| 1. |
- Reinthaler, Eva M., et al.
(författare)
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TPP2 mutation associated with sterile brain inflammation mimicking MS
- 2018
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Ingår i: NEUROLOGY-GENETICS. - 2376-7839. ; 4:6
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Tidskriftsartikel (refereegranskat)abstract
- Objective To ascertain the genetic cause of a consanguineous family from Syria suffering from a sterile brain inflammation mimicking a mild nonprogressive form of MS.Methods We used homozygosity mapping and next-generation sequencing to detect the disease-causing gene in the affected siblings. In addition, we performed RNA and protein expression studies, enzymatic activity assays, immunohistochemistry, and targeted sequencing of further MS cases from Austria, Germany, Canada and Jordan.Results In this study, we describe the identification of a homozygous missense mutation (c.82T>G, p.Cys28Gly) in the tripeptidyl peptidase II (TPP2) gene in all 3 affected siblings of the family. Sequencing of all TPP2-coding exons in 826 MS cases identified one further homozygous missense variant (c.2027C>T, p.Thr676Ile) in a Jordanian MS patient. TPP2 protein expression in whole blood was reduced in the affected siblings. In contrast, TPP2 protein expression in postmortem brain tissue from MS patients without TPP2 mutations was highly upregulated.Conclusions The homozygous TPP2 mutation (p.Cys28Gly) is likely responsible for the inflammation phenotype in this family. TPP2 is an ubiquitously expressed serine peptidase that removes tripeptides from the N-terminal end of longer peptides. TPP2 is involved in various biological processes including the destruction of major histocompatibility complex Class I epitopes. Recessive loss-of-function mutations in TPP2 were described in patients with Evans syndrome, a rare autoimmune disease affecting the hematopoietic system. Based on the gene expression results in our MS autopsy brain samples, we further suggest that TPP2 may play a broader role in the inflammatory process in MS.
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| 2. |
- de Vera, Jean-Pierre, et al.
(författare)
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Limits of Life and the Habitability of Mars : The ESA Space Experiment BIOMEX on the ISS
- 2019
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Ingår i: Astrobiology. - : Mary Ann Liebert. - 1531-1074 .- 1557-8070. ; 19:2, s. 145-157
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Tidskriftsartikel (övrigt vetenskapligt/konstnärligt)abstract
- BIOMEX (BIOlogy and Mars EXperiment) is an ESA/Roscosmos space exposure experiment housed within the exposure facility EXPOSE-R2 outside the Zvezda module on the International Space Station (ISS). The design of the multiuser facility supports-among others-the BIOMEX investigations into the stability and level of degradation of space-exposed biosignatures such as pigments, secondary metabolites, and cell surfaces in contact with a terrestrial and Mars analog mineral environment. In parallel, analysis on the viability of the investigated organisms has provided relevant data for evaluation of the habitability of Mars, for the limits of life, and for the likelihood of an interplanetary transfer of life (theory of lithopanspermia). In this project, lichens, archaea, bacteria, cyanobacteria, snow/permafrost algae, meristematic black fungi, and bryophytes from alpine and polar habitats were embedded, grown, and cultured on a mixture of martian and lunar regolith analogs or other terrestrial minerals. The organisms and regolith analogs and terrestrial mineral mixtures were then exposed to space and to simulated Mars-like conditions by way of the EXPOSE-R2 facility. In this special issue, we present the first set of data obtained in reference to our investigation into the habitability of Mars and limits of life. This project was initiated and implemented by the BIOMEX group, an international and interdisciplinary consortium of 30 institutes in 12 countries on 3 continents. Preflight tests for sample selection, results from ground-based simulation experiments, and the space experiments themselves are presented and include a complete overview of the scientific processes required for this space experiment and postflight analysis. The presented BIOMEX concept could be scaled up to future exposure experiments on the Moon and will serve as a pretest in low Earth orbit.
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| 3. |
- Dutta, Biswanath, et al.
(författare)
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Phonons in magnetically disordered materials : Magnetic versus phononic time scales
- 2020
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Ingår i: Physical Review B. - : AMER PHYSICAL SOC. - 2469-9950 .- 2469-9969. ; 101:9
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Tidskriftsartikel (refereegranskat)abstract
- The lattice dynamics in magnetic materials, such as Fe depends on the degree of disorder of the atomic magnetic moments and the time scale of spin fluctuations. Using first-principles methods, we have studied this effect by determining the force constant matrix in two limits: (i) When spin fluctuations are much faster than the atom vibrations, their combined impact is captured by a spin-space averaged force constant matrix, (ii) when individual spin fluctuations are sufficiently slow to scatter the phonon modes, the itinerant coherent potential approximation with spin-pair resolved force constants (i.e., Phi(up arrow up arrow), Phi(down arrow down arrow), and Phi(up arrow down arrow)) is employed in this paper. The physical consequences for the vibrational spectral functions are analyzed by systematically modifying the input parameters (magnetization and ratio of force constants betweens atoms with equal and opposite spin directions) and by deriving them for the prototype material system bcc Fe from first-principles calculations. In the paramagnetic regime, the two limits yield identical phonon spectra. Below the Curie temperature, however, there are regions in the parametric study that show qualitative differences, including a broadening of the phonon peaks. For bcc Fe, however, the quantitative modifications of phonon frequencies turn out to be small.
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| 4. |
- Gubaev, Konstantin, et al.
(författare)
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Finite-temperature interplay of structural stability, chemical complexity, and elastic properties of bcc multicomponent alloys from ab initio trained machine-learning potentials
- 2021
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Ingår i: Physical Review Materials. - : AMER PHYSICAL SOC. - 2475-9953. ; 5:7
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Tidskriftsartikel (refereegranskat)abstract
- An active learning approach to train machine-learning interatomic potentials (moment tensor potentials) for multicomponent alloys to ab initio data is presented. Employing this approach, the disordered body-centered cubic (bcc) TiZrHfTax system with varying Ta concentration is investigated via molecular dynamics simulations. Our results show a strong interplay between elastic properties and the structural. phase stability, strongly affecting the mechanical properties. Based on these insights we systematically screen composition space for regimes where elastic constants show little or no temperature dependence (elinvar effect).
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| 5. |
- Kostiuchenko, Tatiana, et al.
(författare)
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Short-range order in face-centered cubic VCoNi alloys
- 2020
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Ingår i: Physical Review Materials. - : American Physical Society. - 2475-9953. ; 4:11
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Tidskriftsartikel (refereegranskat)abstract
- Concentrated solid solutions including the class of high entropy alloys (HEAs) have attracted enormous attention recently. Among these alloys a recently developed face-centered cubic (fcc) equiatomic VCoNi alloy revealed extraordinary high yield strength, exceeding previous high-strength fcc CrCoNi and FeCoNiCrMn alloys. Significant lattice distortions had been reported in the VCoNi solid solution. There is, however, a lack of knowledge about potential short-range order (SRO) and its implications for most of these alloys. We performed first-principles calculations and Monte Carlo simulations to compute the degree of SRO for fcc VCoNi, namely, by utilizing the coherent-potential approximation in combination with the generalized perturbation method as well as the supercell method in combination with recently developed machine-learned potentials. We analyze the chemical SRO parameters as well as the impact on other properties such as relaxation energies and lattice distortions.
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| 6. |
- Lang, Daniel, et al.
(författare)
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The Physcomitrella patens chromosome-scale assembly reveals moss genome structure and evolution
- 2018
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Ingår i: The Plant Journal. - : Wiley. - 0960-7412 .- 1365-313X. ; 93:3, s. 515-533
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Tidskriftsartikel (refereegranskat)abstract
- The draft genome of the moss model, Physcomitrella patens, comprised approximately 2000 unordered scaffolds. In order to enable analyses of genome structure and evolution we generated a chromosome-scale genome assembly using genetic linkage as well as (end) sequencing of long DNA fragments. We find that 57% of the genome comprises transposable elements (TEs), some of which may be actively transposing during the life cycle. Unlike in flowering plant genomes, gene-and TE-rich regions show an overall even distribution along the chromosomes. However, the chromosomes are mono-centric with peaks of a class of Copia elements potentially coinciding with centromeres. Gene body methylation is evident in 5.7% of the protein-coding genes, typically coinciding with low GC and low expression. Some giant virus insertions are transcriptionally active and might protect gametes from viral infection via siRNA mediated silencing. Structure-based detection methods show that the genome evolved via two rounds of whole genome duplications (WGDs), apparently common in mosses but not in liverworts and hornworts. Several hundred genes are present in colinear regions conserved since the last common ancestor of plants. These syntenic regions are enriched for functions related to plant-specific cell growth and tissue organization. The P. patens genome lacks the TE-rich pericentromeric and gene-rich distal regions typical for most flowering plant genomes. More non-seed plant genomes are needed to unravel how plant genomes evolve, and to understand whether the P. patens genome structure is typical for mosses or bryophytes.
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| 7. |
- Rao, Ziyuan, et al.
(författare)
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Machine learning-enabled high-entropy alloy discovery
- 2022
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Ingår i: Science. - : American Association for the Advancement of Science (AAAS). - 0036-8075 .- 1095-9203. ; 378:6615, s. 78-84
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Tidskriftsartikel (refereegranskat)abstract
- High-entropy alloys are solid solutions of multiple principal elements that are capable of reaching composition and property regimes inaccessible for dilute materials. Discovering those with valuable properties, however, too often relies on serendipity, because thermodynamic alloy design rules alone often fail in high-dimensional composition spaces. We propose an active learning strategy to accelerate the design of high-entropy Invar alloys in a practically infinite compositional space based on very sparse data. Our approach works as a closed-loop, integrating machine learning with density-functional theory, thermodynamic calculations, and experiments. After processing and characterizing 17 new alloys out of millions of possible compositions, we identified two high-entropy Invar alloys with extremely low thermal expansion coefficients around 2 x 10-6 per degree kelvin at 300 kelvin. We believe this to be a suitable pathway for the fast and automated discovery of high-entropy alloys with optimal thermal, magnetic, and electrical properties.
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| 8. |
- Stockem, Irina, et al.
(författare)
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Anomalous Phonon Lifetime Shortening in Paramagnetic CrN Caused by Spin-Lattice Coupling: A Combined Spin and Ab Initio Molecular Dynamics Study
- 2018
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Ingår i: Physical Review Letters. - : AMER PHYSICAL SOC. - 0031-9007 .- 1079-7114. ; 121:12
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Tidskriftsartikel (refereegranskat)abstract
- We study the mutual coupling of spin fluctuations and lattice vibrations in paramagnetic CrN by combining atomistic spin dynamics and ab initio molecular dynamics. The two degrees of freedom are dynamically coupled, leading to nonadiabatic effects. Those effects suppress the phonon lifetimes at low temperature compared to an adiabatic approach. The dynamic coupling identified here provides an explanation for the experimentally observed unexpected temperature dependence of the thermal conductivity of magnetic semiconductors above the magnetic ordering temperature.
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| 9. |
- Zhang, Xi, et al.
(författare)
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Temperature dependence of the stacking-fault Gibbs energy for Al, Cu, and Ni
- 2018
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Ingår i: Physical Review B. Condensed Matter and Materials Physics. - : American Physical Society (APS). - 1098-0121 .- 1550-235X. ; 98:22
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Tidskriftsartikel (refereegranskat)abstract
- The temperature-dependent intrinsic stacking fault Gibbs energy is computed based on highly converged density-functional-theory (DFT) calculations for the three prototype face-centered cubic metals Al, Cu, and Ni. All relevant temperature-dependent contributions are considered including electronic, vibrational, magnetic, and explicit anharmonic Gibbs energy contributions as well as coupling terms employing state-of-the-art statistical sampling techniques. Particular emphasis is put on a careful comparison of different theoretical concepts to derive the stacking fault energy such as the axial-next-nearest-neighbor-Ising (ANNNI) model or the vacuum-slab approach. Our theoretical results are compared with an extensive set of previous theoretical and experimental data. Large uncertainties in the experimental data highlight the necessity of complementary parameter-free calculations. Specifically, the temperature dependence is experimentally unknown and poorly described by thermodynamic databases. Whereas CALPHAD derived data shows an increase of the stacking fault energy with temperature for two of the systems (Cu and Ni), our results predict a decrease for all studied systems. For Ni, the temperature induced change is in fact so strong that in the temperature interval relevant for super-alloy applications the stacking fault energy falls below one third of the low temperature value. Such large changes clearly call for a revision of the stacking fault energy when modeling or designing alloys based on such elements.
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| 10. |
- Zhu, Li-Fang, et al.
(författare)
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Performance of the standard exchange-correlation functionals in predicting melting properties fully from first principles : Application to Al and magnetic Ni
- 2020
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Ingår i: Physical Review B. - : AMER PHYSICAL SOC. - 2469-9950 .- 2469-9969. ; 101:14
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Tidskriftsartikel (refereegranskat)abstract
- We apply the efficient two-optimized references thermodynamic integration using Langevin dynamics method [Phys. Rey. B 96, 224202 (2017)] to calculate highly accurate melting properties of Al and magnetic Ni from first principles. For Ni we carefully investigate the impact of magnetism on the liquid and solid free energies including longitudinal spin fluctuations and the reverse influence of atomic vibrations on magnetic properties. We show that magnetic fluctuations are effectively canceling out for both phases and are thus not altering the predicted melting temperature. For both elements, the generalized gradient approximation (GGA) and the local-density approximation (LDA) are used for the exchange-correlation functional revealing a reliable ab initio confidence interval capturing the respective experimental melting point, enthalpy of fusion, and entropy of fusion.
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