| 1. |
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| 2. |
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| 3. |
- Beal, Jacob, et al.
(author)
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Robust estimation of bacterial cell count from optical density
- 2020
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In: Communications Biology. - : Springer Science and Business Media LLC. - 2399-3642. ; 3:1
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Journal article (peer-reviewed)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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| 5. |
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| 6. |
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| 7. |
- Klionsky, Daniel J., et al.
(author)
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Guidelines for the use and interpretation of assays for monitoring autophagy
- 2012
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In: Autophagy. - : Informa UK Limited. - 1554-8635 .- 1554-8627. ; 8:4, s. 445-544
-
Research review (peer-reviewed)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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| 8. |
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- 2019
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Journal article (peer-reviewed)
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| 9. |
- Ablikim, M., et al.
(author)
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Amplitude analysis of D0 → K -π+π+π-
- 2017
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In: Physical Review D. - 2470-0010 .- 2470-0029. ; 95:7
-
Journal article (peer-reviewed)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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| 10. |
- Ablikim, M., et al.
(author)
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Amplitude analysis of the KSKS system produced in radiative J /psi decays
- 2018
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In: Physical Review D. - : AMER PHYSICAL SOC. - 2470-0010 .- 2470-0029. ; 98:7
-
Journal article (peer-reviewed)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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| 11. |
- Ablikim, M., et al.
(author)
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Determination of the Spin and Parity of the Z(c)(3900)
- 2017
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In: Physical Review Letters. - : AMER PHYSICAL SOC. - 0031-9007 .- 1079-7114. ; 119:7
-
Journal article (peer-reviewed)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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| 12. |
- Ablikim, M., et al.
(author)
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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
-
In: Physical Review D. - : AMER PHYSICAL SOC. - 2470-0010 .- 2470-0029. ; 95:7
-
Journal article (peer-reviewed)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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| 13. |
- Ablikim, M., et al.
(author)
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Observation of an Anomalous Line Shape of the eta 'pi(+)pi(-) Mass Spectrum near the p(p)over-bar Mass Threshold in J/psi -> gamma eta 'pi(+)pi(-)
- 2016
-
In: Physical Review Letters. - 0031-9007 .- 1079-7114. ; 117:4
-
Journal article (peer-reviewed)abstract
- Using 1.09 x 10(9) J/psi events collected by the BESIII experiment in 2012, we study the J / psi -> gamma eta'pi(+)pi(-) process and observe a significant abrupt change in the slope of the eta'pi(+)pi(-) invariant mass distribution at the proton-antiproton (p (p) over bar) mass threshold. We use two models to characterize the eta'pi(+)pi(-) line shape around 1.85 GeV/c(2): one that explicitly incorporates the opening of a decay threshold in the mass spectrum (Flatte formula), and another that is the coherent sum of two resonant amplitudes. Both fits show almost equally good agreement with data, and suggest the existence of either a broad state around 1.85 GeV/c(2) with strong couplings to the c final states or a narrow state just below the p (p) over bar mass threshold. Although we cannot distinguish between the fits, either one supports the existence of a p (p) over bar moleculelike state or bound state with greater than 7 sigma significance.
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| 14. |
- Ablikim, M., et al.
(author)
-
Observation of e(+)e(-) -> eta ' J/psi center-of-mass energies between 4.189 and 4.600 GeV
- 2016
-
In: PHYSICAL REVIEW D. - 2470-0010. ; 94:3
-
Journal article (peer-reviewed)abstract
- The process e(+)e(-) -> eta' J/psi is observed for the first time with a statistical significance of 8.6 sigma at center-of-mass energy root s = 4.226 GeV and 7.3 sigma at root s = 4.258 GeV using data samples collected with the BESIII detector. The Born cross sections are measured to be (3.7 +/- 0.7 +/- 0.3) and (3.9 +/- 0.8 +/- 0.3) pb at root s = 4.226 and 4.258 GeV, respectively, where the first errors are statistical and the second systematic. Upper limits at the 90% confidence level of the Born cross sections are also reported at other 12 energy points.
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| 15. |
- Ablikim, M., et al.
(author)
-
Observation of the Singly Cabibbo-Suppressed Decay D+ -> omega pi(+) and Evidence for D-0 -> omega pi(0)
- 2016
-
In: Physical Review Letters. - 0031-9007 .- 1079-7114. ; 116:8
-
Journal article (peer-reviewed)abstract
- Based on 2.93 fb(-1) e(+)e(-) collision data taken at center-of-mass energy of 3.773 GeV by the BESIII detector, we report searches for the singly Cabibbo-suppressed decays D+ -> omega pi(+) and D-0 -> omega pi(0). A double tag technique is used to measure the absolute branching fractions B(D+ -> omega pi(+)) = (2.79 +/- 0.57 +/- 0.16) x 10(-4) and B(D-0 +/- omega pi(0)) = (1.17 +/- 0.34 +/- 0.07) x 10(-4), with statistical significances of 5.5 sigma and 4.1 sigma, where the first and second uncertainties are statistical and systematic, respectively.
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| 16. |
- Ablikim, M., et al.
(author)
-
Observation of Ψ(3686) → e+e-ΧcJ and ΧcJ → e+e-J/Ψ
- 2017
-
In: Physical Review Letters. - 0031-9007 .- 1079-7114. ; 118:22
-
Journal article (peer-reviewed)abstract
- Using 4.479 x 10(8) psi(3686) events collected with the BESIII detector, we search for the decays psi(3686) -> e(+)e(-)chi(cJ) and chi(cJ) -> e(+)e(-)J/psi, where J = 0, 1, 2. The decays psi(3686) -> e(+)e(-)chi(cJ) and chi(cJ) -> e(+)e(-)J/psi are observed for the first time. The measured branching fractions are B(psi(3686) -> e(+)e(-)chi(cJ)) = (11.7 +/- 2.5 +/- 1.0) x 10(-4), (8.6 +/- 0.3 +/- 0.6) x 10(-4), (6.9 +/- 0.5 +/- 0.6) x 10(-4) for J = 0, 1, 2, and B(chi(cJ) -> e(+)e(-)J/psi) = (1.51 +/- 0.30 +/- 0.13)x10(-4), (3.73 +/- 0.09 +/- 0.25)x10(-3), (2.48 +/- 0.08 +/- 0.16)x10(-3) for J = 0, 1, 2, respectively. The ratios of the branching fractions B(psi(3686) -> e(+)e(-)chi(cJ))/B(psi(3686) -> gamma chi(cJ)) and B(chi(cJ) -> e(+)e(-)J/psi)/B(chi(cJ) -> gamma J/psi) are also reported. Also, the alpha values of helicity angular distributions of the e(+)e(-) pair are determined for psi(3686) -> e(+)e(-)chi(c1,2) and chi(c1,2) -> e(+)e(-)J/psi.
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| 17. |
- Ablikim, M., et al.
(author)
-
Amplitude Analysis of the Decays eta ' -> pi(+)pi(-)pi(0) and eta' -> pi(0)pi(0)pi(0)
- 2017
-
In: Physical Review Letters. - 0031-9007 .- 1079-7114. ; 118:1
-
Journal article (peer-reviewed)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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| 18. |
- Ablikim, M., et al.
(author)
-
Branching fraction measurement of J/ψ→KSKL and search for J/ψ→KSKS
- 2017
-
In: Physical Review D. - 2470-0010 .- 2470-0029. ; 96:11
-
Journal article (peer-reviewed)abstract
- Using a sample of 1.31 x 10(9) J/Psi events collected with the BESIII detector at the BEPCII collider, we study the decays of J/Psi -> KSKL and KSKS. The branching fraction of J/Psi -> KSKL is determined to be B(J/Psi -> KSKL) = (1.93 +/- 0.01 (stat) +/- 0.05 (syst)) x 10(-4), which significantly improves on previous measurements. No clear signal is observed for the J/Psi -> KSKS process, and the upper limit at the 95% confidence level for its branching fraction is determined to be B(J/Psi -> KSKS) < 1.4 x 10(-8), which improves on the previous searches by 2 orders in magnitude and reaches the order of the Einstein-Podolsky-Rosen expectation.
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| 19. |
- Ablikim, M., et al.
(author)
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Improved measurement of the absolute branching fraction of D+ -> (K)over-bar(0)mu(+)nu(mu)
- 2016
-
In: European Physical Journal C. - : SPRINGER. - 1434-6044 .- 1434-6052. ; 76:7
-
Journal article (peer-reviewed)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.
(author)
-
Improved measurements of branching fractions for eta(c) -> phi phi and omega phi
- 2017
-
In: Physical Review D. - : AMER PHYSICAL SOC. - 2470-0010 .- 2470-0029. ; 95:9
-
Journal article (peer-reviewed)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.
(author)
-
Measurement of cross sections of the interactions e(+)e(-) -> phi phi omega and e(+)e(-) -> phi phi phi at center-of-mass energies from 4.008 to 4.600 GeV
- 2017
-
In: Physics Letters B. - : Elsevier BV. - 0370-2693 .- 1873-2445. ; 774, s. 78-86
-
Journal article (peer-reviewed)abstract
- Using data samples collected with the BESIII detector at the BEPCII collider at six center-of-mass energies between 4.008 and 4.600 GeV, we observe the processes e(+)e(-) -> phi phi omega and e(-)e(-) -> phi phi phi. The Born cross sections are measured and the ratio of the cross sections sigma(e(+)e(-) -> phi phi omega)/sigma(e(-)e(-) -> phi phi phi) is estimated to be 1.75 +/- 0.22 +/- 0.19 averaged over six energy points, where the first uncertainty is statistical and the second is systematic. The results represent first measurements of these interactions.
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| 22. |
- Ablikim, M., et al.
(author)
-
Measurement of e(+)e(-) -> K(K)over-barJ/psi cross sections at center-of-mass energies from 4.189 to 4.600 GeV
- 2018
-
In: Physical Review D. - : AMER PHYSICAL SOC. - 2470-0010 .- 2470-0029. ; 97:7
-
Journal article (peer-reviewed)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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| 23. |
- Ablikim, M., et al.
(author)
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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
-
In: Physical Review D. - 2470-0010 .- 2470-0029. ; 96:3
-
Journal article (peer-reviewed)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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| 24. |
- Ablikim, M., et al.
(author)
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Measurement of the absolute branching fraction of D+ → K̅0 e+νe via K̅0 → π 0 π 0
- 2016
-
In: Chinese Physics C. - : IOP Publishing. - 1674-1137 .- 2058-6132. ; 40:11
-
Journal article (peer-reviewed)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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| 25. |
- Ablikim, M., et al.
(author)
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Measurement of the absolute branching fraction of D*(s0) (2317)(+/-) -> pi D-0(s)+/-
- 2018
-
In: Physical Review D. - : American Physical Society. - 2470-0010 .- 2470-0029. ; 97:5
-
Journal article (peer-reviewed)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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