| 1. |
- 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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| 2. |
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| 3. |
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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
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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. |
- Ablikim, M., et al.
(author)
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Amplitude analysis of the D+ -> K-S(0)pi + (0)(pi) Dalitz plot
- 2014
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In: Physical Review D. - 1550-7998 .- 1550-2368. ; 89:5, s. 052001-
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Journal article (peer-reviewed)abstract
- We perform an analysis of the D+ -> K-S(0)pi + (0)(pi) Dalitz plot using a data set of 2.92 fb(-1) of e(+) e(-) collisions at the (3770) mass accumulated by the BESIII experiment, in which 166694 candidate events are selected with a background of 15.1%. The Dalitz plot is found to be well represented by a combination of six quasitwo- body decay channels [k(SP)(0)(+) (1450)(+,) ] plus a small nonresonant component. Using the fit fractions from this analysis, partial branching ratios are updated with higher precision than previous measurements.
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| 9. |
- Ablikim, M., et al.
(author)
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Measurement of chi(cJ) decaying into eta ' K+K-
- 2014
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In: Physical Review D. - 1550-7998 .- 1550-2368. ; 89:7, s. 074030-
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Journal article (peer-reviewed)abstract
- Using (106.41 +/- 0.86) x 10(6) Psi(3686) events collected with the BESIII detector at BEPCII, we study for the first time the decay chi(cJ) -> eta'K+K- (J = 1, 2), where eta' -> gamma rho(0) and eta' -> eta pi(+)pi(-). A partial wave analysis in the covariant tensor amplitude formalism is performed for the decay chi(c1) -> eta'K+K-. Intermediate processes chi(c1) -> eta'f(2)'(1525) chi(c1) -> K-0*(1430)K-+/-(-/+) (K-0*(1430)(+/-) -> eta'K-+/-) are observed with statistical significances larger than 5 sigma, and their branching fractions are measured.
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| 10. |
- Ablikim, M., et al.
(author)
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Measurement of the branching fraction for psi(3686) -> omega K+K-
- 2014
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In: Physical Review D. - 1550-7998 .- 1550-2368. ; 89:11, s. 112006-
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Journal article (peer-reviewed)abstract
- With 1.06 x 10(8) psi(3686) events collected with the BESIII detector, the branching fraction of psi(3686) -> omega K+K- is measured to be (1.54 +/- 0.04 +/- 0.11) x 10(-4). This is the most precise result to date, due to the largest psi(3686) sample, improved signal reconstruction efficiency, good simulation of the detector performance, and a more accurate knowledge of the continuum contribution. Using the branching fraction of J/psi -> omega K+K-, the ratio B(psi(3868) -> K+K-)/B(J/psi -> K+K-) is determined to be (18.4 +/- 3.7)%. This constitutes a significantly improved test of the 12% rule, with the uncertainty now dominated by the J/psi branching fraction.
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| 11. |
- 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
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In: Physical Review Letters. - 0031-9007 .- 1079-7114. ; 117:4
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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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| 12. |
- Ablikim, M., et al.
(author)
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Observation of eta' -> pi(+) pi(-) pi(+) pi(-) and eta' -> pi(+) pi(-) pi(0) pi(0)
- 2014
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In: Physical Review Letters. - 0031-9007 .- 1079-7114. ; 112:25, s. 251801-
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Journal article (peer-reviewed)abstract
- Using a sample of 1.3 x 10(9) J/psi events collected with the BESIII detector, we report the first observation of eta' -> pi(+) pi(-) pi(+) pi(-) and eta' -> pi(+) pi(-) pi(0) pi(0). The measured branching fractions are B(eta' -> pi(+) pi(-) pi(+) pi(-)) = [8.53 +/- 0.69(stat.) +/- 0.64(syst.)] x 10(-5) and B(eta' -> pi(+) pi(-) pi(0) pi(0)) = [1.82 +/- 0.35(stat.) +/- 0.18(syst.)] x 10(-4), which are consistent with theoretical predictions based on a combination of chiral perturbation theory and vector-meson dominance.
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| 13. |
- Ablikim, M., et al.
(author)
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Observation of J/psi -> p(p)over-bara(0)(980) at BESIII
- 2014
-
In: Physical Review D. - 1550-7998 .- 1550-2368. ; 90:5, s. 052009-
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Journal article (peer-reviewed)abstract
- Using 2.25 x 10(8) J/psi events collected with the BESIII detector at the BEPCII storage rings, we observe for the first time the process J/psi -> p (p) over bara(0)(980) -> pi(0)eta with a significance of 6.5 sigma (3.2 sigma including systematic uncertainties). The product branching fraction of J/psi -> p (p) over bara(0)(980) -> p (p) over bara(0)pi(0)eta is measured to be (6.8 +/- 1.2 +/- 1.3) x 10(-5), where the first error is statistical and the second is systematic. This measurement provides information on the a(0) production near threshold coupling to p (p) over bar and improves the understanding of the dynamics of J/psi decays to four-body processes.
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| 14. |
- Ablikim, M., et al.
(author)
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Precision measurement of the mass of the tau lepton
- 2014
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In: Physical Review D. - 1550-7998 .- 1550-2368. ; 90:1
-
Journal article (peer-reviewed)abstract
- An energy scan near the tau pair production threshold has been performed using the BESIII detector. About 24 pb(-1) of data, distributed over four scan points, were collected. This analysis is based on t pair decays to ee, e mu, eh, h, hh, e.,. and p. final states, where h denotes a charged p or K. The mass of the t lepton is measured from a maximum likelihood fit to the t pair production cross- section data to be m(tau) = 1776.91 +/- 0.12_0.10 - 0.13 _ MeV/c(2), which is currently the most precise value in a single measurement.
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| 15. |
- Ablikim, M., et al.
(author)
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Search for the radiative transitions Psi(3770) -> gamma eta(c) and gamma eta(c) (2S)
- 2014
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In: Physical Review D. - 1550-7998 .- 1550-2368. ; 89:11, s. 112005-
-
Journal article (peer-reviewed)abstract
- By using a 2.92 fb-1 data sample taken at pffisffiffi 3.773 GeV with the BESIII detector operating at the BEPCII collider, we search for the radiative transitions.d3770c and cd2S through the hadronic decays cdcd2S. K0 SK p. No significant excess of signal events above background is observed. We set upper limits at a 90% confidence level for the product branching fractions to be Bdd3770cxBd.c. K0 SK k p < 1.6x10-5 and Bd.d3770cd2SxBd.cd2S. K0 SK p<5.6x10-6. Combining our result with world-average values of Bd.cd.cd2S. K0 SK p, we find the branching fractions Bd.d3770c< 6.8 x 10-4 and Bd.d3770cd2S< 2.0 x 10-3 at a 90% confidence level.
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| 16. |
- Ablikim, M., et al.
(author)
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Search for the rare decays J/y -> D-s(-) rho(+) and J/psi -> <(D)over bar(0)<(K)over bar*(0)
- 2014
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In: Physical Review D. - 1550-7998 .- 1550-2368. ; 89:7, s. 071101-
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Journal article (peer-reviewed)abstract
- A search for the rare decays of J/psi -> D-S(-) rho(+) + c.c. and J/psi -> <(D)over bar(0)<(K)over bar*(0) + c.c. is performed with a data sample of 225.3-million J/psi events collected with the Beijing Spectrometer III detector. No evident signal is observed. Upper limits on the branching fractions are determined to be beta(J/psi -> D-S(-)rho(+) + c.c.) < 1.3 x 10(-5) and beta(J/psi -> <(D)over bar(0)<(K)over bar*(0) + c.c.) < 2.5 x 10(-6) at the 90% confidence level.
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| 17. |
- Ablikim, M., et al.
(author)
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Study of e(+)e(-) -> p(p)over-bar in the vicinity of psi(3770)
- 2014
-
In: Physics Letters B. - : Elsevier BV. - 0370-2693 .- 1873-2445. ; 735, s. 101-107
-
Journal article (peer-reviewed)abstract
- Using 2917 pb(-1) of data accumulated at 3.773 GeV, 44.5 pb(-1) of data accumulated at 3.65 GeV and data accumulated during a psi(3770) line-shape scan with the BESIII detector, the reaction e(+)e(-) -> p (p) over bar is studied considering a possible interference between resonant and continuum amplitudes. The cross section of e(+)e(-) -> psi(3770) -> p (p) over bar, sigma(e(+)e(-)-> psi(3770) -> p (p) over bar), is found to have two solutions, determined to be (0.059(-0.020)(+0.070) +/- 0.012) pb with the phase angle phi = (255.8(-26.6)(+39.0) +/- 4.8). (< 0.166 pb at the 90% confidence level), or sigma(e(+)e(-) -> psi(3770) -> p<(p)over bar>) = (2.57(-0.13)(+0.12) +/- 0.12) pb with phi = (266.9(-6.3)(+6.1) +/- 0.9)degrees both of which agree with a destructive interference. Using the obtained cross section of psi(3770) -> p (p) over bar, the cross section of p (p) over bar -> psi(3770), which is useful information for the future PANDA experiment, is estimated to be either (9.8(-3.9)(+11.8)) nb (< 27.5 nb at 90% C.L.) or (425.6(-43.7)(+42.9)) nb. (C) 2014 The Authors. Published by Elsevier B.V. This is an open access article under the CC BY license.
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| 18. |
- Ablikim, M., et al.
(author)
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Study of e(+)e(-) -> p(p)over-bar pi(0) in the vicinity of the psi(3770)
- 2014
-
In: Physical Review D. - 1550-7998 .- 1550-2368. ; 90:3, s. 032007-
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Journal article (peer-reviewed)abstract
- The process e(+)e(-) -> p (p) over bar pi(0) has been studied by analyzing data collected at root s = 3.773 GeV, root s = 3.650 GeV, and during a psi(3770) line shape scan with the BESIII detector at the BEPCII collider. The Born cross section of p (p) over bar pi(0) in the vicinity of the psi(3770) is measured, and the Born cross section of psi(3770) -> p (p) over bar pi(0) is extracted considering interference between resonant and continuum production amplitudes. Two solutions with the same probability and a significance of 1.5 sigma are found. The solutions for the Born cross section of psi(3770) -> p (p) over bar pi(0) are 33.8 +/- 1.8 +/- 2.1 pb and 0.06(-0.04-0.01)(+0.10+0.01) pb (< 0.22 pb at a 90% confidence level). Using the estimated cross section and a constant decay amplitude approximation, the cross section sigma(p<(p)over bar> -> psi(3770)pi(0)) is calculated for the kinematic situation of the planned (p) over bar ANDA experiment. The maximum cross section corresponding to the two solutions is expected to be less than 0.79 nb at 90% confidence level and 122 +/- 10 nb at a center-of-mass energy of 5.26 GeV.
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| 19. |
-
- 2019
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Journal article (peer-reviewed)
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| 20. |
- 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
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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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| 21. |
- Ablikim, M., et al.
(author)
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Amplitude analysis of the chi(c1) -> eta pi(+)pi(-) decays
- 2017
-
In: Physical Review D. - : AMER PHYSICAL SOC. - 2470-0010 .- 2470-0029. ; 95:3
-
Journal article (peer-reviewed)abstract
- Using 448.0 x 10(6) psi(3686) events collected with the BESIII detector, an amplitude analysis is performed for psi(3686) -> gamma chi(c1), chi(c1) ->eta pi(+)pi(-) decays. The most dominant two- body structure observed is a(0)(980)(+/-) pi(-/+); a(0)(980)(+/-) -> eta pi(+/-.) line shape is modeled using a dispersion relation, and a significant nonzero a(0) (980) coupling to the eta'pi channel is measured. We observe chi(c1) -> a(2)(1700)pi production for the first time, with a significance larger than 17 sigma. The production of mesons with exotic quantum numbers, J(PC) = 1(-+), is investigated, and upper limits for the branching fractions chi(c1) -> pi(1)(1400)(+/-)pi(-/+) , chi(c1) -> pi(1)(1600)(+/-)pi(-/+) and chi(c1) -> pi 1(2015)(+/-)pi(-/+) with subsequent pi(1)(X)(+/-) -> eta pi(+/-) decay, are determined.
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| 22. |
- Ablikim, M., et al.
(author)
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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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| 23. |
- Ablikim, M., et al.
(author)
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Amplitude analysis of the pi(0)pi(0) system produced in radiative J/psi decays
- 2015
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In: Physical Review D. - 1550-7998 .- 1550-2368. ; 92:5
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Journal article (peer-reviewed)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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| 24. |
- Ablikim, M., et al.
(author)
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An improved limit for Gamma(ee) of X(3872) and Gamma(ee) measurement of psi(3686)
- 2015
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In: Physics Letters B. - : Elsevier BV. - 0370-2693 .- 1873-2445. ; 749, s. 414-420
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Journal article (peer-reviewed)abstract
- Using the data sets taken at center-of-mass energies above 4 GeV by the BESIII detector at the BEPCII storage ring, we search for the reaction e(+)e(-) -> gamma(ISR) X(3872) -> gamma(ISR)pi(+)pi(-) J/psi via the Initial State Radiation technique. The production of a resonance with quantum numbers J(PC) = 1(++) such as the X(3872) via single photon e(+)e(-) annihilation is forbidden, but is allowed by a next-to-leading order box diagram. We do not observe a significant signal of X(3872), and therefore give an upper limit for the electronic width times the branching fraction Gamma B-X(3872)(ee)(X(3872) -> pi(+)pi(-) J/psi) < 0.13 eVat the 90% confidence level. This measurement improves upon existing limits by a factor of 46. Using the same final state, we also measure the electronic width of the psi(3686) to be Gamma(psi)(ee)(3686) ee = 2213 +/- 18(stat) +/- 99(sys) eV.
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| 25. |
- Ablikim, M., et al.
(author)
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Dark photon search in the mass range between 1.5 and 3.4 GeV/c
- 2017
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In: Physics Letters B. - : Elsevier BV. - 0370-2693 .- 1873-2445. ; 774, s. 252-257
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Journal article (peer-reviewed)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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