| 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. |
- Wang, Zhaoming, et al.
(författare)
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Imputation and subset-based association analysis across different cancer types identifies multiple independent risk loci in the TERT-CLPTM1L region on chromosome 5p15.33
- 2014
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Ingår i: Human Molecular Genetics. - : Oxford University Press (OUP). - 0964-6906 .- 1460-2083. ; 23:24, s. 6616-6633
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Tidskriftsartikel (refereegranskat)abstract
- Genome-wide association studies (GWAS) have mapped risk alleles for at least 10 distinct cancers to a small region of 63 000 bp on chromosome 5p15.33. This region harbors the TERT and CLPTM1L genes; the former encodes the catalytic subunit of telomerase reverse transcriptase and the latter may play a role in apoptosis. To investigate further the genetic architecture of common susceptibility alleles in this region, we conducted an agnostic subset-based meta-analysis (association analysis based on subsets) across six distinct cancers in 34 248 cases and 45 036 controls. Based on sequential conditional analysis, we identified as many as six independent risk loci marked by common single-nucleotide polymorphisms: five in the TERT gene (Region 1: rs7726159, P = 2.10 × 10(-39); Region 3: rs2853677, P = 3.30 × 10(-36) and PConditional = 2.36 × 10(-8); Region 4: rs2736098, P = 3.87 × 10(-12) and PConditional = 5.19 × 10(-6), Region 5: rs13172201, P = 0.041 and PConditional = 2.04 × 10(-6); and Region 6: rs10069690, P = 7.49 × 10(-15) and PConditional = 5.35 × 10(-7)) and one in the neighboring CLPTM1L gene (Region 2: rs451360; P = 1.90 × 10(-18) and PConditional = 7.06 × 10(-16)). Between three and five cancers mapped to each independent locus with both risk-enhancing and protective effects. Allele-specific effects on DNA methylation were seen for a subset of risk loci, indicating that methylation and subsequent effects on gene expression may contribute to the biology of risk variants on 5p15.33. Our results provide strong support for extensive pleiotropy across this region of 5p15.33, to an extent not previously observed in other cancer susceptibility loci.
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| 3. |
- Cui, Xing-Mei, et al.
(författare)
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Unique UV-Erasable In-Ga-Zn-O TFT Memory With Self-Assembled Pt Nanocrystals
- 2013
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Ingår i: IEEE Electron Device Letters. - 0741-3106 .- 1558-0563. ; 34:8, s. 1011-1013
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Tidskriftsartikel (refereegranskat)abstract
- Semiconducting amorphous indium-gallium-zinc oxide (a-IGZO) films are integrated with an Al2O3/Pt-nanocrystals/ Al2O3 gate-stack to form UV-erasable thin-film transistor (TFT) memory. The threshold voltage (V-th), sub-threshold swing, I-ON/I-OFF ratio, and effective electron mobility of the fabricated devices are 2.1 V, 0.39 V/decade, similar to 10(6), and 8.4 cm(2)/V.s, respectively. A positive V-th shift of 2.25 V is achieved after 1-ms programming at 10 V-th, whereas a negative V-th shift as large as 3.48 V is attained after 5-s UV erasing. In addition, a 10-year memory window of 2.56 V is extrapolated at room temperature. This high-performance a-IGZO TFT memory is suitable for optical touch-panel applications.
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| 4. |
- Li, Wei, et al.
(författare)
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Generalized stacking fault energies of alloys
- 2014
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Ingår i: Journal of Physics. - : IOP Publishing. - 0953-8984 .- 1361-648X. ; 26:26, s. 265005-
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Tidskriftsartikel (refereegranskat)abstract
- The generalized stacking fault energy (gamma surface) provides fundamental physics for understanding the plastic deformation mechanisms. Using the ab initio exact muffin-tin orbitals method in combination with the coherent potential approximation, we calculate the. surface for the disordered Cu-Al, Cu-Zn, Cu-Ga, Cu-Ni, Pd-Ag and Pd-Au alloys. Studying the effect of segregation of the solute to the stacking fault planes shows that only the local chemical composition affects the. surface. The calculated alloying trends are discussed using the electronic band structure of the base and distorted alloys. Based on our. surface results, we demonstrate that the previous revealed 'universal scaling law' between the intrinsic energy barriers (IEBs) is well obeyed in random solid solutions. This greatly simplifies the calculations of the twinning measure parameters or the critical twinning stress. Adopting two twinnability measure parameters derived from the IEBs, we find that in binary Cu alloys, Al, Zn and Ga increase the twinnability, while Ni decreases it. Aluminum and gallium yield similar effects on the twinnability.
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| 5. |
- Li, Wei, et al.
(författare)
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The effect of Al on the 475 degrees C embrittlement of Fe-Cr alloys
- 2013
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Ingår i: Computational materials science. - : Elsevier BV. - 0927-0256 .- 1879-0801. ; 74, s. 101-106
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Tidskriftsartikel (refereegranskat)abstract
- Aluminum addition to ferritic stainless steels was found to effectively suppress the deleterious 475 degrees C embrittlement resulting from the phase decomposition in concentrated Fe-Cr alloys. With the aim of revealing the mechanism behind this prosperous phenomenon, here we investigate the effect of Al on the interfacial energy and formation energy of Fe-Cr solid solutions. The interface between the decomposed Fe-rich alpha and Cr-rich alpha' phases carries a positive excess energy, which is of significant importance on determining the process of phase separation. Using ab initio alloy theory, we show that for the alpha-Fe70Cr20Al10/alpha'-Fe100-x-yCryAlx (0 <= x <= 10, 55 <= y <= 80) interface, the Al content (x) barely changes the interfacial energy. However, for the alpha-Fe100-x-yCryAlx/alpha'-Fe10Cr90 (0 <= x <= 10, 0 <= y <= 25) interface, the interfacial energy increases with Al content due to the variation of the formation energies of the Fe-Cr alloys upon Al alloying. Our ab initio results are supported by CALPHAD calculations, and suggest that the beneficial effect of Al on ferritic steels is mainly due to its thermodynamical effect on the alpha' phase.
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| 6. |
- Li, Yan-Ling, et al.
(författare)
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Formation of Nanofoam carbon and re-emergence of Superconductivity in compressed CaC6
- 2013
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Ingår i: Scientific Reports. - : Springer Science and Business Media LLC. - 2045-2322. ; 3, s. 3331-
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Tidskriftsartikel (refereegranskat)abstract
- Pressure can tune material's electronic properties and control its quantum state, making some systems present disconnected superconducting region as observed in iron chalcogenides and heavy fermion CeCu2Si2. For CaC6 superconductor (T-c of 11.5 K), applying pressure firstTc increases and then suppresses and the superconductivity of this compound is eventually disappeared at about 18 GPa. Here, we report a theoretical finding of the re-emergence of superconductivity in heavily compressed CaC6. The predicted phase III (space group Pmmn) with formation of carbon nanofoam is found to be stable at wide pressure range with a Tc up to 14.7 K at 78 GPa. Diamond-like carbon structure is adhered to the phase IV (Cmcm) for compressed CaC6 after 126 GPa, which has bad metallic behavior, indicating again departure from superconductivity. Re-emerged superconductivity in compressed CaC6 paves a new way to design new-type superconductor by inserting metal into nanoporous host lattice.
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| 7. |
- Li, Yan-Ling, et al.
(författare)
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Pressure-induced superconductivity in CaC2
- 2013
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Ingår i: Proceedings of the National Academy of Sciences of the United States of America. - : National Academy of Sciences. - 0027-8424 .- 1091-6490. ; 110:23, s. 9289-9294
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Tidskriftsartikel (refereegranskat)abstract
- Carbon can exist as isolated dumbbell, 1D chain, 2D plane, and 3D network in carbon solids or carbon-based compounds, which attributes to its rich chemical binding way, including sp-, sp(2)-, and sp(3)-hybridized bonds. sp(2)-hybridizing carbon always captures special attention due to its unique physical and chemical property. Here, using an evolutionary algorithm in conjunction with ab initio method, we found that, under compression, dumbbell carbon in CaC2 can be polymerized first into 1D chain and then into ribbon and further into 2D graphite sheet at higher pressure. The C2/m structure transforms into an orthorhombic Cmcm phase at 0.5 GPa, followed by another orthorhombic Immm phase, which is stabilized in a wide pressure range of 15.2-105.8 GPa and then forced into MgB2-type phase with wide range stability up to at least 1 TPa. Strong electron-phonon coupling. in compressed CaC2 is found, in particular for Immm phase, which has the highest lambda value (0.562-0.564) among them, leading to its high superconducting critical temperature T-c (7.9 similar to 9.8 K), which is comparable with the 11.5 K value of CaC6. Our results show that calcium not only can stabilize carbon sp(2) hybridization at a larger range of pressure but also can contribute in superconducting behavior, which would further ignite experimental and theoretical interest in alkaline-earth metal carbides to uncover their peculiar physical properties under extreme conditions.
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| 8. |
- Loth, Daan W, et al.
(författare)
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Genome-wide association analysis identifies six new loci associated with forced vital capacity
- 2014
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Ingår i: Nature Genetics. - : Springer Science and Business Media LLC. - 1061-4036 .- 1546-1718. ; 46, s. 669-677
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Tidskriftsartikel (refereegranskat)abstract
- Forced vital capacity (FVC), a spirometric measure of pulmonary function, reflects lung volume and is used to diagnose and monitor lung diseases. We performed genome-wide association study meta-analysis of FVC in 52,253 individuals from 26 studies and followed up the top associations in 32,917 additional individuals of European ancestry. We found six new regions associated at genome-wide significance (P < 5 × 10(-8)) with FVC in or near EFEMP1, BMP6, MIR129-2-HSD17B12, PRDM11, WWOX and KCNJ2. Two loci previously associated with spirometric measures (GSTCD and PTCH1) were related to FVC. Newly implicated regions were followed up in samples from African-American, Korean, Chinese and Hispanic individuals. We detected transcripts for all six newly implicated genes in human lung tissue. The new loci may inform mechanisms involved in lung development and the pathogenesis of restrictive lung disease.
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| 9. |
- Lu, Yun-Bi, et al.
(författare)
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Reactive glial cells: increased stiffness correlates with increased intermediate filament expression.
- 2011
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Ingår i: The FASEB journal : official publication of the Federation of American Societies for Experimental Biology. - : Wiley. - 1530-6860. ; 25:2, s. 624-31
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Tidskriftsartikel (refereegranskat)abstract
- Increased stiffness of reactive glial cells may impede neurite growth and contribute to the poor regenerative capabilities of the mammalian central nervous system. We induced reactive gliosis in rodent retina by ischemia-reperfusion and assessed intermediate filament (IF) expression and the viscoelastic properties of dissociated single glial cells in wild-type mice, mice lacking glial fibrillary acidic protein and vimentin (GFAP(-/-)Vim(-/-)) in which glial cells are consequently devoid of IFs, and normal Long-Evans rats. In response to ischemia-reperfusion, glial cells stiffened significantly in wild-type mice and rats but were unchanged in GFAP(-/-)Vim(-/-) mice. Cell stiffness (elastic modulus) correlated with the density of IFs. These results support the hypothesis that rigid glial scars impair nerve regeneration and that IFs are important determinants of cellular viscoelasticity in reactive glia. Thus, therapeutic suppression of IF up-regulation in reactive glial cells may facilitate neuroregeneration.-Lu, Y.-B., Iandiev, I., Hollborn, M., Körber, N., Ulbricht, E., Hirrlinger, P. G., Pannicke, T., Wei, E.-Q., Bringmann, A., Wolburg, H., Wilhelmsson, U., Pekny, M., Wiedemann, P., Reichenbach, A., Käs, J. A. Reactive glial cells: increased stiffness correlates with increased intermediate filament expression.
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| 10. |
- Proletov, Ian, et al.
(författare)
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Primary and secondary glomerulonephritides 1.
- 2014
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Ingår i: Nephrology, dialysis, transplantation : official publication of the European Dialysis and Transplant Association - European Renal Association. - : Oxford University Press (OUP). - 1460-2385. ; 29 Suppl 3:May, s. 186-200
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Tidskriftsartikel (refereegranskat)
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