a layered structure appears highly ordered and highly aligned with the C60 planes oriented parallel to the substrate in the thin film configuration. The order inside the thin film increases with the EG chain length, allowing the systems to achieve mobilities as high as 0.053 cm2 V−1 s−1. Our work elucidates the structure of these interesting semiconducting organic molecules and shows that the synergistic use of X-ray structural analysis and MD simulations is a powerful tool to identify the structure of thin organic films for optoelectronic applications. acknowledgement: J. D. gratefully acknowledges the China Scholarship Council (CSC No. 201606340158) for supporting his PhD studies. S. S. thanks J. Antoja-Lleonart for insightful discussions on simulating the X-ray diffraction patterns. Part of the work was sponsored by NWO Exact and Natural Sciences for the use of supercomputer facilities (Contract no. 17197 7095). Regarding S. S., R. A., R. W. A. H., J. C. H., and M. A. L., this is a publication by the FOM Focus Group “Next Generation Organic Photovoltaics”, participating in the Dutch Institute for Fundamental Energy Research (DIFFER). The ESRF is acknowledged for providing the beamtime. J. D. and G. P. are grateful to the BM26B staff for their great support during the beamtime. M. A. L., D. M. B. are grateful for the financial support of the European Research Council via a Starting Grant (HySPOD, No. 306983). article_processing_charge: No article_type: original author: - first_name: Jingjin full_name: Dong, Jingjin last_name: Dong - first_name: Selim full_name: Sami, Selim last_name: Sami - first_name: Daniel full_name: Balazs, Daniel id: 302BADF6-85FC-11EA-9E3B-B9493DDC885E last_name: Balazs orcid: 0000-0001-7597-043X - first_name: Riccardo full_name: Alessandri, Riccardo last_name: Alessandri - first_name: Fatimeh full_name: Jahani, Fatimeh last_name: Jahani - first_name: Li full_name: Qiu, Li last_name: Qiu - first_name: Siewert J. full_name: Marrink, Siewert J. last_name: Marrink - first_name: Remco W.A. full_name: Havenith, Remco W.A. last_name: Havenith - first_name: Jan C. full_name: Hummelen, Jan C. last_name: Hummelen - first_name: Maria A. full_name: Loi, Maria A. last_name: Loi - first_name: Giuseppe full_name: Portale, Giuseppe last_name: Portale citation: ama: 'Dong J, Sami S, Balazs D, et al. Fullerene derivatives with oligoethylene-glycol side chains: An investigation on the origin of their outstanding transport properties. Journal of Materials Chemistry C. 2021;9(45):16217-16225. doi:10.1039/d1tc02753k' apa: 'Dong, J., Sami, S., Balazs, D., Alessandri, R., Jahani, F., Qiu, L., … Portale, G. (2021). Fullerene derivatives with oligoethylene-glycol side chains: An investigation on the origin of their outstanding transport properties. Journal of Materials Chemistry C. Royal Society of Chemistry. https://doi.org/10.1039/d1tc02753k' chicago: 'Dong, Jingjin, Selim Sami, Daniel Balazs, Riccardo Alessandri, Fatimeh Jahani, Li Qiu, Siewert J. Marrink, et al. “Fullerene Derivatives with Oligoethylene-Glycol Side Chains: An Investigation on the Origin of Their Outstanding Transport Properties.” Journal of Materials Chemistry C. Royal Society of Chemistry, 2021. https://doi.org/10.1039/d1tc02753k.' ieee: 'J. Dong et al., “Fullerene derivatives with oligoethylene-glycol side chains: An investigation on the origin of their outstanding transport properties,” Journal of Materials Chemistry C, vol. 9, no. 45. Royal Society of Chemistry, pp. 16217–16225, 2021.' ista: 'Dong J, Sami S, Balazs D, Alessandri R, Jahani F, Qiu L, Marrink SJ, Havenith RWA, Hummelen JC, Loi MA, Portale G. 2021. Fullerene derivatives with oligoethylene-glycol side chains: An investigation on the origin of their outstanding transport properties. Journal of Materials Chemistry C. 9(45), 16217–16225.' mla: 'Dong, Jingjin, et al. “Fullerene Derivatives with Oligoethylene-Glycol Side Chains: An Investigation on the Origin of Their Outstanding Transport Properties.” Journal of Materials Chemistry C, vol. 9, no. 45, Royal Society of Chemistry, 2021, pp. 16217–25, doi:10.1039/d1tc02753k.' short: J. Dong, S. Sami, D. Balazs, R. Alessandri, F. Jahani, L. Qiu, S.J. Marrink, R.W.A. Havenith, J.C. Hummelen, M.A. Loi, G. Portale, Journal of Materials Chemistry C 9 (2021) 16217–16225. date_created: 2021-12-12T23:01:27Z date_published: 2021-12-07T00:00:00Z date_updated: 2023-08-17T06:18:44Z day: '07' ddc: - '540' department: - _id: MaIb doi: 10.1039/d1tc02753k external_id: isi: - '000688135700001' file: - access_level: open_access checksum: 6b73c214ce54a6894a5854b4364413d7 content_type: application/pdf creator: cchlebak date_created: 2021-12-13T09:24:42Z date_updated: 2021-12-13T09:24:42Z file_id: '10538' file_name: 2021_JMaterChemC_Dong.pdf file_size: 4979390 relation: main_file success: 1 file_date_updated: 2021-12-13T09:24:42Z has_accepted_license: '1' intvolume: ' 9' isi: 1 issue: '45' language: - iso: eng month: '12' oa: 1 oa_version: Published Version page: 16217-16225 publication: Journal of Materials Chemistry C publication_identifier: eissn: - 2050-7526 issn: - 2050-7534 publication_status: published publisher: Royal Society of Chemistry quality_controlled: '1' scopus_import: '1' status: public title: 'Fullerene derivatives with oligoethylene-glycol side chains: An investigation on the origin of their outstanding transport properties' tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 9 year: '2021' ... --- _id: '10533' abstract: - lang: eng text: Flowering plants utilize small RNA molecules to guide DNA methyltransferases to genomic sequences. This RNA-directed DNA methylation (RdDM) pathway preferentially targets euchromatic transposable elements. However, RdDM is thought to be recruited by methylation of histone H3 at lysine 9 (H3K9me), a hallmark of heterochromatin. How RdDM is targeted to euchromatin despite an affinity for H3K9me is unclear. Here we show that loss of histone H1 enhances heterochromatic RdDM, preferentially at nucleosome linker DNA. Surprisingly, this does not require SHH1, the RdDM component that binds H3K9me. Furthermore, H3K9me is dispensable for RdDM, as is CG DNA methylation. Instead, we find that non-CG methylation is specifically associated with small RNA biogenesis, and without H1 small RNA production quantitatively expands to non-CG methylated loci. Our results demonstrate that H1 enforces the separation of euchromatic and heterochromatic DNA methylation pathways by excluding the small RNA-generating branch of RdDM from non-CG methylated heterochromatin. acknowledgement: We thank X Feng for helpful comments on the manuscript. This work was supported by a European Research Council grant MaintainMeth (725746) to DZ. article_number: e72676 article_processing_charge: No article_type: original author: - first_name: Jaemyung full_name: Choi, Jaemyung last_name: Choi - first_name: David B full_name: Lyons, David B last_name: Lyons - first_name: Daniel full_name: Zilberman, Daniel id: 6973db13-dd5f-11ea-814e-b3e5455e9ed1 last_name: Zilberman orcid: 0000-0002-0123-8649 citation: ama: Choi J, Lyons DB, Zilberman D. Histone H1 prevents non-CG methylation-mediated small RNA biogenesis in Arabidopsis heterochromatin. eLife. 2021;10. doi:10.7554/elife.72676 apa: Choi, J., Lyons, D. B., & Zilberman, D. (2021). Histone H1 prevents non-CG methylation-mediated small RNA biogenesis in Arabidopsis heterochromatin. ELife. eLife Sciences Publications. https://doi.org/10.7554/elife.72676 chicago: Choi, Jaemyung, David B Lyons, and Daniel Zilberman. “Histone H1 Prevents Non-CG Methylation-Mediated Small RNA Biogenesis in Arabidopsis Heterochromatin.” ELife. eLife Sciences Publications, 2021. https://doi.org/10.7554/elife.72676. ieee: J. Choi, D. B. Lyons, and D. Zilberman, “Histone H1 prevents non-CG methylation-mediated small RNA biogenesis in Arabidopsis heterochromatin,” eLife, vol. 10. eLife Sciences Publications, 2021. ista: Choi J, Lyons DB, Zilberman D. 2021. Histone H1 prevents non-CG methylation-mediated small RNA biogenesis in Arabidopsis heterochromatin. eLife. 10, e72676. mla: Choi, Jaemyung, et al. “Histone H1 Prevents Non-CG Methylation-Mediated Small RNA Biogenesis in Arabidopsis Heterochromatin.” ELife, vol. 10, e72676, eLife Sciences Publications, 2021, doi:10.7554/elife.72676. short: J. Choi, D.B. Lyons, D. Zilberman, ELife 10 (2021). date_created: 2021-12-10T13:12:08Z date_published: 2021-12-01T00:00:00Z date_updated: 2023-08-17T06:21:08Z day: '01' ddc: - '570' department: - _id: DaZi doi: 10.7554/elife.72676 ec_funded: 1 external_id: isi: - '000754832000001' pmid: - '34850679' file: - access_level: open_access checksum: 22ed4c55fb550f6da02ae55c359be651 content_type: application/pdf creator: dernst date_created: 2022-05-16T10:42:22Z date_updated: 2022-05-16T10:42:22Z file_id: '11384' file_name: 2021_eLife_Choi.pdf file_size: 2715200 relation: main_file success: 1 file_date_updated: 2022-05-16T10:42:22Z has_accepted_license: '1' intvolume: ' 10' isi: 1 keyword: - genetics and molecular biology language: - iso: eng month: '12' oa: 1 oa_version: Published Version pmid: 1 project: - _id: 62935a00-2b32-11ec-9570-eff30fa39068 call_identifier: H2020 grant_number: '725746' name: Quantitative analysis of DNA methylation maintenance with chromatin publication: eLife publication_identifier: issn: - 2050-084X publication_status: published publisher: eLife Sciences Publications quality_controlled: '1' scopus_import: '1' status: public title: Histone H1 prevents non-CG methylation-mediated small RNA biogenesis in Arabidopsis heterochromatin tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 10 year: '2021' ... --- _id: '10536' abstract: - lang: eng text: TGFβ overexpression is commonly detected in cancer patients and correlates with poor prognosis and metastasis. Cancer progression is often associated with an enhanced recruitment of myeloid-derived cells to the tumor microenvironment. Here we show that functional TGFβ-signaling in myeloid cells is required for metastasis to the lungs and the liver. Myeloid-specific deletion of Tgfbr2 resulted in reduced spontaneous lung metastasis, which was associated with a reduction of proinflammatory cytokines in the metastatic microenvironment. Notably, CD8+ T cell depletion in myeloid-specific Tgfbr2-deficient mice rescued lung metastasis. Myeloid-specific Tgfbr2-deficiency resulted in reduced liver metastasis with an almost complete absence of myeloid cells within metastatic foci. On contrary, an accumulation of Tgfβ-responsive myeloid cells was associated with an increased recruitment of monocytes and granulocytes and higher proinflammatory cytokine levels in control mice. Monocytic cells isolated from metastatic livers of Tgfbr2-deficient mice showed increased polarization towards the M1 phenotype, Tnfα and Il-1β expression, reduced levels of M2 markers and reduced production of chemokines responsible for myeloid-cell recruitment. No significant differences in Tgfβ levels were observed at metastatic sites of any model. These data demonstrate that Tgfβ signaling in monocytic myeloid cells suppresses CD8+ T cell activity during lung metastasis, while these cells actively contribute to tumor growth during liver metastasis. Thus, myeloid cells modulate metastasis through different mechanisms in a tissue-specific manner. acknowledgement: The authors acknowledge the assistance of the Laboratory Animal Services Center (LASC) – UZH, Center for Microscopy and Image Analysis, and the Flow Cytometry Center of the University of Zurich. article_number: '765151' article_processing_charge: No article_type: original author: - first_name: Cristina full_name: Stefanescu, Cristina last_name: Stefanescu - first_name: Merel full_name: Van Gogh, Merel last_name: Van Gogh - first_name: Marko full_name: Roblek, Marko id: 3047D808-F248-11E8-B48F-1D18A9856A87 last_name: Roblek orcid: 0000-0001-9588-1389 - first_name: Mathias full_name: Heikenwalder, Mathias last_name: Heikenwalder - first_name: Lubor full_name: Borsig, Lubor last_name: Borsig citation: ama: Stefanescu C, Van Gogh M, Roblek M, Heikenwalder M, Borsig L. TGFβ signaling in myeloid cells promotes lung and liver metastasis through different mechanisms. Frontiers in Oncology. 2021;11. doi:10.3389/fonc.2021.765151 apa: Stefanescu, C., Van Gogh, M., Roblek, M., Heikenwalder, M., & Borsig, L. (2021). TGFβ signaling in myeloid cells promotes lung and liver metastasis through different mechanisms. Frontiers in Oncology. Frontiers. https://doi.org/10.3389/fonc.2021.765151 chicago: Stefanescu, Cristina, Merel Van Gogh, Marko Roblek, Mathias Heikenwalder, and Lubor Borsig. “TGFβ Signaling in Myeloid Cells Promotes Lung and Liver Metastasis through Different Mechanisms.” Frontiers in Oncology. Frontiers, 2021. https://doi.org/10.3389/fonc.2021.765151. ieee: C. Stefanescu, M. Van Gogh, M. Roblek, M. Heikenwalder, and L. Borsig, “TGFβ signaling in myeloid cells promotes lung and liver metastasis through different mechanisms,” Frontiers in Oncology, vol. 11. Frontiers, 2021. ista: Stefanescu C, Van Gogh M, Roblek M, Heikenwalder M, Borsig L. 2021. TGFβ signaling in myeloid cells promotes lung and liver metastasis through different mechanisms. Frontiers in Oncology. 11, 765151. mla: Stefanescu, Cristina, et al. “TGFβ Signaling in Myeloid Cells Promotes Lung and Liver Metastasis through Different Mechanisms.” Frontiers in Oncology, vol. 11, 765151, Frontiers, 2021, doi:10.3389/fonc.2021.765151. short: C. Stefanescu, M. Van Gogh, M. Roblek, M. Heikenwalder, L. Borsig, Frontiers in Oncology 11 (2021). date_created: 2021-12-12T23:01:27Z date_published: 2021-11-18T00:00:00Z date_updated: 2023-08-17T06:20:32Z day: '18' ddc: - '610' department: - _id: DaSi doi: 10.3389/fonc.2021.765151 external_id: isi: - '000726603400001' pmid: - '34868988' file: - access_level: open_access checksum: 56cbac80e6891ce750511a30161b7792 content_type: application/pdf creator: alisjak date_created: 2021-12-13T13:32:37Z date_updated: 2021-12-13T13:32:37Z file_id: '10539' file_name: 2021_Frontiers_Stefanescu.pdf file_size: 9245199 relation: main_file success: 1 file_date_updated: 2021-12-13T13:32:37Z has_accepted_license: '1' intvolume: ' 11' isi: 1 language: - iso: eng month: '11' oa: 1 oa_version: Published Version pmid: 1 publication: Frontiers in Oncology publication_identifier: eissn: - 2234-943X publication_status: published publisher: Frontiers quality_controlled: '1' scopus_import: '1' status: public title: TGFβ signaling in myeloid cells promotes lung and liver metastasis through different mechanisms tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 11 year: '2021' ... --- _id: '10537' abstract: - lang: eng text: We consider the quantum many-body evolution of a homogeneous Fermi gas in three dimensions in the coupled semiclassical and mean-field scaling regime. We study a class of initial data describing collective particle–hole pair excitations on the Fermi ball. Using a rigorous version of approximate bosonization, we prove that the many-body evolution can be approximated in Fock space norm by a quasi-free bosonic evolution of the collective particle–hole excitations. acknowledgement: NB was supported by Gruppo Nazionale per la Fisica Matematica (GNFM). RS was supported by the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (Grant Agreement No. 694227). PTN was supported by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) under Germany’s Excellence Strategy (EXC-2111-390814868). MP was supported by the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (ERC StG MaMBoQ, Grant Agreement No. 802901). BS was supported by the NCCR SwissMAP, the Swiss National Science Foundation through the Grant “Dynamical and energetic properties of Bose-Einstein condensates,” and the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program through the ERC-AdG CLaQS (Grant Agreement No. 834782). article_processing_charge: No article_type: original author: - first_name: Niels P full_name: Benedikter, Niels P id: 3DE6C32A-F248-11E8-B48F-1D18A9856A87 last_name: Benedikter orcid: 0000-0002-1071-6091 - first_name: Phan Thành full_name: Nam, Phan Thành last_name: Nam - first_name: Marcello full_name: Porta, Marcello last_name: Porta - first_name: Benjamin full_name: Schlein, Benjamin last_name: Schlein - first_name: Robert full_name: Seiringer, Robert id: 4AFD0470-F248-11E8-B48F-1D18A9856A87 last_name: Seiringer orcid: 0000-0002-6781-0521 citation: ama: Benedikter NP, Nam PT, Porta M, Schlein B, Seiringer R. Bosonization of fermionic many-body dynamics. Annales Henri Poincaré. 2021. doi:10.1007/s00023-021-01136-y apa: Benedikter, N. P., Nam, P. T., Porta, M., Schlein, B., & Seiringer, R. (2021). Bosonization of fermionic many-body dynamics. Annales Henri Poincaré. Springer Nature. https://doi.org/10.1007/s00023-021-01136-y chicago: Benedikter, Niels P, Phan Thành Nam, Marcello Porta, Benjamin Schlein, and Robert Seiringer. “Bosonization of Fermionic Many-Body Dynamics.” Annales Henri Poincaré. Springer Nature, 2021. https://doi.org/10.1007/s00023-021-01136-y. ieee: N. P. Benedikter, P. T. Nam, M. Porta, B. Schlein, and R. Seiringer, “Bosonization of fermionic many-body dynamics,” Annales Henri Poincaré. Springer Nature, 2021. ista: Benedikter NP, Nam PT, Porta M, Schlein B, Seiringer R. 2021. Bosonization of fermionic many-body dynamics. Annales Henri Poincaré. mla: Benedikter, Niels P., et al. “Bosonization of Fermionic Many-Body Dynamics.” Annales Henri Poincaré, Springer Nature, 2021, doi:10.1007/s00023-021-01136-y. short: N.P. Benedikter, P.T. Nam, M. Porta, B. Schlein, R. Seiringer, Annales Henri Poincaré (2021). date_created: 2021-12-12T23:01:28Z date_published: 2021-12-02T00:00:00Z date_updated: 2023-08-17T06:19:14Z day: '02' department: - _id: RoSe doi: 10.1007/s00023-021-01136-y ec_funded: 1 external_id: arxiv: - '2103.08224' isi: - '000725405700001' isi: 1 language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/2103.08224 month: '12' oa: 1 oa_version: Preprint project: - _id: 25C6DC12-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '694227' name: Analysis of quantum many-body systems publication: Annales Henri Poincaré publication_identifier: issn: - 1424-0637 publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: Bosonization of fermionic many-body dynamics type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 year: '2021' ... --- _id: '10549' abstract: - lang: eng text: We derive optimal-order homogenization rates for random nonlinear elliptic PDEs with monotone nonlinearity in the uniformly elliptic case. More precisely, for a random monotone operator on \mathbb {R}^d with stationary law (that is spatially homogeneous statistics) and fast decay of correlations on scales larger than the microscale \varepsilon >0, we establish homogenization error estimates of the order \varepsilon in case d\geqq 3, and of the order \varepsilon |\log \varepsilon |^{1/2} in case d=2. Previous results in nonlinear stochastic homogenization have been limited to a small algebraic rate of convergence \varepsilon ^\delta . We also establish error estimates for the approximation of the homogenized operator by the method of representative volumes of the order (L/\varepsilon )^{-d/2} for a representative volume of size L. Our results also hold in the case of systems for which a (small-scale) C^{1,\alpha } regularity theory is available. acknowledgement: Open access funding provided by Institute of Science and Technology (IST Austria). SN acknowledges partial support by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) – project number 405009441. article_processing_charge: Yes (via OA deal) article_type: original author: - first_name: Julian L full_name: Fischer, Julian L id: 2C12A0B0-F248-11E8-B48F-1D18A9856A87 last_name: Fischer orcid: 0000-0002-0479-558X - first_name: Stefan full_name: Neukamm, Stefan last_name: Neukamm citation: ama: Fischer JL, Neukamm S. Optimal homogenization rates in stochastic homogenization of nonlinear uniformly elliptic equations and systems. Archive for Rational Mechanics and Analysis. 2021;242(1):343-452. doi:10.1007/s00205-021-01686-9 apa: Fischer, J. L., & Neukamm, S. (2021). Optimal homogenization rates in stochastic homogenization of nonlinear uniformly elliptic equations and systems. Archive for Rational Mechanics and Analysis. Springer Nature. https://doi.org/10.1007/s00205-021-01686-9 chicago: Fischer, Julian L, and Stefan Neukamm. “Optimal Homogenization Rates in Stochastic Homogenization of Nonlinear Uniformly Elliptic Equations and Systems.” Archive for Rational Mechanics and Analysis. Springer Nature, 2021. https://doi.org/10.1007/s00205-021-01686-9. ieee: J. L. Fischer and S. Neukamm, “Optimal homogenization rates in stochastic homogenization of nonlinear uniformly elliptic equations and systems,” Archive for Rational Mechanics and Analysis, vol. 242, no. 1. Springer Nature, pp. 343–452, 2021. ista: Fischer JL, Neukamm S. 2021. Optimal homogenization rates in stochastic homogenization of nonlinear uniformly elliptic equations and systems. Archive for Rational Mechanics and Analysis. 242(1), 343–452. mla: Fischer, Julian L., and Stefan Neukamm. “Optimal Homogenization Rates in Stochastic Homogenization of Nonlinear Uniformly Elliptic Equations and Systems.” Archive for Rational Mechanics and Analysis, vol. 242, no. 1, Springer Nature, 2021, pp. 343–452, doi:10.1007/s00205-021-01686-9. short: J.L. Fischer, S. Neukamm, Archive for Rational Mechanics and Analysis 242 (2021) 343–452. date_created: 2021-12-16T12:12:33Z date_published: 2021-06-30T00:00:00Z date_updated: 2023-08-17T06:23:21Z day: '30' ddc: - '530' department: - _id: JuFi doi: 10.1007/s00205-021-01686-9 external_id: arxiv: - '1908.02273' isi: - '000668431200001' file: - access_level: open_access checksum: cc830b739aed83ca2e32c4e0ce266a4c content_type: application/pdf creator: cchlebak date_created: 2021-12-16T14:58:08Z date_updated: 2021-12-16T14:58:08Z file_id: '10558' file_name: 2021_ArchRatMechAnalysis_Fischer.pdf file_size: 1640121 relation: main_file success: 1 file_date_updated: 2021-12-16T14:58:08Z has_accepted_license: '1' intvolume: ' 242' isi: 1 issue: '1' keyword: - Mechanical Engineering - Mathematics (miscellaneous) - Analysis language: - iso: eng month: '06' oa: 1 oa_version: Published Version page: 343-452 publication: Archive for Rational Mechanics and Analysis publication_identifier: eissn: - 1432-0673 issn: - 0003-9527 publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: Optimal homogenization rates in stochastic homogenization of nonlinear uniformly elliptic equations and systems tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 242 year: '2021' ... --- _id: '10409' abstract: - lang: eng text: We show that Yao’s garbling scheme is adaptively indistinguishable for the class of Boolean circuits of size S and treewidth w with only a SO(w) loss in security. For instance, circuits with constant treewidth are as a result adaptively indistinguishable with only a polynomial loss. This (partially) complements a negative result of Applebaum et al. (Crypto 2013), which showed (assuming one-way functions) that Yao’s garbling scheme cannot be adaptively simulatable. As main technical contributions, we introduce a new pebble game that abstracts out our security reduction and then present a pebbling strategy for this game where the number of pebbles used is roughly O(δwlog(S)) , δ being the fan-out of the circuit. The design of the strategy relies on separators, a graph-theoretic notion with connections to circuit complexity. with only a SO(w) loss in security. For instance, circuits with constant treewidth are as a result adaptively indistinguishable with only a polynomial loss. This (partially) complements a negative result of Applebaum et al. (Crypto 2013), which showed (assuming one-way functions) that Yao’s garbling scheme cannot be adaptively simulatable. As main technical contributions, we introduce a new pebble game that abstracts out our security reduction and then present a pebbling strategy for this game where the number of pebbles used is roughly O(δwlog(S)) , δ being the fan-out of the circuit. The design of the strategy relies on separators, a graph-theoretic notion with connections to circuit complexity. acknowledgement: We are grateful to Daniel Wichs for helpful discussions on the landscape of adaptive security of Yao’s garbling. We would also like to thank Crypto 2021 and TCC 2021 reviewers for their detailed review and suggestions, which helped improve presentation considerably. alternative_title: - LNCS article_processing_charge: No author: - first_name: Chethan full_name: Kamath Hosdurg, Chethan id: 4BD3F30E-F248-11E8-B48F-1D18A9856A87 last_name: Kamath Hosdurg - first_name: Karen full_name: Klein, Karen id: 3E83A2F8-F248-11E8-B48F-1D18A9856A87 last_name: Klein - first_name: Krzysztof Z full_name: Pietrzak, Krzysztof Z id: 3E04A7AA-F248-11E8-B48F-1D18A9856A87 last_name: Pietrzak orcid: 0000-0002-9139-1654 citation: ama: 'Kamath Hosdurg C, Klein K, Pietrzak KZ. On treewidth, separators and Yao’s garbling. In: 19th International Conference. Vol 13043. Springer Nature; 2021:486-517. doi:10.1007/978-3-030-90453-1_17' apa: 'Kamath Hosdurg, C., Klein, K., & Pietrzak, K. Z. (2021). On treewidth, separators and Yao’s garbling. In 19th International Conference (Vol. 13043, pp. 486–517). Raleigh, NC, United States: Springer Nature. https://doi.org/10.1007/978-3-030-90453-1_17' chicago: Kamath Hosdurg, Chethan, Karen Klein, and Krzysztof Z Pietrzak. “On Treewidth, Separators and Yao’s Garbling.” In 19th International Conference, 13043:486–517. Springer Nature, 2021. https://doi.org/10.1007/978-3-030-90453-1_17. ieee: C. Kamath Hosdurg, K. Klein, and K. Z. Pietrzak, “On treewidth, separators and Yao’s garbling,” in 19th International Conference, Raleigh, NC, United States, 2021, vol. 13043, pp. 486–517. ista: 'Kamath Hosdurg C, Klein K, Pietrzak KZ. 2021. On treewidth, separators and Yao’s garbling. 19th International Conference. TCC: Theory of Cryptography, LNCS, vol. 13043, 486–517.' mla: Kamath Hosdurg, Chethan, et al. “On Treewidth, Separators and Yao’s Garbling.” 19th International Conference, vol. 13043, Springer Nature, 2021, pp. 486–517, doi:10.1007/978-3-030-90453-1_17. short: C. Kamath Hosdurg, K. Klein, K.Z. Pietrzak, in:, 19th International Conference, Springer Nature, 2021, pp. 486–517. conference: end_date: 2021-11-11 location: Raleigh, NC, United States name: 'TCC: Theory of Cryptography' start_date: 2021-11-08 date_created: 2021-12-05T23:01:43Z date_published: 2021-11-04T00:00:00Z date_updated: 2023-08-17T06:21:38Z day: '04' department: - _id: KrPi doi: 10.1007/978-3-030-90453-1_17 ec_funded: 1 external_id: isi: - '000728364000017' isi: 1 language: - iso: eng main_file_link: - open_access: '1' url: https://eprint.iacr.org/2021/926 month: '11' oa: 1 oa_version: Preprint page: 486-517 project: - _id: 258AA5B2-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '682815' name: Teaching Old Crypto New Tricks publication: 19th International Conference publication_identifier: eissn: - 1611-3349 isbn: - 9-783-0309-0452-4 issn: - 0302-9743 publication_status: published publisher: Springer Nature quality_controlled: '1' related_material: record: - id: '10044' relation: earlier_version status: public scopus_import: '1' status: public title: On treewidth, separators and Yao’s garbling type: conference user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: '13043 ' year: '2021' ...