| 1. |
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| 2. |
- 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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| 3. |
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| 4. |
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- 2019
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Tidskriftsartikel (refereegranskat)
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| 5. |
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| 6. |
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| 7. |
- Cui, Wen, et al.
(författare)
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Reversible pressure-induced polymerization of Fe(C5H5)(2) doped C-70
- 2013
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Ingår i: Carbon. - : Pergamon-Elsevier Science. - 0008-6223 .- 1873-3891. ; 62, s. 447-454
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Tidskriftsartikel (refereegranskat)abstract
- High pressure Raman, IR and X-ray diffraction (XRD) studies have been carried out on C-70(Fe(C5H5)(2))(2) (hereafter, "C-70(Fc)(2)") sheets. Theoretical calculation is further used to analyze the Electron Localization Function (ELF) and charge transfer in the crystal and thus to understand the transformation of C-70(Fc)(2) under pressure. Our results show that even at room temperature dimeric phase and one dimensional (1D) polymer phase of C-70 molecules can be formed at about 3 and 8 GPa, respectively. The polymerization is found to be reversible Upon decompression and the reversibility is related to the pressure-tuned charge transfer, as well as the overridden steric repulsion of counter ions. According to the layered structure of the intercalated ferrocene molecules formed in the crystal, we suggest that ferrocene acts as not only a spacer to restrict the polymerization of C-70 molecules within a layer, but also as charge reservoir to tune the polymerization process. This supplies a possible way for us to design the polymerization of fullerenes at suitable conditions.
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| 8. |
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| 9. |
- Jiang, Pengfei, et al.
(författare)
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VLBI astrometry on the white dwarf pulsar AR Scorpii
- 2023
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Ingår i: Monthly Notices of the Royal Astronomical Society. - : Oxford University Press (OUP). - 0035-8711 .- 1365-2966. ; 520:2, s. 2942-2951
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Tidskriftsartikel (refereegranskat)abstract
- AR Scorpii (AR Sco), the only-known radio-pulsing white dwarf binary, shows unusual pulsating emission at the radio, infrared, optical, and ultraviolet bands. To determine its astrometric parameters at the radio band independently, we conducted multi-epoch Very Long Baseline Interferometry (VLBI) phase-referencing observations with the European VLBI Network at 5 GHz and the Chinese VLBI Network plus the Warkworth 30-m telescope (New Zealand) at 8.6 GHz. By using the differential VLBI astrometry, we provide high-precision astrometric measurements on the parallax (pi = 8.52(-0.07)(+0.04) mas) and proper motion (mu(alpha) = 9.48(-0.07)(+0.04) mas yr(-1), mu(delta) = -51.32(-0.38)(+0.22) mas yr (-1)). The new VLBI results agree with the optical Gaia astrometry. Our kinematic analysis reveals that the Galactic space velocities of AR Sco are quite consistent with that of both intermediate polars and polars. Combined with the previous tightest VLBI constraint on the size, our parallax distance suggests that the radio emission of AR Sco should be located within the light cylinder of its white dwarf.
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| 10. |
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| 11. |
- Liu, Dedi, et al.
(författare)
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In situ Raman and photoluminescence study on pressure-induced phase transition in C60 nanotubes
- 2012
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Ingår i: Journal of Raman Spectroscopy. - : Wiley. - 0377-0486 .- 1097-4555. ; 43:6, s. 737-740
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Tidskriftsartikel (refereegranskat)abstract
- Single crystalline C60 nanotubes having face-centered-cubic structure with diameters in the nanometer range were synthesized by a solution method. In situ Raman and photoluminescence spectroscopy under high pressure were employed to study the structural stabilities and transitions of the pristine C60 nanotubes. A phase transition, probably because of the orientational ordering of C60 molecules, from face-centered-cubic structure to simple cubic structure occurred at the pressure between 1.46 and 2.26 GPa. At above 20.41 GPa, the Raman spectrum became very diffuse and lost its fine structure in all wavenumber regions, and only two broad and asymmetry peaks initially centered at 1469 and 1570cm-1 were observed, indicating an occurrence of amorphization. This amorphous phase remained to be reversible until 31.1 GPa, and it became irreversible to the ambient pressure after the pressure cycle of 34.3 GPa was applied.
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| 12. |
- Liu, Dedi, et al.
(författare)
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Pressure-induced phase transitions of C70 nanotubes
- 2011
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Ingår i: The Journal of Physical Chemistry C. - : American Chemical Society. - 1932-7447 .- 1932-7455. ; 115:18, s. 8918-8922
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Tidskriftsartikel (refereegranskat)abstract
- Single crystalline C70 nanotubes having a face-centered-cubic (fcc) structure with diameters on a nanometer scale were synthesized by a facile solution method. In situ high pressure Raman spectroscopy and X-ray diffraction have been employed to study the structural stability and phase transitions of the pristine sample. We show that the molecular orientation-related phase transition from the fcc structure to a rhombohedral structure occurs at about 1.5 GPa, which is 1 GPa higher than in bulk C70. Also, the C70 molecules themselves are more stable in the nanotubes than in bulk crystals, manifested by a partial amorphization at 20 GPa. The crystal structure of C70 nanotubes could partially return to the initial structure after a pressure cycle above 30.8 GPa, and the C70 molecules were intact up to 43 GPa. The bulk modulus of C70 nanotubes is measured to be 50 GPa, which is twice larger than that of bulk C70.
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| 13. |
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| 14. |
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| 15. |
- Wan, Lu Ming, et al.
(författare)
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Heparanase Facilitates PMA-Induced Megakaryocytic Differentiation in K562 Cells via Interleukin 6/STAT3 Pathway
- 2020
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Ingår i: Thrombosis and Haemostasis. - : GEORG THIEME VERLAG KG. - 0340-6245 .- 2567-689X. ; 120:4, s. 647-657
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Tidskriftsartikel (refereegranskat)abstract
- Heparanase (HPSE) is an endo-beta-D-glucuronidase that cleaves heparan sulfate and hence participates in remodeling of the extracellular matrix, leading to release of cytokines that are immobilized by binding to heparan sulfate proteoglycans (HSPGs), and consequently activating signaling pathways. This function of HPSE is correlated to its expression level that is normally very low in majority of the tissues. Exceptionally, human platelets express high level of HPSE, suggesting a unique physiological role in this cell. Using K562 cell line, we found a progressive increase of HPSE during the megakaryocytic differentiation. Analysis of a series of megakaryocytic differentiation-related heparin-binding proteins (HBPs) in the cell culture medium revealed an exclusive positive correlation between the level of interleukin 6 (IL-6) and HPSE expression. IL-6 modulated megakaryocytic differentiation through activation of STAT3. Further, we demonstrated that overexpression of HPSE potentiates megakaryocytic differentiation, whereas elimination of HPSE led to a delayed differentiation. This function of HPSE is associated with its activity, as overexpression of inactive HPSE had no effect on IL-6 production and megakaryocytic differentiation. The role of HPSE is further supported by the observation in an umbilical cord blood CD34+ cells megakaryocytic differentiation model. Our data propose a novel role for HPSE in platelets production by a HPSE/IL-6/STAT3 positive feedback loop that specifically regulates megakaryocytes maturation.
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| 16. |
- Wen, Jiansen, et al.
(författare)
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Copper-based perovskites and perovskite-like halides : A review from the perspective of molecular level
- 2024
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Ingår i: Nano Energy. - : Elsevier. - 2211-2855 .- 2211-3282. ; 128
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Forskningsöversikt (refereegranskat)abstract
- The toxicity of lead and instability are crucial factors hindering the commercialization of lead-based halide perovskite materials. In recent years, copper has been considered as one of the promising alternatives to lead in perovskites due to its abundance, environmental friendliness, and unique electronic structure. A bunch of new copper-based perovskite-like materials have been synthesized and their physical properties and chemical stabilities have been explored. However, there is still a lack of a comprehensive and systematic overview regarding copper-based perovskites and perovskite-like halides from the molecular level perspective. Therefore, focusing on the molecular structure, this review provides a summary of the crystal structures, electronic properties, and application principles of copper-based all-inorganic and organic-inorganic hybrid perovskites and perovskite-like halides. Furthermore, we have discussed the limitations of copper-based perovskites and perovskite-like halides, as well as provided our outlook on their future development directions.
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| 17. |
- Zhang, Guojie, et al.
(författare)
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Comparative genomics reveals insights into avian genome evolution and adaptation
- 2014
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Ingår i: Science. - : American Association for the Advancement of Science (AAAS). - 0036-8075 .- 1095-9203. ; 346:6215, s. 1311-1320
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Tidskriftsartikel (refereegranskat)abstract
- Birds are the most species-rich class of tetrapod vertebrates and have wide relevance across many research fields. We explored bird macroevolution using full genomes from 48 avian species representing all major extant clades. The avian genome is principally characterized by its constrained size, which predominantly arose because of lineage-specific erosion of repetitive elements, large segmental deletions, and gene loss. Avian genomes furthermore show a remarkably high degree of evolutionary stasis at the levels of nucleotide sequence, gene synteny, and chromosomal structure. Despite this pattern of conservation, we detected many non-neutral evolutionary changes in protein-coding genes and noncoding regions. These analyses reveal that pan-avian genomic diversity covaries with adaptations to different lifestyles and convergent evolution of traits.
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| 18. |
- Bailey, Matthew H., et al.
(författare)
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Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples
- 2020
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Ingår i: Nature Communications. - : Springer Science and Business Media LLC. - 2041-1723. ; 11:1
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Tidskriftsartikel (refereegranskat)abstract
- The Cancer Genome Atlas (TCGA) and International Cancer Genome Consortium (ICGC) curated consensus somatic mutation calls using whole exome sequencing (WES) and whole genome sequencing (WGS), respectively. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, which aggregated whole genome sequencing data from 2,658 cancers across 38 tumour types, we compare WES and WGS side-by-side from 746 TCGA samples, finding that ~80% of mutations overlap in covered exonic regions. We estimate that low variant allele fraction (VAF < 15%) and clonal heterogeneity contribute up to 68% of private WGS mutations and 71% of private WES mutations. We observe that ~30% of private WGS mutations trace to mutations identified by a single variant caller in WES consensus efforts. WGS captures both ~50% more variation in exonic regions and un-observed mutations in loci with variable GC-content. Together, our analysis highlights technological divergences between two reproducible somatic variant detection efforts.
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| 19. |
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| 20. |
- Cacciani, Nicola, et al.
(författare)
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A prospective clinical study on the mechanisms underlying critical illness myopathy : A time-course approach
- 2022
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Ingår i: Journal of Cachexia, Sarcopenia and Muscle. - : John Wiley & Sons. - 2190-5991 .- 2190-6009. ; 13:6, s. 2669-2682
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Tidskriftsartikel (refereegranskat)abstract
- Background: Critical illness myopathy (CIM) is a consequence of modern critical care resulting in general muscle wasting and paralyses of all limb and trunk muscles, resulting in prolonged weaning from the ventilator, intensive care unit (ICU) treatment and rehabilitation. CIM is associated with severe morbidity/mortality and significant negative socioeconomic consequences, which has become increasingly evident during the current COVID-19 pandemic, but underlying mechanisms remain elusive.Methods: Ten neuro-ICU patients exposed to long-term controlled mechanical ventilation were followed with repeated muscle biopsies, electrophysiology and plasma collection three times per week for up to 12 days. Single muscle fibre contractile recordings were conducted on the first and final biopsy, and a multiomics approach was taken to analyse gene and protein expression in muscle and plasma at all collection time points.Results: (i) A progressive preferential myosin loss, the hallmark of CIM, was observed in all neuro-ICU patients during the observation period (myosin:actin ratio decreased from 2.0 in the first to 0.9 in the final biopsy, P < 0.001). The myosin loss was coupled to a general transcriptional downregulation of myofibrillar proteins (P < 0.05; absolute fold change >2) and activation of protein degradation pathways (false discovery rate [FDR] <0.1), resulting in significant muscle fibre atrophy and loss in force generation capacity, which declined >65% during the 12 day observation period (muscle fibre cross-sectional area [CSA] and maximum single muscle fibre force normalized to CSA [specific force] declined 30% [P < 0.007] and 50% [P < 0.0001], respectively). (ii) Membrane excitability was not affected as indicated by the maintained compound muscle action potential amplitude upon supramaximal stimulation of upper and lower extremity motor nerves. (iii) Analyses of plasma revealed early activation of inflammatory and proinflammatory pathways (FDR < 0.1), as well as a redistribution of zinc ions from plasma.Conclusions: The mechanical ventilation-induced lung injury with release of cytokines/chemokines and the complete mechanical silencing uniquely observed in immobilized ICU patients affecting skeletal muscle gene/protein expression are forwarded as the dominant factors triggering CIM.
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| 21. |
- Chatziioannou, Aristotelis, et al.
(författare)
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Blood-based omic profiling supports female susceptibility to tobacco smoke-induced cardiovascular diseases
- 2017
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Ingår i: Scientific Reports. - : Springer Science and Business Media LLC. - 2045-2322. ; 7
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Tidskriftsartikel (refereegranskat)abstract
- We recently reported that differential gene expression and DNA methylation profiles in blood leukocytes of apparently healthy smokers predicts with remarkable efficiency diseases and conditions known to be causally associated with smoking, suggesting that blood-based omic profiling of human populations may be useful for linking environmental exposures to potential health effects. Here we report on the sex-specific effects of tobacco smoking on transcriptomic and epigenetic features derived from genome-wide profiling in white blood cells, identifying 26 expression probes and 92 CpG sites, almost all of which are affected only in female smokers. Strikingly, these features relate to numerous genes with a key role in the pathogenesis of cardiovascular disease, especially thrombin signaling, including the thrombin receptors on platelets F2R (coagulation factor II (thrombin) receptor; PAR1) and GP5 (glycoprotein 5), as well as HMOX1 (haem oxygenase 1) and BCL2L1 (BCL2-like 1) which are involved in protection against oxidative stress and apoptosis, respectively. These results are in concordance with epidemiological evidence of higher female susceptibility to tobacco-induced cardiovascular disease and underline the potential of blood-based omic profiling in hazard and risk assessment.
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| 22. |
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| 23. |
- Chen, Wen, 1988, et al.
(författare)
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VLBI Astrometry of radio stars to link radio and optical celestial reference frames. I. HD 199178 & AR Lacertae
- 2023
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Ingår i: Monthly Notices of the Royal Astronomical Society. - 0035-8711 .- 1365-2966. ; 524:4, s. 5357-5367
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Tidskriftsartikel (refereegranskat)abstract
- To accurately link the radio and optical Celestial Reference Frames (CRFs) at optical bright end, i.e. with GaiaG-band magnitude ≾13, increasing number and improving sky distribution of radio stars with accurate astrometric parameters from both Very Long Baseline Interferometry (VLBI) and Gaia measurements are mandatory. We selected two radio stars HD 199178 and AR Lacertae as the target for a pilot program for the frame link, using the Very Long Baseline Array at 15 GHz at six epochs spanning about 1 yr, to measure their astrometric parameters. The measured parallax of HD 199178 is 8.949 ± 0.059 mas and the proper motion is μαcos δ = 26.393 ± 0.093 and μδ = −0.950 ± 0.083 mas yr−1, while the parallax of AR Lac is 23.459 ± 0.094 mas and the proper motion is μαcos δ = −51.906 ± 0.138 and μδ = 46.732 ± 0.131 mas yr−1. Our VLBI measured astrometric parameters have accuracies about 4–5 times better than the corresponding historic VLBI measurements and comparable accuracies with those from Gaia, validating the feasibility of frame link using radio stars. With the updated astrometric parameters for these two stars, there is a ∼25 per cent reduction of the uncertainties on the Y-axis for both orientation and spin parameters.
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| 24. |
- Cramer, Joel, et al.
(författare)
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Spin transport across antiferromagnets induced by the spin Seebeck effect
- 2018
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Ingår i: Journal of Physics D. - : IOP PUBLISHING LTD. - 0022-3727 .- 1361-6463. ; 51:14
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Tidskriftsartikel (refereegranskat)abstract
- For prospective spintronics devices based on the propagation of pure spin currents, antiferromagnets are an interesting class of materials that potentially entail a number of advantages as compared to ferromagnets. Here, we present a detailed theoretical study of magnonic spin current transport in ferromagnetic-antiferromagnetic multilayers by using atomistic spin dynamics simulations. The relevant length scales of magnonic spin transport in antiferromagnets are determined. We demonstrate the transfer of angular momentum from a ferromagnet into an antiferromagnet due to the excitation of only one magnon branch in the antiferromagnet. As an experimental system, we ascertain the transport across an antiferromagnet in Y3Fe5O12 vertical bar Ir20Mn80 vertical bar Pt heterostructures. We determine the spin transport signals for spin currents generated in the Y3Fe5O12 by the spin Seebeck effect and compare to measurements of the spin Hall magnetoresistance in the heterostructure stack. By means of temperature-dependent and thickness-dependent measurements, we deduce conclusions on the spin transport mechanism across Ir20Mn80 and furthermore correlate it to its paramagnetic-antiferromagnetic phase transition.
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| 25. |
- Cui, Wen, et al.
(författare)
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Synthesis of alkali-metal-doped C60 nanotubes
- 2011
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Ingår i: Diamond and Related Materials. - : Elsevier BV. ; , s. 93-96
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Konferensbidrag (refereegranskat)abstract
- C60 nanotubes have been synthesized by a solution–solution method. After degassing in a dynamic vacuum, the C60 nanotubes were doped with alkali metals by means of vapor evaporation method. Different temperatures have been studied to evaporate the alkali metals for the doping experiments. Raman spectrum was further employed to analyze the doping concentration of the obtained samples. It was found that all three alkali metals (Li, Na and K) used can be efficiently doped into the C60 nanotubes, forming AxC60 nanotubes. The doping concentration of Li, Na changed from low to high level, depending on the experiment temperatures, while K doping always gave saturated doping. The melt points, the ionic sizes and vapor pressures of alkali metals were thought to affect the final doping results.
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