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| 2. |
- 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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| 3. |
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- 2019
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Tidskriftsartikel (refereegranskat)
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| 4. |
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| 5. |
- 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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| 6. |
- Ablikim, M., et al.
(författare)
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Amplitude analysis of the KSKS system produced in radiative J /psi decays
- 2018
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Ingår i: Physical Review D. - : AMER PHYSICAL SOC. - 2470-0010 .- 2470-0029. ; 98:7
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Tidskriftsartikel (refereegranskat)abstract
- An amplitude analysis of the KSKS system produced in radiative J/psi decays is performed using the (1310.6 +/- 7.0) x 10(6) nip decays collected by the BESIII detector. Two approaches are presented. A mass-dependent analysis is performed by parametrizing the KSKS invariant mass spectrum as a sum of Breit-aligner line shapes. Additionally, a mass-independent analysis is performed to extract a piecewise function that describes the dynamics of the KSKS system while making minimal assumptions about the properties and number of poles in the amplitude. The dominant amplitudes in the mass-dependent analysis include the f(0)(1710), f(0)(2200), and f(2)'(1525). The mass-independent results, which are made available as input for further studies, are consistent with those of the mass-dependent analysis and are useful for a systematic study of hadronic interactions. The branching fraction of radiative J/psi decays to KSKS is measured to be (8.1 +/- 0.4) x 10(-4), where the uncertainty is systematic and the statistical uncertainty is negligible.
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| 7. |
- Ablikim, M., et al.
(författare)
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Measurement of e(+)e(-) -> K(K)over-barJ/psi cross sections at center-of-mass energies from 4.189 to 4.600 GeV
- 2018
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Ingår i: Physical Review D. - : AMER PHYSICAL SOC. - 2470-0010 .- 2470-0029. ; 97:7
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Tidskriftsartikel (refereegranskat)abstract
- We investigate the process e(+)e(-) -> K (K) over barJ/psi at center-of-mass energies from 4.189 to 4.600 GeV using 4.7 fb(-1) of data collected by the BESIII detector at the BEPCII collider. The Born cross sections for the reactions e(+)e(-) -> K(+)K(-)J/psi and K(S)(0)K(S)(0)J/psi are measured as a function of center-of-mass energy. The energy dependence of the cross section for e(+)e(-) -> K(+)K(-)J/psi is shown to differ from that for pi(+)pi(-)J/psi in the region around the Y(4260). In addition, there is evidence for a structure around 4.5 GeV in the e(+)e(-) -> K(+)K(-)J/psi cross section that is not present in pi(+)pi(-)J/psi.
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| 8. |
- Ablikim, M., et al.
(författare)
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Measurement of e(+)e(-) -> pi(+)pi(-) psi(3686) from 4.008 to 4.600 GeV and observation of a charged structure in the pi(+/-)psi(3686) mass spectrum
- 2017
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Ingår i: Physical Review D. - 2470-0010 .- 2470-0029. ; 96:3
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Tidskriftsartikel (refereegranskat)abstract
- We study the process e(+)e(-) -> p(+)p(-)psi(3686) using 5.1 fb(-1) of data collected at 16 center-of-mass energy (root s) points from 4.008 to 4.600 GeV by the BESIII detector operating at the BEPCII collider. The measured Born cross sections for e(+)e(-) -> p(+)p(-)psi(3686) are consistent with previous results, but with much improved precision. A fit to the cross section shows contributions from two structures: the first has M = 4209.5 +/- 7.4 +/- 1.4 MeV/c(2) and Gamma = 80.1 +/- 24.6 +/- 2.9 MeV, and the second has M = 4383.8 +/- 4.2 +/- 0.8 MeV/c(2) and Gamma = 84.2 +/- 12.5 +/- 2.1 MeV, where the first errors are statistical and the second systematic. The lower-mass resonance is observed in the process e(+)e(-) -> p(+)p(-)psi(3686) for the first time with a statistical significance of 5.8 sigma. A charged charmoniumlike structure is observed in the pi(+/-)psi(3686) invariant mass spectrum for data at root s = 4.416 GeV. A fit with an S-wave Breit-Wigner function yields a mass M = 4032.1 +/- 2.4 MeV/c(2), where the errors are statistical only. However, there are still unresolved discrepancies between the fit model and data. The width of the intermediate state varies in a wide range for different kinematic regions within the data set. Therefore, no simple interpretation of the data has been found, and a future data sample with larger statistics and more theoretical input will be required to better understand this issue.
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| 9. |
- Ablikim, M., et al.
(författare)
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Measurement of singly Cabibbo-suppressed decays D-0 → π0π0π0, π0π0η, π0ηη and ηηη
- 2018
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Ingår i: Physics Letters B. - : ELSEVIER SCIENCE BV. - 0370-2693 .- 1873-2445. ; 781, s. 368-375
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Tidskriftsartikel (refereegranskat)abstract
- Using a data sample of e(+)e(-) collision data corresponding to an integrated luminosity of 2.93 fb(-1) collected with the BESIII detector at a center-of-mass energy of root s = 3.773 GeV, we search for the singly Cabibbo-suppressed decays D-0 -> pi(0)pi(0)pi(0), pi(0)pi(0)eta, pi(0)eta eta and eta eta eta using the double tag method. The absolute branching fractions are measured to be B(D-0 -> pi(0)pi(0)pi(0)) = (2.0 +/- 0.4 +/- 0.3) x 10(-4), B(D-0 -> pi(0)pi(0)eta) = (3.8 +/- 1.1 +/- 0.7) x 10(-4) and B(D-0 -> pi(0)eta eta) = (7.3 +/- 1.6 +/- 1.5) x 10(-4) with the statistical significances of 4.8 sigma, 3.8 sigma and 5.5 sigma, respectively, where the first uncertainties are statistical and the second ones systematic. No significant signal of D-0 -> eta eta eta is found, and the upper limit on its decay branching fraction is set to be B(D-0 -> eta eta eta) < 1.3 x 10(-4) at the 90% confidence level.
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| 10. |
- Ablikim, M., et al.
(författare)
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Measurement of the absolute branching fraction of D*(s0) (2317)(+/-) -> pi D-0(s)+/-
- 2018
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Ingår i: Physical Review D. - : American Physical Society. - 2470-0010 .- 2470-0029. ; 97:5
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Tidskriftsartikel (refereegranskat)abstract
- The process e(+)e(-) -> D*D-+(s)*(s0) (2317)(-) + c.c. is observed for the first time with the data sample of 567 pb(-1) collected with the BESIII detector operating at the BEPCII collider at a center-of-mass energy root s = 4.6 GeV. The statistical significance of the D*(s0) (2317)(+/-) signal is 5.8 sigma and the mass is measured to be (2318.3 +/- 1.2 +/- 1.2) MeV/c(2). The absolute branching fraction B(D*(s0) (2317)(+/-) -> pi D-0(s)+/-) is measured as 1.00(-0.14)(+0.00) (stat)(-0.14)(+0.00) (syst) for the first time. The uncertainties are statistical and systematic, respectively.
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