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Formalin‐fixed, paraffin‐embedded (FFPE ), biobanked tissue samples offer an invaluable resource for clinical and biomarker research. Here, we developed a pressure cycling technology (PCT )‐SWATH mass spectrometry workflow to analyze FFPE tissue proteomes and applied it to the stratification of prostate cancer (PC a) and diffuse large B‐cell lymphoma (DLBCL ) samples. We show that the proteome patterns of FFPE PC a tissue samples and their analogous fresh‐frozen (FF ) counterparts have a high degree of similarity and we confirmed multiple proteins consistently regulated in PC a tissues in an independent sample cohort. We further demonstrate temporal stability of proteome patterns from FFPE samples that were stored between 1 and 15 years in a biobank and show a high degree of the proteome pattern similarity between two types of histological regions in small FFPE samples, that is, punched tissue biopsies and thin tissue sections of micrometer thickness, despite the existence of a certain degree of biological variations. Applying the method to two independent DLBCL cohorts, we identified myeloperoxidase, a peroxidase enzyme, as a novel prognostic marker. In summary, this study presents a robust proteomic method to analyze bulk and biopsy FFPE tissues and reports the first systematic comparison of proteome maps generated from FFPE and FF samples. Our data demonstrate the practicality and superiority of FFPE over FF samples for proteome in biomarker discovery. Promising biomarker candidates for PC a and DLBCL have been discovered.
Improved measurement of the branching fraction of h_(c) → γη^(′)/η and search for h_(c) → γπ⁰
(2024)
The processes hc→γP(P=η′, η, π0)) are studied with a sample of (27.12±0.14)×108 ψ(3686) events collected by the BESIII detector at the BEPCII collider. The branching fractions of hc→γη′ and hc→γη are measured to be (1.40±0.11±0.04±0.10)×10−3 and (3.77±0.55±0.13±0.26)×10−4, respectively, where the first uncertainties are statistical, the second systematic, and the third from the branching fraction of ψ(3686)→π0hc. The ratio Rhc=B(hc→γη)B(hc→γη′) is calculated to be (27.0±4.4±1.0)%. The measurements are consistent with the previous results with improved precision by a factor of 2. The results are valuable for gaining a deeper understanding of η−η′ mixing, and its manifestation within quantum chromodynamics. No significant signal is found for the decay hc→γπ0, and an upper limit is placed on its branching fraction of B(hc→γπ0)<5.0×10−5, at the 90\% confidence level.
Using a sample of 106 million 𝜓(3686) decays, 𝜓(3686)→𝛾𝜒𝑐𝐽(𝐽=0,1,2) and 𝜓(3686)→𝛾𝜒𝑐𝐽,𝜒𝑐𝐽→𝛾𝐽/𝜓(𝐽=1,2) events are utilized to study inclusive 𝜒𝑐𝐽→anything, 𝜒𝑐𝐽→hadrons, and 𝐽/𝜓→anything distributions, including distributions of the number of charged tracks, electromagnetic calorimeter showers, and 𝜋0s, and to compare them with distributions obtained from the BESIII Monte Carlo simulation. Information from each Monte Carlo simulated decay event is used to construct matrices connecting the detected distributions to the input predetection “produced” distributions. Assuming these matrices also apply to data, they are used to predict the analogous produced distributions of the decay events. Using these, the charged particle multiplicities are compared with results from MARK I. Further, comparison of the distributions of the number of photons in data with those in Monte Carlo simulation indicates that G-parity conservation should be taken into consideration in the simulation.
Based on 4.5 fb−1 data taken at seven center-of-mass energies ranging from 4.600 to 4.699 GeV with the BESIII detector at the BEPCII collider, we measure the branching fractions of Λ + c → Σ + + hadrons relative to Λ + c → Σ +π +π −. Combining with the world average branching fraction of Λ + c → Σ +π +π −, their branching fractions are measured to be (0.377 ± 0.042 ± 0.020 ± 0.021)% for Λ + c → Σ +K+K−, (0.200 ± 0.023 ± 0.011 ± 0.011)% for Λ + c → Σ+K+π−, (0.414 ± 0.080 ± 0.030 ± 0.023)% for Λ + c → Σ +φ and (0.197 ± 0.036 ± 0.009 ± 0.011)% for Λ + c → Σ +K+K−(non-φ). In all the above results, the first uncertainties are statistical, the second are systematic and the third are from external input of the branching fraction of Λ + c → Σ +π +π −. Since no signal for Λ + c → Σ +K+π−π 0 is observed, the upper limit of its branching fraction is determined to be 0.13% at the 90% confidence level.
The Born cross sections and effective form factors for process 𝑒+𝑒−→Ξ−¯Ξ+ are measured at eight center-of-mass energies between 2.644 and 3.080 GeV, using a total integrated luminosity of 363.9 pb−1 𝑒+𝑒− collision data collected with the BESIII detector at BEPCII. After performing a fit to the Born cross section of 𝑒+𝑒−→Ξ−¯Ξ+, no significant threshold effect is observed.
Measurement of cross sections for e⁺e⁻ → μ⁺μ⁻ at center-of-mass energies from 3.80 to 4.60 GeV
(2020)
The observed cross sections for 𝑒+𝑒−→𝜇+𝜇− at energies from 3.8 to 4.6 GeV are measured using data samples taken with the BESIII detector operated at the BEPCII collider. We measure the muonic widths and determine the branching fractions of the charmonium states 𝜓(4040), 𝜓(4160), and 𝜓(4415) decaying to 𝜇+𝜇−, as well as making a first determination of the phase of the amplitudes. In addition, we observe evidence for a structure in the dimuon cross section near 4.220 GeV/𝑐2, which we denote as 𝑆(4220). Analyzing a coherent sum of amplitudes yields eight solutions, one of which gives a mass of 𝑀𝑆(4220) = 4216.7±8.9±4.1 MeV/𝑐2, a total width of Γtot S(4220) = 47.2±22.8±10.5 MeV, and a muonic width of Γ𝜇𝜇 𝑆(4220) = 1.53±1.26±0.54 keV, where the first uncertainties are statistical and the second systematic. The eight solutions give the central values of the mass, total width, muonic width to be, respectively, in the range from 4212.8 to 4219.4 MeV/𝑐2, from 36.4 to 49.6 MeV, and from 1.09 to 1.53 keV. The statistical significance of the 𝑆(4220) signal is 3.9𝜎. Correcting the total dimuon cross section for radiative effects yields a statistical significance for this structure of 8.1𝜎.
Using data samples with an integrated luminosity of 22.42 fb−1 collected by the BESIII detector operating at the BEPCII storage ring, we measure the cross sections of the 𝑒+𝑒−→𝜂𝐽/𝜓 process at center-of-mass energies from 3.808 to 4.951 GeV. Three structures are observed in the line shape of the measured cross sections. A maximum-likelihood fit with 𝜓(4040), two additional resonances, and a nonresonant component are performed. The mass and width of the first additional state are (4219.7±2.5±4.5) MeV/𝑐2 and (80.7±4.4±1.4) MeV, respectively, consistent with the 𝜓(4230). For the second state, the mass and width are (4386±13±17) MeV/𝑐2 and (177±32±13) MeV, respectively, consistent with the 𝜓(4360). The first uncertainties are statistical, and the second ones are systematic. The statistical significance of 𝜓(4040) is 8.0𝜎 and those for 𝜓(4230) and 𝜓(4360) are more than 10.0𝜎.
Using data samples with an integrated luminosity of 22.42 fb−1 collected by the BESIII detector operating at the BEPCII storage ring, we measure the cross sections of the $e^{+}e^{-}\rightarrow\etaJ/\psi$ process at center-of-mass energies from 3.808 to 4.951 GeV. Three structures are observed in the line shape of the measured cross sections. A maximum-likelihood fit with ψ(4040), two additional resonances, and a non-resonant component is performed. The mass and width of the first additional state are (4219.7±2.5±4.5)MeV/c2 and (80.7±4.4±1.4)MeV, respectively, consistent with the ψ(4230). For the second state, the mass and width are (4386±13±17)MeV/c2 and (177±32±13)MeV, respectively, consistent with the ψ(4360). The first uncertainties are statistical and the second ones are systematic. The statistical significance of ψ(4040) is 8.0σ and those for ψ(4230) and ψ(4360) are more than 10.0σ.
The Born cross sections for the process e+e−→ωη′ are measured at 22 center-of-mass energies from 2.000 to 3.080 GeV using data collected with the BESIII detector at the BEPCII collider. A resonant structure is observed with a statistical significance of 9.6σ. A Breit-Wigner fit determines its mass to be MR=(2153±30±31) MeV/c2 and its width to be ΓR=(167±77±7) MeV, where the first uncertainties are statistical and the second are systematic.
The cross sections of the 𝑒+𝑒−→𝜙𝜂′ process at center-of-mass energies from 3.508 to 4.951 GeV are measured with high precision using 26.1 fb−1 data collected with the BESIII detector operating at the BEPCII storage ring. The cross sections are of the order of a few picobarn and decrease as the center-of-mass energy increases as 𝑠−𝑛/2 with 𝑛=4.35±0.14. This result is in agreement with the Nambu-Jona-Lasinio model prediction of 𝑛=3.5±0.9. In addition, the charmless decay 𝜓(3770)→𝜙𝜂′ is searched for by fitting the measured cross sections, yet no significant signal is observed. The upper limit of ℬ(𝜓(3770)→𝜙𝜂′) at the 90% confidence level is determined to be 2.3×10−5.