| 1. |
- Munk, P., et al.
(author)
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Genomic analysis of sewage from 101 countries reveals global landscape of antimicrobial resistance
- 2022
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In: Nature Communications. - : Springer Science and Business Media LLC. - 2041-1723. ; 13:1
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Journal article (peer-reviewed)abstract
- Antimicrobial resistance (AMR) is a major threat to global health. Understanding the emergence, evolution, and transmission of individual antibiotic resistance genes (ARGs) is essential to develop sustainable strategies combatting this threat. Here, we use metagenomic sequencing to analyse ARGs in 757 sewage samples from 243 cities in 101 countries, collected from 2016 to 2019. We find regional patterns in resistomes, and these differ between subsets corresponding to drug classes and are partly driven by taxonomic variation. The genetic environments of 49 common ARGs are highly diverse, with most common ARGs carried by multiple distinct genomic contexts globally and sometimes on plasmids. Analysis of flanking sequence revealed ARG-specific patterns of dispersal limitation and global transmission. Our data furthermore suggest certain geographies are more prone to transmission events and should receive additional attention.
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| 2. |
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| 3. |
- Verra, L., et al.
(author)
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Controlled Growth of the Self-Modulation of a Relativistic Proton Bunch in Plasma
- 2022
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In: Physical Review Accelerators and Beams. - : American Physical Society. - 2469-9888. ; 25:7
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Journal article (peer-reviewed)abstract
- A long, narrow, relativistic charged particle bunch propagating in plasma is subject to the self -modulation (SM) instability. We show that SM of a proton bunch can be seeded by the wakefields driven by a preceding electron bunch. SM timing reproducibility and control are at the level of a small fraction of the modulation period. With this seeding method, we independently control the amplitude of the seed wakefields with the charge of the electron bunch and the growth rate of SM with the charge of the proton bunch. Seeding leads to larger growth of the wakefields than in the instability case.
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| 4. |
- Tedersoo, L., et al.
(author)
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The Global Soil Mycobiome consortium dataset for boosting fungal diversity research
- 2021
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In: Fungal Diversity. - : Springer Science and Business Media LLC. - 1560-2745 .- 1878-9129. ; 111, s. 573-588
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Journal article (peer-reviewed)abstract
- Fungi are highly important biotic components of terrestrial ecosystems, but we still have a very limited understanding about their diversity and distribution. This data article releases a global soil fungal dataset of the Global Soil Mycobiome consortium (GSMc) to boost further research in fungal diversity, biogeography and macroecology. The dataset comprises 722,682 fungal operational taxonomic units (OTUs) derived from PacBio sequencing of full-length ITS and 18S-V9 variable regions from 3200 plots in 108 countries on all continents. The plots are supplied with geographical and edaphic metadata. The OTUs are taxonomically and functionally assigned to guilds and other functional groups. The entire dataset has been corrected by excluding chimeras, index-switch artefacts and potential contamination. The dataset is more inclusive in terms of geographical breadth and phylogenetic diversity of fungi than previously published data. The GSMc dataset is available over the PlutoF repository.
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| 5. |
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The Seventeenth Data Release of the Sloan Digital Sky Surveys : Complete Release of MaNGA, MaStar, and APOGEE-2 Data
- 2022
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In: Astrophysical Journal Supplement Series. - : Institute of Physics (IOP). - 0067-0049 .- 1538-4365. ; 259:2
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Journal article (peer-reviewed)abstract
- This paper documents the seventeenth data release (DR17) from the Sloan Digital Sky Surveys; the fifth and final release from the fourth phase (SDSS-IV). DR17 contains the complete release of the Mapping Nearby Galaxies at Apache Point Observatory (MaNGA) survey, which reached its goal of surveying over 10,000 nearby galaxies. The complete release of the MaNGA Stellar Library accompanies this data, providing observations of almost 30,000 stars through the MaNGA instrument during bright time. DR17 also contains the complete release of the Apache Point Observatory Galactic Evolution Experiment 2 survey that publicly releases infrared spectra of over 650,000 stars. The main sample from the Extended Baryon Oscillation Spectroscopic Survey (eBOSS), as well as the subsurvey Time Domain Spectroscopic Survey data were fully released in DR16. New single-fiber optical spectroscopy released in DR17 is from the SPectroscipic IDentification of ERosita Survey subsurvey and the eBOSS-RM program. Along with the primary data sets, DR17 includes 25 new or updated value-added catalogs. This paper concludes the release of SDSS-IV survey data. SDSS continues into its fifth phase with observations already underway for the Milky Way Mapper, Local Volume Mapper, and Black Hole Mapper surveys.
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| 6. |
- Pihl, E., et al.
(author)
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Ten new insights in climate science 2020- A horizon scan
- 2020
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In: Global Sustainability. - : Cambridge University Press. - 2059-4798.
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Journal article (peer-reviewed)abstract
- Non-technical summary We summarize some of the past year's most important findings within climate change-related research. New research has improved our understanding of Earth's sensitivity to carbon dioxide, finds that permafrost thaw could release more carbon emissions than expected and that the uptake of carbon in tropical ecosystems is weakening. Adverse impacts on human society include increasing water shortages and impacts on mental health. Options for solutions emerge from rethinking economic models, rights-based litigation, strengthened governance systems and a new social contract. The disruption caused by COVID-19 could be seized as an opportunity for positive change, directing economic stimulus towards sustainable investments. Technical summary A synthesis is made of ten fields within climate science where there have been significant advances since mid-2019, through an expert elicitation process with broad disciplinary scope. Findings include: (1) a better understanding of equilibrium climate sensitivity; (2) abrupt thaw as an accelerator of carbon release from permafrost; (3) changes to global and regional land carbon sinks; (4) impacts of climate change on water crises, including equity perspectives; (5) adverse effects on mental health from climate change; (6) immediate effects on climate of the COVID-19 pandemic and requirements for recovery packages to deliver on the Paris Agreement; (7) suggested long-term changes to governance and a social contract to address climate change, learning from the current pandemic, (8) updated positive cost-benefit ratio and new perspectives on the potential for green growth in the short- A nd long-term perspective; (9) urban electrification as a strategy to move towards low-carbon energy systems and (10) rights-based litigation as an increasingly important method to address climate change, with recent clarifications on the legal standing and representation of future generations. Social media summary Stronger permafrost thaw, COVID-19 effects and growing mental health impacts among highlights of latest climate science.
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| 7. |
- Garcia-Tenorio, R., et al.
(author)
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From radiometry to chronology of a marine sediment core: A Pb-210 dating interlaboratory comparison exercise organised by the IAEA
- 2020
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In: Marine Pollution Bulletin. - : PERGAMON-ELSEVIER SCIENCE LTD. - 0025-326X .- 1879-3363. ; 159
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Journal article (peer-reviewed)abstract
- Laboratories from 14 countries (with different levels of expertise in radionuclide measurements and Pb-210 dating) participated in an interlaboratory comparison exercise (ILC) related to the application of Pb-210 sediment dating technique within the framework of the IAEA Coordinated Research Project. The laboratories were provided with samples from a composite sediment core and were required to provide massic activities of several radionuclides and an age versus depth model from the obtained results, using the most suitable Pb-210 dating model. Massic concentrations of Zn and Cu were also determined to be used for chronology validation. The ILC results indicated good analytical performances while the dating results didnt demonstrate the same degree of competence in part due to the different experience in dating of the participant laboratories. The ILC exercise enabled evaluation of the difficulties faced by laboratories implementing Pb-210 dating methods and identified some limitations in providing reliable chronologies.
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| 8. |
- Noske, G. D., et al.
(author)
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A Crystallographic Snapshot of SARS-CoV-2 Main Protease Maturation Process : SARS-CoV-2 Mpro maturation
- 2021
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In: Journal of Molecular Biology. - : Elsevier BV. - 0022-2836. ; 433:18
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Journal article (peer-reviewed)abstract
- SARS-CoV-2 is the causative agent of COVID-19. The dimeric form of the viral Mpro is responsible for the cleavage of the viral polyprotein in 11 sites, including its own N and C-terminus. The lack of structural information for intermediary forms of Mpro is a setback for the understanding its self-maturation process. Herein, we used X-ray crystallography combined with biochemical data to characterize multiple forms of SARS-CoV-2 Mpro. For the immature form, we show that extra N-terminal residues caused conformational changes in the positioning of domain-three over the active site, hampering the dimerization and diminishing its activity. We propose that this form preludes the cis and trans-cleavage of N-terminal residues. Using fragment screening, we probe new cavities in this form which can be used to guide therapeutic development. Furthermore, we characterized a serine site-directed mutant of the Mpro bound to its endogenous N and C-terminal residues during dimeric association stage of the maturation process. We suggest this form is a transitional state during the C-terminal trans-cleavage. This data sheds light in the structural modifications of the SARS-CoV-2 main protease during its self-maturation process.
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| 9. |
- Barsanti, M., et al.
(author)
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Challenges and limitations of the Pb-210 sediment dating method : Results from an IAEA modelling interlaboratory comparison exercise
- 2020
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In: Quaternary Geochronology. - : Elsevier. - 1871-1014 .- 1878-0350. ; 59
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Journal article (peer-reviewed)abstract
- The Pb-210 sediment dating is the most widely used method to determine recent (similar to 100-150 years) chronologies and sediment accumulation rates in aquatic environments and has been used effectively for reconstruction of diverse environmental processes associated with global change. Owing to the relative accessibility of the Pb-210 methodology, many environmental chronologies have been produced, but not always critically assessed. Sometimes, sedimentary processes such as compaction, local mixing, erosion, or episodic sedimentation are not taken into account, nor the validity of the fundamental premises and proper estimation of uncertainties assessed. A Pb-210 dating interlaboratory comparison modelling exercise was designed within the framework of the IAEA (International Atomic Energy Agency) Coordinated Research Project "Study of temporal trends of pollution in selected coastal areas by the application of isotopic and nuclear tools" (CRP K41016), to identify potential problems associated with the use of Pb-210 dating models and to suggest best practices to obtain reliable reconstructions. The exercise involved 14 laboratories worldwide with different levels of expertise in the application of the Pb-210 dating methods. The dating exercise was performed using Pb-210, Ra-226 and Cs-137 activity data from two sediment cores (coastal and lacustrine sediments), and the participants were requested to provide their Pb-210 chronologies based on dating models. This modelling exercise evidenced the limitations and constraints of Pb-210 method when supplementary and validation information is not available. The exercise highlighted the relevance of solid understanding of the fundamentals, assumptions and limitations of the Pb-210 dating method and its validation, and allowed identifying key aspects to improve the reliability of Pb-210 dating process, including: a critical examination and interpretation of the Pb-210 activity depth profile; an appropriate selection of the Pb-210 dating model according to the characteristics of the Pb-210 activity profile and the environmental setting taking into account sediment compaction in the calculations; a sound identification of the Pb-210 equilibrium depth and the estimation of the Pb-210 inventory ensuring the best possible estimation of interpolated Pb-210 values when needed; and the use of independent markers to corroborate the age models.
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| 10. |
- Godoy, N., et al.
(author)
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ISPY - NaCo Imaging Survey for Planets around Young stars : CenteR: The impact of centering and frame selection
- 2022
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In: Astronomy and Astrophysics. - : EDP Sciences. - 0004-6361 .- 1432-0746. ; 663
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Journal article (peer-reviewed)abstract
- Context. Direct imaging has made significant progress over the past decade, in part thanks to a new generation of instruments and excellent adaptive optic systems, but also thanks to advanced post-processing techniques. The combination of these two factors allowed the detection of several giant planets with separations as close as 0.2 arcsec with contrasts typically reaching 9-10 magnitudes at nearinfrared wavelengths. Observing strategies and data rates vary depending on the instrument and the wavelength, with L- and M-band observations yielding tens of thousands of images to be combined.Aims. We present a new approach, tailored for VLT/NaCo observations performed with the Annular Groove Phase Mask (AGPM) coronagraph, but that can be applied to other instruments using similar coronagraphs. Our pipeline aims to improve the post-processing of the observations on two fronts: identifying the location of the star behind the AGPM to better align the science frames and performing frame selection.Methods. Our method relies on finding the position of the AGPM in the sky frame observations, and correlating it with the circular aperture of the coronagraphic mask. This relationship allows us to retrieve the location of the AGPM in the science frames. We are then able to model the torus shape visible in the sky-subtracted science frames, as a combination of negative and positive 2D Gaussian functions. The model provides additional information that is useful to design our frame selection criteria. Results. We tested our pipeline on three targets (β Pictoris, R CrA, and HD 34282), two of which have companions at intermediate and close separations, and the third hosts a bright circumstellar disk. We find that the centering of the science frames has a significant impact on the signal-to-noise ratio (S/N) of the companions. Our results suggest that the best reduction is achieved when performing the principal component analysis centered on the location of the AGPM and derotating the frames centered at the location of the star before collapsing the final datacube. We improved the S/N of companions around β Pictoris and R CrA by 24 +/- 3% and 117 +/- 11% respectively, compared to other state-of-the-art reductions. We find that the companion position for all the centering strategies are consistent within 3 σ. Finally, we find that even for NaCo observations with tens of thousands of frames, frame selection yields just marginal improvement for point sources, but may improve the final images for objects with extended emission such as disks.Conclusions. We propose a novel approach to identify the location of the star behind a coronagraph even when it cannot easily be determined by other methods. We led a thorough study on the importance of frame selection, concluding that the improvements are marginal in most cases, but may yield better contrast in some specific cases. Our approach can be applied to the wealth of archival NaCo data and, assuming that the field of view includes the edges of the coronagraphic mask, its implementation can be adapted to other instruments with coronagraphs similar to the AGPM used on NaCo (e.g., Keck/NIRC2, LBT/LMIRCam).
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