| 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. |
- Ji, Cheng, et al.
(författare)
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Crystallography of low Z material at ultrahigh pressure : Case study on solid hydrogen
- 2020
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Ingår i: Matter and Radiation at Extremes. - : American Institute of Physics (AIP). - 2468-2047 .- 2468-080X. ; 5:3
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Tidskriftsartikel (refereegranskat)abstract
- Diamond anvil cell techniques have been improved to allow access to the multimegabar ultrahigh-pressure region for exploring novel phenomena in condensed matter. However, the only way to determine crystal structures of materials above 100 GPa, namely, X-ray diffraction (XRD), especially for low Z materials, remains nontrivial in the ultrahigh-pressure region, even with the availability of brilliant synchrotron X-ray sources. In this work, we perform a systematic study, choosing hydrogen (the lowest X-ray scatterer) as the subject, to understand how to better perform XRD measurements of low Z materials at multimegabar pressures. The techniques that we have developed have been proved to be effective in measuring the crystal structure of solid hydrogen up to 254 GPa at room temperature [C. Ji et al., Nature 573, 558–562 (2019)]. We present our discoveries and experiences with regard to several aspects of this work, namely, diamond anvil selection, sample configuration for ultrahigh-pressure XRD studies, XRD diagnostics for low Z materials, and related issues in data interpretation and pressure calibration. We believe that these methods can be readily extended to other low Z materials and can pave the way for studying the crystal structure of hydrogen at higher pressures, eventually testing structural models of metallic hydrogen.
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| 4. |
- Ji, Cheng, et al.
(författare)
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Ultrahigh-pressure isostructural electronic transitions in hydrogen
- 2019
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Ingår i: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 573:7775, s. 558-562
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Tidskriftsartikel (refereegranskat)abstract
- High-pressure transitions are thought to modify hydrogen molecules to a molecular metallic solid and finally to an atomic metal(1), which is predicted to have exotic physical properties and the topology of a two-component (electron and proton) superconducting superfluid condensate(2,3). Therefore, understanding such transitions remains an important objective in condensed matter physics(4,5). However, measurements of the crystal structure of solid hydrogen, which provides crucial information about the metallization of hydrogen under compression, are lacking for most high-pressure phases, owing to the considerable technical challenges involved in X-ray and neutron diffraction measurements under extreme conditions. Here we present a single-crystal X-ray diffraction study of solid hydrogen at pressures of up to 254 gigapascals that reveals the crystallographic nature of the transitions from phase I to phases III and IV. Under compression, hydrogen molecules remain in the hexagonal close-packed (hcp) crystal lattice structure, accompanied by a monotonic increase in anisotropy. In addition, the pressure-dependent decrease of the unit cell volume exhibits a slope change when entering phase IV, suggesting a second-order isostructural phase transition. Our results indicate that the precursor to the exotic two-component atomic hydrogen may consist of electronic transitions caused by a highly distorted hcp Brillouin zone and molecular-symmetry breaking.
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| 5. |
- Mao, Wendy L., et al.
(författare)
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Distortions and stabilization of simple-cubic calcium at high pressure and low temperature
- 2010
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Ingår i: Proceedings of the National Academy of Sciences of the United States of America. - : Proceedings of the National Academy of Sciences. - 0027-8424 .- 1091-6490. ; 107:22, s. 9965-9968
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Tidskriftsartikel (refereegranskat)abstract
- Ca-III, the first superconducting calcium phase under pressure, was identified as simple-cubic (sc) by previous X-ray diffraction (XRD) experiments. In contrast, all previous theoretical calculations showed that sc had a higher enthalpy than many proposed structures and had an imaginary (unstable) phonon branch. By using our newly developed submicrometer high-pressure single-crystal XRD, cryogenic high-pressure XRD, and theoretical calculations, we demonstrate that Ca-III is neither exactly sc nor any of the lower-enthalpy phases, but sustains the sc-like, primitive unit by a rhombohedral distortion at 300 K and a monoclinic distortion below 30 K. This surprising discovery reveals a scenario that the high-pressure structure of calcium does not go to the zero-temperature global enthalpy minimum but is dictated by high-temperature anharmonicity and low-temperature metastability fine-tuned with phonon stability at the local minimum.
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| 6. |
- Zeng, Qiao-Shi, et al.
(författare)
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Substitutional alloy of Ce and Al
- 2009
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Ingår i: Proceedings of the National Academy of Sciences of the United States of America. - : Proceedings of the National Academy of Sciences. - 0027-8424 .- 1091-6490. ; 106:8, s. 2515-2518
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Tidskriftsartikel (refereegranskat)abstract
- The formation of substitutional alloys has been restricted to elements with similar atomic radii and electronegativity. Using high-pressure at 298 K, we synthesized a face-centered cubic disordered alloy of highly dissimilar elements (large Ce and small Al atoms) by compressing the Ce3Al intermetallic compound > 15 GPa or the Ce3Al metallic glass > 25 GPa. Synchrotron X-ray diffraction, Ce L-3-edge absorption spectroscopy, and ab initio calculations revealed that the pressure-induced Kondo volume collapse and 4f electron delocalization of Ce reduced the differences between Ce and Al and brought them within the Hume-Rothery (HR) limit for substitutional alloying. The alloy remained after complete release of pressure, which was also accompanied by the transformation of Ce back to its ambient 4f electron localized state and reversal of the Kondo volume collapse, resulting in a non-HR alloy at ambient conditions.
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| 7. |
- Belonoshko, Anatoly B., et al.
(författare)
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Atomic Diffusion in Solid Molecular Hydrogen
- 2013
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Ingår i: Scientific Reports. - : Springer Science and Business Media LLC. - 2045-2322. ; 3, s. 2340-
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Tidskriftsartikel (refereegranskat)abstract
- We performed ab initio molecular dynamics simulations of the C2c and Cmca-12 phases of hydrogen at pressures from 210 to 350 GPa. These phases were predicted to be stable at 0 K and pressures above 200 GPa. However, systematic studies of temperature impact on properties of these phases have not been performed so far. Filling this gap, we observed that on temperature increase diffusion sets in the Cmca-12 phase, being absent in C2c. We explored the mechanism of diffusion and computed melting curve of hydrogen at extreme pressures. The results suggest that the recent experiments claiming conductive hydrogen at the pressure around 260 GPa and ambient temperature might be explained by the diffusion. The diffusion might also be the reason for the difference in Raman spectra obtained in recent experiments.
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| 8. |
- Ding, Yang, et al.
(författare)
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Structural phase transition of vanadium at 69 GPa
- 2007
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Ingår i: Physical Review Letters. - 0031-9007 .- 1079-7114. ; 98:8
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Tidskriftsartikel (refereegranskat)abstract
- A phase transition was observed at 63-69 GPa and room temperature in vanadium with synchrotron x-ray diffraction. The transition is characterized as a rhombohedral lattice distortion of the body-centered-cubic vanadium without a discontinuity in the pressure-volume data, thus representing a novel type of transition that has never been observed in elements. Instead of driven by the conventional s-d electronic transition mechanism, the phase transition could be associated with the softening of C-44 trigonal elasticity tensor that originates from the combination of Fermi surface nesting, band Jahn-Teller distortion, and electronic topological transition.
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| 9. |
- Ji, Cheng, et al.
(författare)
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Stability of Ar(H2)2 to 358 GPa
- 2017
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Ingår i: Proceedings of the National Academy of Sciences of the United States of America. - : Proceedings of the National Academy of Sciences. - 0027-8424 .- 1091-6490. ; 114:14, s. 3596-3600
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Tidskriftsartikel (refereegranskat)abstract
- "Chemical precompression" through introducing impurity atoms into hydrogen has been proposed as a method to facilitate metallization of hydrogen under external pressure. Here we selected Ar(H-2)(2), a hydrogen-rich compound with molecular hydrogen, to explore the effect of "doping" on the intermolecular interaction of H-2 molecules and metallization at ultrahigh pressure. Ar(H-2)(2) was studied experimentally by synchrotron X-ray diffraction to 265 GPa, by Raman and optical absorption spectroscopy to 358 GPa, and theoretically using the density-functional theory. Our measurements of the optical bandgap and the vibron frequency show that Ar(H-2)(2) retains 2-eV bandgap and H-2 molecular units up to 358 GPa. This is attributed to reduced intermolecular interactions between H-2 molecules in Ar(H-2)(2) compared with that in solid H-2. A splitting of the molecular vibron mode above 216 GPa suggests an orientational ordering transition, which is not accompanied by a change in lattice symmetry. The experimental and theoretical equations of state of Ar(H-2)(2) provide direct insight into the structure and bonding of this hydrogen-rich system, suggesting a negative chemical pressure on H-2 molecules brought about by doping of Ar.
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| 10. |
- Kotmool, Komsilp, et al.
(författare)
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Revealing an unusual transparent phase of superhard iron tetraboride under high pressure
- 2014
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Ingår i: Proceedings of the National Academy of Sciences of the United States of America. - : Proceedings of the National Academy of Sciences. - 0027-8424 .- 1091-6490. ; 111:48, s. 17050-17053
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Tidskriftsartikel (refereegranskat)abstract
- First principles-based electronic structure calculations of super-hard iron tetraboride (FeB4) under high pressure have been undertaken in this study. Starting with a "conventional" superconducting phase of this material under high pressure leads to an unexpected phase transition toward a semiconducting one. This transition occurred at 53.7 GPa, and this pressure acts as a demarcation between two distinct crystal symmetries, metallic orthorhombic and semiconducting tetragonal phases, with Pnnm and I4(1)/acd space groups, respectively. In this work, the electron-phonon coupling-derived superconducting T-c has been determined up to 60 GPa and along with optical band gap variation with increasing pressure up to 300 GPa. The dynamic stability has been confirmed by phonon dispersion calculations throughout this study.
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