| 1. |
- Beal, Jacob, et al.
(författare)
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Robust estimation of bacterial cell count from optical density
- 2020
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Ingår i: Communications Biology. - : Springer Science and Business Media LLC. - 2399-3642. ; 3:1
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Tidskriftsartikel (refereegranskat)abstract
- Optical density (OD) is widely used to estimate the density of cells in liquid culture, but cannot be compared between instruments without a standardized calibration protocol and is challenging to relate to actual cell count. We address this with an interlaboratory study comparing three simple, low-cost, and highly accessible OD calibration protocols across 244 laboratories, applied to eight strains of constitutive GFP-expressing E. coli. Based on our results, we recommend calibrating OD to estimated cell count using serial dilution of silica microspheres, which produces highly precise calibration (95.5% of residuals <1.2-fold), is easily assessed for quality control, also assesses instrument effective linear range, and can be combined with fluorescence calibration to obtain units of Molecules of Equivalent Fluorescein (MEFL) per cell, allowing direct comparison and data fusion with flow cytometry measurements: in our study, fluorescence per cell measurements showed only a 1.07-fold mean difference between plate reader and flow cytometry data.
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| 2. |
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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. |
- Ablikim, M., et al.
(författare)
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Measurement of the integrated Luminosities of cross-section scan data samples around the psi(3770) mass region
- 2018
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Ingår i: Chinese Physics C. - : SCIENCE PRESS. - 1674-1137 .- 2058-6132. ; 42:6
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Tidskriftsartikel (refereegranskat)abstract
- To investigate the nature of the psi(3770) resonance and to measure the cross section for e(+)e(-) -> D (D) over bar, a cross-section scan data sample, distributed among 41 center-of-mass energy points from 3.73 to 3.89 GeV, was taken with the BESIII detector operated at the BEPCII collider in the year 2010. By analyzing the large angle Bhabha scattering events, we measure the integrated luminosity of the data sample at each center-of-mass energy point. The total integrated luminosity of the data sample is 76.16 +/- 0.04 +/- 0.61 pb(-1), where the first uncertainty is statistical and the second systematic.
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| 6. |
- 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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| 7. |
- 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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| 8. |
- 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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| 9. |
- Abelev, B., et al.
(författare)
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Charged jet cross sections and properties in proton-proton collisions at root s=7 TeV
- 2015
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Ingår i: Physical Review D (Particles, Fields, Gravitation and Cosmology). - 1550-2368. ; 91:11
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Tidskriftsartikel (refereegranskat)abstract
- The differential charged jet cross sections, jet fragmentation distributions, and jet shapes are measured in minimum bias proton-proton collisions at center-of-mass energy root s = 7 TeV using the ALICE detector at the LHC. Jets are reconstructed from charged particle momenta in the midrapidity region using the sequential recombination k(T) and anti-k(T) as well as the SISCone jet finding algorithms with several resolution parameters in the range R = 0.2-0.6. Differential jet production cross sections measured with the three jet finders are in agreement in the transverse momentum (p(T)) interval 20 < p(T)(jet,ch) < 100 GeV/c. They are also consistent with prior measurements carried out at the LHC by the ATLAS Collaboration. The jet charged particle multiplicity rises monotonically with increasing jet p(T), in qualitative agreement with prior observations at lower energies. The transverse profiles of leading jets are investigated using radial momentum density distributions as well as distributions of the average radius containing 80% (< R-80 >) of the reconstructed jet p(T). The fragmentation of leading jets with R = 0.4 using scaled p(T) spectra of the jet constituents is studied. The measurements are compared to model calculations from event generators (PYTHIA, PHOJET, HERWIG). The measured radial density distributions and < R-80 > distributions are well described by the PYTHIA model (tune Perugia-2011). The fragmentation distributions are better described by HERWIG.
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| 10. |
- Abelev, B., et al.
(författare)
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Elliptic flow of identified hadrons in Pb-Pb collisions at root(NN)-N-s=2.76 Tev
- 2015
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Ingår i: Journal of High Energy Physics. - 1029-8479. ; :6
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Tidskriftsartikel (refereegranskat)abstract
- The elliptic flow coefficient (v(2)) of identified particles in Pb-Pb collisions at root s(NN) = 2.76 TeV was measured with the ALICE detector at the Large Hadron Collider (LHC). The results were obtained with the Scalar Product method, a two-particle correlation technique, using a pseudo-rapidity gap of |Delta eta| > 0.9 between the identified hadron under study and the reference particles. The v (2) is reported for pi(+/-), K-+/-, K-S(0), p+(p) over bar, phi, Lambda+(Lambda) over bar, Xi+(Xi) over bar (+) and Omega(-)+(Omega) over bar (+) in several collision centralities. In the low transverse momentum (p(T)) region, p(T) < 3 GeV/c, v(2)(p(T)) exhibits a particle mass dependence consistent with elliptic flow accompanied by the transverse radial expansion of the system with a common velocity field. The experimental data for pi (+/-) and the combined K-+/- and K-S(0) results, are described fairly well by hydrodynamic calculations coupled to a hadronic cascade model (VISHNU) for central collisions. However, the same calculations fail to reproduce the v(2)(p(T)) for p+(p) over bar, phi, Lambda+(Lambda) over bar, Xi+(Xi) over bar (+). For transverse momentum values larger than about 3 GeV/c, particles tend to group according to their type, i.e. mesons and baryons. The present measurements exhibit deviations from the number of constituent quark (NCQ) scaling at the level of +/- 20% for p(T) > 3 GeV/c.
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