| 1. |
- Klionsky, Daniel J., et al.
(författare)
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Guidelines for the use and interpretation of assays for monitoring autophagy
- 2012
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Ingår i: Autophagy. - : Informa UK Limited. - 1554-8635 .- 1554-8627. ; 8:4, s. 445-544
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Forskningsöversikt (refereegranskat)abstract
- In 2008 we published the first set of guidelines for standardizing research in autophagy. Since then, research on this topic has continued to accelerate, and many new scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Accordingly, it is important to update these guidelines for monitoring autophagy in different organisms. Various reviews have described the range of assays that have been used for this purpose. Nevertheless, there continues to be confusion regarding acceptable methods to measure autophagy, especially in multicellular eukaryotes. A key point that needs to be emphasized is that there is a difference between measurements that monitor the numbers or volume of autophagic elements (e.g., autophagosomes or autolysosomes) at any stage of the autophagic process vs. those that measure flux through the autophagy pathway (i.e., the complete process); thus, a block in macroautophagy that results in autophagosome accumulation needs to be differentiated from stimuli that result in increased autophagic activity, defined as increased autophagy induction coupled with increased delivery to, and degradation within, lysosomes (in most higher eukaryotes and some protists such as Dictyostelium) or the vacuole (in plants and fungi). In other words, it is especially important that investigators new to the field understand that the appearance of more autophagosomes does not necessarily equate with more autophagy. In fact, in many cases, autophagosomes accumulate because of a block in trafficking to lysosomes without a concomitant change in autophagosome biogenesis, whereas an increase in autolysosomes may reflect a reduction in degradative activity. Here, we present a set of guidelines for the selection and interpretation of methods for use by investigators who aim to examine macroautophagy and related processes, as well as for reviewers who need to provide realistic and reasonable critiques of papers that are focused on these processes. These guidelines are not meant to be a formulaic set of rules, because the appropriate assays depend in part on the question being asked and the system being used. In addition, we emphasize that no individual assay is guaranteed to be the most appropriate one in every situation, and we strongly recommend the use of multiple assays to monitor autophagy. In these guidelines, we consider these various methods of assessing autophagy and what information can, or cannot, be obtained from them. Finally, by discussing the merits and limits of particular autophagy assays, we hope to encourage technical innovation in the field.
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| 2. |
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| 3. |
- Hudson, Lawrence N., et al.
(författare)
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The PREDICTS database : a global database of how local terrestrial biodiversity responds to human impacts
- 2014
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Ingår i: Ecology and Evolution. - : Wiley. - 2045-7758. ; 4:24, s. 4701-4735
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Tidskriftsartikel (refereegranskat)abstract
- Biodiversity continues to decline in the face of increasing anthropogenic pressures such as habitat destruction, exploitation, pollution and introduction of alien species. Existing global databases of species' threat status or population time series are dominated by charismatic species. The collation of datasets with broad taxonomic and biogeographic extents, and that support computation of a range of biodiversity indicators, is necessary to enable better understanding of historical declines and to project - and avert - future declines. We describe and assess a new database of more than 1.6 million samples from 78 countries representing over 28,000 species, collated from existing spatial comparisons of local-scale biodiversity exposed to different intensities and types of anthropogenic pressures, from terrestrial sites around the world. The database contains measurements taken in 208 (of 814) ecoregions, 13 (of 14) biomes, 25 (of 35) biodiversity hotspots and 16 (of 17) megadiverse countries. The database contains more than 1% of the total number of all species described, and more than 1% of the described species within many taxonomic groups - including flowering plants, gymnosperms, birds, mammals, reptiles, amphibians, beetles, lepidopterans and hymenopterans. The dataset, which is still being added to, is therefore already considerably larger and more representative than those used by previous quantitative models of biodiversity trends and responses. The database is being assembled as part of the PREDICTS project (Projecting Responses of Ecological Diversity In Changing Terrestrial Systems - ). We make site-level summary data available alongside this article. The full database will be publicly available in 2015.
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| 4. |
- Smiljanic, R., et al.
(författare)
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The Gaia-ESO Survey: The analysis of high-resolution UVES spectra of FGK-type stars
- 2014
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Ingår i: Astronomy & Astrophysics. - : EDP Sciences. - 0004-6361 .- 1432-0746. ; 570
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Tidskriftsartikel (refereegranskat)abstract
- Context. The ongoing Gaia-ESO Public Spectroscopic Survey is using FLAMES at the VLT to obtain high-quality medium-resolution Giraffe spectra for about 10(5) stars and high-resolution UVES spectra for about 5000 stars. With UVES, the Survey has already observed 1447 FGK-type stars. Aims. These UVES spectra are analyzed in parallel by several state-of-the-art methodologies. Our aim is to present how these analyses were implemented, to discuss their results, and to describe how a final recommended parameter scale is defined. We also discuss the precision (method-to-method dispersion) and accuracy (biases with respect to the reference values) of the final parameters. These results are part of the Gaia-ESO second internal release and will be part of its first public release of advanced data products. Methods. The final parameter scale is tied to the scale defined by the Gaia benchmark stars, a set of stars with fundamental atmospheric parameters. In addition, a set of open and globular clusters is used to evaluate the physical soundness of the results. Each of the implemented methodologies is judged against the benchmark stars to define weights in three different regions of the parameter space. The final recommended results are the weighted medians of those from the individual methods. Results. The recommended results successfully reproduce the atmospheric parameters of the benchmark stars and the expected T-eff-log g relation of the calibrating clusters. Atmospheric parameters and abundances have been determined for 1301 FGK-type stars observed with UVES. The median of the method-to-method dispersion of the atmospheric parameters is 55K for T-eff, 0.13dex for log g and 0.07 dex for [Fe/H]. Systematic biases are estimated to be between 50-100 K for T-eff, 0.10-0.25 dex for log g and 0.05-0.10 dex for [Fe/H]. Abundances for 24 elements were derived: C, N, O, Na, Mg, Al, Si, Ca, Sc, Ti, V, Cr, Mn, Fe, Co, Ni, Cu, Zn, Y, Zr, Mo, Ba, Nd, and Eu. The typical method-to-method dispersion of the abundances varies between 0.10 and 0.20 dex. Conclusions. The Gaia-ESO sample of high-resolution spectra of FGK-type stars will be among the largest of its kind analyzed in a homogeneous way. The extensive list of elemental abundances derived in these stars will enable significant advances in the areas of stellar evolution and Milky Way formation and evolution.
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| 5. |
- Cantat-Gaudin, T., et al.
(författare)
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The Gaia-ESO Survey: Stellar content and elemental abundances in the massive cluster NGC 6705
- 2014
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Ingår i: Astronomy & Astrophysics. - : EDP Sciences. - 0004-6361 .- 1432-0746. ; 569
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Tidskriftsartikel (refereegranskat)abstract
- Context. Chemically inhomogeneous populations are observed in most globular clusters, but not in open clusters. Cluster mass seems to play a key role in the existence of multiple populations. Aims. Studying the chemical homogeneity of the most massive open clusters is needed to better understand the mechanism of their formation and determine the mass limit under which clusters cannot host multiple populations. Here we studied NGC 6705, which is a young and massive open cluster located towards the inner region of the Milky Way. This cluster is located inside the solar circle. This makes it an important tracer of the inner disk abundance gradient. Methods. This study makes use of BVI and ri photometry and comparisons with theoretical isochrones to derive the age of NGC 6705. We study the density profile of the cluster and the mass function to infer the cluster mass. Based on abundances of the chemical elements distributed in the first internal data release of the Gaia-ESO Survey, we study elemental ratios and the chemical homogeneity of the red clump stars. Radial velocities enable us to study the rotation and internal kinematics of the cluster. Results. The estimated ages range from 250 to 316 Myr, depending on the adopted stellar model. Luminosity profiles and mass functions show strong signs of mass segregation. We derive the mass of the cluster from its luminosity function and from the kinematics, finding values between 3700 M-circle dot and 11 000 M-circle dot. After selecting the cluster members from their radial velocities, we obtain a metallicity of [Fe/H] = 0.10 +/- 0.06 based on 21 candidate members. Moreover, NGC 6705 shows no sign of the typical correlations or anti-correlations between Al, Mg, Si, and Na, which are expected in multiple populations. This is consistent with our cluster mass estimate, which is lower than the required mass limit proposed in the literature to develop multiple populations.
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| 6. |
- Damiani, F., et al.
(författare)
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Gaia-ESO Survey: Empirical classification of VLT/Giraffe stellar spectra in the wavelength range 6440-6810 angstrom in the gamma Velorum cluster, and calibration of spectral indices
- 2014
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Ingår i: Astronomy & Astrophysics. - : EDP Sciences. - 0004-6361 .- 1432-0746. ; 566
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Tidskriftsartikel (refereegranskat)abstract
- We present a study of spectral diagnostics available from optical spectra with R = 17 000 obtained with the VLT/Giraffe HR15n setup, using observations from the Gaia-ESO Survey, on the gamma Vel young cluster, with the purpose of classifying these stars and finding their fundamental parameters. We define several spectroscopic indices, sampling the amplitude of TiO bands, the H alpha line core and wings, and temperature- and gravity-sensitive sets of lines, each useful as a T-eff or log g indicator over a limited range of stellar spectral types. H alpha line indices are also useful as chromospheric activity or accretion indicators. Furthermore, we use all indices to define additional global T-eff - and logg-sensitive indices tau and gamma, valid for the entire range of types in the observed sample. We find a clear difference between gravity indices of main-sequence and pre-main-sequence stars, as well as a much larger difference between these and giant stars. The potentially great usefulness of the (gamma, t) diagram as a distance-independent age measurement tool for young clusters is discussed. We discuss the effect on the defined indices of classical T Tauri star veiling, which is however detected in only a few stars in the present sample. Then, we present tests and calibrations of these indices, on the basis of both photometry and literature reference spectra, from the UVES Paranal Observatory Project and the ELODIE 3.1 Library. The known properties of these stars, spanning a wide range of stellar parameters, enable us to obtain a good understanding of the performances of our new spectral indices. For non-peculiar stars with known temperature, gravity, and metallicity, we are able to calibrate quantitatively our indices, and derive stellar parameters for a wide range of stellar types. To this aim, a new composite index is defined, providing a good metallicity indicator. The ability of our indices to select peculiar, or otherwise rare classes of stars is also established. For pre-main-sequence stars outside the parameter range of the ELODIE dataset, index calibration relies on model isochrones. We check our calibrations against current Gaia-ESO UVES results, plus a number of Survey benchmark stars, and also against Gaia-ESO observations of young clusters, which contribute to establishing the good performance of our method across a wide range of stellar parameters. Our gravity determination for late-type PMS stars is found to be accurate enough to let us obtain gravity-based age estimates for PMS clusters. Finally, our gravity determinations support the existence of an older pre-main-sequence population in the gamma Vel sky region, in agreement with evidence obtained from the lithium depletion pattern of the same stars.
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| 7. |
- Sacco, G. G., et al.
(författare)
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The Gaia-ESO Survey: processing FLAMES-UVES spectra
- 2014
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Ingår i: Astronomy & Astrophysics. - : EDP Sciences. - 0004-6361 .- 1432-0746. ; 565
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Tidskriftsartikel (refereegranskat)abstract
- The Gaia-ESO Survey is a large public spectroscopic survey that aims to derive radial velocities and fundamental parameters of about 10(5) Milky Way stars in the field and in clusters. Observations are carried out with the multi-object optical spectrograph FLAMES, using simultaneously the medium-resolution (R similar to 20 000) GIRAFFE spectrograph and the high-resolution (R similar to 47 000) UVES spectrograph. In this paper we describe the methods and the software used for the data reduction, the derivation of the radial velocities, and the quality control of the FLAMES-UVES spectra. Data reduction has been performed using a workflow specifically developed for this project. This workflow runs the ESO public pipeline optimizing the data reduction for the Gaia-ESO Survey, automatically performs sky subtraction, barycentric correction and normalisation, and calculates radial velocities and a first guess of the rotational velocities. The quality control is performed using the output parameters from the ESO pipeline, by a visual inspection of the spectra and by the analysis of the signal-to-noise ratio of the spectra. Using the observations of the first 18 months, specifically targets observed multiple times at different epochs, stars observed with both GIRAFFE and UVES, and observations of radial velocity standards, we estimated the precision and the accuracy of the radial velocities. The statistical error on the radial velocities is sigma similar to 0.4 km s(-1) and is mainly due to uncertainties in the zero point of the wavelength calibration. However, we found a systematic bias with respect to the GIRAFFE spectra (similar to 0.9 km s(-1)) and to the radial velocities of the standard stars (similar to 0.5 km s(-1)) retrieved from the literature. This bias will be corrected in the future data releases, when a common zero point for all the set-ups and instruments used for the survey is be established.
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| 8. |
- Gilmore, G., et al.
(författare)
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The Gaia-ESO Public Spectroscopic Survey
- 2012
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Ingår i: The Messenger. - 0254-4423. ; 147, s. 25-31
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Tidskriftsartikel (refereegranskat)abstract
- The Gaia-ESO Public Spectroscopic Survey has begun and will obtain high quality spectroscopy of some 100000 Milky Way stars, in the field and in open clusters, down to magnitude 19, systematically covering all the major components of the Milky Way. This survey will provide the first homogeneous overview of the distributions of kinematics and chemical element abundances in the Galaxy. The motivation, organisation and implementation of the Gaia-ESO Survey are described, emphasising the complementarity with the ESA Gaia mission. Spectra from the very first observing run of the survey are presented.
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| 9. |
- Aneheim, Emma, 1982, et al.
(författare)
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Fission product interactions with nitrogen donor ligands used for spent nuclear fuel treatment
- 2013
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Ingår i: Polyhedron. - : Elsevier BV. - 0277-5387. ; 50:1, s. 154-163
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Tidskriftsartikel (refereegranskat)abstract
- The so called BTBP (bis-triazine bi-pyridine)-type molecules have been developed for liquid-liquid extraction in the advanced reprocessing of used nuclear fuel. One solvent composition that has proven to be promising for such an application is the combination of CyMe4-BTBP and tri-butyl phosphate (TBP) in cyclohexanone. This solvent can extract the actinides successfully but unfortunately some fission products are also co-extracted. One of the most problematic fission products is palladium, but silver and cadmium are also extracted by the proposed solvent, which has been investigated here. In this study it was found that CyMe4-BTBP in cyclohexanone, when extracting palladium from nitric acid, forms complexes that are soluble both in the organic and aqueous phase. The predominant complex observed in both phases established with mass spectrometry and confirmed by NMR is a 1:1 complex, contrary to silver that forms 2:2 complexes and cadmium that forms 1:2 complexes. The nitrate dependency of the palladium extraction from nitric acid into a BTBP containing organic phase was found to be two. However, with higher ionic strengths, such as under process conditions, the palladium was found to be salted out into the organic phase.
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| 10. |
- Bubnova, Olga, et al.
(författare)
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Corrigendum: Semi-metallic polymers
- 2014
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Ingår i: Nature Materials. - : Springer Science and Business Media LLC. - 1476-1122 .- 1476-4660. ; 13, s. 662-662
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Tidskriftsartikel (refereegranskat)
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