| 41. |
- Thul, Peter J., et al.
(författare)
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A subcellular map of the human proteome
- 2017
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Ingår i: Science. - : American Association for the Advancement of Science. - 0036-8075 .- 1095-9203. ; 356:6340
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Tidskriftsartikel (refereegranskat)abstract
- Resolving the spatial distribution of the human proteome at a subcellular level can greatly increase our understanding of human biology and disease. Here we present a comprehensive image-based map of subcellular protein distribution, the Cell Atlas, built by integrating transcriptomics and antibody-based immunofluorescence microscopy with validation by mass spectrometry. Mapping the in situ localization of 12,003 human proteins at a single-cell level to 30 subcellular structures enabled the definition of the proteomes of 13 major organelles. Exploration of the proteomes revealed single-cell variations in abundance or spatial distribution and localization of about half of the proteins to multiple compartments. This subcellular map can be used to refine existing protein-protein interaction networks and provides an important resource to deconvolute the highly complex architecture of the human cell.
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| 42. |
- Voisin, Sarah, et al.
(författare)
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Exercise is associated with younger methylome and transcriptome profiles in human skeletal muscle
- 2024
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Ingår i: Aging Cell. - 1474-9726. ; , s. 1-15
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Tidskriftsartikel (refereegranskat)abstract
- Exercise training prevents age-related decline in muscle function. Targeting epigenetic aging is a promising actionable mechanism and late-life exercise mitigates epigenetic aging in rodent muscle. Whether exercise training can decelerate, or reverse epigenetic aging in humans is unknown. Here, we performed a powerful meta-analysis of the methylome and transcriptome of an unprecedented number of human skeletal muscle samples (n = 3176). We show that: (1) individuals with higher baseline aerobic fitness have younger epigenetic and transcriptomic profiles, (2) exercise training leads to significant shifts of epigenetic and transcriptomic patterns toward a younger profile, and (3) muscle disuse "ages" the transcriptome. Higher fitness levels were associated with attenuated differential methylation and transcription during aging. Furthermore, both epigenetic and transcriptomic profiles shifted toward a younger state after exercise training interventions, while the transcriptome shifted toward an older state after forced muscle disuse. We demonstrate that exercise training targets many of the age-related transcripts and DNA methylation loci to maintain younger methylome and transcriptome profiles, specifically in genes related to muscle structure, metabolism, and mitochondrial function. Our comprehensive analysis will inform future studies aiming to identify the best combination of therapeutics and exercise regimes to optimize longevity.
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| 43. |
- Vujasinovic, M, et al.
(författare)
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Low Bone Mineral Density and Risk for Osteoporotic Fractures in Patients with Chronic Pancreatitis
- 2021
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Ingår i: Nutrients. - : MDPI AG. - 2072-6643. ; 13:7
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Tidskriftsartikel (refereegranskat)abstract
- Introduction: Chronic pancreatitis (CP) can lead to malnutrition, an established risk factor for low bone mineral density (BMD) and fractures. This study aims to determine the prevalence of low BMD, assess fracture incidence and explore risk factors for fractures in patients with CP. Patients and methods: We performed a retrospective analysis of all patients treated for CP at Karolinska University Hospital between January 1999 and December 2020. Electronic medical records were retrieved to assess demographic, laboratory and clinical data. Patients subjected to dual-energy X-ray absorptiometry (DXA) were categorised as either low BMD or normal BMD. We investigated whether the rate of fractures, defined by chart review, differed between these groups using Cox regression, adjusting the model for age, sex and body mass index (BMI). Additional within-group survival analysis was conducted to identify potential risk factors. Results: DXA was performed in 23% of patients with definite CP. Some 118 patients were included in the final analysis. Low BMD was present in 63 (53.4%) patients. Mean age at CP diagnosis in the total cohort was 53.1 years and was significantly lower in patients with normal BMD than in patients with low BMD (45.5 vs. 59.8, p < 0.001). Significant differences were observed in smoking status and disease aetiology, i.e., a higher proportion of patients with low BMD were current or former smokers, with nicotine or alcohol being a more common cause of CP (p < 0.05). Total follow-up time was 898 person-years. Fractures were found in 33 (28.0%) patients: in 5 of 55 patients (16.7%) with normal DXA and in 28 of 63 patients (44.4%) with low BMD (adjusted hazard ratio = 3.4, 95% confidence interval (CI) = 1.2–9.6). Patients with at least 3 months of consecutive pancreatic enzyme replacement therapy (PERT) or vitamin D treatment had a longer median time to fracture after CP diagnosis. Conclusion: DXA was only performed in 23% of patients with definite CP in this study, indicating a low adherence to current European guidelines. A low BMD was found in 53.4% of patients with CP, and 44% of the patients with a low BMD experienced a fracture during follow-up. Moreover, the fracture rate in patients with low BMD increased compared to those with normal BMD.
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| 44. |
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| 45. |
- Adibekyan, V., et al.
(författare)
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Sun-like stars unlike the Sun : Clues for chemical anomalies of cool stars
- 2017
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Ingår i: Astronomical Notes - Astronomische Nachrichten. - : WILEY-V C H VERLAG GMBH. - 0004-6337 .- 1521-3994. ; 338:4, s. 442-452
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Tidskriftsartikel (refereegranskat)abstract
- We present a summary of the splinter session Sun-like stars unlike the Sun that was held on June 9, 2016, as part of the Cool Stars 19 conference (Uppsala, Sweden), in which the main limitations (in the theory and observations) in the derivation of very precise stellar parameters and chemical abundances of Sun-like stars were discussed. The most important and most debated processes that can produce chemical peculiarities in solar-type stars were outlined and discussed. Finally, in an open discussion between all the participants, we tried to identify new pathways and prospects toward future solutions of the currently open questions.
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| 46. |
- Amarsi, A. M., et al.
(författare)
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3D non-LTE line formation of neutral carbon in the Sun
- 2019
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Ingår i: Astronomy and Astrophysics. - : EDP Sciences. - 0004-6361 .- 1432-0746. ; 624
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Tidskriftsartikel (refereegranskat)abstract
- Carbon abundances in late-type stars are important in a variety of astrophysical contexts. However C I lines, one of the main abundance diagnostics, are sensitive to departures from local thermodynamic equilibrium (LTE). We present a model atom for non-LTE analyses of C I lines, that uses a new, physically-motivated recipe for the rates of neutral hydrogen impact excitation. We analyse C I lines in the solar spectrum, employing a three-dimensional (3D) hydrodynamic model solar atmosphere and 3D non-LTE radiative transfer. We find negative non-LTE abundance corrections for C I lines in the solar photosphere, in accordance with previous studies, reaching up to around 0.1 dex in the disk-integrated flux. We also present the first fully consistent 3D non-LTE solar carbon abundance determination: we infer log is an element of(C) = 8.44 ± 0.02, in good agreement with the current standard value. Our models reproduce the observed solar centre-to-limb variations of various C I lines, without any adjustments to the rates of neutral hydrogen impact excitation, suggesting that the proposed recipe may be a solution to the long-standing problem of how to reliably model inelastic collisions with neutral hydrogen in late-type stellar atmospheres.
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| 47. |
- Amarsi, A. M., et al.
(författare)
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Carbon and oxygen in metal-poor halo stars
- 2019
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Ingår i: Astronomy and Astrophysics. - : EDP SCIENCES S A. - 0004-6361 .- 1432-0746. ; 622
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Tidskriftsartikel (refereegranskat)abstract
- Carbon and oxygen are key tracers of the Galactic chemical evolution; in particular, a reported upturn in [C/O] towards decreasing [O/H] in metal-poor halo stars could be a signature of nucleosynthesis by massive Population III stars. We reanalyse carbon, oxygen, and iron abundances in 39 metal-poor turn-off stars. For the first time, we take into account 3D hydrodynamic effects together with departures from local thermodynamic equilibrium (LTE) when determining both the stellar parameters and the elemental abundances, by deriving effective temperatures from 3D non-LTE H beta profiles, surface gravities from Gaia parallaxes, iron abundances from 3D LTE Fe ii equivalent widths, and carbon and oxygen abundances from 3D non-LTE C-I and O-I equivalent widths. We find that [C/Fe] stays flat with [Fe/H], whereas [O/Fe] increases linearly up to 0.75 dex with decreasing [Fe/H] down to -3.0 dex. Therefore [C/O] monotonically decreases towards decreasing [C/H], in contrast to previous findings, mainly because the non-LTE e ff ects for O i at low [Fe/H] are weaker with our improved calculations.
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| 48. |
- Amarsi, A. M., et al.
(författare)
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Effective temperature determinations of late-type stars based on 3D non-LTE Balmer line formation
- 2018
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Ingår i: Astronomy and Astrophysics. - : EDP Sciences. - 0004-6361 .- 1432-0746. ; 615
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Tidskriftsartikel (refereegranskat)abstract
- Hydrogen Balmer lines are commonly used as spectroscopic effective temperature diagnostics of late-type stars. However, reliable inferences require accurate model spectra, and the absolute accuracy of classical methods that are based on one-dimensional (1D) hydrostatic model atmospheres and local thermodynamic equilibrium (LTE) is still unclear. To investigate this, we carry out 3D non-LTE calculations for the Balmer lines, performed, for the first time, over an extensive grid of 3D hydrodynamic STAGGER model atmospheres. For H alpha, H beta, and H gamma we find significant 1D non-LTE versus 3D non-LTE differences (3D effects): the outer wings tend to be stronger in 3D models, particularly for H gamma, while the inner wings can be weaker in 3D models, particularly for H alpha. For H alpha, we also find significant 3D LTE versus 3D non-LTE differences (non-LTE effects): in warmer stars (T-eff approximate to 6500 K) the inner wings tend to be weaker in non-LTE models, while at lower effective temperatures (T-eff approximate to 4500 K) the inner wings can be stronger in non-LTE models; the non-LTE effects are more severe at lower metallicities. We test our 3D non-LTE models against observations of well-studied benchmark stars. For the Sun, we infer concordant effective temperatures from H alpha, H beta, and H gamma; however the value is too low by around 50 K which could signal residual modelling shortcomings. For other benchmark stars, our 3D non-LTE models generally reproduce the effective temperatures to within 1 sigma uncertainties. For H alpha, the absolute 3D effects and non-LTE effects can separately reach around 100 K, in terms of inferred effective temperatures. For metal-poor turn-off stars, 1D LTE models of H alpha can underestimate effective temperatures by around 150 K. Our 3D non-LTE model spectra are publicly available, and can be used for more reliable spectroscopic effective temperature determinations.
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| 49. |
- Amarsi, A. M., et al.
(författare)
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Inelastic O plus H collisions and the O I 777 nm solar centre-to-limb variation
- 2018
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Ingår i: Astronomy and Astrophysics. - : EDP SCIENCES S A. - 0004-6361 .- 1432-0746. ; 616
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Tidskriftsartikel (refereegranskat)abstract
- The O I 777 nm triplet is a key diagnostic of oxygen abundances in the atmospheres of FGK-type stars; however, it is sensitive to departures from local thermodynamic equilibrium (LTE). The accuracy of non-LTE line formation calculations has hitherto been limited by errors in the inelastic O+H collisional rate coefficients; several recent studies have used the Drawin recipe, albeit with a correction factor S-H that is calibrated to the solar centre-to-limb variation of the triplet. We present a new model oxygen atom that incorporates inelastic O+H collisional rate coefficients using an asymptotic two-electron model based on linear combinations of atomic orbitals, combined with a free electron model based on the impulse approximation. Using a 3D hydrodynamic STAGGER model solar atmosphere and 3D non-LTE line formation calculations, we demonstrate that this physically motivated approach is able to reproduce the solar centre-to-limb variation of the triplet to 0.02 dex, without any calibration of the inelastic collisional rate coefficients or other free parameters. We infer log epsilon(O) = 8.69 +/- 0.03 from the triplet alone, strengthening the case for a low solar oxygen abundance.
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| 50. |
- Amarsi, A. M., et al.
(författare)
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Non-LTE line formation of Fe in late-type stars - III. 3D non-LTE analysis of metal-poor stars
- 2016
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Ingår i: Monthly notices of the Royal Astronomical Society. - : Oxford University Press (OUP). - 0035-8711 .- 1365-2966. ; 463:2, s. 1518-1533
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Tidskriftsartikel (refereegranskat)abstract
- As one of the most important elements in astronomy, iron abundance determinations need to be as accurate as possible. We investigate the accuracy of spectroscopic iron abundance analyses using archetypal metal-poor stars. We perform detailed 3D non-LTE radiative transfer calculations based on 3D hydrodynamic STAGGER model atmospheres, and employ a new model atom that includes new quantum-mechanical neutral hydrogen collisional rate coefficients. With the exception of the red giant HD122563, we find that the 3D non-LTE models achieve Fe I/Fe II excitation and ionization balance as well as not having any trends with equivalent width to within modelling uncertainties of 0.05 dex, all without having to invoke any microturbulent broadening; for HD122563 we predict that the current best parallax-based surface gravity is overestimated by 0.5 dex. Using a 3D non-LTE analysis, we infer iron abundances from the 3D model atmospheres that are roughly 0.1 dex higher than corresponding abundances from 1D MARCS model atmospheres; these differences go in the same direction as the non-LTE effects themselves. We make available grids of departure coefficients, equivalent widths and abundance corrections, calculated on 1D MARCS model atmospheres and horizontally and temporally averaged 3D STAGGER model atmospheres.
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