| 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. |
- Abelev, Betty, et al.
(författare)
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Measurement of prompt J/psi and beauty hadron production cross sections at mid-rapidity in pp collisions at root s=7 TeV
- 2012
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Ingår i: Journal of High Energy Physics. - 1029-8479. ; :11
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Tidskriftsartikel (refereegranskat)abstract
- The ALICE experiment at the LHC has studied J/psi production at mid-rapidity in pp collisions at root s = 7 TeV through its electron pair decay on a data sample corresponding to an integrated luminosity L-int = 5.6 nb(-1). The fraction of J/psi from the decay of long-lived beauty hadrons was determined for J/psi candidates with transverse momentum p(t) > 1,3 GeV/c and rapidity vertical bar y vertical bar < 0.9. The cross section for prompt J/psi mesons, i.e. directly produced J/psi and prompt decays of heavier charmonium states such as the psi(2S) and chi(c) resonances, is sigma(prompt J/psi) (p(t) > 1.3 GeV/c, vertical bar y vertical bar < 0.9) = 8.3 +/- 0.8(stat.) +/- 1.1 (syst.)(-1.4)(+1.5) (syst. pol.) mu b. The cross section for the production of b-hadrons decaying to J/psi with p(t) > 1.3 GeV/c and vertical bar y vertical bar < 0.9 is a sigma(J/psi <- hB) (p(t) > 1.3 GeV/c, vertical bar y vertical bar < 0.9) = 1.46 +/- 0.38 (stat.)(-0.32)(+0.26) (syst.) mu b. The results are compared to QCD model predictions. The shape of the p(t) and y distributions of b-quarks predicted by perturbative QCD model calculations are used to extrapolate the measured cross section to derive the b (b) over bar pair total cross section and d sigma/dy at mid-rapidity.
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| 3. |
- Deng, Min, et al.
(författare)
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Genome-wide association analyses in Han Chinese identify two new susceptibility loci for amyotrophic lateral sclerosis
- 2013
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Ingår i: Nature Genetics. - : Nature Publishing Group. - 1061-4036 .- 1546-1718. ; 45:6, s. 697-
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Tidskriftsartikel (refereegranskat)abstract
- To identify susceptibility genes for amyotrophic lateral sclerosis (ALS), we conducted a genome-wide association study (GWAS) in 506 individuals with sporadic ALS and 1,859 controls of Han Chinese ancestry. Ninety top SNPs suggested by the current GWAS and 6 SNPs identified by previous GWAS were analyzed in an independent cohort of 706 individuals with ALS and 1,777 controls of Han Chinese ancestry. We discovered two new susceptibility loci for ALS at 1q32 (CAMK1G, rs6703183, P-combined = 2.92 x 10(-8), odds ratio (OR) = 1.31) and 22p11 (CABIN1 and SUSD2, rs8141797, P-combined = 2.35 x 10(-9), OR = 1.52). These two loci explain 12.48% of the overall variance in disease risk in the Han Chinese population. We found no association evidence for the previously reported loci in the Han Chinese population, suggesting genetic heterogeneity of disease susceptibility for ALS between ancestry groups. Our study identifies two new susceptibility loci and suggests new pathogenic mechanisms of ALS.
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| 4. |
- 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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| 5. |
- Abelev, Betty, et al.
(författare)
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Long-range angular correlations on the near and away side in p-Pb collisions at root S-NN=5.02 TeV
- 2013
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Ingår i: Physics Letters. Section B: Nuclear, Elementary Particle and High-Energy Physics. - : Elsevier BV. - 0370-2693. ; 719:1-3, s. 29-41
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Tidskriftsartikel (refereegranskat)abstract
- Angular correlations between charged trigger and associated particles are measured by the ALICE detector in p-Pb collisions at a nucleon-nucleon centre-of-mass energy of 5.02 TeV for transverse momentum ranges within 0.5 < P-T,P-assoc < P-T,P-trig < 4 GeV/c. The correlations are measured over two units of pseudorapidity and full azimuthal angle in different intervals of event multiplicity, and expressed as associated yield per trigger particle. Two long-range ridge-like structures, one on the near side and one on the away side, are observed when the per-trigger yield obtained in low-multiplicity events is subtracted from the one in high-multiplicity events. The excess on the near-side is qualitatively similar to that recently reported by the CMS Collaboration, while the excess on the away-side is reported for the first time. The two-ridge structure projected onto azimuthal angle is quantified with the second and third Fourier coefficients as well as by near-side and away-side yields and widths. The yields on the near side and on the away side are equal within the uncertainties for all studied event multiplicity and p(T) bins, and the widths show no significant evolution with event multiplicity or p(T). These findings suggest that the near-side ridge is accompanied by an essentially identical away-side ridge. (c) 2013 CERN. Published by Elsevier B.V. All rights reserved.
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| 6. |
- Jarvis, Erich D., et al.
(författare)
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Whole-genome analyses resolve early branches in the tree of life of modern birds
- 2014
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Ingår i: Science. - : American Association for the Advancement of Science (AAAS). - 0036-8075 .- 1095-9203. ; 346:6215, s. 1320-1331
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Tidskriftsartikel (refereegranskat)abstract
- To better determine the history of modern birds, we performed a genome-scale phylogenetic analysis of 48 species representing all orders of Neoaves using phylogenomic methods created to handle genome-scale data. We recovered a highly resolved tree that confirms previously controversial sister or close relationships. We identified the first divergence in Neoaves, two groups we named Passerea and Columbea, representing independent lineages of diverse and convergently evolved land and water bird species. Among Passerea, we infer the common ancestor of core landbirds to have been an apex predator and confirm independent gains of vocal learning. Among Columbea, we identify pigeons and flamingoes as belonging to sister clades. Even with whole genomes, some of the earliest branches in Neoaves proved challenging to resolve, which was best explained by massive protein-coding sequence convergence and high levels of incomplete lineage sorting that occurred during a rapid radiation after the Cretaceous-Paleogene mass extinction event about 66 million years ago.
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| 7. |
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| 8. |
- Bianchi, Marco, et al.
(författare)
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Robust Surface Doping of Bi2Se3 by Rubidium Intercalation
- 2012
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Ingår i: ACS Nano. - : American Chemical Society (ACS). - 1936-086X .- 1936-0851. ; 6:8, s. 7009-7015
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Tidskriftsartikel (refereegranskat)abstract
- Rubidium adsorption on the surface of the topological insulator Bi2Se3 is found to induce a strong downward band bending, leading to the appearance of a quantum-confined two-dimensional electron gas state (2DEG) in the conduction band. The 2DEG shows a strong Rashba-type spin orbit splitting, and it has previously been pointed out that this has relevance to nanoscale spintronics devices. The adsorption of Rb atoms, on the other hand, renders the surface very reactive, and exposure to oxygen leads to a rapid degrading of the 2DEG. We show that intercalating the Rb atoms, presumably into the van der Waals gaps in the quintuple layer structure of Bi2Se3, drastically reduces the surface reactivity while not affecting the promising electronic structure. The intercalation process is observed above room temperature and accelerated with increasing initial Rb coverage, an effect that is ascribed to the Coulomb interaction between the charged Rb ions. Coulomb repulsion is also thought to be responsible for a uniform distribution of Rb on the surface.
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| 9. |
- Brackmann, Christian, et al.
(författare)
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Characterization of ammonia two-photon laser-induced fluorescence for gas-phase diagnostics
- 2014
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Ingår i: Applied Physics B. - : Springer Science and Business Media LLC. - 0946-2171 .- 1432-0649. ; 115:1, s. 25-33
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Tidskriftsartikel (refereegranskat)abstract
- Two-photon laser-induced fluorescence (LIF) of ammonia (NH3) with excitation of the C'-X transition at 304.8 nm and fluorescence detection in the 565 nm C'-A band has been investigated, targeting combustion diagnostics. The impact of laser irradiance, temperature, and pressure has been studied, and simulation of NH3-spectra, fitted to experimental data, facilitated interpretation of the results. The LIF-signal showed quadratic dependence on laser irradiance up to 2 GW/cm(2). Stimulated emission, resulting in loss of excited molecules, is induced above 10 GW/cm(2), i.e., above irradiances attainable for LIF imaging. Maximum LIF-signal was obtained for excitation at the 304.8 nm bandhead; however, lower temperature sensitivity over the range 400-700 K can be obtained probing lines around 304.9 nm. A decrease in fluorescence signal was observed with pressure up to 5 bar absolute and attributed to collisional quenching. A detection limit of 800 ppm, at signal-to-noise ratio 1.5, was identified for single-shot LIF imaging over an area of centimeter scale, whereas for single-point measurements, the technique shows potential for sub-ppm detection. Moreover, high-quality NH3-imaging has been achieved in laminar and turbulent premixed flames. Altogether, two-photon fluorescence provides a useful tool for imaging NH3-detection in combustion diagnostics.
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| 10. |
- Chang, Bo, et al.
(författare)
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HYDROPHILIC-SUPERHYDROPHOBIC PATTERNED SURFACE FOR PARALLEL MICROASSEMBLY
- 2014
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Ingår i: Technical Digest of the 25th Micromechanics and Microsystems Europe Conference (MME 2014), Istanbul, Turkey, 2014.
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Konferensbidrag (refereegranskat)abstract
- In this paper, a hydrophilic-superhydrophobic patterned surface is investigated for parallel microassembly of 200 µm × 200 µm chips with receptor sites of the same dimensions, allowing for correction of significant error as compared to the state-of-the-art. The hydrophilic-superhydrophobic pattered surface consists of 200 µm × 200 µm silicondioxide receptor sites with black silicon substrate coated with fluorocarbon polymer. The measured contact angle of water on the silicon dioxide padsand the background are 50° and 170°, respectively.The water mist-induced hybrid microassembly technique is used to carry out the experimental studies on hydrophilic-superhydrophobic pattered surface for parallel microassembly. The experimental results show that the parallel microassembly of chips can not only be achieved on hydrophilic-superhydrophobic patterned surface, but also demonstrate significant error correction capability. With extreme large initial placement error, where achip is placed next to a receptor site and has zero overlapping with the receptor site, the chip is still able to align with the receptor site. The results also indicate that the reliability of the microassembly process can be greatly enhanced using hydrophilic patterns with super-hydrophobic background.
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