| 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. |
- Yi, Chuixiang, et al.
(författare)
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Climate control of terrestrial carbon exchange across biomes and continents
- 2010
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Ingår i: Environmental Research Letters. - : IOP Publishing. - 1748-9326. ; 5:3
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Tidskriftsartikel (refereegranskat)abstract
- Understanding the relationships between climate and carbon exchange by terrestrial ecosystems is critical to predict future levels of atmospheric carbon dioxide because of the potential accelerating effects of positive climate-carbon cycle feedbacks. However, directly observed relationships between climate and terrestrial CO2 exchange with the atmosphere across biomes and continents are lacking. Here we present data describing the relationships between net ecosystem exchange of carbon (NEE) and climate factors as measured using the eddy covariance method at 125 unique sites in various ecosystems over six continents with a total of 559 site-years. We find that NEE observed at eddy covariance sites is (1) a strong function of mean annual temperature at mid-and high-latitudes, (2) a strong function of dryness at mid-and low-latitudes, and (3) a function of both temperature and dryness around the mid-latitudinal belt (45 degrees N). The sensitivity of NEE to mean annual temperature breaks down at similar to 16 degrees C (a threshold value of mean annual temperature), above which no further increase of CO2 uptake with temperature was observed and dryness influence overrules temperature influence.
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| 4. |
- Abelev, B., et al.
(författare)
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Azimuthal anisotropy of D-meson production in Pb-Pb collisions at root s(NN)=2.76 TeV
- 2014
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Ingår i: Physical Review C (Nuclear Physics). - 0556-2813. ; 90:3
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Tidskriftsartikel (refereegranskat)abstract
- The production of the prompt charmed mesonsD(0), D+, andD(*+) relative to the reaction plane was measured in Pb-Pb collisions at a center-of-mass energy per nucleon-nucleon collision of root s(NN) = 2.76 TeV with the ALICE detector at the CERN Large Hadron Collider. D mesons were reconstructed via their hadronic decays at central rapidity in the transverse-momentum (pT) interval 2-16 GeV/c. The azimuthal anisotropy is quantified in terms of the second coefficient v(2) in a Fourier expansion of the D-meson azimuthal distribution and in terms of the nuclear modification factor R-AA, measured in the direction of the reaction plane and orthogonal to it. The v(2) coefficient was measured with three different methods and in three centrality classes in the interval 0%-50%. A positive v(2) is observed in midcentral collisions (30%-50% centrality class), with a mean value of 0.204(-0.036)(+0.099) (tot.unc.) in the interval 2 < pT < 6 GeV/c, which decreases towards more central collisions (10%-30% and 0%-10% classes). The positive v(2) is also reflected in the nuclear modification factor, which shows a stronger suppression in the direction orthogonal to the reaction plane formidcentral collisions. The measurements are compared to theoretical calculations of charm-quark transport and energy loss in high-density strongly interacting matter at high temperature. The models that include substantial elastic interactions with an expanding medium provide a good description of the observed anisotropy. However, they are challenged to simultaneously describe the strong suppression of high-pT yield of D mesons in central collisions and their azimuthal anisotropy in noncentral collisions.
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| 5. |
- Abelev, B., et al.
(författare)
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Beauty production in pp collisions at root s=2.76 TeV measured via semi-electronic decays
- 2014
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Ingår i: Physics Letters. Section B: Nuclear, Elementary Particle and High-Energy Physics. - : Elsevier BV. - 0370-2693. ; 738, s. 97-108
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Tidskriftsartikel (refereegranskat)abstract
- The ALICE Collaboration at the LHC reports measurement of the inclusive production cross section of electrons from semi-leptonic decays of beauty hadrons with rapidity |y| < 0.8 and transverse momentum 1 < p(T)< 10 GeV/c, in pp collisions at root s = 2.76 TeV. Electrons not originating from semi-electronic decay of beauty hadrons are suppressed using the impact parameter of the corresponding tracks. The production cross section of beauty decay electrons is compared to the result obtained with an alternative method which uses the distribution of the azimuthal angle between heavy-flavour decay electrons and charged hadrons. Perturbative QCD predictions agree with the measured cross section within the experimental and theoretical uncertainties. The integrated visible cross section, sigma(b -> e) = 3.47 +/- 0.40(stat)(+1.12)(-1.33)(sys) +/- 0.07(norm) mu b, was extrapolated to full phase space using Fixed Order plus Next-to-Leading Log (FONLL) calculations to obtain the total b (b) over bar production cross section, sigma(b (b) over bar) = 130 +/- 15.1(stat)(+42.1)(-49.8)(sys)(+3.4)(-3.1)(extr) +/- 2.5(norm) +/- 4.4(BR) mu b. (C) 2014 The Authors. Published by Elsevier B.V.
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| 6. |
- Abelev, B., et al.
(författare)
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Centrality, rapidity and transverse momentum dependence of J/Psi suppression in Pb-Pb collisions at root(NN)-N-S=2.76TeV
- 2014
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Ingår i: Physics Letters. Section B: Nuclear, Elementary Particle and High-Energy Physics. - : Elsevier BV. - 0370-2693. ; 734, s. 314-327
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Tidskriftsartikel (refereegranskat)abstract
- The inclusive J/.nuclear modification factor (R-AA) in Pb-Pb collisions at root(NN)-N-S = 2.76TeVhas been measured by ALICE as a function of centrality in the e+ e-decay channel at mid-rapidity (| y| < 0.8) and as a function of centrality, transverse momentum and rapidity in the + -decay channel at forward-rapidity (2.5 < y < 4). The J/.yields measured in Pb-Pb are suppressed compared to those in ppcollisions scaled by the number of binary collisions. The RAAintegrated over a centrality range corresponding to 90% of the inelastic Pb-Pb cross section is 0.72 - 0.06(stat.) - 0.10(syst.) at mid-rapidity and 0.58 - 0.01(stat.) - 0.09(syst.) at forward-rapidity. At low transverse momentum, significantly larger values of RAAare measured at forward-rapidity compared to measurements at lower energy. These features suggest that a contribution to the J/.yield originates from charm quark (re) combination in the deconfined partonic medium. (C) 2014 The Authors. Published by Elsevier B. V.
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| 7. |
- Abelev, B, et al.
(författare)
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Directed Flow of Charged Particles at Midrapidity Relative to the Spectator Plane in Pb-Pb Collisions at sqrt[s_{NN}]=2.76 TeV.
- 2013
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Ingår i: Physical Review Letters. - 1079-7114. ; 111:23
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Tidskriftsartikel (refereegranskat)abstract
- The directed flow of charged particles at midrapidity is measured in Pb-Pb collisions at sqrt[s_{NN}]=2.76 TeV relative to the collision symmetry plane defined by the spectator nucleons. A negative slope of the rapidity-odd directed flow component with approximately 3 times smaller magnitude than found at the highest RHIC energy is observed. This suggests a smaller longitudinal tilt of the initial system and disfavors the strong fireball rotation predicted for the LHC energies. The rapidity-even directed flow component is measured for the first time with spectators and found to be independent of pseudorapidity with a sign change at transverse momenta p_{T} between 1.2 and 1.7 GeV/c. Combined with the observation of a vanishing rapidity-even p_{T} shift along the spectator deflection this is strong evidence for dipolelike initial density fluctuations in the overlap zone of the nuclei. Similar trends in the rapidity-even directed flow and the estimate from two-particle correlations at midrapidity, which is larger by about a factor of 40, indicate a weak correlation between fluctuating participant and spectator symmetry planes. These observations open new possibilities for investigation of the initial conditions in heavy-ion collisions with spectator nucleons.
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| 8. |
- Abelev, B., et al.
(författare)
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Energy dependence of the transverse momentum distributions of charged particles in pp collisions measured by ALICE
- 2013
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Ingår i: European Physical Journal C. Particles and Fields. - : Springer Science and Business Media LLC. - 1434-6044. ; 73:12
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Tidskriftsartikel (refereegranskat)abstract
- Differential cross sections of charged particles in inelastic pp collisions as a function of pT have been measured at root s = 0.9, 2.76 and 7 TeV at the LHC. The pT spectra are compared to NLO-pQCD calculations. Though the differential cross section for an individual root s cannot be described by NLO-pQCD, the relative increase of cross section with root s is in agreement with NLO-pQCD. Based on these measurements and observations, procedures are discussed to construct pp reference spectra at root s = 2.76 and 5.02 TeV up to pT = 50 GeV/c as required for the calculation of the nuclear modification factor in nucleus-nucleus and proton-nucleus collisions.
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| 9. |
- Abelev, B., et al.
(författare)
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Event-by-event mean p(T) fluctuations in pp and Pb-Pb collisions at the LHC
- 2014
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Ingår i: European Physical Journal C. Particles and Fields. - : Springer Science and Business Media LLC. - 1434-6044. ; 74:10
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Tidskriftsartikel (refereegranskat)abstract
- Event-by-event fluctuations of the mean transverse momentum of charged particles produced in pp collisions at root s = 0.9, 2.76 and 7 TeV, and Pb-Pb collisions at root S-NN = 2.76 TeV are studied as a function of the charged-particle multiplicity using the ALICE detector at the LHC. Dynamical fluctuations indicative of correlated particle emission are observed in all systems. The results in pp collisions show little dependence on collision energy. The Monte Carlo event generators PYTHIA and PHOJET are in qualitative agreement with the data. Peripheral Pb-Pb data exhibit a similar-multiplicity dependence as that observed in pp. In central Pb-Pb, the results deviate from this trend, featuring a significant reduction of the fluctuation strength. The results in Pb-Pb are in qualitative agreement with previous measurements in Au-Au at lower collision energies and with expectations from models that incorporate collective phenomena.
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