| 1. |
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| 2. |
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| 3. |
- 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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| 4. |
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- 2019
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Tidskriftsartikel (refereegranskat)
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| 5. |
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| 6. |
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| 7. |
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| 8. |
- 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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| 9. |
- Aad, G, et al.
(författare)
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- 2015
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swepub:Mat__t
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| 10. |
- Sampson, Joshua N., et al.
(författare)
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Analysis of Heritability and Shared Heritability Based on Genome-Wide Association Studies for 13 Cancer Types
- 2015
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Ingår i: Journal of the National Cancer Institute. - : Oxford University Press (OUP). - 0027-8874 .- 1460-2105. ; 107:12
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Tidskriftsartikel (refereegranskat)abstract
- Background: Studies of related individuals have consistently demonstrated notable familial aggregation of cancer. We aim to estimate the heritability and genetic correlation attributable to the additive effects of common single-nucleotide polymorphisms (SNPs) for cancer at 13 anatomical sites. Methods: Between 2007 and 2014, the US National Cancer Institute has generated data from genome-wide association studies (GWAS) for 49 492 cancer case patients and 34 131 control patients. We apply novel mixed model methodology (GCTA) to this GWAS data to estimate the heritability of individual cancers, as well as the proportion of heritability attributable to cigarette smoking in smoking-related cancers, and the genetic correlation between pairs of cancers. Results: GWAS heritability was statistically significant at nearly all sites, with the estimates of array-based heritability, h(l)(2), on the liability threshold (LT) scale ranging from 0.05 to 0.38. Estimating the combined heritability of multiple smoking characteristics, we calculate that at least 24% (95% confidence interval [CI] = 14% to 37%) and 7% (95% CI = 4% to 11%) of the heritability for lung and bladder cancer, respectively, can be attributed to genetic determinants of smoking. Most pairs of cancers studied did not show evidence of strong genetic correlation. We found only four pairs of cancers with marginally statistically significant correlations, specifically kidney and testes (rho = 0.73, SE = 0.28), diffuse large B-cell lymphoma (DLBCL) and pediatric osteosarcoma (rho = 0.53, SE = 0.21), DLBCL and chronic lymphocytic leukemia (CLL) (rho = 0.51, SE = 0.18), and bladder and lung (rho = 0.35, SE = 0.14). Correlation analysis also indicates that the genetic architecture of lung cancer differs between a smoking population of European ancestry and a nonsmoking Asian population, allowing for the possibility that the genetic etiology for the same disease can vary by population and environmental exposures. Conclusion: Our results provide important insights into the genetic architecture of cancers and suggest new avenues for investigation.
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| 11. |
- Ablikim, M., et al.
(författare)
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Observation of a Neutral Structure near the D(D)over-bar* Mass Threshold in e(+)e(-) -> (D(D)over-bar*)(0)pi(0) at root s=4.226 and 4.257 GeV
- 2015
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Ingår i: Physical Review Letters. - 0031-9007 .- 1079-7114. ; 115:22
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Tidskriftsartikel (refereegranskat)abstract
- A neutral structure in the D (D) over bar* system around the D (D) over bar* mass threshold is observed with a statistical significance greater than 10 sigma in the processes e(+)e(-) -> D+D*(-)pi(0) + c.c. and e(+)e(-) -> D-0(D) over bar*(0)pi(0) + c.c. at root s = 4.226 and 4.257 GeV in the BESIII experiment. The structure is denoted as Z(c)(3885)(0). Assuming the presence of a resonance, its pole mass and width are determined to be [3885.7(-5.7)(+4.3) (stat) +/- 8.4(syst)] MeV/c(2) and [35(-12)(+11) (stat) +/- 15(syst)] MeV, respectively. The Born cross sections are measured to be sigma[e(+)e(-) -> Z(c)(3885)(0)pi(0); Z(c)(3885)(0) -> D (D) over bar*] = [77 +/- 13(stat) +/- 17(syst)] pb at 4.226 GeV and [47 +/- 9(stat) +/- 10(syst)] pb at 4.257 GeV. The ratio of decay rates B[Z(c)(3885)(0) -> D+D*(-) + c.c.]/B[Z(c)(3885)(0) -> D-0(D) over bar*(0) + c.c.] is determined to be 0.96 +/- 0.18(stat) +/- 0.12(syst), consistent with no isospin violation in the process, Z(c)(3885)(0) -> D (D) over bar*.
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| 12. |
- Ablikim, M., et al.
(författare)
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Study of D+ -> K-pi(+)e(+)nu(e)
- 2016
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Ingår i: PHYSICAL REVIEW D. - 2470-0010. ; 94:3
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Tidskriftsartikel (refereegranskat)abstract
- We present an analysis of the decay D+ -> K-pi(+)e(+)nu(e) based on data collected by the BESIII experiment at the psi(3770) resonance. Using a nearly background-free sample of 18262 events, we measure the branching fraction B(D+ -> K-pi+e+nu e) = (3.77 +/- 0.03 +/- 0.08)%. For 0.8 < m(K pi) < 1.0 GeV/c(2), the partial branching fraction is B(D+ -> K-pi+e+nu e)([0.8,1.0]) = (3.39 +/- 0.03 +/- 0.08)%. A partial wave analysis shows that the dominant (K) over bar* (892)degrees component is accompanied by an S-wave contribution accounting for (6.05 +/- 0.22 +/- 0.18)% of the total rate and that other components are negligible. The parameters of the (K) over bar* (892)degrees resonance and of the form factors based on the spectroscopic pole dominance predictions are also measured. We also present a measurement of the (K) over bar* (892)degrees helicity basis form factors in a model-independent way.
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| 13. |
- Ablikim, M., et al.
(författare)
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Amplitude analysis of D0 → K -π+π+π-
- 2017
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Ingår i: Physical Review D. - 2470-0010 .- 2470-0029. ; 95:7
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Tidskriftsartikel (refereegranskat)abstract
- We present an amplitude analysis of the decay D0 → K -π+π+π- based on a data sample of 2.93 fb−1 acquired by the BESIII detector at the ψ(3770) resonance. With a nearly background free sample of about 16000 events, we investigate the substructure of the decay and determine the relative fractions and the phases among the different intermediate processes. Our amplitude model includes the two-body decays D0 → ¯K*0ρ0, D0 → K−a+1(1260) and D0 → K−1(1270)π+, the three-body decays D0 →¯K*0π+π− and D0 → K−π+ρ0, as well as the four-body nonresonant decay D0 → K−π+π+π−. The dominant intermediate process is D0 → K−a+1(1260), accounting for a fit fraction of 54.6%.
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| 14. |
- Ablikim, M., et al.
(författare)
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Amplitude Analysis of the Decays eta ' -> pi(+)pi(-)pi(0) and eta' -> pi(0)pi(0)pi(0)
- 2017
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Ingår i: Physical Review Letters. - 0031-9007 .- 1079-7114. ; 118:1
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Tidskriftsartikel (refereegranskat)abstract
- Based on a sample of 1.31 x 10(9) J/Psi events collected with the BESIII detector, an amplitude analysis of the isospin-violating decays eta' -> pi(+)pi(-)pi(0) and eta' -> pi(0)pi(0)pi(0) is performed. A significant P-wave contribution from eta' -> rho(+/-)eta(-/+) is observed for the first time in eta' -> pi(+)pi(-)pi(0). The branching fraction is determined to be B(eta' -> rho(+/-)pi(-/+)) = (7.44 +/- 0.60 +/- 1.26 +/- 1.84) x 10(-4), where the first uncertainty is statistical, the second systematic, and the third model dependent. In addition to the nonresonant S-wave component, there is a significant sigma meson component. The branching fractions of the combined S-wave components are determined to be B(eta' -> pi(+)pi(-)pi(0))(S) = (37.63 +/- 0.77 +/- 2.22 +/- 4.48) x 10(-4) and B(eta' -> pi(0)pi(0)pi(0)) = (35.22 +/- 0.82 +/- 2.54) x 10(-4), respectively. The latter one is consistent with previous BESIII measurements.
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| 15. |
- Ablikim, M., et al.
(författare)
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Amplitude analysis of the pi(0)pi(0) system produced in radiative J/psi decays
- 2015
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Ingår i: Physical Review D. - 1550-7998 .- 1550-2368. ; 92:5
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Tidskriftsartikel (refereegranskat)abstract
- An amplitude analysis of the pi(0)pi(0) system produced in radiative J/psi decays is presented. In particular, a piecewise function that describes the dynamics of the pi(0)pi(0) system is determined as a function of M pi(0)pi(0) from an analysis of the (1.311 +/- 0.011) x 10(9) J/psi decays collected by the BESIII detector. The goal of this analysis is to provide a description of the scalar and tensor components of the pi(0)pi(0) system while making minimal assumptions about the properties or number of poles in the amplitude. Such a model-independent description allows one to integrate these results with other related results from complementary reactions in the development of phenomenological models, which can then be used to directly fit experimental data to obtain parameters of interest. The branching fraction of J/psi -> pi(0)pi(0) is determined to be (1.15 +/- 0.05) x 10(-3), where the uncertainty is systematic only and the statistical uncertainty is negligible.
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| 16. |
- Ablikim, M., et al.
(författare)
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Analysis of D+ -> (K)over-bar(0)e(+)nu(e) and D+ -> pi(0)e(+)nu(e) semileptonic decays
- 2017
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Ingår i: Physical Review D. - : AMER PHYSICAL SOC. - 2470-0010 .- 2470-0029. ; 96:1
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Tidskriftsartikel (refereegranskat)abstract
- Using 2.93 fb(-1) of data taken at 3.773 GeV with the BESIII detector operated at the BEPCII collider, we study the semileptonic decays D+ -> (K) over bar (0)e(+)nu(e) and D+ -> pi(0)e(+)nu(e). We measure the absolute decay branching fractions B(D+ -> (K) over bar (0)e(+)nu(e)) = (8.60 +/- 0.06 +/- 0.15) x 10(-2) and B(D+ -> pi(0)e(+)nu(e)) = (3.63 +/- 0.08 +/- 0.05) x 10(-3), where the first uncertainties are statistical and the second systematic. We also measure the differential decay rates and study the form factors of these two decays. With the values of |V-cs| and |V-cd| from Particle Data Group fits assuming Cabibbo-Kobayashi-Maskawa (CKM) unitarity, we obtain the values of the form factors at q(2) = 0, f(+)(K)(0) = 0.725 +/- 0.004 +/- 0.012, and f(+)(pi)(0) = 0.622 +/- 0.012 +/- 0.003. Taking input from recent lattice QCD calculations of these form factors, we determine values of the CKM matrix elements |V-cs| = 0.944 +/- 0.005 +/- 0.015 +/- 0.024 and |V-cd| = 0.210 +/- 0.004 +/- 0.001 +/- 0.009, where the third uncertainties are theoretical.
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| 17. |
- Ablikim, M., et al.
(författare)
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Dark photon search in the mass range between 1.5 and 3.4 GeV/c
- 2017
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Ingår i: Physics Letters B. - : Elsevier BV. - 0370-2693 .- 1873-2445. ; 774, s. 252-257
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Tidskriftsartikel (refereegranskat)abstract
- Using a data set of 2.93 fb taken at a center-of-mass energy root s = 3.773 GeV with the BESIII detector at the BEPCII collider, we perform a search for an extra U(1) gauge boson, also denoted as a dark photon. We examine the initial state radiation reactions e(+)e(-) -> e(+)e(-) gamma(ISR) and e(+)e(-) -> mu(+)mu(-) gamma(ISR) for this search, where the dark photon would appear as an enhancement in the invariant mass distribution of the leptonic pairs. We observe no obvious enhancement in the mass range between 1.5 and 3.4 GeV/c(2) and set a 90% confidence level upper limit on the mixing strength of the dark photon and the Standard Model photon. We obtain a competitive limit in the tested mass range.
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| 18. |
- Ablikim, M., et al.
(författare)
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Determination of the Spin and Parity of the Z(c)(3900)
- 2017
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Ingår i: Physical Review Letters. - : AMER PHYSICAL SOC. - 0031-9007 .- 1079-7114. ; 119:7
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Tidskriftsartikel (refereegranskat)abstract
- The spin and parity of the Z(c)(3900)(+/-) state are determined to be J(P) = 1(+) with a statistical significance larger than 7 sigma over other quantum numbers in a partial wave analysis of the process e(+)e(-) -> pi(+)pi(-) J/psi We use a data sample of 1.92 fb(-1) accumulated at root s = 4.23 and 4.26 GeV with the BESIII experiment. When parametrizing the Z(c)(3900)(+/-) with a Flatte-like formula, we determine its pole mass M-pole = (3881.2 +/- 4.2(stat) +/- 52.7(syst)) MeV/c(2) and pole width Gamma(pole) = (51.8 +/- 4.6(stat) +/- 36.0(syst)) MeV. We also measure cross sections for the process e(+)e(-) -> Z(c)(3900)(+)pi(-) + c.c. -> J/psi pi(+)pi(-) and determine an upper limit at the 90% confidence level for the process e(+)e(-) -> Z(c)(4020)(+)pi(-) + c.c. -> J/psi pi(+)pi(-).
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| 19. |
- Ablikim, M., et al.
(författare)
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Improved measurement of the absolute branching fraction of D+ -> (K)over-bar(0)mu(+)nu(mu)
- 2016
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Ingår i: European Physical Journal C. - : SPRINGER. - 1434-6044 .- 1434-6052. ; 76:7
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Tidskriftsartikel (refereegranskat)abstract
- By analyzing 2.93 fb(-1) of data collected at root s = 3.773 GeV with the BESIII detector, we measure the absolute branching fraction B(D+ -> (K) over bar (0) (+)(mu)nu(mu)) = (8.72 +/- 0.07(stat). +/- 0.18(sys).) %, which is consistent with previous measurements within uncertainties but with significantly improved precision. Combining the Particle Data Group values of B(D-0 -> K- mu(+)nu(mu)), B(D+-> (K) over bar (0)e(+)nu(e)), and the lifetimes of the D-0 and D+ mesons with the value of B(D+ -> (K) over bar (0)mu(+)nu(mu)) measured in this work, we determine the following ratios of partial widths: Gamma (D-0 -> (K) over bar (-)mu(+)nu(mu))/Gamma (D+ -> (K) over bar (0)mu+nu(mu)) = 0.963 +/- 0.044 and Gamma (D+ -> (K) over bar (0) mu+nu(mu))/Gamma(D+ -> (K) over bar (0)e+nu(e)) = 0.988 +/- 0.033.
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| 20. |
- Ablikim, M., et al.
(författare)
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Improved measurements of branching fractions for eta(c) -> phi phi and omega phi
- 2017
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Ingår i: Physical Review D. - : AMER PHYSICAL SOC. - 2470-0010 .- 2470-0029. ; 95:9
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Tidskriftsartikel (refereegranskat)abstract
- Using (223.7 +/- 1.4) x 10(6) J / Psi events accumulated with the BESIII detector, we study eta(c) decays to phi phi and omega phi final states. The branching fraction of n(c) -> phi phi is measured to be Br(eta(c) -> phi phi) = (2.5 +/- 0(-0.7)(+0.3) +/- 0.6) X 10(-3,) where the first uncertainty is statistical, the second is systematic, and the third is from the uncertainty of Br(J / Psi -> gamma eta(C)). No significant signal for the double Okubo-Zweig-Iizuka suppressed decay of eta(c) -> omega phi is observed, and the upper limit on the branching fraction is determined to be Br(eta(c) -> omega phi) < 2.5 x 10(-4) at the 90% confidence level.
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| 21. |
- Ablikim, M., et al.
(författare)
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Measurement of higher-order multipole amplitudes in psi(3686) -> gamma chi(c1,2) with chi(c1,2) -> gamma J/psi and search for the transition eta(c)(2S) -> gamma J/psi
- 2017
-
Ingår i: Physical Review D. - : AMER PHYSICAL SOC. - 2470-0010 .- 2470-0029. ; 95:7
-
Tidskriftsartikel (refereegranskat)abstract
- Using 106 x 10(6) psi(3686) events collected with the BESIII detector, we measure multipole amplitudes for the decay psi(3686) ->; gamma chi(c1,2) -> gamma gamma J/psi beyond the dominant electric-dipole amplitudes. The normalized magnetic-quadrupole (M2) amplitude for psi(3686) -> gamma chi(c1,2) -> gamma gamma J/psi and the normalized electric-dipole amplitudes for psi(3686) -> gamma chi(c2) -> gamma J/psi and determined. The M2 amplitudes for psi(3686) -> gamma chi(c1) and ; chi(c1,2) -> gamma J/psi are found to differ significantly from zero and are consistent with theoretical predictions. We also obtain the ratios of M2 contributions of psi(3686) and J/psi decays to;2,chi(c1,2,) b(2)(1/)b(2)(2) = 1.35 +/- 0.72 and a(2)(1/)a(2)(2) = 0.617 +/- 0.083,,which agree well with theoretical expectations. By considering the multipole contributions of chi(c1,2), we measure the product branching fractions for the cascade decays psi(3686) -> gamma chi(c 0,1,2) -> gamma gamma J/psi and search for the process eta(c)(2s) -> gamma J/psi through psi(3686) -> gamma eta(c)(2s).The product branching fraction for psi(3686) -> gamma chi(c0) -> gamma gamma J/psi is 3 sigma larger than published measurements, while those of psi(3686) -> gamma chi(c1,2) -> gamma gamma J/psi are consistent. No significant signal for the decay psi(3686) -> gamma eta(c) (2s) -> gamma gamma J/psi is observed, and the upper limit of the product branching fraction at the 90% confidence level is determined.
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| 22. |
- Ablikim, M., et al.
(författare)
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Measurement of the absolute branching fraction of D+ → K̅0 e+νe via K̅0 → π 0 π 0
- 2016
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Ingår i: Chinese Physics C. - : IOP Publishing. - 1674-1137 .- 2058-6132. ; 40:11
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Tidskriftsartikel (refereegranskat)abstract
- By analyzing 2.93 fb(-1) data collected at the center-of-mass energy root s = 3.773 GeV with the BESIII detector, we measure the absolute branching fraction of the semileptonic decay D+ -> (K) over bar (0)e(+)nu(e) to be B(D (+) -> (K) over bar (0)e(+)nu(e)) = (8.59 +/- 0.14 +/- 0.21)% using (K) over bar (0) -> K-S(0) -> pi(0) pi(0), where the first uncertainty is statistical and the second systematic. Our result is consistent with previous measurements within uncertainties..
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| 23. |
- Ablikim, M., et al.
(författare)
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Measurement of the branching fractions of D-s(+) -> eta ' X and D-s(+) -> eta 'rho(+) in e(+)e(-) -> Ds+Ds-
- 2015
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Ingår i: Physics Letters B. - : Elsevier BV. - 0370-2693 .- 1873-2445. ; 750, s. 466-474
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Tidskriftsartikel (refereegranskat)abstract
- We study D-s(+) decays to final states involving the eta' with a 482 pb(-1) data sample collected at root s = 4.009 GeV with the BESIII detector at the BEPCII collider. We measure the branching fractions B(D-s(+) -> eta'X) = (8.8 +/- 1.8 +/- 0.5)% and B(D-s(+) > eta'rho(+)) = (5.8 +/- 1.4 +/- 0.4)% where the first uncertainty is statistical and the second is systematic. In addition, we estimate an upper limit on the non-resonant branching ratio B(D-s(+) -> eta'pi(+)pi(0)) < 5.1% at the 90% confidence level. Our results are consistent with CLEO's recent measurements and help to resolve the disagreement between the theoretical prediction and CLEO's previous measurement of B(D-s(+) -> eta'rho(+)).
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| 24. |
- Ablikim, M., et al.
(författare)
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Measurement of the Ds<(+)-> l(+)ve branching fractions and the decay constant fDs
- 2016
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Ingår i: PHYSICAL REVIEW D. - 2470-0010. ; 94:7
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Tidskriftsartikel (refereegranskat)abstract
- Using 482 pb(-1) of e(+) e(-) collision data collected at a center-of-mass energy of root s = 4.009 GeV with the BESIII detector, we measure the branching fractions of the decays D-s(+) -> u(+)v(u) and D-s(+) -> tau(+)v(tau). By constraining the ratio of decay rates of Ds(+) to tau(+)v(u) and to u(+)v(u) to the Standard Model prediction, the branching fractions are determined to be B(D-s(+) -> u(+)v(u) = (0.495 +/- 0.067 +/- 0.026)% and B(D-s(+) -> tau(+)v(tau) = (4.83 +/- 0.65 +/- 0.26)% Using these branching fractions, we obtain a value for the decay constant f(Ds+) of (241.0 +/- 16.3 +/- 6.5) MeV, where the first error is statistical and the second systematic.
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| 25. |
- Ablikim, M., et al.
(författare)
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Measurement of the leptonic decay width of J/psi using initial state radiation
- 2016
-
Ingår i: Physics Letters B. - : Elsevier BV. - 0370-2693 .- 1873-2445. ; 761, s. 98-103
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Tidskriftsartikel (refereegranskat)abstract
- Using a data set of 2.93 fb(-1) taken at a center-of-mass energy of root s = 3.773 GeV with the BESIII detector at the BEPCII collider, we measure the process e(+) e(-) -> J/psi gamma -> mu(+)mu(-)gamma and determine the product of the branching fraction and the electronic width B-mu mu . Gamma(ee) = (333.4 +/- 2.5(stat) +/- 4.4(sys)) eV. Using the earlier-published BESIII result for B-mu mu = (5.973 +/- 0.007(stat) +/- 0.037(sys))%, we derive the J/psi electronic width Gamma(ee) = (5.58 +/- 0.05(stat) +/- 0.08(sys)) keV. (C) 2016 The Author(s). Published by Elsevier B.V.
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