--- OA_place: publisher OA_type: diamond _id: '18493' abstract: - lang: eng text: "Context. The escape of Lyman-α photons at redshifts greater than two is an ongoing subject of study and an important quantity to further understanding of Lyman-α emitters (LAEs), the transmission of Lyman-α photons through the interstellar medium and intergalactic medium, and the impact these LAEs have on cosmic reionisation.\r\n\r\nAims. This study aims to assess the Lyman-α escape fraction, fesc, Lyα, over the redshift range 2.9 < z < 6.7, focusing on Very Large Telescope/Multi Unit Spectroscopic Explorer (VLT/MUSE) selected, gravitationally lensed, intrinsically faint LAEs. These galaxies are of particular interest as the potential drivers of cosmic reionisation.\r\n\r\nMethods. We assessed fesc, Lyα in two ways: through an individual study of 96 LAEs behind the A2744 lensing cluster, with James Webb Space Telescope/Near-Infrared Camera (JWST/NIRCam) and HST data, and through a study of the global evolution of fesc, Lyα using the state-of-the-art luminosity functions for LAEs and the UV-selected ‘parent’ population (dust-corrected). We compared these studies to those in the literature based on brighter samples.\r\n\r\nResults. We find a negligible redshift evolution of fesc, Lyα for our individual galaxies; it is likely that it was washed out by significant intrinsic scatter. We observed a more significant evolution towards higher escape fractions with decreasing UV magnitude and fit this relation. When comparing the two luminosity functions to derive fesc, Lyα in a global sense, we saw agreement with previous literature when integrating the luminosity functions to a bright limit. However, when integrating using a faint limit equivalent to the observational limits of our samples, we observed enhanced values of fesc, Lyα, particularly around z ∼ 6, where fesc, Lyα becomes consistent with 100% escape. This indicates for the faint regimes we sampled that galaxies towards reionisation tend to allow very large fractions of Lyman-α photons to escape. We interpret this as evidence of a lack of any significant dust in these populations; our sample is likely dominated by young, highly star-forming chemically unevolved galaxies. Finally, we assessed the contribution of the LAE population to reionisation using our latest values for fesc, Lyα and the LAE luminosity density. The dependence on the escape fraction of Lyman continuum photons is strong, but for values similar to those observed recently in z ∼ 3 LAEs and high-redshift analogues, LAEs could provide all the ionising emissivity necessary for reionisation." acknowledgement: "This work is done based on observations made with ESO Telescopes at the La Silla Paranal Observatory under programme IDs 060.A-9345, 092.A-0472, 094.A-0115, 095.A-0181, 096.A-0710, 097.A0269, 100.A-0249, and 294.A-5032. Also based on observations obtained with the\r\nNASA/ESA Hubble Space Telescope, retrieved from the Mikulski Archive for Space Telescopes (MAST) at the Space Telescope Science Institute (STScI). STScI is operated by the Association of Universities for Research in Astronomy, Inc. under NASA contract NAS 5-26555. All plots in this paper were created using Matplotlib (Hunter 2007). Part of this work was supported by the French CNRS, the Aix-Marseille University, the French Programme National de Cosmologie et Galaxies (PNCG) of CNRS/INSU with INP and IN2P3, co-funded by CEA and CNES. This work also received support from the French government under the France 2030 investment plan, as part of the Excellence Initiative of Aix-Marseille University - A*MIDEX (AMX-19-IET-008 - IPhU).\r\nFinancial support from the World Laboratory, the Odon Vallet Foundation and VNSC is gratefully acknowledged. Tran Thi Thai was funded by Vingroup JSC and supported by the Master, PhD Scholarship Programme of Vingroup Innovation Foundation (VINIF), Institute of Big Data, code VINIF.2023.TS.108. This research was funded by Vingroup Innovation Foundation under project code VINIF.2023.DA.057." article_number: A302 article_processing_charge: No article_type: original arxiv: 1 author: - first_name: I. full_name: Goovaerts, I. last_name: Goovaerts - first_name: T. T. full_name: Thai, T. T. last_name: Thai - first_name: R. full_name: Pello, R. last_name: Pello - first_name: P. full_name: Tuan-Anh, P. last_name: Tuan-Anh - first_name: N. full_name: Laporte, N. last_name: Laporte - first_name: Jorryt J full_name: Matthee, Jorryt J id: 7439a258-f3c0-11ec-9501-9df22fe06720 last_name: Matthee orcid: 0000-0003-2871-127X - first_name: T. full_name: Nanayakkara, T. last_name: Nanayakkara - first_name: J. full_name: Pharo, J. last_name: Pharo citation: ama: Goovaerts I, Thai TT, Pello R, et al. Charting the Lyman-α escape fraction in the range 2.9 < z < 6.7 and consequences for the LAE reionisation contribution. Astronomy and Astrophysics. 2024;690. doi:10.1051/0004-6361/202451432 apa: Goovaerts, I., Thai, T. T., Pello, R., Tuan-Anh, P., Laporte, N., Matthee, J. J., … Pharo, J. (2024). Charting the Lyman-α escape fraction in the range 2.9 < z < 6.7 and consequences for the LAE reionisation contribution. Astronomy and Astrophysics. EDP Sciences. https://doi.org/10.1051/0004-6361/202451432 chicago: Goovaerts, I., T. T. Thai, R. Pello, P. Tuan-Anh, N. Laporte, Jorryt J Matthee, T. Nanayakkara, and J. Pharo. “Charting the Lyman-α Escape Fraction in the Range 2.9 < z < 6.7 and Consequences for the LAE Reionisation Contribution.” Astronomy and Astrophysics. EDP Sciences, 2024. https://doi.org/10.1051/0004-6361/202451432. ieee: I. Goovaerts et al., “Charting the Lyman-α escape fraction in the range 2.9 < z < 6.7 and consequences for the LAE reionisation contribution,” Astronomy and Astrophysics, vol. 690. EDP Sciences, 2024. ista: Goovaerts I, Thai TT, Pello R, Tuan-Anh P, Laporte N, Matthee JJ, Nanayakkara T, Pharo J. 2024. Charting the Lyman-α escape fraction in the range 2.9 < z < 6.7 and consequences for the LAE reionisation contribution. Astronomy and Astrophysics. 690, A302. mla: Goovaerts, I., et al. “Charting the Lyman-α Escape Fraction in the Range 2.9 < z < 6.7 and Consequences for the LAE Reionisation Contribution.” Astronomy and Astrophysics, vol. 690, A302, EDP Sciences, 2024, doi:10.1051/0004-6361/202451432. short: I. Goovaerts, T.T. Thai, R. Pello, P. Tuan-Anh, N. Laporte, J.J. Matthee, T. Nanayakkara, J. Pharo, Astronomy and Astrophysics 690 (2024). date_created: 2024-11-03T23:01:45Z date_published: 2024-10-01T00:00:00Z date_updated: 2025-09-08T14:28:28Z day: '01' ddc: - '520' department: - _id: JoMa doi: 10.1051/0004-6361/202451432 external_id: arxiv: - '2408.00517' isi: - '001339205700015' file: - access_level: open_access checksum: 4007e2b0fadf93bea61c5bec3fc97e87 content_type: application/pdf creator: dernst date_created: 2024-11-04T08:04:44Z date_updated: 2024-11-04T08:04:44Z file_id: '18495' file_name: 2024_AstronomyAstrophysics_Goovaerts.pdf file_size: 2008461 relation: main_file success: 1 file_date_updated: 2024-11-04T08:04:44Z has_accepted_license: '1' intvolume: ' 690' isi: 1 language: - iso: eng month: '10' oa: 1 oa_version: Published Version publication: Astronomy and Astrophysics publication_identifier: eissn: - 1432-0746 issn: - 0004-6361 publication_status: published publisher: EDP Sciences quality_controlled: '1' scopus_import: '1' status: public title: Charting the Lyman-α escape fraction in the range 2.9 < z < 6.7 and consequences for the LAE reionisation contribution 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: 317138e5-6ab7-11ef-aa6d-ffef3953e345 volume: 690 year: '2024' ... --- DOAJ_listed: '1' OA_place: publisher OA_type: gold _id: '18494' abstract: - lang: eng text: We expect luminous (M 1450 ≲ −26.5) high-redshift quasars to trace the highest-density peaks in the early Universe. Here, we present observations of four z ≳ 6 quasar fields using JWST/NIRCam in the imaging and wide-field slitless spectroscopy mode and report a wide range in the number of detected [O iii]-emitting galaxies in the quasars’ environments, ranging between a density enhancement of δ ≈ 65 within a 2 cMpc radius—one of the largest protoclusters during the Epoch of Reionization discovered to date—to a density contrast consistent with zero, indicating the presence of a UV-luminous quasar in a region comparable to the average density of the Universe. By measuring the two-point cross-correlation function of quasars and their surrounding galaxies, as well as the galaxy autocorrelation function, we infer a correlation length of quasars at 〈z〉 = 6.25 of r 0 QQ = 22.0 − 2.9 + 3.0 cMpc h − 1 , while we obtain a correlation length of the [O iii]-emitting galaxies of r 0 GG = 4.1 ± 0.3 cMpc h − 1 . By comparing the correlation functions to dark-matter-only simulations we estimate the minimum mass of the quasars’ host dark matter halos to be log 10 ( M halo , min / M ⊙ ) = 12.43 − 0.15 + 0.13 (and log 10 ( M halo , min [ OIII ] / M ⊙ ) = 10.56 − 0.03 + 0.05 for the [O iii] emitters), indicating that (a) luminous quasars do not necessarily reside within the most overdense regions in the early Universe, and that (b) the UV-luminous duty cycle of quasar activity at these redshifts is f duty ≪ 1. Such short quasar activity timescales challenge our understanding of early supermassive black hole growth and provide evidence for highly dust-obscured growth phases or episodic, radiatively inefficient accretion rates. acknowledgement: "The authors would like to thank the anonymous referee for the thoughtful comments, which significantly improved our manuscript, and Jan-Torge Schindler, Jiamu Huang, and Feige Wang for helpful discussions.\r\n\r\nJ.F.H. and E.P. acknowledge support from the European Research Council (ERC) under the European Unions Horizon 2020 research and innovation program (grant agreement No. 885301). J.M. acknowledges support from the European Union (ERC, AGENTS, 101076224).\r\n\r\nThis work is based on observations made with the NASA/ESA/CSA James Webb Space Telescope. The JWST data presented in this article were obtained from the Mikulski Archive for Space Telescopes at the Space Telescope Science Institute, which is operated by the Association of Universities for Research in Astronomy, Inc., under NASA contract NAS 5-03127 for JWST. The specific observations analyzed are associated with program #1243 and can be accessed via doi:10.17909/m5mp-5v90.\r\n\r\nThis work used the DiRAC Memory Intensive service (Cosma8) at the University of Durham, which is part of the STFC DiRAC HPC Facility (www.dirac.ac.uk). Access to DiRAC resources was granted through a Directors Discretionary Time allocation in 2023/24, under the auspices of the UKRI-funded DiRAC Federation Project. The equipment was funded by BEIS capital funding via STFC capital grants ST/K00042X/1, ST/P002293/1, ST/R002371/1, and ST/S002502/1, Durham University and STFC operations grant ST/R000832/1. DiRAC is part of the National e-Infrastructure.\r\n\r\nWe thank the Instituto de Astrofisica de Andalucia (IAA-CSIC), Centro de Supercomputacion de Galicia (CESGA), and Spanish Academic and Research Network (RedIRIS) in Spain for hosting Uchuu DR1, DR2, and DR3 in the Skies & Universes site for cosmological simulations. The Uchuu simulations were carried out on the Aterui II supercomputer at the Center for Computational Astrophysics, CfCA, of the National Astronomical Observatory of Japan, and the K computer at the RIKEN Advanced Institute for Computational Science. The Uchuu Data Releases efforts have made use of the skunIAA_RedIRIS and skun6IAA computer facilities managed by the IAA-CSIC in Spain (MICINN EU-Feder grant EQC2018-004366-P)." article_number: '275' article_processing_charge: Yes article_type: original author: - first_name: Anna Christina full_name: Eilers, Anna Christina last_name: Eilers - first_name: Ruari full_name: Mackenzie, Ruari last_name: Mackenzie - first_name: Elia full_name: Pizzati, Elia last_name: Pizzati - first_name: Jorryt J full_name: Matthee, Jorryt J id: 7439a258-f3c0-11ec-9501-9df22fe06720 last_name: Matthee orcid: 0000-0003-2871-127X - first_name: Joseph F. full_name: Hennawi, Joseph F. last_name: Hennawi - first_name: Haowen full_name: Zhang, Haowen last_name: Zhang - first_name: Rongmon full_name: Bordoloi, Rongmon last_name: Bordoloi - first_name: Daichi full_name: Kashino, Daichi last_name: Kashino - first_name: Simon J. full_name: Lilly, Simon J. last_name: Lilly - first_name: Rohan P. full_name: Naidu, Rohan P. last_name: Naidu - first_name: Robert A. full_name: Simcoe, Robert A. last_name: Simcoe - first_name: Minghao full_name: Yue, Minghao last_name: Yue - first_name: Carlos S. full_name: Frenk, Carlos S. last_name: Frenk - first_name: John C. full_name: Helly, John C. last_name: Helly - first_name: Matthieu full_name: Schaller, Matthieu last_name: Schaller - first_name: Joop full_name: Schaye, Joop last_name: Schaye citation: ama: Eilers AC, Mackenzie R, Pizzati E, et al. EIGER. VI. The correlation function, host halo mass, and duty cycle of luminous quasars at z ≳ 6. Astrophysical Journal. 2024;974(2). doi:10.3847/1538-4357/ad778b apa: Eilers, A. C., Mackenzie, R., Pizzati, E., Matthee, J. J., Hennawi, J. F., Zhang, H., … Schaye, J. (2024). EIGER. VI. The correlation function, host halo mass, and duty cycle of luminous quasars at z ≳ 6. Astrophysical Journal. IOP Publishing. https://doi.org/10.3847/1538-4357/ad778b chicago: Eilers, Anna Christina, Ruari Mackenzie, Elia Pizzati, Jorryt J Matthee, Joseph F. Hennawi, Haowen Zhang, Rongmon Bordoloi, et al. “EIGER. VI. The Correlation Function, Host Halo Mass, and Duty Cycle of Luminous Quasars at z ≳ 6.” Astrophysical Journal. IOP Publishing, 2024. https://doi.org/10.3847/1538-4357/ad778b. ieee: A. C. Eilers et al., “EIGER. VI. The correlation function, host halo mass, and duty cycle of luminous quasars at z ≳ 6,” Astrophysical Journal, vol. 974, no. 2. IOP Publishing, 2024. ista: Eilers AC, Mackenzie R, Pizzati E, Matthee JJ, Hennawi JF, Zhang H, Bordoloi R, Kashino D, Lilly SJ, Naidu RP, Simcoe RA, Yue M, Frenk CS, Helly JC, Schaller M, Schaye J. 2024. EIGER. VI. The correlation function, host halo mass, and duty cycle of luminous quasars at z ≳ 6. Astrophysical Journal. 974(2), 275. mla: Eilers, Anna Christina, et al. “EIGER. VI. The Correlation Function, Host Halo Mass, and Duty Cycle of Luminous Quasars at z ≳ 6.” Astrophysical Journal, vol. 974, no. 2, 275, IOP Publishing, 2024, doi:10.3847/1538-4357/ad778b. short: A.C. Eilers, R. Mackenzie, E. Pizzati, J.J. Matthee, J.F. Hennawi, H. Zhang, R. Bordoloi, D. Kashino, S.J. Lilly, R.P. Naidu, R.A. Simcoe, M. Yue, C.S. Frenk, J.C. Helly, M. Schaller, J. Schaye, Astrophysical Journal 974 (2024). date_created: 2024-11-03T23:01:45Z date_published: 2024-10-01T00:00:00Z date_updated: 2025-09-08T14:29:05Z day: '01' ddc: - '520' department: - _id: JoMa doi: 10.3847/1538-4357/ad778b external_id: isi: - '001338877100001' file: - access_level: open_access checksum: 1fcac3d11d01d91cf2bb4963b6e10b22 content_type: application/pdf creator: dernst date_created: 2024-11-04T08:42:23Z date_updated: 2024-11-04T08:42:23Z file_id: '18496' file_name: 2024_AstrophysicalJour_Eilers.pdf file_size: 1042470 relation: main_file success: 1 file_date_updated: 2024-11-04T08:42:23Z has_accepted_license: '1' intvolume: ' 974' isi: 1 issue: '2' language: - iso: eng month: '10' oa: 1 oa_version: Published Version project: - _id: bd9b2118-d553-11ed-ba76-db24564edfea grant_number: '101076224' name: Young galaxies as tracers and agents of cosmic reionization publication: Astrophysical Journal publication_identifier: eissn: - 1538-4357 issn: - 0004-637X publication_status: published publisher: IOP Publishing quality_controlled: '1' scopus_import: '1' status: public title: EIGER. VI. The correlation function, host halo mass, and duty cycle of luminous quasars at z ≳ 6 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: 317138e5-6ab7-11ef-aa6d-ffef3953e345 volume: 974 year: '2024' ... --- OA_place: publisher OA_type: gold _id: '18515' abstract: - lang: eng text: "Understanding the role of evolutionary processes in shaping genetic variation has been a\r\nprimary goal in evolutionary genetics. In this regard, a key question is how genetically\r\ndistinct populations evolve in the face of gene flow, thereby generating genetic and\r\nphenotypic divergence and reproductive isolation (RI). This requires quantifying the role\r\nand relative contributions of prezygotic and postzygotic isolating mechanisms on the\r\nreduction of gene exchange between populations, and identifying regions in the genome\r\nthat mediate RI, which is often polygenic. Further, this needs distinguishing neutral and\r\nselected regions in the genome, and discerning how selection influences patterns of neutral\r\ndivergence.\r\nPopulation structure, defined as any deviation from panmixia, such as geographic distribution, movement and mating patterns of individuals, influences how genetic variation is\r\nstructured in space and shapes the neutral null model. Availability of large scale spatial\r\ngenomic datasets now enables us to detect signatures of population structure in genetic\r\ndata and infer population genetic parameters. Such inferences are crucial and have wide\r\napplications in biodiversity, conservation genetics, population management and medical\r\ngenetics. However, inferences are based on assumptions that do not always match the\r\ncomplex reality, thus leading to erroneous conclusions. Moreover, the role and interaction\r\nof heterogeneous population density and dispersal, which are ubiquitous in nature, has\r\nbeen challenging to study owing to their mathematical complexity. In such scenarios,\r\nfeedback between theory, data and simulations can prove to be useful.\r\nIn this thesis, I examine the effect of population structure on neutral genetic variation\r\nand barriers to gene exchange in hybridising populations, thereby bridging together the\r\nfields of spatial population genetics and speciation.\r\nDespite being a key concept in speciation, reproductive isolation (RI) lacks a quantitative\r\ndefinition and has been used and measured differently across different fields. Chapter 2\r\ngives a quantitative definition of RI, in terms of the effect of genetic differences on gene\r\nflow. We give analytical predictions for RI in a range of scenarios, in terms of effective migration rates for discrete populations and barrier strength for continuous populations.\r\nIn addition to this, we discuss current measures of RI and their limitations, and propose\r\nthe need for new measures that combine organismal and genetic perspectives of RI.\r\nIn chapter 3, I examine the combined effect of assortative mating, sexual selection\r\nand viability selection on RI. For this, we consider a polygenic ‘magic’ trait under a\r\nmainland-island model. We obtain novel theoretical predictions for molecular divergence\r\nin terms of effective migration rates, which bears a simple relationship to measurable\r\nfitness components of migrants and various early generation hybrids. We explore the\r\nconditions under which local adaptation can be maintained despite maladaptive gene flow\r\nand quantify the relative contributions of viability and sexual selection to genome-wide\r\nbarriers to gene flow.\r\nThe next two chapters of the thesis focus on a hybrid zone of Antirrhinum majus that\r\nconsist of two subspecies- the magenta flowered A. m. pseudomajus and the yellow\r\nflowered A.m. striatum. Previous studies have suggested that flower colour is target of\r\npollinator mediated selection and is influenced only by few genes. While these regions\r\nshow high genetic differentiation between the subspecies, the rest of the genome is seen\r\nto be well mixed. Chapter 4 examines the effects of heterogeneous population density\r\nand leptokurtic dispersal on isolation by distance and the distribution of heterozygosity\r\nby focusing on non-flower colour markers.\r\nChapter 5 analyses cline shapes and associations among 6 focal flower colour markers to\r\nunderstand how selection and dispersal maintain this hybrid zone. We see sharp coincident\r\nstepped clines at all loci and positive associations throughout the hybrid zone, contrary to\r\nthe expected patterns from diffusive gene flow. With a novel scheme of inferring dispersal\r\ncombined with multilocus simulations, we show that stepped clines do not reflect genetic\r\nbarriers to gene flow, but are rather a result of long-distance migration. This framework\r\nallows us to get realistic estimates gene flow and selection and shows how traditional cline\r\nanalysis may lead to inaccurate conclusions when assumptions of the theory are not met.\r\nOverall, this thesis investigates how different features of population structure leave\r\ndetectable signatures in genetic variation, namely in patterns of isolation by distance,\r\nlinkage disequilibrium and genetic divergence. It also highlights how effective migration\r\nrates provide useful way of analysing polygenic architectures and shed new light into\r\nhybrid zones. In doing so, I identify scenarios when simple models become insufficient\r\nand suggest possibe directions by combining genetic data with simulations." acknowledged_ssus: - _id: ScienComp acknowledgement: "I also acknowledge the funding agencies Marie Curie COFUND Doctoral Fellowship,\r\nAustrian Science Fund FWF (grant P32166) and ERC (grant PR1000ERC02) for financially\r\nsupporting my research over the years." alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Parvathy full_name: Surendranadh, Parvathy id: 455235B8-F248-11E8-B48F-1D18A9856A87 last_name: Surendranadh orcid: 0000-0001-6395-386X citation: ama: Surendranadh P. Effect of population structure on neutral genetic variation and barriers to gene exchange. 2024. doi:10.15479/at:ista:18515 apa: Surendranadh, P. (2024). Effect of population structure on neutral genetic variation and barriers to gene exchange. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:18515 chicago: Surendranadh, Parvathy. “Effect of Population Structure on Neutral Genetic Variation and Barriers to Gene Exchange.” Institute of Science and Technology Austria, 2024. https://doi.org/10.15479/at:ista:18515. ieee: P. Surendranadh, “Effect of population structure on neutral genetic variation and barriers to gene exchange,” Institute of Science and Technology Austria, 2024. ista: Surendranadh P. 2024. Effect of population structure on neutral genetic variation and barriers to gene exchange. Institute of Science and Technology Austria. mla: Surendranadh, Parvathy. Effect of Population Structure on Neutral Genetic Variation and Barriers to Gene Exchange. Institute of Science and Technology Austria, 2024, doi:10.15479/at:ista:18515. short: P. Surendranadh, Effect of Population Structure on Neutral Genetic Variation and Barriers to Gene Exchange, Institute of Science and Technology Austria, 2024. corr_author: '1' date_created: 2024-11-06T21:25:37Z date_published: 2024-11-07T00:00:00Z date_updated: 2026-04-07T12:56:52Z day: '07' ddc: - '576' degree_awarded: PhD department: - _id: GradSch - _id: NiBa doi: 10.15479/at:ista:18515 file: - access_level: open_access checksum: c32cf7bc75748d9c551d8eb70178bbec content_type: application/pdf creator: psurendr date_created: 2024-11-07T10:59:29Z date_updated: 2024-11-07T10:59:29Z file_id: '18519' file_name: PhD_Thesis__Parvathy_071124_PDFA.pdf file_size: 37019760 relation: main_file success: 1 - access_level: closed checksum: 4417e02d54084d89e75734e18caaa96d content_type: application/zip creator: psurendr date_created: 2024-11-07T10:59:42Z date_updated: 2024-11-07T10:59:42Z file_id: '18520' file_name: PhD Thesis- Parvathy_071124.zip file_size: 41198857 relation: source_file file_date_updated: 2024-11-07T10:59:42Z has_accepted_license: '1' language: - iso: eng license: https://creativecommons.org/licenses/by-nc-sa/4.0/ month: '11' oa: 1 oa_version: Published Version page: '219' project: - _id: 05959E1C-7A3F-11EA-A408-12923DDC885E grant_number: P32166 name: Snapdragon Speciation - _id: bd6958e0-d553-11ed-ba76-86eba6a76c00 grant_number: '101055327' name: Understanding the evolution of continuous genomes publication_identifier: issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria status: public supervisor: - first_name: Nicholas H full_name: Barton, Nicholas H id: 4880FE40-F248-11E8-B48F-1D18A9856A87 last_name: Barton orcid: 0000-0002-8548-5240 title: Effect of population structure on neutral genetic variation and barriers to gene exchange tmp: image: /images/cc_by_nc_sa.png legal_code_url: https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode name: Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0) short: CC BY-NC-SA (4.0) type: dissertation user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd year: '2024' ... --- DOAJ_listed: '1' OA_place: publisher OA_type: gold _id: '18522' abstract: - lang: eng text: The Golgi apparatus is essential for protein sorting, yet its quality control mechanisms are poorly understood. Here we show that the Dsc ubiquitin ligase complex uses its rhomboid pseudo-protease subunit, Dsc2, to assess the hydrophobic length of α-helical transmembrane domains (TMDs) at the Golgi. Thereby the Dsc complex likely interacts with orphaned ER and Golgi proteins that have shorter TMDs and ubiquitinates them for targeted degradation. Some Dsc substrates will be extracted by Cdc48 for endosome and Golgi associated proteasomal degradation (EGAD), while others will undergo ESCRT dependent vacuolar degradation. Some substrates are degraded by both, EGAD- or ESCRT pathways. The accumulation of Dsc substrates entails a specific increase in glycerophospholipids with shorter and asymmetric fatty acyl chains. Hence, the Dsc complex mediates the selective degradation of orphaned proteins at the sorting center of cells, which prevents their spreading across other organelles and thereby preserves cellular membrane protein and lipid composition. acknowledgement: 'We thank Snezhana Oliferenko, Hesso Farhan, Chris Dunworth, and Lukas A Huber for critically reading the manuscript, Ming Li, Peter Espenshade, Sebastien Leon, and Scott Emr for reagents, Bob Kaufmann for help in characterizing the Dsc2 L1 loop mutant. This research was funded in part by the Austrian Science Fund (FWF) (10.55776/P32161, 10.55776/P34907, 10.55776/DOC82 to DT, and 10.55776/P36187 to OS), by a Lipotype lipidomics excellence award (LEA 2019) to OS, by a Luxembourg National Research Fund (FNR): Grant #13571826 to YW, and by European Union’s Horizon 2020 research and innovation program under the Marie Skłodowska-Curie grant agreement No. 847681 (to KRL). For open access purposes, the author has applied a CC BY public copyright license to any author accepted manuscript version arising from this submission.' article_number: '9257' article_processing_charge: Yes article_type: original author: - first_name: Yannick full_name: Weyer, Yannick last_name: Weyer - first_name: Sinead I. full_name: Schwabl, Sinead I. last_name: Schwabl - first_name: Xuechen full_name: Tang, Xuechen last_name: Tang - first_name: Astha full_name: Purwar, Astha last_name: Purwar - first_name: Konstantin full_name: Siegmann, Konstantin last_name: Siegmann - first_name: Angela full_name: Ruepp, Angela last_name: Ruepp - first_name: Theresia full_name: Dunzendorfer-Matt, Theresia last_name: Dunzendorfer-Matt - first_name: Michael A. full_name: Widerin, Michael A. last_name: Widerin - first_name: Veronika full_name: Niedrist, Veronika last_name: Niedrist - first_name: Noa J.M. full_name: Mutsters, Noa J.M. last_name: Mutsters - first_name: Maria G. full_name: Tettamanti, Maria G. last_name: Tettamanti - first_name: Sabine full_name: Weys, Sabine id: caffa136-9669-11ed-9092-ceac12ac9c05 last_name: Weys - first_name: Bettina full_name: Sarg, Bettina last_name: Sarg - first_name: Leopold full_name: Kremser, Leopold last_name: Kremser - first_name: Klaus R. full_name: Liedl, Klaus R. last_name: Liedl - first_name: Oliver full_name: Schmidt, Oliver last_name: Schmidt - first_name: David full_name: Teis, David last_name: Teis citation: ama: Weyer Y, Schwabl SI, Tang X, et al. The Dsc ubiquitin ligase complex identifies transmembrane degrons to degrade orphaned proteins at the Golgi. Nature Communications. 2024;15. doi:10.1038/s41467-024-53676-6 apa: Weyer, Y., Schwabl, S. I., Tang, X., Purwar, A., Siegmann, K., Ruepp, A., … Teis, D. (2024). The Dsc ubiquitin ligase complex identifies transmembrane degrons to degrade orphaned proteins at the Golgi. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-024-53676-6 chicago: Weyer, Yannick, Sinead I. Schwabl, Xuechen Tang, Astha Purwar, Konstantin Siegmann, Angela Ruepp, Theresia Dunzendorfer-Matt, et al. “The Dsc Ubiquitin Ligase Complex Identifies Transmembrane Degrons to Degrade Orphaned Proteins at the Golgi.” Nature Communications. Springer Nature, 2024. https://doi.org/10.1038/s41467-024-53676-6. ieee: Y. Weyer et al., “The Dsc ubiquitin ligase complex identifies transmembrane degrons to degrade orphaned proteins at the Golgi,” Nature Communications, vol. 15. Springer Nature, 2024. ista: Weyer Y, Schwabl SI, Tang X, Purwar A, Siegmann K, Ruepp A, Dunzendorfer-Matt T, Widerin MA, Niedrist V, Mutsters NJM, Tettamanti MG, Weys S, Sarg B, Kremser L, Liedl KR, Schmidt O, Teis D. 2024. The Dsc ubiquitin ligase complex identifies transmembrane degrons to degrade orphaned proteins at the Golgi. Nature Communications. 15, 9257. mla: Weyer, Yannick, et al. “The Dsc Ubiquitin Ligase Complex Identifies Transmembrane Degrons to Degrade Orphaned Proteins at the Golgi.” Nature Communications, vol. 15, 9257, Springer Nature, 2024, doi:10.1038/s41467-024-53676-6. short: Y. Weyer, S.I. Schwabl, X. Tang, A. Purwar, K. Siegmann, A. Ruepp, T. Dunzendorfer-Matt, M.A. Widerin, V. Niedrist, N.J.M. Mutsters, M.G. Tettamanti, S. Weys, B. Sarg, L. Kremser, K.R. Liedl, O. Schmidt, D. Teis, Nature Communications 15 (2024). date_created: 2024-11-10T23:01:58Z date_published: 2024-12-01T00:00:00Z date_updated: 2026-03-05T11:20:12Z day: '01' ddc: - '570' doi: 10.1038/s41467-024-53676-6 external_id: isi: - '001345548100007' pmid: - '39461958' file: - access_level: open_access checksum: 32c986fc3babec999c03a5c043310f40 content_type: application/pdf creator: dernst date_created: 2025-01-22T14:36:33Z date_updated: 2025-01-22T14:36:33Z file_id: '18870' file_name: 2024_NatureComm_Weyer.pdf file_size: 5634494 relation: main_file success: 1 file_date_updated: 2025-01-22T14:36:33Z has_accepted_license: '1' intvolume: ' 15' isi: 1 language: - iso: eng month: '12' 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: The Dsc ubiquitin ligase complex identifies transmembrane degrons to degrade orphaned proteins at the Golgi tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 15 year: '2024' ... --- DOAJ_listed: '1' OA_place: publisher OA_type: gold _id: '18523' abstract: - lang: eng text: "Recent observations from the EIGER JWST program have measured for the first time the quasar–galaxy cross-correlation function at z ≈ 6. The autocorrelation function of faint z ≈ 6 quasars was also recently estimated. These measurements provide key insights into the properties of quasars and galaxies at high redshift and their relation with the host dark matter haloes. In this work, we interpret these data building upon an empirical quasar population model that has been applied successfully to quasar clustering and demographic measurements at z ≈ 2–4. We use a new, large-volume N-body simulation with more than a trillion particles, FLAMINGO-10k, to model quasars and galaxies simultaneously. We successfully reproduce observations of z ≈ 6 quasars and galaxies (i.e. their clustering properties and luminosity functions), and infer key quantities such as their luminosity–halo mass relation, the mass function of their host haloes, and their duty cycle/occupation fraction. Our key findings\r\nare (i) quasars reside on average in ≈ 1012.5 M haloes (corresponding to ≈ 5σ fluctuations in the initial conditions of the linear density field), but the distribution of host halo masses is quite broad; (ii) the duty cycle of (UV-bright) quasar activity is relatively low (≈ 1 per cent); (iii) galaxies (that are bright in [O III]) live in much smaller haloes (≈ 1010.9 M) and have a larger duty cycle (occupation fraction) of ≈ 13 per cent. Finally, we focus on the inferred properties of quasars and present a homogeneous analysis of their evolution with redshift. The picture that emerges reveals a strong evolution of the host halo mass and duty cycle of quasars at z ≈ 2–6, and calls for new investigations of the role of quasar activity across cosmic time." acknowledgement: "We are grateful to Junya Arita and the SHELLQs team for sharing their data on the quasar autocorrelation function and to Jan-Torge Schindler for discussion on the QLF. We acknowledge helpful conversations with the ENIGMA group at UC Santa Barbara and Leiden University. EP is grateful to Rob McGibbon and Victor Forouhar Moreno for help with the simulation outputs, and to Timo Kist, Jiamu Huang, and Vikram Khaire for comments on an early version of the manuscript. JFH and EP acknowledge support from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (grant agreement No 885301). This work is partly supported by funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement No 860744 (BiD4BESt). FW acknowledges support from NSF grant AST-2308258. This work used the DiRAC Memory Intensive service (Cosma8) at the University of Durham, which is part of the STFC DiRAC HPC Facility (www.dirac.ac.uk). Access to DiRAC resources was granted through a Director’s Discretionary Time allocation in 2023/24, under the auspices of the UKRI-funded\r\nDiRAC Federation Project. The equipment was funded by BEIS capital funding via STFC capital grants ST/K00042X/1, ST/P002293/1, ST/R002371/1, and ST/S002502/1, Durham University, and STFC operations grant ST/R000832/1. DiRAC is part of the National e-Infrastructure." article_processing_charge: Yes article_type: original author: - first_name: Elia full_name: Pizzati, Elia last_name: Pizzati - first_name: Joseph F. full_name: Hennawi, Joseph F. last_name: Hennawi - first_name: Joop full_name: Schaye, Joop last_name: Schaye - first_name: Matthieu full_name: Schaller, Matthieu last_name: Schaller - first_name: Anna Christina full_name: Eilers, Anna Christina last_name: Eilers - first_name: Feige full_name: Wang, Feige last_name: Wang - first_name: Carlos S. full_name: Frenk, Carlos S. last_name: Frenk - first_name: Willem full_name: Elbers, Willem last_name: Elbers - first_name: John C. full_name: Helly, John C. last_name: Helly - first_name: Ruari full_name: Mackenzie, Ruari last_name: Mackenzie - first_name: Jorryt J full_name: Matthee, Jorryt J id: 7439a258-f3c0-11ec-9501-9df22fe06720 last_name: Matthee orcid: 0000-0003-2871-127X - first_name: Rongmon full_name: Bordoloi, Rongmon last_name: Bordoloi - first_name: Daichi full_name: Kashino, Daichi last_name: Kashino - first_name: Rohan P. full_name: Naidu, Rohan P. last_name: Naidu - first_name: Minghao full_name: Yue, Minghao last_name: Yue citation: ama: Pizzati E, Hennawi JF, Schaye J, et al. A unified model for the clustering of quasars and galaxies at z ≈ 6. Monthly Notices of the Royal Astronomical Society. 2024;534(4):3155-3175. doi:10.1093/mnras/stae2307 apa: Pizzati, E., Hennawi, J. F., Schaye, J., Schaller, M., Eilers, A. C., Wang, F., … Yue, M. (2024). A unified model for the clustering of quasars and galaxies at z ≈ 6. Monthly Notices of the Royal Astronomical Society. Oxford University Press. https://doi.org/10.1093/mnras/stae2307 chicago: Pizzati, Elia, Joseph F. Hennawi, Joop Schaye, Matthieu Schaller, Anna Christina Eilers, Feige Wang, Carlos S. Frenk, et al. “A Unified Model for the Clustering of Quasars and Galaxies at z ≈ 6.” Monthly Notices of the Royal Astronomical Society. Oxford University Press, 2024. https://doi.org/10.1093/mnras/stae2307. ieee: E. Pizzati et al., “A unified model for the clustering of quasars and galaxies at z ≈ 6,” Monthly Notices of the Royal Astronomical Society, vol. 534, no. 4. Oxford University Press, pp. 3155–3175, 2024. ista: Pizzati E, Hennawi JF, Schaye J, Schaller M, Eilers AC, Wang F, Frenk CS, Elbers W, Helly JC, Mackenzie R, Matthee JJ, Bordoloi R, Kashino D, Naidu RP, Yue M. 2024. A unified model for the clustering of quasars and galaxies at z ≈ 6. Monthly Notices of the Royal Astronomical Society. 534(4), 3155–3175. mla: Pizzati, Elia, et al. “A Unified Model for the Clustering of Quasars and Galaxies at z ≈ 6.” Monthly Notices of the Royal Astronomical Society, vol. 534, no. 4, Oxford University Press, 2024, pp. 3155–75, doi:10.1093/mnras/stae2307. short: E. Pizzati, J.F. Hennawi, J. Schaye, M. Schaller, A.C. Eilers, F. Wang, C.S. Frenk, W. Elbers, J.C. Helly, R. Mackenzie, J.J. Matthee, R. Bordoloi, D. Kashino, R.P. Naidu, M. Yue, Monthly Notices of the Royal Astronomical Society 534 (2024) 3155–3175. date_created: 2024-11-10T23:01:58Z date_published: 2024-11-01T00:00:00Z date_updated: 2025-09-08T14:40:22Z day: '01' ddc: - '520' department: - _id: JoMa doi: 10.1093/mnras/stae2307 external_id: isi: - '001335663900008' file: - access_level: open_access checksum: 9ea6285dd1d04d7a9e7b40a4c9e11edb content_type: application/pdf creator: dernst date_created: 2024-11-12T07:17:26Z date_updated: 2024-11-12T07:17:26Z file_id: '18542' file_name: 2024_MonthlyNRoyalAstronSoc_Pizzati.pdf file_size: 2954312 relation: main_file success: 1 file_date_updated: 2024-11-12T07:17:26Z has_accepted_license: '1' intvolume: ' 534' isi: 1 issue: '4' language: - iso: eng month: '11' oa: 1 oa_version: Published Version page: 3155-3175 publication: Monthly Notices of the Royal Astronomical Society publication_identifier: eissn: - 1365-2966 issn: - 0035-8711 publication_status: published publisher: Oxford University Press quality_controlled: '1' scopus_import: '1' status: public title: A unified model for the clustering of quasars and galaxies at z ≈ 6 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: 317138e5-6ab7-11ef-aa6d-ffef3953e345 volume: 534 year: '2024' ... --- OA_place: publisher OA_type: hybrid _id: '18527' abstract: - lang: eng text: "Context. Galaxies evolve through a dynamic exchange of material with their immediate surrounding environment, the so-called circumgalactic medium (CGM). Understanding the physics of gas flows and the nature of the CGM is fundamental to studying galaxy evolution, especially at 4 ≤ z ≤ 6 (i.e., after the Epoch of Reionization) when galaxies rapidly assembled their masses and reached their chemical maturity. Galactic outflows are predicted to enrich the CGM with metals, although it has also been suggested that gas stripping in systems undergoing a major merger may play a role.\r\n\r\nAims. In this work, we explore the metal enrichment of the medium around merging galaxies at z ∼ 4.5, observed by the ALMA Large Program to INvestigate [CII] at Early times (ALPINE). To do so, we study the nature of the [CII] 158 μm emission in the CGM around these systems, using simulations to help disentangle the mechanisms contributing to the CGM metal pollution.\r\n\r\nMethods. By adopting an updated classification of major merger systems in the ALPINE survey, we selected and analyzed merging galaxies whose components can be spatially and/or spectrally resolved in a robust way. This makes it possible to distinguish between the [CII] emission coming from the single components of the system and that coming from the system as a whole. We also made use of the dustyGadget cosmological simulation to select synthetic analogs of observed galaxies and guide the interpretation of the observational results.\r\n\r\nResults. We find a large diffuse [CII] envelope (≳20 kpc) embedding all the merging systems, with at least 25% of the total [CII] emission coming from the medium between the galaxies. Using predictions from dustyGadget, we suggest that this emission has a multi-fold nature, with dynamical interactions between galaxies playing a major role in stripping the gas and enriching the medium with heavy elements." acknowledgement: 'The authors would like to thank the anonymous referee for the useful suggestions which improved this article. This paper is based on data obtained with the ALMA Observatory, under Large Program 2017.1.00428.L. ALMA is a partnership of ESO (representing its member states), NSF (USA), and NINS (Japan), together with NRC (Canada), MOST and ASIAA (Taiwan), and KASI (Republic of Korea), in cooperation with the Republic of Chile. The Joint ALMA Observatory is operated by ESO, AUI/NRAO and NAOJ. CDC would like to thank the GESO group at the European Southern Observatory (ESO) for the useful discussions while preparing this manuscript. The simulated data underlying this article will be shared on reasonable request to the corresponding author. CDC acknowledged support from Sapienza University of Rome program “Bando per la mobilità individuale all’estero” (DR n.1607 del 14 June 2021) during the visiting period (June-November 2022) at ESO Garching, Germany. LG and RS acknowledge support from the PRIN 2022 MUR project 2022CB3PJ3 – First Light And Galaxy aSsembly (FLAGS) funded by the European Union – Next Generation EU, and from the Amaldi Research Center funded by the MIUR program “Dipartimento di Eccellenza” (CUP:B81I18001170001). MR acknowledges support from the Narodowe Centrum Nauki (UMO-2020/38/E/ST9/00077) and support from the Foundation for Polish Science (FNP) under the program START 063.2023. We have benefited from the publicly available software CASA and CARTA and programming language Python, including the numpy (https://numpy.org), matplotlib (https://matplotlib.org), scipy (https://scipy.org) and astropy (http://www.astropy.org) packages. ' article_number: A255 article_processing_charge: No article_type: original arxiv: 1 author: - first_name: Claudia full_name: Di Cesare, Claudia id: 2d002343-372f-11ef-98ec-a164d20427cb last_name: Di Cesare - first_name: M. full_name: Ginolfi, M. last_name: Ginolfi - first_name: L. full_name: Graziani, L. last_name: Graziani - first_name: R. full_name: Schneider, R. last_name: Schneider - first_name: M. full_name: Romano, M. last_name: Romano - first_name: G. full_name: Popping, G. last_name: Popping citation: ama: Di Cesare C, Ginolfi M, Graziani L, Schneider R, Romano M, Popping G. Carbon envelopes around merging galaxies at z ~ 4.5. Astronomy and Astrophysics. 2024;690. doi:10.1051/0004-6361/202449164 apa: Di Cesare, C., Ginolfi, M., Graziani, L., Schneider, R., Romano, M., & Popping, G. (2024). Carbon envelopes around merging galaxies at z ~ 4.5. Astronomy and Astrophysics. EDP Sciences. https://doi.org/10.1051/0004-6361/202449164 chicago: Di Cesare, Claudia, M. Ginolfi, L. Graziani, R. Schneider, M. Romano, and G. Popping. “Carbon Envelopes around Merging Galaxies at z ~ 4.5.” Astronomy and Astrophysics. EDP Sciences, 2024. https://doi.org/10.1051/0004-6361/202449164. ieee: C. Di Cesare, M. Ginolfi, L. Graziani, R. Schneider, M. Romano, and G. Popping, “Carbon envelopes around merging galaxies at z ~ 4.5,” Astronomy and Astrophysics, vol. 690. EDP Sciences, 2024. ista: Di Cesare C, Ginolfi M, Graziani L, Schneider R, Romano M, Popping G. 2024. Carbon envelopes around merging galaxies at z ~ 4.5. Astronomy and Astrophysics. 690, A255. mla: Di Cesare, Claudia, et al. “Carbon Envelopes around Merging Galaxies at z ~ 4.5.” Astronomy and Astrophysics, vol. 690, A255, EDP Sciences, 2024, doi:10.1051/0004-6361/202449164. short: C. Di Cesare, M. Ginolfi, L. Graziani, R. Schneider, M. Romano, G. Popping, Astronomy and Astrophysics 690 (2024). corr_author: '1' date_created: 2024-11-10T23:02:00Z date_published: 2024-10-01T00:00:00Z date_updated: 2025-09-08T14:35:57Z day: '01' ddc: - '520' department: - _id: JoMa doi: 10.1051/0004-6361/202449164 external_id: arxiv: - '2401.03020' isi: - '001332213700013' file: - access_level: open_access checksum: 24c65a64047aba156f39b01425269bdb content_type: application/pdf creator: dernst date_created: 2024-11-11T08:54:11Z date_updated: 2024-11-11T08:54:11Z file_id: '18533' file_name: 2024_AstronomyAstrophysics_diCesare.pdf file_size: 8033864 relation: main_file success: 1 file_date_updated: 2024-11-11T08:54:11Z has_accepted_license: '1' intvolume: ' 690' isi: 1 language: - iso: eng month: '10' oa: 1 oa_version: Published Version publication: Astronomy and Astrophysics publication_identifier: eissn: - 1432-0746 issn: - 0004-6361 publication_status: published publisher: EDP Sciences quality_controlled: '1' scopus_import: '1' status: public title: Carbon envelopes around merging galaxies at z ~ 4.5 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: 317138e5-6ab7-11ef-aa6d-ffef3953e345 volume: 690 year: '2024' ... --- DOAJ_listed: '1' OA_place: publisher OA_type: gold _id: '18581' abstract: - lang: eng text: "Background: Human induced pluripotent stem cells represent a scalable source of youthful tissue progenitors and secretomes for regenerative therapies. The aim of our study was to investigate the potential of conditioned medium (CM) from hiPSC-mesenchymal progenitors (hiPSC-MPs) to stimulate osteogenic differentiation of human bone marrow-derived mesenchymal stromal cells (MSCs). We also investigated whether prolonged cultivation or osteogenic pre-differentiation of hiPSC-MPs could enhance the stimulatory activity of CM.\r\nMethods: MSCs were isolated from 13 donors (age 20–90 years). CM derived from hiPSC-MPs was added to the MSC cultures and the effects on proliferation and osteogenic differentiation were examined after 14 days and 6 weeks. The stimulatory activity of hiPSC-MP-CM was compared with the activity of MSC-derived CM and with the activity of CM prepared from hiPSC-MPs pre-cultured in growth or osteogenic medium for 14 days. Comparative proteomic analysis of CM was performed to gain insight into the molecular components responsible for the stimulatory activity.\r\nResults: Primary bone marrow-derived MSC exhibited variability, with a tendency towards lower proliferation and tri-lineage differentiation in older donors. hiPSC-MP-CM increased the proliferation and alkaline phosphatase activity of MSC from several adult/aged donors after 14 days of continuous supplementation under osteogenic conditions. However, CM supplementation failed to improve the mineralization of MSC pellets after 6 weeks under osteogenic conditions. hiPSC-MP-CM showed greater enhancement of proliferation and ALP activity than CM derived from bone marrow-derived MSCs. Moreover, 14-day cultivation but not osteogenic pre-differentiation of hiPSC-MPs strongly enhanced CM stimulatory activity. Quantitative proteomic analysis of d14-CM revealed a distinct profile of components that formed a highly interconnected associations network with two clusters, one functionally associated with binding and organization of actin/cytoskeletal components and the other with structural constituents of the extracellular matrix, collagen, and growth factor binding. Several hub proteins were identified that were reported to have functions in cell-extracellular matrix interaction, osteogenic differentiation and development.\r\nConclusions: Our data show that hiPSC-MP-CM enhances early osteogenic differentiation of human bone marrow-derived MSCs and that prolonged cultivation of hiPSC-MPs enhances CM-stimulatory activity. Proteomic analysis of the upregulated protein components provides the basis for further optimization of hiPSC-MP-CM for bone regenerative therapies." acknowledgement: "We thank the personnel of the Lorenz-Böhler-Unfallkrankenhaus for providing the human tissue waste for primary cell isolation and the New York Stem Cell Foundation Research Institute for providing the human induced pluripotent stem cell line 1013 A and its mesenchymal progenitors. We also thank all our colleagues at the Ludwig Boltzmann Institute for Traumatology for their suggestions and ongoing support of the project. InstaText writing tool (https://instatext.io) was used to edit the English language of the final manuscript.\r\nThis work has received funding from the European Union’s Horizon 2020 research and innovation program under the Marie Sklodowska-Curie actions (grant agreement No. 657716) and the Transforming European Industry call H2020-NMBP-TRIND-2020 (grant agreement No. 953134), as well as by the FFG Industrienahe Dissertation program (grant agreement No. 867803 and 853056), the FEMtech Praktika program (grant agreement No. 852154, 868917 and 877951) and the Production of the Future program (grant agreement No. 877452)." article_number: '434' article_processing_charge: Yes article_type: original author: - first_name: Darja full_name: Marolt Presen, Darja last_name: Marolt Presen - first_name: Vanessa full_name: Goeschl, Vanessa last_name: Goeschl - first_name: Dominik full_name: Hanetseder, Dominik last_name: Hanetseder - first_name: Laura full_name: Ogrin, Laura last_name: Ogrin - first_name: Alexandra Larissa full_name: Stetco, Alexandra Larissa last_name: Stetco - first_name: Anja full_name: Tansek, Anja last_name: Tansek - first_name: Laura full_name: Pozenel, Laura last_name: Pozenel - first_name: Bella full_name: Bruszel, Bella id: 70abbbb3-88ea-11ec-8e0a-e8c939944834 last_name: Bruszel - first_name: Goran full_name: Mitulovic, Goran last_name: Mitulovic - first_name: Johannes full_name: Oesterreicher, Johannes last_name: Oesterreicher - first_name: Johannes full_name: Zipperle, Johannes last_name: Zipperle - first_name: Barbara full_name: Schaedl, Barbara last_name: Schaedl - first_name: Wolfgang full_name: Holnthoner, Wolfgang last_name: Holnthoner - first_name: Johannes full_name: Grillari, Johannes last_name: Grillari - first_name: Heinz full_name: Redl, Heinz last_name: Redl citation: ama: Marolt Presen D, Goeschl V, Hanetseder D, et al. Prolonged cultivation enhances the stimulatory activity of hiPSC mesenchymal progenitor-derived conditioned medium. Stem Cell Research and Therapy. 2024;15. doi:10.1186/s13287-024-03960-5 apa: Marolt Presen, D., Goeschl, V., Hanetseder, D., Ogrin, L., Stetco, A. L., Tansek, A., … Redl, H. (2024). Prolonged cultivation enhances the stimulatory activity of hiPSC mesenchymal progenitor-derived conditioned medium. Stem Cell Research and Therapy. Springer Nature. https://doi.org/10.1186/s13287-024-03960-5 chicago: Marolt Presen, Darja, Vanessa Goeschl, Dominik Hanetseder, Laura Ogrin, Alexandra Larissa Stetco, Anja Tansek, Laura Pozenel, et al. “Prolonged Cultivation Enhances the Stimulatory Activity of HiPSC Mesenchymal Progenitor-Derived Conditioned Medium.” Stem Cell Research and Therapy. Springer Nature, 2024. https://doi.org/10.1186/s13287-024-03960-5. ieee: D. Marolt Presen et al., “Prolonged cultivation enhances the stimulatory activity of hiPSC mesenchymal progenitor-derived conditioned medium,” Stem Cell Research and Therapy, vol. 15. Springer Nature, 2024. ista: Marolt Presen D, Goeschl V, Hanetseder D, Ogrin L, Stetco AL, Tansek A, Pozenel L, Bruszel B, Mitulovic G, Oesterreicher J, Zipperle J, Schaedl B, Holnthoner W, Grillari J, Redl H. 2024. Prolonged cultivation enhances the stimulatory activity of hiPSC mesenchymal progenitor-derived conditioned medium. Stem Cell Research and Therapy. 15, 434. mla: Marolt Presen, Darja, et al. “Prolonged Cultivation Enhances the Stimulatory Activity of HiPSC Mesenchymal Progenitor-Derived Conditioned Medium.” Stem Cell Research and Therapy, vol. 15, 434, Springer Nature, 2024, doi:10.1186/s13287-024-03960-5. short: D. Marolt Presen, V. Goeschl, D. Hanetseder, L. Ogrin, A.L. Stetco, A. Tansek, L. Pozenel, B. Bruszel, G. Mitulovic, J. Oesterreicher, J. Zipperle, B. Schaedl, W. Holnthoner, J. Grillari, H. Redl, Stem Cell Research and Therapy 15 (2024). date_created: 2024-11-24T23:01:47Z date_published: 2024-12-01T00:00:00Z date_updated: 2025-09-09T11:41:12Z day: '01' ddc: - '570' department: - _id: LifeSc doi: 10.1186/s13287-024-03960-5 external_id: isi: - '001356479400001' pmid: - '39551765' file: - access_level: open_access checksum: 91edba8edde30d781dce89fdd5cadc39 content_type: application/pdf creator: dernst date_created: 2024-12-10T08:28:17Z date_updated: 2024-12-10T08:28:17Z file_id: '18641' file_name: 2024_StemCellResearch_Presen.pdf file_size: 6690494 relation: main_file success: 1 file_date_updated: 2024-12-10T08:28:17Z has_accepted_license: '1' intvolume: ' 15' isi: 1 language: - iso: eng license: https://creativecommons.org/licenses/by-nc-nd/4.0/ month: '12' oa: 1 oa_version: Published Version pmid: 1 publication: Stem Cell Research and Therapy publication_identifier: eissn: - 1757-6512 publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: Prolonged cultivation enhances the stimulatory activity of hiPSC mesenchymal progenitor-derived conditioned medium 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: 317138e5-6ab7-11ef-aa6d-ffef3953e345 volume: 15 year: '2024' ... --- DOAJ_listed: '1' OA_place: publisher OA_type: gold _id: '18584' abstract: - lang: eng text: In this paper, we describe the "Medium Bands, Mega Science" JWST Cycle 2 survey (JWST-GO-4111) and demonstrate the power of these data to reveal both the spatially integrated and spatially resolved properties of galaxies from the local Universe to the era of cosmic dawn. Executed in 2023 November, MegaScience obtained ∼30 arcmin2 of deep multiband NIRCam imaging centered on the z ∼ 0.3 A2744 cluster, including 11 medium-band filters and the two shortest-wavelength broadband filters, F070W and F090W. Together, MegaScience and the UNCOVER Cycle 1 treasury program provide a complete set of deep (∼28–30 magAB) images in all NIRCam medium- and broadband filters. This unique data set allows us to precisely constrain photometric redshifts, map stellar populations and dust attenuation for large samples of distant galaxies, and examine the connection between galaxy structures and formation histories. MegaScience also includes ∼17 arcmin2 of NIRISS parallel imaging in two broadband and four medium-band filters from 0.9 to 4.8 μm, expanding the footprint where robust spectral energy distribution (SED) fitting is possible. We provide example SEDs and multiband cutouts at a variety of redshifts, and use a catalog of JWST spectroscopic redshifts to show that MegaScience improves both the scatter and catastrophic outlier rate of photometric redshifts by factors of 2–3. Additionally, we demonstrate the spatially resolved science enabled by MegaScience by presenting maps of the [O iii] line emission and continuum emission in three spectroscopically confirmed z > 6 galaxies. We show that line emission in reionization-era galaxies can be clumpy, extended, and spatially offset from continuum emission, implying that galaxy assembly histories are complex even at these early epochs. We publicly release fully reduced mosaics and photometric catalogs for both the NIRCam primary and NIRISS parallel fields (jwst-uncover.github.io/megascience). acknowledgement: "K.A.S. thanks Shelly Meyett, the MegaScience Program Coordinator, for invaluable assistance designing WOPR 88967 and ensuring that this program was fully observed. This proposal was conceived of and developed at the International Space Science Institute (ISSI) in Bern, through ISSI International Team project #562. This work is based on observations made with the NASA/ESA/CSA James Webb Space Telescope. The raw data were obtained from the Mikulski Archive for Space Telescopes at the Space Telescope Science Institute, which is operated by the Association of Universities for Research in Astronomy, Inc., under NASA contract NAS 5-03127 for JWST. These observations are associated with JWST Cycle 2 GO program #4111, and this project has gratefully made use of a large number of public JWST programs in the A2744 field including JWST-GO-2641, JWST-ERS-1324, JWST-DD-2756, JWST-GO-2883, JWST-GO-3538, and JWST-GO-3516. Support for program JWST-GO-4111 was provided by NASA through a grant from the Space Telescope Science Institute, which is operated by the Associations of Universities for Research in Astronomy, Incorporated, under NASA contract NAS5-26555.\r\n\r\nThe Cosmic Dawn Center is funded by the Danish National Research Foundation (DNRF) under grant #140. P.D. acknowledges support from the NWO grant 016.VIDI.189.162 (\"ODIN\") and warmly thanks the European Commission's and University of Groningen's CO-FUND Rosalind Franklin program. This work has received funding from the Swiss State Secretariat for Education, Research and Innovation (SERI) under contract number MB22.00072, as well as from the Swiss National Science Foundation (SNSF) through project grant 200020_207349. The work of C.C.W. is supported by NOIRLab, which is managed by the Association of Universities for Research in Astronomy (AURA) under a cooperative agreement with the National Science Foundation. T.B.M. was supported by a CIERA Fellowship. H.A. is supported by CNES, focused on the JWST mission, and by the Programme National Cosmology and Galaxies (PNCG) of CNRS/INSU with INP and IN2P3, co-funded by CEA and CNES. The BGU lensing group acknowledges support by grant No. 2020750 from the United States–Israel Binational Science Foundation (BSF) and grant No. 2109066 from the United States National Science Foundation (NSF); by the Ministry of Science & Technology, Israel; and by the Israel Science Foundation grant No. 864/23. Y.F. acknowledges support from JSPS KAKENHI grant No. JP22K21349 and JP23K13149. R.P. and D.M. acknowledge funding from JWST-GO-02561.013 and JWST-GO-04111.035." article_number: '101' article_processing_charge: Yes article_type: original arxiv: 1 author: - first_name: Katherine A. full_name: Suess, Katherine A. last_name: Suess - first_name: John R. full_name: Weaver, John R. last_name: Weaver - first_name: Sedona H. full_name: Price, Sedona H. last_name: Price - first_name: Richard full_name: Pan, Richard last_name: Pan - first_name: Bingjie full_name: Wang, Bingjie last_name: Wang - first_name: Rachel full_name: Bezanson, Rachel last_name: Bezanson - first_name: Gabriel full_name: Brammer, Gabriel last_name: Brammer - first_name: Sam E. full_name: Cutler, Sam E. last_name: Cutler - first_name: Ivo full_name: Labbé, Ivo last_name: Labbé - first_name: Joel full_name: Leja, Joel last_name: Leja - first_name: Christina C. full_name: Williams, Christina C. last_name: Williams - first_name: Katherine E. full_name: Whitaker, Katherine E. last_name: Whitaker - first_name: Hakim full_name: Atek, Hakim last_name: Atek - first_name: Pratika full_name: Dayal, Pratika last_name: Dayal - first_name: Anna full_name: De Graaff, Anna last_name: De Graaff - first_name: Robert full_name: Feldmann, Robert last_name: Feldmann - first_name: Marijn full_name: Franx, Marijn last_name: Franx - first_name: Yoshinobu full_name: Fudamoto, Yoshinobu last_name: Fudamoto - first_name: Seiji full_name: Fujimoto, Seiji last_name: Fujimoto - first_name: Lukas J. full_name: Furtak, Lukas J. last_name: Furtak - first_name: Andy D. full_name: Goulding, Andy D. last_name: Goulding - first_name: Jenny E. full_name: Greene, Jenny E. last_name: Greene - first_name: Gourav full_name: Khullar, Gourav last_name: Khullar - first_name: Vasily full_name: Kokorev, Vasily last_name: Kokorev - first_name: Mariska full_name: Kriek, Mariska last_name: Kriek - first_name: Brian full_name: Lorenz, Brian last_name: Lorenz - first_name: Danilo full_name: Marchesini, Danilo last_name: Marchesini - first_name: Michael V. full_name: Maseda, Michael V. last_name: Maseda - first_name: Jorryt J full_name: Matthee, Jorryt J id: 7439a258-f3c0-11ec-9501-9df22fe06720 last_name: Matthee orcid: 0000-0003-2871-127X - first_name: Tim B. full_name: Miller, Tim B. last_name: Miller - first_name: Ikki full_name: Mitsuhashi, Ikki last_name: Mitsuhashi - first_name: Lamiya A. full_name: Mowla, Lamiya A. last_name: Mowla - first_name: Adam full_name: Muzzin, Adam last_name: Muzzin - first_name: Rohan P. full_name: Naidu, Rohan P. last_name: Naidu - first_name: Themiya full_name: Nanayakkara, Themiya last_name: Nanayakkara - first_name: Erica J. full_name: Nelson, Erica J. last_name: Nelson - first_name: Pascal A. full_name: Oesch, Pascal A. last_name: Oesch - first_name: David J. full_name: Setton, David J. last_name: Setton - first_name: Heath full_name: Shipley, Heath last_name: Shipley - first_name: Renske full_name: Smit, Renske last_name: Smit - first_name: Justin S. full_name: Spilker, Justin S. last_name: Spilker - first_name: Pieter full_name: Van Dokkum, Pieter last_name: Van Dokkum - first_name: Adi full_name: Zitrin, Adi last_name: Zitrin citation: ama: 'Suess KA, Weaver JR, Price SH, et al. Medium bands, mega science: A JWST/NIRCam medium-band imaging survey of A2744. Astrophysical Journal. 2024;976(1). doi:10.3847/1538-4357/ad75fe' apa: 'Suess, K. A., Weaver, J. R., Price, S. H., Pan, R., Wang, B., Bezanson, R., … Zitrin, A. (2024). Medium bands, mega science: A JWST/NIRCam medium-band imaging survey of A2744. Astrophysical Journal. IOP Publishing. https://doi.org/10.3847/1538-4357/ad75fe' chicago: 'Suess, Katherine A., John R. Weaver, Sedona H. Price, Richard Pan, Bingjie Wang, Rachel Bezanson, Gabriel Brammer, et al. “Medium Bands, Mega Science: A JWST/NIRCam Medium-Band Imaging Survey of A2744.” Astrophysical Journal. IOP Publishing, 2024. https://doi.org/10.3847/1538-4357/ad75fe.' ieee: 'K. A. Suess et al., “Medium bands, mega science: A JWST/NIRCam medium-band imaging survey of A2744,” Astrophysical Journal, vol. 976, no. 1. IOP Publishing, 2024.' ista: 'Suess KA, Weaver JR, Price SH, Pan R, Wang B, Bezanson R, Brammer G, Cutler SE, Labbé I, Leja J, Williams CC, Whitaker KE, Atek H, Dayal P, De Graaff A, Feldmann R, Franx M, Fudamoto Y, Fujimoto S, Furtak LJ, Goulding AD, Greene JE, Khullar G, Kokorev V, Kriek M, Lorenz B, Marchesini D, Maseda MV, Matthee JJ, Miller TB, Mitsuhashi I, Mowla LA, Muzzin A, Naidu RP, Nanayakkara T, Nelson EJ, Oesch PA, Setton DJ, Shipley H, Smit R, Spilker JS, Van Dokkum P, Zitrin A. 2024. Medium bands, mega science: A JWST/NIRCam medium-band imaging survey of A2744. Astrophysical Journal. 976(1), 101.' mla: 'Suess, Katherine A., et al. “Medium Bands, Mega Science: A JWST/NIRCam Medium-Band Imaging Survey of A2744.” Astrophysical Journal, vol. 976, no. 1, 101, IOP Publishing, 2024, doi:10.3847/1538-4357/ad75fe.' short: K.A. Suess, J.R. Weaver, S.H. Price, R. Pan, B. Wang, R. Bezanson, G. Brammer, S.E. Cutler, I. Labbé, J. Leja, C.C. Williams, K.E. Whitaker, H. Atek, P. Dayal, A. De Graaff, R. Feldmann, M. Franx, Y. Fudamoto, S. Fujimoto, L.J. Furtak, A.D. Goulding, J.E. Greene, G. Khullar, V. Kokorev, M. Kriek, B. Lorenz, D. Marchesini, M.V. Maseda, J.J. Matthee, T.B. Miller, I. Mitsuhashi, L.A. Mowla, A. Muzzin, R.P. Naidu, T. Nanayakkara, E.J. Nelson, P.A. Oesch, D.J. Setton, H. Shipley, R. Smit, J.S. Spilker, P. Van Dokkum, A. Zitrin, Astrophysical Journal 976 (2024). date_created: 2024-11-24T23:01:48Z date_published: 2024-11-14T00:00:00Z date_updated: 2025-09-09T11:40:09Z day: '14' ddc: - '520' department: - _id: JoMa doi: 10.3847/1538-4357/ad75fe external_id: arxiv: - '2404.13132' isi: - '001355710500001' file: - access_level: open_access checksum: dcd854acee73ce998d70a4ce634ead6d content_type: application/pdf creator: dernst date_created: 2024-12-10T08:18:53Z date_updated: 2024-12-10T08:18:53Z file_id: '18640' file_name: 2024_AstrophysicalJournal_Suess.pdf file_size: 13352667 relation: main_file success: 1 file_date_updated: 2024-12-10T08:18:53Z has_accepted_license: '1' intvolume: ' 976' isi: 1 issue: '1' language: - iso: eng month: '11' oa: 1 oa_version: Published Version publication: Astrophysical Journal publication_identifier: eissn: - 1538-4357 issn: - 0004-637X publication_status: published publisher: IOP Publishing quality_controlled: '1' scopus_import: '1' status: public title: 'Medium bands, mega science: A JWST/NIRCam medium-band imaging survey of A2744' 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: 317138e5-6ab7-11ef-aa6d-ffef3953e345 volume: 976 year: '2024' ... --- DOAJ_listed: '1' OA_place: publisher OA_type: gold _id: '18585' abstract: - lang: eng text: We present the census of Hβ+[OIII] 4960,5008 Åemitters at 6.87 galaxies. We report a rapid decline of the [OIII] luminosity density at z≳6−7 which cannot be explained by the evolution of the cosmic star-formation rate density. Finally we find that FRESCO detects in only 2h galaxies likely accounting for ∼10−20% of the ionising budget at z=7−8 (assuming an escape fraction of 10%), raising the prospect of directly detecting a significant fraction of the sources of reionisation with JWST. acknowledgement: "The authors thank the anonymous referee for comments and suggestions which improved this paper. RAM thanks R. Kannan for sharing emission line luminosities from THESAN and H. Katz for similar data from an early version of the SPHINX20 data release (we use the final data release in this paper). The authors thank the CONGRESS team for proposing and designing their program with a zero exclusive access period.\r\nRAM, PA, ACP, and AW acknowledge support from the Swiss National Science Foundation (SNSF) through project grant 200020_207349. PA, AW, EG, and MX acknowledge support from the Swiss State Secretariat for Education, Research and Innovation (SERI) under contract number MB22.00072. YF acknowledges support by JSPS KAKENHI grant number JP22K21349 and JP23K13149. RPN acknowledges support for this work provided by NASA through the NASA Hubble Fellowship grant HST-HF2-51515.001-A awarded by the Space Telescope Science Institute, which is operated by the Association of Universities for Research in Astronomy, Incorporated, under NASA contract NAS5-26555. MS acknowledges support from the European Research Commission Grant 101088789 (SFEER), from the CIDEGENT/2021/059 grant by Generalitat Valenciana, and from project PID2019-109592GB-I00/AEI/10.13039/501100011033 by the Spanish Ministerio de Ciencia e Innovación - Agencia Estatal de Investigación. The Cosmic Dawn Center (DAWN) is funded by the Danish National Research Foundation under grant no. 140. Cloud-based data processing and file storage for this work is provided by the AWS Cloud Credits for Research program. RJB and MS acknowledges support from NWO grant TOP1.16.057.\r\nThis work is based on observations made with the NASA/ESA/CSA JWST. The raw data were obtained from the Mikulski Archive for Space Telescopes at the Space Telescope Science Institute, which is operated by the Association of Universities for Research in Astronomy, Inc., under NASA contract NAS 5-03127 for JWST. These observations are associated with JWST Cycle 1 GO program #1895. Support for program JWST-GO-1895 was provided by NASA through a grant from the Space Telescope Science Institute, which is operated by the Associations of Universities for Research in Astronomy, Incorporated, under NASA contract NAS5-26555." article_processing_charge: Yes article_type: original author: - first_name: R. A. full_name: Meyer, R. A. last_name: Meyer - first_name: P. A. full_name: Oesch, P. A. last_name: Oesch - first_name: E. full_name: Giovinazzo, E. last_name: Giovinazzo - first_name: A. full_name: Weibel, A. last_name: Weibel - first_name: G. full_name: Brammer, G. last_name: Brammer - first_name: Jorryt J full_name: Matthee, Jorryt J id: 7439a258-f3c0-11ec-9501-9df22fe06720 last_name: Matthee orcid: 0000-0003-2871-127X - first_name: R. P. full_name: Naidu, R. P. last_name: Naidu - first_name: R. J. full_name: Bouwens, R. J. last_name: Bouwens - first_name: J. full_name: Chisholm, J. last_name: Chisholm - first_name: A. full_name: Covelo-Paz, A. last_name: Covelo-Paz - first_name: Y. full_name: Fudamoto, Y. last_name: Fudamoto - first_name: M. full_name: Maseda, M. last_name: Maseda - first_name: E. full_name: Nelson, E. last_name: Nelson - first_name: I. full_name: Shivaei, I. last_name: Shivaei - first_name: M. full_name: Xiao, M. last_name: Xiao - first_name: T. full_name: Herard-Demanche, T. last_name: Herard-Demanche - first_name: G. D. full_name: Illingworth, G. D. last_name: Illingworth - first_name: J. full_name: Kerutt, J. last_name: Kerutt - first_name: Ivan full_name: Kramarenko, Ivan id: 9a9394cb-3200-11ee-973b-f5ba2a8b16e4 last_name: Kramarenko orcid: 0000-0001-5346-6048 - first_name: I. full_name: Labbe, I. last_name: Labbe - first_name: E. full_name: Leonova, E. last_name: Leonova - first_name: D. full_name: Magee, D. last_name: Magee - first_name: J. full_name: Matharu, J. last_name: Matharu - first_name: G. full_name: Prieto Lyon, G. last_name: Prieto Lyon - first_name: N. full_name: Reddy, N. last_name: Reddy - first_name: D. full_name: Schaerer, D. last_name: Schaerer - first_name: A. full_name: Shapley, A. last_name: Shapley - first_name: M. full_name: Stefanon, M. last_name: Stefanon - first_name: M. A. full_name: Wozniak, M. A. last_name: Wozniak - first_name: S. full_name: Wuyts, S. last_name: Wuyts citation: ama: 'Meyer RA, Oesch PA, Giovinazzo E, et al. JWST FRESCO: A comprehensive census of H β + [O iii] emitters at 6.8 < z < 9.0 in the GOODS fields. Monthly Notices of the Royal Astronomical Society. 2024;535(1):1067-1094. doi:10.1093/mnras/stae2353' apa: 'Meyer, R. A., Oesch, P. A., Giovinazzo, E., Weibel, A., Brammer, G., Matthee, J. J., … Wuyts, S. (2024). JWST FRESCO: A comprehensive census of H β + [O iii] emitters at 6.8 < z < 9.0 in the GOODS fields. Monthly Notices of the Royal Astronomical Society. Oxford University Press. https://doi.org/10.1093/mnras/stae2353' chicago: 'Meyer, R. A., P. A. Oesch, E. Giovinazzo, A. Weibel, G. Brammer, Jorryt J Matthee, R. P. Naidu, et al. “JWST FRESCO: A Comprehensive Census of H β + [O Iii] Emitters at 6.8 < z < 9.0 in the GOODS Fields.” Monthly Notices of the Royal Astronomical Society. Oxford University Press, 2024. https://doi.org/10.1093/mnras/stae2353.' ieee: 'R. A. Meyer et al., “JWST FRESCO: A comprehensive census of H β + [O iii] emitters at 6.8 < z < 9.0 in the GOODS fields,” Monthly Notices of the Royal Astronomical Society, vol. 535, no. 1. Oxford University Press, pp. 1067–1094, 2024.' ista: 'Meyer RA, Oesch PA, Giovinazzo E, Weibel A, Brammer G, Matthee JJ, Naidu RP, Bouwens RJ, Chisholm J, Covelo-Paz A, Fudamoto Y, Maseda M, Nelson E, Shivaei I, Xiao M, Herard-Demanche T, Illingworth GD, Kerutt J, Kramarenko I, Labbe I, Leonova E, Magee D, Matharu J, Prieto Lyon G, Reddy N, Schaerer D, Shapley A, Stefanon M, Wozniak MA, Wuyts S. 2024. JWST FRESCO: A comprehensive census of H β + [O iii] emitters at 6.8 < z < 9.0 in the GOODS fields. Monthly Notices of the Royal Astronomical Society. 535(1), 1067–1094.' mla: 'Meyer, R. A., et al. “JWST FRESCO: A Comprehensive Census of H β + [O Iii] Emitters at 6.8 < z < 9.0 in the GOODS Fields.” Monthly Notices of the Royal Astronomical Society, vol. 535, no. 1, Oxford University Press, 2024, pp. 1067–94, doi:10.1093/mnras/stae2353.' short: R.A. Meyer, P.A. Oesch, E. Giovinazzo, A. Weibel, G. Brammer, J.J. Matthee, R.P. Naidu, R.J. Bouwens, J. Chisholm, A. Covelo-Paz, Y. Fudamoto, M. Maseda, E. Nelson, I. Shivaei, M. Xiao, T. Herard-Demanche, G.D. Illingworth, J. Kerutt, I. Kramarenko, I. Labbe, E. Leonova, D. Magee, J. Matharu, G. Prieto Lyon, N. Reddy, D. Schaerer, A. Shapley, M. Stefanon, M.A. Wozniak, S. Wuyts, Monthly Notices of the Royal Astronomical Society 535 (2024) 1067–1094. date_created: 2024-11-24T23:01:49Z date_published: 2024-11-01T00:00:00Z date_updated: 2025-09-08T14:47:58Z day: '01' ddc: - '520' department: - _id: JoMa doi: 10.1093/mnras/stae2353 external_id: isi: - '001348009500001' file: - access_level: open_access checksum: efe0ce3580e01459f3be78eb111b35a9 content_type: application/pdf creator: dernst date_created: 2024-12-03T12:52:13Z date_updated: 2024-12-03T12:52:13Z file_id: '18613' file_name: 2024_MonthlyNRoyalAstronSoc_Meyer.pdf file_size: 29476699 relation: main_file success: 1 file_date_updated: 2024-12-03T12:52:13Z has_accepted_license: '1' intvolume: ' 535' isi: 1 issue: '1' language: - iso: eng month: '11' oa: 1 oa_version: Published Version page: 1067-1094 publication: Monthly Notices of the Royal Astronomical Society publication_identifier: eissn: - 1365-2966 issn: - 0035-8711 publication_status: published publisher: Oxford University Press quality_controlled: '1' scopus_import: '1' status: public title: 'JWST FRESCO: A comprehensive census of H β + [O iii] emitters at 6.8 < z < 9.0 in the GOODS fields' 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: 317138e5-6ab7-11ef-aa6d-ffef3953e345 volume: 535 year: '2024' ... --- DOAJ_listed: '1' OA_place: publisher OA_type: gold _id: '18628' abstract: - lang: eng text: 'Arctic tidewater glaciers are retreating, serving as key indicators of global warming. This study aims to assess how subglacial hydrology affects glacier front retreat by comparing two glacier–fjord models of the Hansbreen glacier: one incorporating a detailed subglacial hydrology model and another simplifying the subglacial discharge to a single channel centered in the flow line. We first validate the subglacial hydrology model by comparing its discharge channels with observations of plume activity. Simulations conducted from April to December 2010 revealed that the glacier front position aligns more closely with the observations in the coupled model than in the simplified version. Furthermore, the mass loss due to calving and submarine melting is greater in the coupled model, with the calving mass loss reaching 6 Mt by the end of the simulation compared to 4 Mt in the simplified model. These findings highlight the critical role of subglacial hydrology in predicting glacier dynamics and emphasize the importance of detailed modeling in understanding the responses of Arctic tidewater glaciers to climate change.' acknowledgement: "E. De Andrés is supported by Margarita-Salas Grant No. UP2021-035 under the Next Generation-EU program. This research was also funded by grant PID2020-113051RB-C31 from MCIN/AEI/10.13039/501100011033/FEDER, UE.\r\nWe gratefully acknowledge Michal Cieply and Dariusz Ignatiuk from the Faculty of Natural Sciences, University of Silesia in Katowice, Poland, for their essential contributions to the Hansbreen data collection. We also extend our sincere thanks to Waldemar Walczowski from the Institute of Oceanology, Polish Academy of Sciences, Sopot, Poland, for providing Hansbuka data. Additionally, we would like to thank two anonymous reviewers for their constructive feedback, which helped to enhance the quality and clarity of this work." article_number: '193' article_processing_charge: Yes article_type: original author: - first_name: Eva full_name: De Andrés, Eva last_name: De Andrés - first_name: José M full_name: Muñoz Hermosilla, José M id: e1037a6d-646e-11ef-b402-e0ed9ab0901e last_name: Muñoz Hermosilla - first_name: Kaian full_name: Shahateet, Kaian last_name: Shahateet - first_name: Jaime full_name: Otero, Jaime last_name: Otero citation: ama: 'De Andrés E, Muñoz Hermosilla JM, Shahateet K, Otero J. The importance of solving Subglaciar hydrology in modeling glacier retreat: A case study of Hansbreen, Svalbard. Hydrology. 2024;11(11). doi:10.3390/hydrology11110193' apa: 'De Andrés, E., Muñoz Hermosilla, J. M., Shahateet, K., & Otero, J. (2024). The importance of solving Subglaciar hydrology in modeling glacier retreat: A case study of Hansbreen, Svalbard. Hydrology. MDPI. https://doi.org/10.3390/hydrology11110193' chicago: 'De Andrés, Eva, José M Muñoz Hermosilla, Kaian Shahateet, and Jaime Otero. “The Importance of Solving Subglaciar Hydrology in Modeling Glacier Retreat: A Case Study of Hansbreen, Svalbard.” Hydrology. MDPI, 2024. https://doi.org/10.3390/hydrology11110193.' ieee: 'E. De Andrés, J. M. Muñoz Hermosilla, K. Shahateet, and J. Otero, “The importance of solving Subglaciar hydrology in modeling glacier retreat: A case study of Hansbreen, Svalbard,” Hydrology, vol. 11, no. 11. MDPI, 2024.' ista: 'De Andrés E, Muñoz Hermosilla JM, Shahateet K, Otero J. 2024. The importance of solving Subglaciar hydrology in modeling glacier retreat: A case study of Hansbreen, Svalbard. Hydrology. 11(11), 193.' mla: 'De Andrés, Eva, et al. “The Importance of Solving Subglaciar Hydrology in Modeling Glacier Retreat: A Case Study of Hansbreen, Svalbard.” Hydrology, vol. 11, no. 11, 193, MDPI, 2024, doi:10.3390/hydrology11110193.' short: E. De Andrés, J.M. Muñoz Hermosilla, K. Shahateet, J. Otero, Hydrology 11 (2024). corr_author: '1' date_created: 2024-12-08T23:01:55Z date_published: 2024-11-12T00:00:00Z date_updated: 2024-12-09T09:43:48Z day: '12' ddc: - '550' department: - _id: FrPe doi: 10.3390/hydrology11110193 file: - access_level: open_access checksum: 0665c5bfca97782bf0b041f23dd7e8d7 content_type: application/pdf creator: dernst date_created: 2024-12-09T09:43:33Z date_updated: 2024-12-09T09:43:33Z file_id: '18635' file_name: 2024_Hydrology_deAndres.pdf file_size: 5709093 relation: main_file success: 1 file_date_updated: 2024-12-09T09:43:33Z has_accepted_license: '1' intvolume: ' 11' issue: '11' language: - iso: eng month: '11' oa: 1 oa_version: Published Version publication: Hydrology publication_identifier: eissn: - 2306-5338 publication_status: published publisher: MDPI quality_controlled: '1' related_material: record: - id: '18634' relation: used_in_publication status: public scopus_import: '1' status: public title: 'The importance of solving Subglaciar hydrology in modeling glacier retreat: A case study of Hansbreen, Svalbard' tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 11 year: '2024' ... --- OA_place: publisher OA_type: gold _id: '18847' abstract: - lang: eng text: "Machine Learning and AI have the potential to transform data-driven\r\nscientific discovery, enabling accurate predictions for several scientific\r\nphenomena. As many scientific questions are inherently causal, this paper looks\r\nat the causal inference task of treatment effect estimation, where the outcome\r\nof interest is recorded in high-dimensional observations in a Randomized\r\nControlled Trial (RCT). Despite being the simplest possible causal setting and\r\na perfect fit for deep learning, we theoretically find that many common choices\r\nin the literature may lead to biased estimates. To test the practical impact of\r\nthese considerations, we recorded ISTAnt, the first real-world benchmark for\r\ncausal inference downstream tasks on high-dimensional observations as an RCT\r\nstudying how garden ants (Lasius neglectus) respond to microparticles applied\r\nonto their colony members by hygienic grooming. Comparing 6 480 models\r\nfine-tuned from state-of-the-art visual backbones, we find that the sampling\r\nand modeling choices significantly affect the accuracy of the causal estimate,\r\nand that classification accuracy is not a proxy thereof. We further validated\r\nthe analysis, repeating it on a synthetically generated visual data set\r\ncontrolling the causal model. Our results suggest that future benchmarks should\r\ncarefully consider real downstream scientific questions, especially causal\r\nones. Further, we highlight guidelines for representation learning methods to\r\nhelp answer causal questions in the sciences." acknowledgement: We thank Piersilvio De Bartolomeis, and the full Causal Learning and Artificial Intelligence (CLAI) group at ISTA for the extremely helpful discussions. Riccardo Cadei was supported by a Google Research Scholar Award and a Google Initiated Gift to Francesco Locatello. We thank the Social Immunity team at ISTA particularly Michaela Hönigsberger and Wilfrid Jean Louis, for supporting the ecological experiment and Farnaz Beikzadeh Abbasi, Luisa Fiebig and Martin Estermann for annotating ant behavior in ISTAnt. article_processing_charge: No arxiv: 1 author: - first_name: Riccardo full_name: Cadei, Riccardo id: 0fa8b76f-72f0-11ef-b75a-a5da96e5ad6b last_name: Cadei - first_name: Lukas full_name: Lindorfer, Lukas id: 85f0e6d3-06b3-11ec-8982-8c5049fa4455 last_name: Lindorfer - first_name: Sylvia full_name: Cremer, Sylvia id: 2F64EC8C-F248-11E8-B48F-1D18A9856A87 last_name: Cremer orcid: 0000-0002-2193-3868 - first_name: Cordelia full_name: Schmid, Cordelia last_name: Schmid - first_name: Francesco full_name: Locatello, Francesco id: 26cfd52f-2483-11ee-8040-88983bcc06d4 last_name: Locatello orcid: 0000-0002-4850-0683 citation: ama: 'Cadei R, Lindorfer L, Cremer S, Schmid C, Locatello F. Smoke and mirrors in causal downstream tasks. In: ICML 2024 Workshop AI4Science. Vol 38. Curran Associates; 2024.' apa: Cadei, R., Lindorfer, L., Cremer, S., Schmid, C., & Locatello, F. (2024). Smoke and mirrors in causal downstream tasks. In ICML 2024 Workshop AI4Science (Vol. 38). Curran Associates. chicago: Cadei, Riccardo, Lukas Lindorfer, Sylvia Cremer, Cordelia Schmid, and Francesco Locatello. “Smoke and Mirrors in Causal Downstream Tasks.” In ICML 2024 Workshop AI4Science, Vol. 38. Curran Associates, 2024. ieee: R. Cadei, L. Lindorfer, S. Cremer, C. Schmid, and F. Locatello, “Smoke and mirrors in causal downstream tasks,” in ICML 2024 Workshop AI4Science, 2024, vol. 38. ista: 'Cadei R, Lindorfer L, Cremer S, Schmid C, Locatello F. 2024. Smoke and mirrors in causal downstream tasks. ICML 2024 Workshop AI4Science. ICML: International Conference on Machine Learning vol. 38.' mla: Cadei, Riccardo, et al. “Smoke and Mirrors in Causal Downstream Tasks.” ICML 2024 Workshop AI4Science, vol. 38, Curran Associates, 2024. short: R. Cadei, L. Lindorfer, S. Cremer, C. Schmid, F. Locatello, in:, ICML 2024 Workshop AI4Science, Curran Associates, 2024. conference: end_date: 2024-07-26 name: 'ICML: International Conference on Machine Learning' start_date: 2024-07-26 corr_author: '1' date_created: 2025-01-14T07:27:26Z date_published: 2024-09-25T00:00:00Z date_updated: 2025-07-10T11:51:50Z day: '25' ddc: - '000' - '570' department: - _id: SyCr - _id: FrLo - _id: GradSch external_id: arxiv: - '2405.17151' file: - access_level: open_access checksum: beedf05388bbdb7ddda81ec3d5ec7026 content_type: application/pdf creator: dernst date_created: 2025-01-27T11:42:24Z date_updated: 2025-01-27T11:42:24Z file_id: '18896' file_name: 2024_ICML_Cadei.pdf file_size: 4453014 relation: main_file success: 1 file_date_updated: 2025-01-27T11:42:24Z has_accepted_license: '1' intvolume: ' 38' language: - iso: eng month: '09' oa: 1 oa_version: Published Version publication: ICML 2024 Workshop AI4Science publication_status: published publisher: Curran Associates quality_controlled: '1' related_material: link: - relation: software url: https://github.com/CausalLearningAI/ISTAnt record: - id: '18895' relation: research_data status: public - id: '19509' relation: is_continued_by status: for_moderation scopus_import: '1' status: public title: Smoke and mirrors in causal downstream tasks tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 38 year: '2024' ... --- DOAJ_listed: '1' OA_place: publisher OA_type: gold _id: '18940' abstract: - lang: eng text: BMP signaling has a conserved function in patterning the dorsal-ventral body axis in Bilateria and the directive axis in anthozoan cnidarians. So far, cnidarian studies have focused on the role of different BMP signaling network components in regulating pSMAD1/5 gradient formation. Much less is known about the target genes downstream of BMP signaling. To address this, we generated a genome-wide list of direct pSMAD1/5 target genes in the anthozoan Nematostella vectensis, several of which were conserved in Drosophila and Xenopus. Our ChIP-seq analysis revealed that many of the regulatory molecules with documented bilaterally symmetric expression in Nematostella are directly controlled by BMP signaling. We identified several so far uncharacterized BMP-dependent transcription factors and signaling molecules, whose bilaterally symmetric expression may be indicative of their involvement in secondary axis patterning. One of these molecules is zswim4-6, which encodes a novel nuclear protein that can modulate the pSMAD1/5 gradient and potentially promote BMP-dependent gene repression. acknowledgement: This work was funded by the Austrian Science Foundation (FWF) grants P26962-B21 and P32705-B to GG and by the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (grant agreement No 637840 [QUANTPATTERN] and 863952 [ACE-OF-SPACE]) to PM. We thank Michaela Schwaiger, Taras Kreslavsky, Hiromi Tagoh, and Patricio Ferrer Murguia for their help with the ChIP protocol, Matthias Richter and Christian Hofer for their assistance with in situ analyses, Emilio Gonzalez Morales for making the measurements for Figure 6—figure supplement 3, Catrin Weiler for the assistance in cloning zebrafish zswim5, David Mörsdorf for critically reading the manuscript and help with data visualization, and the Core Facility for Cell Imaging and Ultrastructure Research of the University of Vienna for access to the confocal microscope. article_processing_charge: Yes article_type: original author: - first_name: Paul full_name: Knabl, Paul last_name: Knabl - first_name: Alexandra full_name: Schauer, Alexandra id: 30A536BA-F248-11E8-B48F-1D18A9856A87 last_name: Schauer orcid: 0000-0001-7659-9142 - first_name: Autumn P full_name: Pomreinke, Autumn P last_name: Pomreinke - first_name: Bob full_name: Zimmermann, Bob last_name: Zimmermann - first_name: Katherine W full_name: Rogers, Katherine W last_name: Rogers - first_name: Daniel full_name: Čapek, Daniel last_name: Čapek - first_name: Patrick full_name: Müller, Patrick last_name: Müller - first_name: Grigory full_name: Genikhovich, Grigory last_name: Genikhovich citation: ama: Knabl P, Schauer A, Pomreinke AP, et al. Analysis of SMAD1/5 target genes in a sea anemone reveals ZSWIM4-6 as a novel BMP signaling modulator. eLife. 2024;13. doi:10.7554/elife.80803 apa: Knabl, P., Schauer, A., Pomreinke, A. P., Zimmermann, B., Rogers, K. W., Čapek, D., … Genikhovich, G. (2024). Analysis of SMAD1/5 target genes in a sea anemone reveals ZSWIM4-6 as a novel BMP signaling modulator. ELife. eLife Sciences Publications. https://doi.org/10.7554/elife.80803 chicago: Knabl, Paul, Alexandra Schauer, Autumn P Pomreinke, Bob Zimmermann, Katherine W Rogers, Daniel Čapek, Patrick Müller, and Grigory Genikhovich. “Analysis of SMAD1/5 Target Genes in a Sea Anemone Reveals ZSWIM4-6 as a Novel BMP Signaling Modulator.” ELife. eLife Sciences Publications, 2024. https://doi.org/10.7554/elife.80803. ieee: P. Knabl et al., “Analysis of SMAD1/5 target genes in a sea anemone reveals ZSWIM4-6 as a novel BMP signaling modulator,” eLife, vol. 13. eLife Sciences Publications, 2024. ista: Knabl P, Schauer A, Pomreinke AP, Zimmermann B, Rogers KW, Čapek D, Müller P, Genikhovich G. 2024. Analysis of SMAD1/5 target genes in a sea anemone reveals ZSWIM4-6 as a novel BMP signaling modulator. eLife. 13. mla: Knabl, Paul, et al. “Analysis of SMAD1/5 Target Genes in a Sea Anemone Reveals ZSWIM4-6 as a Novel BMP Signaling Modulator.” ELife, vol. 13, eLife Sciences Publications, 2024, doi:10.7554/elife.80803. short: P. Knabl, A. Schauer, A.P. Pomreinke, B. Zimmermann, K.W. Rogers, D. Čapek, P. Müller, G. Genikhovich, ELife 13 (2024). date_created: 2025-01-29T08:48:34Z date_published: 2024-02-07T00:00:00Z date_updated: 2025-01-29T08:56:21Z day: '07' ddc: - '570' department: - _id: CaHe doi: 10.7554/elife.80803 file: - access_level: open_access checksum: 24548a184215d3f4547bba535ccfd7b1 content_type: application/pdf creator: dernst date_created: 2025-01-29T08:50:18Z date_updated: 2025-01-29T08:50:18Z file_id: '18941' file_name: 2024_eLife_Knabl.pdf file_size: 11855972 relation: main_file success: 1 file_date_updated: 2025-01-29T08:50:18Z has_accepted_license: '1' intvolume: ' 13' language: - iso: eng month: '02' oa: 1 oa_version: Published Version publication: eLife publication_identifier: issn: - 2050-084X publication_status: published publisher: eLife Sciences Publications quality_controlled: '1' scopus_import: '1' status: public title: Analysis of SMAD1/5 target genes in a sea anemone reveals ZSWIM4-6 as a novel BMP signaling modulator tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 13 year: '2024' ... --- DOAJ_listed: '1' OA_place: repository OA_type: gold _id: '18951' abstract: - lang: eng text: "We consider local dynamics of the dimer model (perfect matchings) on hypercubic boxes [n] \r\nd . These consist of successively switching the dimers along alternating cycles of prescribed (small) lengths. We study the connectivity properties of the dimer configuration space equipped with these transitions. Answering a question of Freire, Klivans, Milet, and Saldanha, we show that in three dimensions any configuration admits an alternating cycle of length at most 6. We further establish that any configuration on [n] d features order n d−2 alternating cycles of length at most 4d−2. We also prove that the dynamics of dimer configurations on the unit hypercube of dimension d is ergodic when switching alternating cycles of length at most 4d−4. Finally, in the planar but non-bipartite case, we show that parallelogram-shaped boxes in the triangular lattice are ergodic for switching alternating cycles of lengths 4 and 6 only, thus improving a result of Kenyon and Rémila, which also uses 8-cycles. None of our proofs make reference to height functions." article_processing_charge: Yes article_type: original arxiv: 1 author: - first_name: Ivailo full_name: Hartarsky, Ivailo last_name: Hartarsky - first_name: Lyuben full_name: Lichev, Lyuben id: 9aa8388e-d003-11ee-8458-c4c1d7447977 last_name: Lichev - first_name: Fabio Lucio full_name: Toninelli, Fabio Lucio last_name: Toninelli citation: ama: Hartarsky I, Lichev L, Toninelli FL. Local dimer dynamics in higher dimensions. Annales de l’Institut Henri Poincaré D, Combinatorics, Physics and their Interactions. 2024. doi:10.4171/aihpd/200 apa: Hartarsky, I., Lichev, L., & Toninelli, F. L. (2024). Local dimer dynamics in higher dimensions. Annales de l’Institut Henri Poincaré D, Combinatorics, Physics and Their Interactions. EMS Press. https://doi.org/10.4171/aihpd/200 chicago: Hartarsky, Ivailo, Lyuben Lichev, and Fabio Lucio Toninelli. “Local Dimer Dynamics in Higher Dimensions.” Annales de l’Institut Henri Poincaré D, Combinatorics, Physics and Their Interactions. EMS Press, 2024. https://doi.org/10.4171/aihpd/200. ieee: I. Hartarsky, L. Lichev, and F. L. Toninelli, “Local dimer dynamics in higher dimensions,” Annales de l’Institut Henri Poincaré D, Combinatorics, Physics and their Interactions. EMS Press, 2024. ista: Hartarsky I, Lichev L, Toninelli FL. 2024. Local dimer dynamics in higher dimensions. Annales de l’Institut Henri Poincaré D, Combinatorics, Physics and their Interactions. mla: Hartarsky, Ivailo, et al. “Local Dimer Dynamics in Higher Dimensions.” Annales de l’Institut Henri Poincaré D, Combinatorics, Physics and Their Interactions, EMS Press, 2024, doi:10.4171/aihpd/200. short: I. Hartarsky, L. Lichev, F.L. Toninelli, Annales de l’Institut Henri Poincaré D, Combinatorics, Physics and Their Interactions (2024). date_created: 2025-01-29T10:57:09Z date_published: 2024-08-26T00:00:00Z date_updated: 2025-07-08T08:39:55Z day: '26' department: - _id: MaKw doi: 10.4171/aihpd/200 external_id: arxiv: - '2304.10930' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.48550/arXiv.2304.10930 month: '08' oa: 1 oa_version: Preprint publication: Annales de l’Institut Henri Poincaré D, Combinatorics, Physics and their Interactions publication_identifier: eissn: - 2308-5835 issn: - 2308-5827 publication_status: epub_ahead publisher: EMS Press quality_controlled: '1' scopus_import: '1' status: public title: Local dimer dynamics in higher dimensions type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2024' ... --- OA_place: publisher OA_type: hybrid _id: '18970' abstract: - lang: eng text: Given a smooth projective curve C, nonabelian Hodge theory gives a diffeomorphism between two different moduli spaces associated to C. The first is the moduli space of Higgs bundles on C of rank n, which is equipped with the structure of an algebraic completely integrable Hamiltonian system. The second is the character variety of representations of the fundamental group of C into GL(n). In 2012, de Cataldo, Hausel, and Migliorini [1] proposed the P=W conjecture which identifies the perverse filtration on the cohomology of the Higgs moduli space with the weight filtration on the cohomology of the character variety. Recently, in 2022, two independent proofs of the P=W Conjecture appeared, in work of Maulik &Shen [2] and Hausel, Mellit, Minets &Schiffmann [6]. The aim of the Arbeitsgemeinschaft was to understand the P=W Conjecture and these two recent proofs. acknowledgement: "The MFO and the workshop organizers would like to thank the\r\nNational Science Foundation for supporting the participation of junior researchers\r\nby the grant DMS-2230648, “US Junior Oberwolfach Fellows”. Moreover, the\r\nMFO and the workshop organizers would like to thank the Oberwolfach Foundation for supporting the participation of junior researchers in the Arbeitsgemeinschaft." article_processing_charge: No article_type: original author: - first_name: Tamás full_name: Hausel, Tamás id: 4A0666D8-F248-11E8-B48F-1D18A9856A87 last_name: Hausel orcid: 0000-0002-9582-2634 - first_name: Davesh full_name: Maulik, Davesh last_name: Maulik - first_name: Anton full_name: Mellit, Anton last_name: Mellit - first_name: Olivier full_name: Schiffmann, Olivier last_name: Schiffmann - first_name: Junliang full_name: Shen, Junliang last_name: Shen citation: ama: 'Hausel T, Maulik D, Mellit A, Schiffmann O, Shen J. Arbeitsgemeinschaft: Geometry and representation theory around the P=W conjecture. Oberwolfach Reports. 2024;21(2):949-1004. doi:10.4171/owr/2024/16' apa: 'Hausel, T., Maulik, D., Mellit, A., Schiffmann, O., & Shen, J. (2024). Arbeitsgemeinschaft: Geometry and representation theory around the P=W conjecture. Oberwolfach Reports. EMS Press. https://doi.org/10.4171/owr/2024/16' chicago: 'Hausel, Tamás, Davesh Maulik, Anton Mellit, Olivier Schiffmann, and Junliang Shen. “Arbeitsgemeinschaft: Geometry and Representation Theory around the P=W Conjecture.” Oberwolfach Reports. EMS Press, 2024. https://doi.org/10.4171/owr/2024/16.' ieee: 'T. Hausel, D. Maulik, A. Mellit, O. Schiffmann, and J. Shen, “Arbeitsgemeinschaft: Geometry and representation theory around the P=W conjecture,” Oberwolfach Reports, vol. 21, no. 2. EMS Press, pp. 949–1004, 2024.' ista: 'Hausel T, Maulik D, Mellit A, Schiffmann O, Shen J. 2024. Arbeitsgemeinschaft: Geometry and representation theory around the P=W conjecture. Oberwolfach Reports. 21(2), 949–1004.' mla: 'Hausel, Tamás, et al. “Arbeitsgemeinschaft: Geometry and Representation Theory around the P=W Conjecture.” Oberwolfach Reports, vol. 21, no. 2, EMS Press, 2024, pp. 949–1004, doi:10.4171/owr/2024/16.' short: T. Hausel, D. Maulik, A. Mellit, O. Schiffmann, J. Shen, Oberwolfach Reports 21 (2024) 949–1004. date_created: 2025-01-29T15:34:22Z date_published: 2024-05-05T00:00:00Z date_updated: 2025-01-29T15:39:55Z day: '05' ddc: - '500' department: - _id: TaHa doi: 10.4171/owr/2024/16 has_accepted_license: '1' intvolume: ' 21' issue: '2' language: - iso: eng license: https://creativecommons.org/licenses/by-sa/4.0/ main_file_link: - open_access: '1' url: https://doi.org/10.4171/owr/2024/16 month: '05' oa: 1 oa_version: Published Version page: 949-1004 publication: Oberwolfach Reports publication_identifier: eissn: - 1660-8941 issn: - 1660-8933 publication_status: published publisher: EMS Press quality_controlled: '1' status: public title: 'Arbeitsgemeinschaft: Geometry and representation theory around the P=W conjecture' tmp: image: /images/cc_by_sa.png legal_code_url: https://creativecommons.org/licenses/by-sa/4.0/legalcode name: Creative Commons Attribution-ShareAlike 4.0 International Public License (CC BY-SA 4.0) short: CC BY-SA (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 21 year: '2024' ... --- _id: '14543' abstract: - lang: eng text: The acyl-CoA-binding domain-containing protein 6 (ACBD6) is ubiquitously expressed, plays a role in the acylation of lipids and proteins, and regulates the N-myristoylation of proteins via N-myristoyltransferase enzymes (NMTs). However, its precise function in cells is still unclear, as is the consequence of ACBD6 defects on human pathophysiology. Utilizing exome sequencing and extensive international data sharing efforts, we identified 45 affected individuals from 28 unrelated families (consanguinity 93%) with bi-allelic pathogenic, predominantly loss-of-function (18/20) variants in ACBD6. We generated zebrafish and Xenopus tropicalis acbd6 knockouts by CRISPR/Cas9 and characterized the role of ACBD6 on protein N-myristoylation with YnMyr chemical proteomics in the model organisms and human cells, with the latter also being subjected further to ACBD6 peroxisomal localization studies. The affected individuals (23 males and 22 females), with ages ranging from 1 to 50 years old, typically present with a complex and progressive disease involving moderate-to-severe global developmental delay/intellectual disability (100%) with significant expressive language impairment (98%), movement disorders (97%), facial dysmorphism (95%), and mild cerebellar ataxia (85%) associated with gait impairment (94%), limb spasticity/hypertonia (76%), oculomotor (71%) and behavioural abnormalities (65%), overweight (59%), microcephaly (39%) and epilepsy (33%). The most conspicuous and common movement disorder was dystonia (94%), frequently leading to early-onset progressive postural deformities (97%), limb dystonia (55%), and cervical dystonia (31%). A jerky tremor in the upper limbs (63%), a mild head tremor (59%), parkinsonism/hypokinesia developing with advancing age (32%), and simple motor and vocal tics were among other frequent movement disorders. Midline brain malformations including corpus callosum abnormalities (70%), hypoplasia/agenesis of the anterior commissure (66%), short midbrain and small inferior cerebellar vermis (38% each), as well as hypertrophy of the clava (24%) were common neuroimaging findings. acbd6-deficient zebrafish and Xenopus models effectively recapitulated many clinical phenotypes reported in patients including movement disorders, progressive neuromotor impairment, seizures, microcephaly, craniofacial dysmorphism, and midbrain defects accompanied by developmental delay with increased mortality over time. Unlike ACBD5, ACBD6 did not show a peroxisomal localisation and ACBD6-deficiency was not associated with altered peroxisomal parameters in patient fibroblasts. Significant differences in YnMyr-labelling were observed for 68 co- and 18 post-translationally N-myristoylated proteins in patient-derived fibroblasts. N-Myristoylation was similarly affected in acbd6-deficient zebrafish and Xenopus tropicalis models, including Fus, Marcks, and Chchd-related proteins implicated in neurological diseases. The present study provides evidence that bi-allelic pathogenic variants in ACBD6 lead to a distinct neurodevelopmental syndrome accompanied by complex and progressive cognitive and movement disorders. article_processing_charge: No article_type: original author: - first_name: Rauan full_name: Kaiyrzhanov, Rauan last_name: Kaiyrzhanov - first_name: Aboulfazl full_name: Rad, Aboulfazl last_name: Rad - first_name: Sheng-Jia full_name: Lin, Sheng-Jia last_name: Lin - first_name: Aida full_name: Bertoli-Avella, Aida last_name: Bertoli-Avella - first_name: Wouter W full_name: Kallemeijn, Wouter W last_name: Kallemeijn - first_name: Annie full_name: Godwin, Annie last_name: Godwin - first_name: Maha S full_name: Zaki, Maha S last_name: Zaki - first_name: Kevin full_name: Huang, Kevin id: 3b3d2888-1ff6-11ee-9fa6-8f209ca91fe3 last_name: Huang orcid: 0000-0002-2512-7812 - first_name: Tracy full_name: Lau, Tracy last_name: Lau - first_name: Cassidy full_name: Petree, Cassidy last_name: Petree - first_name: Stephanie full_name: Efthymiou, Stephanie last_name: Efthymiou - first_name: Ehsan full_name: Ghayoor Karimiani, Ehsan last_name: Ghayoor Karimiani - first_name: Maja full_name: Hempel, Maja last_name: Hempel - first_name: Elizabeth A full_name: Normand, Elizabeth A last_name: Normand - first_name: Sabine full_name: Rudnik-Schöneborn, Sabine last_name: Rudnik-Schöneborn - first_name: Ulrich A full_name: Schatz, Ulrich A last_name: Schatz - first_name: Marc P full_name: Baggelaar, Marc P last_name: Baggelaar - first_name: Muhammad full_name: Ilyas, Muhammad last_name: Ilyas - first_name: Tipu full_name: Sultan, Tipu last_name: Sultan - first_name: Javeria Raza full_name: Alvi, Javeria Raza last_name: Alvi - first_name: Manizha full_name: Ganieva, Manizha last_name: Ganieva - first_name: Ben full_name: Fowler, Ben last_name: Fowler - first_name: Ruxandra full_name: Aanicai, Ruxandra last_name: Aanicai - first_name: Gulsen full_name: Akay Tayfun, Gulsen last_name: Akay Tayfun - first_name: Abdulaziz full_name: Al Saman, Abdulaziz last_name: Al Saman - first_name: Abdulrahman full_name: Alswaid, Abdulrahman last_name: Alswaid - first_name: Nafise full_name: Amiri, Nafise last_name: Amiri - first_name: Nilufar full_name: Asilova, Nilufar last_name: Asilova - first_name: Vorasuk full_name: Shotelersuk, Vorasuk last_name: Shotelersuk - first_name: Patra full_name: Yeetong, Patra last_name: Yeetong - first_name: Matloob full_name: Azam, Matloob last_name: Azam - first_name: Meisam full_name: Babaei, Meisam last_name: Babaei - first_name: Gholamreza full_name: Bahrami Monajemi, Gholamreza last_name: Bahrami Monajemi - first_name: Pouria full_name: Mohammadi, Pouria last_name: Mohammadi - first_name: Saeed full_name: Samie, Saeed last_name: Samie - first_name: Selina Husna full_name: Banu, Selina Husna last_name: Banu - first_name: Jorge Pinto full_name: Basto, Jorge Pinto last_name: Basto - first_name: Fanny full_name: Kortüm, Fanny last_name: Kortüm - first_name: Mislen full_name: Bauer, Mislen last_name: Bauer - first_name: Peter full_name: Bauer, Peter last_name: Bauer - first_name: Christian full_name: Beetz, Christian last_name: Beetz - first_name: Masoud full_name: Garshasbi, Masoud last_name: Garshasbi - first_name: Awatif full_name: Hameed Issa, Awatif last_name: Hameed Issa - first_name: Wafaa full_name: Eyaid, Wafaa last_name: Eyaid - first_name: Hind full_name: Ahmed, Hind last_name: Ahmed - first_name: Narges full_name: Hashemi, Narges last_name: Hashemi - first_name: Kazem full_name: Hassanpour, Kazem last_name: Hassanpour - first_name: Isabella full_name: Herman, Isabella last_name: Herman - first_name: Sherozjon full_name: Ibrohimov, Sherozjon last_name: Ibrohimov - first_name: Ban A full_name: Abdul-Majeed, Ban A last_name: Abdul-Majeed - first_name: Maria full_name: Imdad, Maria last_name: Imdad - first_name: Maksudjon full_name: Isrofilov, Maksudjon last_name: Isrofilov - first_name: Qassem full_name: Kaiyal, Qassem last_name: Kaiyal - first_name: Suliman full_name: Khan, Suliman last_name: Khan - first_name: Brian full_name: Kirmse, Brian last_name: Kirmse - first_name: Janet full_name: Koster, Janet last_name: Koster - first_name: Charles Marques full_name: Lourenço, Charles Marques last_name: Lourenço - first_name: Tadahiro full_name: Mitani, Tadahiro last_name: Mitani - first_name: Oana full_name: Moldovan, Oana last_name: Moldovan - first_name: David full_name: Murphy, David last_name: Murphy - first_name: Maryam full_name: Najafi, Maryam last_name: Najafi - first_name: Davut full_name: Pehlivan, Davut last_name: Pehlivan - first_name: Maria Eugenia full_name: Rocha, Maria Eugenia last_name: Rocha - first_name: Vincenzo full_name: Salpietro, Vincenzo last_name: Salpietro - first_name: Miriam full_name: Schmidts, Miriam last_name: Schmidts - first_name: Adel full_name: Shalata, Adel last_name: Shalata - first_name: Mohammad full_name: Mahroum, Mohammad last_name: Mahroum - first_name: Jawabreh Kassem full_name: Talbeya, Jawabreh Kassem last_name: Talbeya - first_name: Robert W full_name: Taylor, Robert W last_name: Taylor - first_name: Dayana full_name: Vazquez, Dayana last_name: Vazquez - first_name: Annalisa full_name: Vetro, Annalisa last_name: Vetro - first_name: Hans R full_name: Waterham, Hans R last_name: Waterham - first_name: Mashaya full_name: Zaman, Mashaya last_name: Zaman - first_name: Tina A full_name: Schrader, Tina A last_name: Schrader - first_name: Wendy K full_name: Chung, Wendy K last_name: Chung - first_name: Renzo full_name: Guerrini, Renzo last_name: Guerrini - first_name: James R full_name: Lupski, James R last_name: Lupski - first_name: Joseph full_name: Gleeson, Joseph last_name: Gleeson - first_name: Mohnish full_name: Suri, Mohnish last_name: Suri - first_name: Yalda full_name: Jamshidi, Yalda last_name: Jamshidi - first_name: Kailash P full_name: Bhatia, Kailash P last_name: Bhatia - first_name: Barbara full_name: Vona, Barbara last_name: Vona - first_name: Michael full_name: Schrader, Michael last_name: Schrader - first_name: Mariasavina full_name: Severino, Mariasavina last_name: Severino - first_name: Matthew full_name: Guille, Matthew last_name: Guille - first_name: Edward W full_name: Tate, Edward W last_name: Tate - first_name: Gaurav K full_name: Varshney, Gaurav K last_name: Varshney - first_name: Henry full_name: Houlden, Henry last_name: Houlden - first_name: Reza full_name: Maroofian, Reza last_name: Maroofian citation: ama: Kaiyrzhanov R, Rad A, Lin S-J, et al. Bi-allelic ACBD6 variants lead to a neurodevelopmental syndrome with progressive and complex movement disorders. Brain. 2024;147(4):1436-1456. doi:10.1093/brain/awad380 apa: Kaiyrzhanov, R., Rad, A., Lin, S.-J., Bertoli-Avella, A., Kallemeijn, W. W., Godwin, A., … Maroofian, R. (2024). Bi-allelic ACBD6 variants lead to a neurodevelopmental syndrome with progressive and complex movement disorders. Brain. Oxford University Press. https://doi.org/10.1093/brain/awad380 chicago: Kaiyrzhanov, Rauan, Aboulfazl Rad, Sheng-Jia Lin, Aida Bertoli-Avella, Wouter W Kallemeijn, Annie Godwin, Maha S Zaki, et al. “Bi-Allelic ACBD6 Variants Lead to a Neurodevelopmental Syndrome with Progressive and Complex Movement Disorders.” Brain. Oxford University Press, 2024. https://doi.org/10.1093/brain/awad380. ieee: R. Kaiyrzhanov et al., “Bi-allelic ACBD6 variants lead to a neurodevelopmental syndrome with progressive and complex movement disorders,” Brain, vol. 147, no. 4. Oxford University Press, pp. 1436–1456, 2024. ista: Kaiyrzhanov R, Rad A, Lin S-J, Bertoli-Avella A, Kallemeijn WW, Godwin A, Zaki MS, Huang K, Lau T, Petree C, Efthymiou S, Ghayoor Karimiani E, Hempel M, Normand EA, Rudnik-Schöneborn S, Schatz UA, Baggelaar MP, Ilyas M, Sultan T, Alvi JR, Ganieva M, Fowler B, Aanicai R, Akay Tayfun G, Al Saman A, Alswaid A, Amiri N, Asilova N, Shotelersuk V, Yeetong P, Azam M, Babaei M, Bahrami Monajemi G, Mohammadi P, Samie S, Banu SH, Basto JP, Kortüm F, Bauer M, Bauer P, Beetz C, Garshasbi M, Hameed Issa A, Eyaid W, Ahmed H, Hashemi N, Hassanpour K, Herman I, Ibrohimov S, Abdul-Majeed BA, Imdad M, Isrofilov M, Kaiyal Q, Khan S, Kirmse B, Koster J, Lourenço CM, Mitani T, Moldovan O, Murphy D, Najafi M, Pehlivan D, Rocha ME, Salpietro V, Schmidts M, Shalata A, Mahroum M, Talbeya JK, Taylor RW, Vazquez D, Vetro A, Waterham HR, Zaman M, Schrader TA, Chung WK, Guerrini R, Lupski JR, Gleeson J, Suri M, Jamshidi Y, Bhatia KP, Vona B, Schrader M, Severino M, Guille M, Tate EW, Varshney GK, Houlden H, Maroofian R. 2024. Bi-allelic ACBD6 variants lead to a neurodevelopmental syndrome with progressive and complex movement disorders. Brain. 147(4), 1436–1456. mla: Kaiyrzhanov, Rauan, et al. “Bi-Allelic ACBD6 Variants Lead to a Neurodevelopmental Syndrome with Progressive and Complex Movement Disorders.” Brain, vol. 147, no. 4, Oxford University Press, 2024, pp. 1436–56, doi:10.1093/brain/awad380. short: R. Kaiyrzhanov, A. Rad, S.-J. Lin, A. Bertoli-Avella, W.W. Kallemeijn, A. Godwin, M.S. Zaki, K. Huang, T. Lau, C. Petree, S. Efthymiou, E. Ghayoor Karimiani, M. Hempel, E.A. Normand, S. Rudnik-Schöneborn, U.A. Schatz, M.P. Baggelaar, M. Ilyas, T. Sultan, J.R. Alvi, M. Ganieva, B. Fowler, R. Aanicai, G. Akay Tayfun, A. Al Saman, A. Alswaid, N. Amiri, N. Asilova, V. Shotelersuk, P. Yeetong, M. Azam, M. Babaei, G. Bahrami Monajemi, P. Mohammadi, S. Samie, S.H. Banu, J.P. Basto, F. Kortüm, M. Bauer, P. Bauer, C. Beetz, M. Garshasbi, A. Hameed Issa, W. Eyaid, H. Ahmed, N. Hashemi, K. Hassanpour, I. Herman, S. Ibrohimov, B.A. Abdul-Majeed, M. Imdad, M. Isrofilov, Q. Kaiyal, S. Khan, B. Kirmse, J. Koster, C.M. Lourenço, T. Mitani, O. Moldovan, D. Murphy, M. Najafi, D. Pehlivan, M.E. Rocha, V. Salpietro, M. Schmidts, A. Shalata, M. Mahroum, J.K. Talbeya, R.W. Taylor, D. Vazquez, A. Vetro, H.R. Waterham, M. Zaman, T.A. Schrader, W.K. Chung, R. Guerrini, J.R. Lupski, J. Gleeson, M. Suri, Y. Jamshidi, K.P. Bhatia, B. Vona, M. Schrader, M. Severino, M. Guille, E.W. Tate, G.K. Varshney, H. Houlden, R. Maroofian, Brain 147 (2024) 1436–1456. date_created: 2023-11-16T12:36:51Z date_published: 2024-04-01T00:00:00Z date_updated: 2024-07-16T08:23:24Z day: '01' ddc: - '570' department: - _id: GradSch doi: 10.1093/brain/awad380 extern: '1' external_id: pmid: - '37951597' file: - access_level: open_access checksum: 0ee7a8ab9300225d60968f7a3e3cfa0d content_type: application/pdf creator: dernst date_created: 2024-07-16T08:22:13Z date_updated: 2024-07-16T08:22:13Z file_id: '17254' file_name: 2024_Brain_Kaiyrzhanov.pdf file_size: 2641456 relation: main_file success: 1 file_date_updated: 2024-07-16T08:22:13Z has_accepted_license: '1' intvolume: ' 147' issue: '4' keyword: - Neurology (clinical) language: - iso: eng month: '04' oa: 1 oa_version: Submitted Version page: 1436-1456 pmid: 1 publication: Brain publication_identifier: eissn: - 1460-2156 issn: - 0006-8950 publication_status: published publisher: Oxford University Press quality_controlled: '1' scopus_import: '1' status: public title: Bi-allelic ACBD6 variants lead to a neurodevelopmental syndrome with progressive and complex movement disorders tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 147 year: '2024' ... --- _id: '14828' abstract: - lang: eng text: Production of hydrogen at large scale requires development of non-noble, inexpensive, and high-performing catalysts for constructing water-splitting devices. Herein, we report the synthesis of Zn-doped NiO heterostructure (ZnNiO) catalysts at room temperature via a coprecipitation method followed by drying (at 80 °C, 6 h) and calcination at an elevated temperature of 400 °C for 5 h under three distinct conditions, namely, air, N2, and vacuum. The vacuum-synthesized catalyst demonstrates a low overpotential of 88 mV at −10 mA cm–2 and a small Tafel slope of 73 mV dec–1 suggesting relatively higher charge transfer kinetics for hydrogen evolution reactions (HER) compared with the specimens synthesized under N2 or O2 atmosphere. It also demonstrates an oxygen evolution (OER) overpotential of 260 mV at 10 mA cm–2 with a low Tafel slope of 63 mV dec–1. In a full-cell water-splitting device, the vacuum-synthesized ZnNiO heterostructure demonstrates a cell voltage of 1.94 V at 50 mA cm–2 and shows remarkable stability over 24 h at a high current density of 100 mA cm–2. It is also demonstrated in this study that Zn-doping, surface, and interface engineering in transition-metal oxides play a crucial role in efficient electrocatalytic water splitting. Also, the results obtained from density functional theory (DFT + U = 0–8 eV), where U is the on-site Coulomb repulsion parameter also known as Hubbard U, based electronic structure calculations confirm that Zn doping constructively modifies the electronic structure, in both the valence band and the conduction band, and found to be suitable in tailoring the carrier’s effective masses of electrons and holes. The decrease in electron’s effective masses together with large differences between the effective masses of electrons and holes is noticed, which is found to be mainly responsible for achieving the best water-splitting performance from a 9% Zn-doped NiO sample prepared under vacuum. acknowledgement: This work was supported by the Technology Innovation Program (20011622, Development of Battery System Applied High-Efficiency Heat Control Polymer and Part Component) funded by the Ministry of Trade, Industry & Energy (MOTIE, Korea). Author acknowledge to Prof. Tsunehiro Takeuchi from Toyota Technological Institute, Nagoya, Japan for the support of computational resources. article_processing_charge: No article_type: original author: - first_name: Gundegowda Kalligowdanadoddi full_name: Kiran, Gundegowda Kalligowdanadoddi last_name: Kiran - first_name: Saurabh full_name: Singh, Saurabh id: 12d625da-9cb3-11ed-9667-af09d37d3f0a last_name: Singh orcid: 0000-0003-2209-5269 - first_name: Neelima full_name: Mahato, Neelima last_name: Mahato - first_name: Thupakula Venkata Madhukar full_name: Sreekanth, Thupakula Venkata Madhukar last_name: Sreekanth - first_name: Gowra Raghupathy full_name: Dillip, Gowra Raghupathy last_name: Dillip - first_name: Kisoo full_name: Yoo, Kisoo last_name: Yoo - first_name: Jonghoon full_name: Kim, Jonghoon last_name: Kim citation: ama: Kiran GK, Singh S, Mahato N, et al. Interface engineering modulation combined with electronic structure modification of Zn-doped NiO heterostructure for efficient water-splitting activity. ACS Applied Energy Materials. 2024;7(1):214-229. doi:10.1021/acsaem.3c02519 apa: Kiran, G. K., Singh, S., Mahato, N., Sreekanth, T. V. M., Dillip, G. R., Yoo, K., & Kim, J. (2024). Interface engineering modulation combined with electronic structure modification of Zn-doped NiO heterostructure for efficient water-splitting activity. ACS Applied Energy Materials. American Chemical Society. https://doi.org/10.1021/acsaem.3c02519 chicago: Kiran, Gundegowda Kalligowdanadoddi, Saurabh Singh, Neelima Mahato, Thupakula Venkata Madhukar Sreekanth, Gowra Raghupathy Dillip, Kisoo Yoo, and Jonghoon Kim. “Interface Engineering Modulation Combined with Electronic Structure Modification of Zn-Doped NiO Heterostructure for Efficient Water-Splitting Activity.” ACS Applied Energy Materials. American Chemical Society, 2024. https://doi.org/10.1021/acsaem.3c02519. ieee: G. K. Kiran et al., “Interface engineering modulation combined with electronic structure modification of Zn-doped NiO heterostructure for efficient water-splitting activity,” ACS Applied Energy Materials, vol. 7, no. 1. American Chemical Society, pp. 214–229, 2024. ista: Kiran GK, Singh S, Mahato N, Sreekanth TVM, Dillip GR, Yoo K, Kim J. 2024. Interface engineering modulation combined with electronic structure modification of Zn-doped NiO heterostructure for efficient water-splitting activity. ACS Applied Energy Materials. 7(1), 214–229. mla: Kiran, Gundegowda Kalligowdanadoddi, et al. “Interface Engineering Modulation Combined with Electronic Structure Modification of Zn-Doped NiO Heterostructure for Efficient Water-Splitting Activity.” ACS Applied Energy Materials, vol. 7, no. 1, American Chemical Society, 2024, pp. 214–29, doi:10.1021/acsaem.3c02519. short: G.K. Kiran, S. Singh, N. Mahato, T.V.M. Sreekanth, G.R. Dillip, K. Yoo, J. Kim, ACS Applied Energy Materials 7 (2024) 214–229. corr_author: '1' date_created: 2024-01-17T12:48:35Z date_published: 2024-01-08T00:00:00Z date_updated: 2024-10-09T21:07:53Z day: '08' department: - _id: MaIb doi: 10.1021/acsaem.3c02519 external_id: isi: - '001138342900001' intvolume: ' 7' isi: 1 issue: '1' keyword: - Electrical and Electronic Engineering - Materials Chemistry - Electrochemistry - Energy Engineering and Power Technology - Chemical Engineering (miscellaneous) language: - iso: eng month: '01' oa_version: None page: 214-229 publication: ACS Applied Energy Materials publication_identifier: issn: - 2574-0962 publication_status: published publisher: American Chemical Society quality_controlled: '1' scopus_import: '1' status: public title: Interface engineering modulation combined with electronic structure modification of Zn-doped NiO heterostructure for efficient water-splitting activity type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 7 year: '2024' ... --- OA_place: publisher OA_type: hybrid _id: '14841' abstract: - lang: eng text: De novo heterozygous variants in KCNC2 encoding the voltage-gated potassium (K+) channel subunit Kv3.2 are a recently described cause of developmental and epileptic encephalopathy (DEE). A de novo variant in KCNC2 c.374G > A (p.Cys125Tyr) was identified via exome sequencing in a patient with DEE. Relative to wild-type Kv3.2, Kv3.2-p.Cys125Tyr induces K+ currents exhibiting a large hyperpolarizing shift in the voltage dependence of activation, accelerated activation, and delayed deactivation consistent with a relative stabilization of the open conformation, along with increased current density. Leveraging the cryogenic electron microscopy (cryo-EM) structure of Kv3.1, molecular dynamic simulations suggest that a strong π-π stacking interaction between the variant Tyr125 and Tyr156 in the α-6 helix of the T1 domain promotes a relative stabilization of the open conformation of the channel, which underlies the observed gain of function. A multicompartment computational model of a Kv3-expressing parvalbumin-positive cerebral cortex fast-spiking γ-aminobutyric acidergic (GABAergic) interneuron (PV-IN) demonstrates how the Kv3.2-Cys125Tyr variant impairs neuronal excitability and dysregulates inhibition in cerebral cortex circuits to explain the resulting epilepsy. acknowledgement: This work was supported by an ERC Consolidator Grant (SYNAPSEEK) to T.P.V., the NOMIS Foundation through the NOMIS Fellowships program at IST Austria to C.B.C., a Jefferson Synaptic Biology Center Pilot Project Grant to M.C., NIH NINDS U54 NS108874 (PI, Alfred L. George), and NIH NINDS R01 NS122887 to E.M.G. The computations were enabled by resources provided by the Swedish National Infrastructure for Computing (SNIC) at the PDC Center for High-Performance Computing, KTH Royal Institute of Technology, partially funded by the Swedish Research Council through grant agreement no. 2018-05973. We thank Akshay Sridhar for the fruitful discussion of the project. article_number: e2307776121 article_processing_charge: Yes (in subscription journal) article_type: original author: - first_name: Jerome full_name: Clatot, Jerome last_name: Clatot - first_name: Christopher full_name: Currin, Christopher id: e8321fc5-3091-11eb-8a53-83f309a11ac9 last_name: Currin orcid: 0000-0002-4809-5059 - first_name: Qiansheng full_name: Liang, Qiansheng last_name: Liang - first_name: Tanadet full_name: Pipatpolkai, Tanadet last_name: Pipatpolkai - first_name: Shavonne L. full_name: Massey, Shavonne L. last_name: Massey - first_name: Ingo full_name: Helbig, Ingo last_name: Helbig - first_name: Lucie full_name: Delemotte, Lucie last_name: Delemotte - first_name: Tim P full_name: Vogels, Tim P id: CB6FF8D2-008F-11EA-8E08-2637E6697425 last_name: Vogels orcid: 0000-0003-3295-6181 - first_name: Manuel full_name: Covarrubias, Manuel last_name: Covarrubias - first_name: Ethan M. full_name: Goldberg, Ethan M. last_name: Goldberg citation: ama: Clatot J, Currin C, Liang Q, et al. A structurally precise mechanism links an epilepsy-associated KCNC2 potassium channel mutation to interneuron dysfunction. Proceedings of the National Academy of Sciences of the United States of America. 2024;121(3). doi:10.1073/pnas.2307776121 apa: Clatot, J., Currin, C., Liang, Q., Pipatpolkai, T., Massey, S. L., Helbig, I., … Goldberg, E. M. (2024). A structurally precise mechanism links an epilepsy-associated KCNC2 potassium channel mutation to interneuron dysfunction. Proceedings of the National Academy of Sciences of the United States of America. National Academy of Sciences. https://doi.org/10.1073/pnas.2307776121 chicago: Clatot, Jerome, Christopher Currin, Qiansheng Liang, Tanadet Pipatpolkai, Shavonne L. Massey, Ingo Helbig, Lucie Delemotte, Tim P Vogels, Manuel Covarrubias, and Ethan M. Goldberg. “A Structurally Precise Mechanism Links an Epilepsy-Associated KCNC2 Potassium Channel Mutation to Interneuron Dysfunction.” Proceedings of the National Academy of Sciences of the United States of America. National Academy of Sciences, 2024. https://doi.org/10.1073/pnas.2307776121. ieee: J. Clatot et al., “A structurally precise mechanism links an epilepsy-associated KCNC2 potassium channel mutation to interneuron dysfunction,” Proceedings of the National Academy of Sciences of the United States of America, vol. 121, no. 3. National Academy of Sciences, 2024. ista: Clatot J, Currin C, Liang Q, Pipatpolkai T, Massey SL, Helbig I, Delemotte L, Vogels TP, Covarrubias M, Goldberg EM. 2024. A structurally precise mechanism links an epilepsy-associated KCNC2 potassium channel mutation to interneuron dysfunction. Proceedings of the National Academy of Sciences of the United States of America. 121(3), e2307776121. mla: Clatot, Jerome, et al. “A Structurally Precise Mechanism Links an Epilepsy-Associated KCNC2 Potassium Channel Mutation to Interneuron Dysfunction.” Proceedings of the National Academy of Sciences of the United States of America, vol. 121, no. 3, e2307776121, National Academy of Sciences, 2024, doi:10.1073/pnas.2307776121. short: J. Clatot, C. Currin, Q. Liang, T. Pipatpolkai, S.L. Massey, I. Helbig, L. Delemotte, T.P. Vogels, M. Covarrubias, E.M. Goldberg, Proceedings of the National Academy of Sciences of the United States of America 121 (2024). date_created: 2024-01-21T23:00:56Z date_published: 2024-01-16T00:00:00Z date_updated: 2025-09-04T11:47:47Z day: '16' ddc: - '570' department: - _id: TiVo doi: 10.1073/pnas.2307776121 ec_funded: 1 external_id: isi: - '001167401000001' pmid: - '38194456' file: - access_level: open_access checksum: f498c643be81895dd3a69ee90115a782 content_type: application/pdf creator: dernst date_created: 2025-04-23T13:51:16Z date_updated: 2025-04-23T13:51:16Z file_id: '19613' file_name: 2024_PNAS_Clatot.pdf file_size: 3060109 relation: main_file success: 1 file_date_updated: 2025-04-23T13:51:16Z has_accepted_license: '1' intvolume: ' 121' isi: 1 issue: '3' language: - iso: eng month: '01' oa: 1 oa_version: Published Version pmid: 1 project: - _id: 0aacfa84-070f-11eb-9043-d7eb2c709234 call_identifier: H2020 grant_number: '819603' name: Learning the shape of synaptic plasticity rules for neuronal architectures and function through machine learning. publication: Proceedings of the National Academy of Sciences of the United States of America publication_identifier: eissn: - 1091-6490 publication_status: published publisher: National Academy of Sciences quality_controlled: '1' related_material: link: - relation: software url: 'https://github.com/ChrisCurrin/pv-kcnc2 ' scopus_import: '1' status: public title: A structurally precise mechanism links an epilepsy-associated KCNC2 potassium channel mutation to interneuron dysfunction 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: 317138e5-6ab7-11ef-aa6d-ffef3953e345 volume: 121 year: '2024' ... --- _id: '14933' abstract: - lang: eng text: Centrioles are part of centrosomes and cilia, which are microtubule organising centres (MTOC) with diverse functions. Despite their stability, centrioles can disappear during differentiation, such as in oocytes, but little is known about the regulation of their structural integrity. Our previous research revealed that the pericentriolar material (PCM) that surrounds centrioles and its recruiter, Polo kinase, are downregulated in oogenesis and sufficient for maintaining both centrosome structural integrity and MTOC activity. We now show that the expression of specific components of the centriole cartwheel and wall, including ANA1/CEP295, is essential for maintaining centrosome integrity. We find that Polo kinase requires ANA1 to promote centriole stability in cultured cells and eggs. In addition, ANA1 expression prevents the loss of centrioles observed upon PCM-downregulation. However, the centrioles maintained by overexpressing and tethering ANA1 are inactive, unlike the MTOCs observed upon tethering Polo kinase. These findings demonstrate that several centriole components are needed to maintain centrosome structure. Our study also highlights that centrioles are more dynamic than previously believed, with their structural stability relying on the continuous expression of multiple components. acknowledgement: We thank all members of the Cell Cycle and Regulation Lab for the discussions and for the critical reading of the manuscript. We thank Tomer Avidor-Reiss (University of Toledo, Toledo, OH), Daniel St. Johnston (The Gurdon Institute, Cambridge, UK), David Glover (University of Cambridge, Cambridge, UK), Jingyan Fu (Agricultural University, Beijing, China) Jordan Raff (University of Oxford, Oxford, UK) and Timothy Megraw (Florida State University, Tallahassee, FL) for sharing tools. We acknowledge the technical support of Instituto Gulbenkian de Ciência (IGC)‘s Advanced Imaging Facility, in particular Gabriel Martins, Nuno Pimpão Martins and José Marques. We also thank Tiago Paixão from the IGC’s Quantitative & Digital Science Unit and Marco Louro from the CCR lab for the support provided on statistical analysis. IGC’s Advanced Imaging Facility (AIF-UIC) is supported by the national Portuguese funding ref# PPBI-POCI-01-0145-FEDER -022122. We thank the IGC’s Fly Facility, supported by CONGENTO (LISBOA-01-0145-FEDER-022170). This work was supported by an ERC grant (ERC-2015-CoG-683258) awarded to MBD and a grant from the Portuguese Research Council (FCT) awarded to APM (PTDC/BIA-BID/32225/2017). article_processing_charge: Yes (in subscription journal) article_type: original author: - first_name: Ana full_name: Pimenta-Marques, Ana last_name: Pimenta-Marques - first_name: Tania full_name: Perestrelo, Tania last_name: Perestrelo - first_name: Patricia full_name: Dos Reis Rodrigues, Patricia id: 26E95904-5160-11E9-9C0B-C5B0DC97E90F last_name: Dos Reis Rodrigues orcid: 0000-0003-1681-508X - first_name: Paulo full_name: Duarte, Paulo last_name: Duarte - first_name: Ana full_name: Ferreira-Silva, Ana last_name: Ferreira-Silva - first_name: Mariana full_name: Lince-Faria, Mariana last_name: Lince-Faria - first_name: Mónica full_name: Bettencourt-Dias, Mónica last_name: Bettencourt-Dias citation: ama: Pimenta-Marques A, Perestrelo T, Dos Reis Rodrigues P, et al. Ana1/CEP295 is an essential player in the centrosome maintenance program regulated by Polo kinase and the PCM. EMBO Reports. 2024;25(1):102-127. doi:10.1038/s44319-023-00020-6 apa: Pimenta-Marques, A., Perestrelo, T., Dos Reis Rodrigues, P., Duarte, P., Ferreira-Silva, A., Lince-Faria, M., & Bettencourt-Dias, M. (2024). Ana1/CEP295 is an essential player in the centrosome maintenance program regulated by Polo kinase and the PCM. EMBO Reports. Embo Press. https://doi.org/10.1038/s44319-023-00020-6 chicago: Pimenta-Marques, Ana, Tania Perestrelo, Patricia Dos Reis Rodrigues, Paulo Duarte, Ana Ferreira-Silva, Mariana Lince-Faria, and Mónica Bettencourt-Dias. “Ana1/CEP295 Is an Essential Player in the Centrosome Maintenance Program Regulated by Polo Kinase and the PCM.” EMBO Reports. Embo Press, 2024. https://doi.org/10.1038/s44319-023-00020-6. ieee: A. Pimenta-Marques et al., “Ana1/CEP295 is an essential player in the centrosome maintenance program regulated by Polo kinase and the PCM,” EMBO Reports, vol. 25, no. 1. Embo Press, pp. 102–127, 2024. ista: Pimenta-Marques A, Perestrelo T, Dos Reis Rodrigues P, Duarte P, Ferreira-Silva A, Lince-Faria M, Bettencourt-Dias M. 2024. Ana1/CEP295 is an essential player in the centrosome maintenance program regulated by Polo kinase and the PCM. EMBO Reports. 25(1), 102–127. mla: Pimenta-Marques, Ana, et al. “Ana1/CEP295 Is an Essential Player in the Centrosome Maintenance Program Regulated by Polo Kinase and the PCM.” EMBO Reports, vol. 25, no. 1, Embo Press, 2024, pp. 102–27, doi:10.1038/s44319-023-00020-6. short: A. Pimenta-Marques, T. Perestrelo, P. Dos Reis Rodrigues, P. Duarte, A. Ferreira-Silva, M. Lince-Faria, M. Bettencourt-Dias, EMBO Reports 25 (2024) 102–127. date_created: 2024-02-04T23:00:53Z date_published: 2024-01-10T00:00:00Z date_updated: 2025-04-23T07:39:52Z day: '10' ddc: - '570' department: - _id: MiSi doi: 10.1038/s44319-023-00020-6 external_id: pmid: - '38200359' file: - access_level: open_access checksum: 53c3ef43d9bd6d7bff3ffcf57d763cac content_type: application/pdf creator: dernst date_created: 2024-02-05T12:35:03Z date_updated: 2024-02-05T12:35:03Z file_id: '14941' file_name: 2023_EmboReports_PimentaMarques.pdf file_size: 9645056 relation: main_file success: 1 file_date_updated: 2024-02-05T12:35:03Z has_accepted_license: '1' intvolume: ' 25' issue: '1' language: - iso: eng month: '01' oa: 1 oa_version: Published Version page: 102-127 pmid: 1 publication: EMBO Reports publication_identifier: eissn: - 1469-3178 publication_status: published publisher: Embo Press quality_controlled: '1' scopus_import: '1' status: public title: Ana1/CEP295 is an essential player in the centrosome maintenance program regulated by Polo kinase and the PCM tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 25 year: '2024' ... --- _id: '14938' abstract: - lang: eng text: High elevation headwater catchments are complex hydrological systems that seasonally buffer water and release it in the form of snow and ice melt, modulating downstream runoff regimes and water availability. In High Mountain Asia (HMA), where a wide range of climates from semi-arid to monsoonal exist, the importance of the cryospheric contributions to the water budget varies with the amount and seasonal distribution of precipitation. Losses due to evapotranspiration and sublimation are to date largely unquantified components of the water budget in such catchments, although they can be comparable in magnitude to glacier melt contributions to streamflow. &#xD;Here, we simulate the hydrology of three high elevation headwater catchments in distinct climates in HMA over 10 years using an ecohydrological model geared towards high-mountain areas including snow and glaciers, forced with reanalysis data. &#xD;Our results show that evapotranspiration and sublimation together are most important at the semi-arid site, Kyzylsu, on the northernmost slopes of the Pamir mountain range. Here, the evaporative loss amounts to 28% of the water throughput, which we define as the total water added to, or removed from the water balance within a year. In comparison, evaporative losses are 19% at the Central Himalayan site Langtang and 13% at the wettest site, 24K, on the Southeastern Tibetan Plateau. At the three sites, respectively, sublimation removes 15%, 13% and 6% of snowfall, while evapotranspiration removes the equivalent of 76%, 28% and 19% of rainfall. In absolute terms, and across a comparable elevation range, the highest ET flux is 413 mm yr-1 at 24K, while the highest sublimation flux is 91 mm yr-1 at Kyzylsu. During warm and dry years, glacier melt was found to only partially compensate for the annual supply deficit. acknowledgement: "We would like to thank the team at the Center for the Research of Glaciers, Tajik National Academy of Sciences, Abduhamid Kayumov, Khusrav Kabutov, Ardamehr Halimov, among others, for their invaluable support over multiple field seasons in Kyzylsu. We thank Wei Yang, Zhao Xhuanxi and Zhen Cheng from the Institute of Tibetan Plateau Research, Chinese Academy of Sciences, for facilitating and supporting fieldwork and for sharing crucial data from the Parlung 24K catchment. We thank Reeju Shrestha and Himalayan Research Expeditions for their great support in Langtang. We extend our thanks to Jakob Steiner and the team at ICIMOD for their relentless efforts in data acquisition and curation in Langtang. Additionally, we are indebted to Masashi Niwano from the Meteorological Research Institute, Japan Meteorological Agency, for providing NHM atmospheric simulation outputs, which proved very valuable in the downscaling process.\r\nThis project has received funding from the European Research Council (ERC) under the European Union's Horizon 2020 research and innovation program Grant Agreements No. 772751 (RAVEN, Rapid mass losses of debris-covered glaciers in High Mountain Asia). Further funding was provided by JSPS-SNSF (Japan Society for the Promotion of Science and Swiss National Science Foundation) Bilateral Programmes project (HOPE, High-elevation precipitation in High Mountain Asia; Grant 183633). Fieldwork support for Tajikistan was received from the Swiss Polar Institute Flagship Programme PAMIR, SPI-FLAG-2021-001. The project also received funding from the ESA and NRSCC Dragon 5 cooperation project 'Cryosphere-hydrosphere interactions of the Asian water towers: using remote sensing to drive hyper-resolution ecohydrological modeling' (grant no. 59199). The National Natural Science Foundation of China (41961134035) financially supported the data collection at 24K." article_number: '044057' article_processing_charge: Yes article_type: original author: - first_name: Stefan full_name: Fugger, Stefan id: 86698d64-c4c6-11ee-af02-cdf1e6a7d31f last_name: Fugger - first_name: Thomas full_name: Shaw, Thomas id: 3caa3f91-1f03-11ee-96ce-e0e553054d6e last_name: Shaw orcid: 0000-0001-7640-6152 - first_name: Achille full_name: Jouberton, Achille last_name: Jouberton - first_name: Evan full_name: Miles, Evan last_name: Miles - first_name: Pascal full_name: Buri, Pascal id: 317987aa-9421-11ee-ac5a-b941b041abba last_name: Buri - first_name: Michael full_name: McCarthy, Michael id: 22a2674a-61ce-11ee-94b5-d18813baf16f last_name: McCarthy - first_name: Catriona Louise full_name: Fyffe, Catriona Louise id: 001b0422-8d15-11ed-bc51-cab6c037a228 last_name: Fyffe - first_name: Simone full_name: Fatichi, Simone last_name: Fatichi - first_name: Marin full_name: Kneib, Marin last_name: Kneib - first_name: Peter full_name: Molnar, Peter last_name: Molnar - first_name: Francesca full_name: Pellicciotti, Francesca id: b28f055a-81ea-11ed-b70c-a9fe7f7b0e70 last_name: Pellicciotti orcid: 0000-0002-5554-8087 citation: ama: Fugger S, Shaw T, Jouberton A, et al. Hydrological regimes and evaporative flux partitioning at the climatic ends of High Mountain Asia. Environmental Research Letters. 2024;19. doi:10.1088/1748-9326/ad25a0 apa: Fugger, S., Shaw, T., Jouberton, A., Miles, E., Buri, P., McCarthy, M., … Pellicciotti, F. (2024). Hydrological regimes and evaporative flux partitioning at the climatic ends of High Mountain Asia. Environmental Research Letters. IOP Publishing. https://doi.org/10.1088/1748-9326/ad25a0 chicago: Fugger, Stefan, Thomas Shaw, Achille Jouberton, Evan Miles, Pascal Buri, Michael McCarthy, Catriona Louise Fyffe, et al. “Hydrological Regimes and Evaporative Flux Partitioning at the Climatic Ends of High Mountain Asia.” Environmental Research Letters. IOP Publishing, 2024. https://doi.org/10.1088/1748-9326/ad25a0. ieee: S. Fugger et al., “Hydrological regimes and evaporative flux partitioning at the climatic ends of High Mountain Asia,” Environmental Research Letters, vol. 19. IOP Publishing, 2024. ista: Fugger S, Shaw T, Jouberton A, Miles E, Buri P, McCarthy M, Fyffe CL, Fatichi S, Kneib M, Molnar P, Pellicciotti F. 2024. Hydrological regimes and evaporative flux partitioning at the climatic ends of High Mountain Asia. Environmental Research Letters. 19, 044057. mla: Fugger, Stefan, et al. “Hydrological Regimes and Evaporative Flux Partitioning at the Climatic Ends of High Mountain Asia.” Environmental Research Letters, vol. 19, 044057, IOP Publishing, 2024, doi:10.1088/1748-9326/ad25a0. short: S. Fugger, T. Shaw, A. Jouberton, E. Miles, P. Buri, M. McCarthy, C.L. Fyffe, S. Fatichi, M. Kneib, P. Molnar, F. Pellicciotti, Environmental Research Letters 19 (2024). corr_author: '1' date_created: 2024-02-05T09:01:11Z date_published: 2024-04-09T00:00:00Z date_updated: 2025-09-04T11:57:57Z day: '09' ddc: - '550' department: - _id: FrPe doi: 10.1088/1748-9326/ad25a0 external_id: isi: - '001198892300001' file: - access_level: open_access checksum: 27999359b51c30fec6d81e48cdf0ee0d content_type: application/pdf creator: dernst date_created: 2024-07-22T09:14:44Z date_updated: 2024-07-22T09:14:44Z file_id: '17295' file_name: 2024_EnvironmResearch_Fugger.pdf file_size: 4433401 relation: main_file success: 1 file_date_updated: 2024-07-22T09:14:44Z has_accepted_license: '1' intvolume: ' 19' isi: 1 keyword: - Public Health - Environmental and Occupational Health - General Environmental Science - Renewable Energy - Sustainability and the Environment language: - iso: eng month: '04' oa: 1 oa_version: Published Version publication: Environmental Research Letters publication_identifier: issn: - 1748-9326 publication_status: published publisher: IOP Publishing quality_controlled: '1' scopus_import: '1' status: public title: Hydrological regimes and evaporative flux partitioning at the climatic ends of High Mountain Asia 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: 317138e5-6ab7-11ef-aa6d-ffef3953e345 volume: 19 year: '2024' ... --- APC_amount: 11700 EUR OA_place: publisher OA_type: hybrid _id: '14979' abstract: - lang: eng text: Poxviruses are among the largest double-stranded DNA viruses, with members such as variola virus, monkeypox virus and the vaccination strain vaccinia virus (VACV). Knowledge about the structural proteins that form the viral core has remained sparse. While major core proteins have been annotated via indirect experimental evidence, their structures have remained elusive and they could not be assigned to individual core features. Hence, which proteins constitute which layers of the core, such as the palisade layer and the inner core wall, has remained enigmatic. Here we show, using a multi-modal cryo-electron microscopy (cryo-EM) approach in combination with AlphaFold molecular modeling, that trimers formed by the cleavage product of VACV protein A10 are the key component of the palisade layer. This allows us to place previously obtained descriptions of protein interactions within the core wall into perspective and to provide a detailed model of poxvirus core architecture. Importantly, we show that interactions within A10 trimers are likely generalizable over members of orthopox- and parapoxviruses. acknowledged_ssus: - _id: ScienComp - _id: LifeSc - _id: EM-Fac acknowledgement: "We thank A. Bergthaler (Research Center for Molecular Medicine of the Austrian Academy of Sciences) for providing VACV WR. We thank A. Nicholas and his team at the ISTA proteomics facility, and S. Elefante at the ISTA Scientific Computing facility for their support. We also thank F. Fäßler, D. Porley, T. Muthspiel and other members of the Schur group for support and helpful discussions. We also thank D. Castaño-Díez for support with Dynamo. We thank D. Farrell for his help optimizing the Rosetta protocol to refine the atomic model into the cryo-EM map with symmetry.\r\n\r\nF.K.M.S. acknowledges support from ISTA and EMBO. F.K.M.S. also received support from the Austrian Science Fund (FWF) grant P31445. This publication has been made possible in part by CZI grant DAF2021-234754 and grant https://doi.org/10.37921/812628ebpcwg from the Chan Zuckerberg Initiative DAF, an advised fund of Silicon Valley Community Foundation (funder https://doi.org/10.13039/100014989) awarded to F.K.M.S.\r\n\r\nThis research was also supported by the Scientific Service Units (SSUs) of ISTA through resources provided by Scientific Computing (SciComp), the Life Science Facility (LSF), and the Electron Microscopy Facility (EMF). We also acknowledge the use of COSMIC45 and Colabfold46." article_processing_charge: Yes (in subscription journal) article_type: original author: - first_name: Julia full_name: Datler, Julia id: 3B12E2E6-F248-11E8-B48F-1D18A9856A87 last_name: Datler orcid: 0000-0002-3616-8580 - first_name: Jesse full_name: Hansen, Jesse id: 1063c618-6f9b-11ec-9123-f912fccded63 last_name: Hansen orcid: 0000-0001-7967-2085 - first_name: Andreas full_name: Thader, Andreas id: 3A18A7B8-F248-11E8-B48F-1D18A9856A87 last_name: Thader - first_name: Alois full_name: Schlögl, Alois id: 45BF87EE-F248-11E8-B48F-1D18A9856A87 last_name: Schlögl orcid: 0000-0002-5621-8100 - first_name: Lukas W full_name: Bauer, Lukas W id: 0c894dcf-897b-11ed-a09c-8186353224b0 last_name: Bauer - first_name: Victor-Valentin full_name: Hodirnau, Victor-Valentin id: 3661B498-F248-11E8-B48F-1D18A9856A87 last_name: Hodirnau orcid: 0000-0003-3904-947X - first_name: Florian KM full_name: Schur, Florian KM id: 48AD8942-F248-11E8-B48F-1D18A9856A87 last_name: Schur orcid: 0000-0003-4790-8078 citation: ama: Datler J, Hansen J, Thader A, et al. Multi-modal cryo-EM reveals trimers of protein A10 to form the palisade layer in poxvirus cores. Nature Structural & Molecular Biology. 2024;31:1114-1123. doi:10.1038/s41594-023-01201-6 apa: Datler, J., Hansen, J., Thader, A., Schlögl, A., Bauer, L. W., Hodirnau, V.-V., & Schur, F. K. (2024). Multi-modal cryo-EM reveals trimers of protein A10 to form the palisade layer in poxvirus cores. Nature Structural & Molecular Biology. Springer Nature. https://doi.org/10.1038/s41594-023-01201-6 chicago: Datler, Julia, Jesse Hansen, Andreas Thader, Alois Schlögl, Lukas W Bauer, Victor-Valentin Hodirnau, and Florian KM Schur. “Multi-Modal Cryo-EM Reveals Trimers of Protein A10 to Form the Palisade Layer in Poxvirus Cores.” Nature Structural & Molecular Biology. Springer Nature, 2024. https://doi.org/10.1038/s41594-023-01201-6. ieee: J. Datler et al., “Multi-modal cryo-EM reveals trimers of protein A10 to form the palisade layer in poxvirus cores,” Nature Structural & Molecular Biology, vol. 31. Springer Nature, pp. 1114–1123, 2024. ista: Datler J, Hansen J, Thader A, Schlögl A, Bauer LW, Hodirnau V-V, Schur FK. 2024. Multi-modal cryo-EM reveals trimers of protein A10 to form the palisade layer in poxvirus cores. Nature Structural & Molecular Biology. 31, 1114–1123. mla: Datler, Julia, et al. “Multi-Modal Cryo-EM Reveals Trimers of Protein A10 to Form the Palisade Layer in Poxvirus Cores.” Nature Structural & Molecular Biology, vol. 31, Springer Nature, 2024, pp. 1114–23, doi:10.1038/s41594-023-01201-6. short: J. Datler, J. Hansen, A. Thader, A. Schlögl, L.W. Bauer, V.-V. Hodirnau, F.K. Schur, Nature Structural & Molecular Biology 31 (2024) 1114–1123. corr_author: '1' date_created: 2024-02-12T09:59:45Z date_published: 2024-07-01T00:00:00Z date_updated: 2026-04-07T12:59:44Z day: '01' ddc: - '570' department: - _id: FlSc - _id: ScienComp - _id: EM-Fac doi: 10.1038/s41594-023-01201-6 external_id: isi: - '001158144600002' pmid: - '38316877' file: - access_level: open_access checksum: bda7bf65d81455480efaed8ca293b0db content_type: application/pdf creator: dernst date_created: 2024-07-22T11:27:22Z date_updated: 2024-07-22T11:27:22Z file_id: '17307' file_name: 2024_NatureStrucBio_Datler.pdf file_size: 17485494 relation: main_file success: 1 file_date_updated: 2024-07-22T11:27:22Z has_accepted_license: '1' intvolume: ' 31' isi: 1 keyword: - Molecular Biology - Structural Biology language: - iso: eng month: '07' oa: 1 oa_version: Published Version page: 1114-1123 pmid: 1 project: - _id: 26736D6A-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P31445 name: Structural conservation and diversity in retroviral capsid publication: Nature Structural & Molecular Biology publication_identifier: eissn: - 1545-9985 issn: - 1545-9993 publication_status: published publisher: Springer Nature quality_controlled: '1' related_material: link: - description: News on ISTA Website relation: press_release url: https://ista.ac.at/en/news/down-to-the-core-of-poxviruses/ record: - id: '18766' relation: dissertation_contains status: public scopus_import: '1' status: public title: Multi-modal cryo-EM reveals trimers of protein A10 to form the palisade layer in poxvirus cores 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: 317138e5-6ab7-11ef-aa6d-ffef3953e345 volume: 31 year: '2024' ...