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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.
A search has been performed for the semileptonic decays D0→K0SK−e+νe, D+→K0SK0Se+νe and D+→K+K−e+νe, using 7.9 fb−1 of e+e− annihilation data collected at the center-of-mass energy s√=3.773 GeV by the BESIII detector operating at the BEPCII collider. No significant signals are observed, and upper limits are set at the 90\% confidence level of 2.13×10−5, 1.54×10−5 and 2.10×10−5 for the branching fractions of D0→K0SK−e+νe, D+→K0SK0Se+νe and D+→K+K−e+νe, respectively.
We present cross sections for the reaction e+e−→K0SK0L at center-of-mass energies ranging from 3.51 GeV to 4.95 GeV using data samples collected in the BESIII experiment, corresponding to a total integrated luminosity of 26.5 fb−1. The ratio of neutral-to-charged kaon form factors at large momentum transfers (12 GeV2<Q2<25 GeV2) is determined to be 0.21±0.01, which indicates a small but significant effect of flavor-SU(3) breaking in the kaon wave function, and consequently excludes the possibility that flavor-SU(3) breaking is the primary reason for the strong experimental violation of the pQCD prediction |F(π±)|/|F(K±)|=f2π/f2K, where F(π±) and F(K±) are the form factors, and fπ and fK are the decay constants of charged pions and kaons, respectively. We also observe a significant signal for the charmless decay ψ(3770)→K0SK0L for the first time. Within a 1σ contour of the likelihood value, the the branching fraction for ψ(3770)→K0SK0L is determined to be B=(2.63+1.40−1.59)×10−5, and the relative phase between the continuum and ψ(3770) amplitudes is ϕ=(−0.39+0.05−0.10)π. The branching fraction is in good agreement with the S- and D-wave charmonia mixing scheme proposed in the interpretation of the "ρπ puzzle" between J/ψ and ψ(3686) decays.
We search for the semi-leptonic decays Λ + c → Λπ+π−e+νe and Λ + c → pK0 Sπ−e+νe in a sample of 4.5 fb−1 of e+e− annihilation data collected in the center-of-mass energy region between 4.600 GeV and 4.699 GeV by the BESIII detector at the BEPCII. No significant signals are observed, and the upper limits on the decay branching fractions are set to be B(Λ+c → Λπ+π−e+νe ) < 3.9 × 10−4 and B(Λ + c → pK0Sπ−e+νe ) < 3.3 × 10−4 at the 90% confidence level, respectively.
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.
With data samples collected with the BESIII detector at seven energy points at √s = 3.68 − 3.71 GeV, corresponding to an integrated luminosity of 333 pb−1, we present a study of the Λ transverse polarization in the e+e− → ΛΛ¯ reaction. The signifcance of polarization by combining the seven energy points is found to be 2.6σ including the systematic uncertainty, which implies a non-zero phase between the transition amplitudes of the ΛΛ¯ helicity states. The modulus ratio and the relative phase of EM-psionic form factors combined with all energy points are measured to be RΨ = 0.71+0.10−0.10 ± 0.03 and ∆ΦΨ = 23+8.8−8.0 ± 1.6◦, where the frst uncertainties are statistical and the second 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.
Using 2.93 fb−1 of e+e− collision data collected with the BESIII detector at the center-of-mass energy 3.773 GeV, we perform the first amplitude analysis of the decay D+ → π+π0π0 and determine the relative magnitudes and phases of different intermediate processes. The absolute branching fraction of D+ → π+π0π0 is measured to be (2.888 ± 0.058stat. ± 0.069syst.)%. The dominant intermediate processes are D+ → a1(1260)+(→ ρ+π0) and D+ → *0ρ+, with branching fractions of (8.66 ± 1.04stat. ± 1.39syst.) × 10−3 and (9.70 ± 0.81stat. ± 0.53syst.) × 10−3, respectively.
Evidence for the singly Cabibbo suppressed decay Λ+c→pπ0 is reported for the first time with a statistical significance of 3.7σ based on 6.0 fb−1 of e+e− collision data collected at center-of-mass energies between 4.600 and 4.843 GeV with the BESIII detector at the BEPCII collider. The absolute branching fraction of Λ+c→pπ0 is measured to be (1.56+0.72−0.58±0.20)×10−4. Combining with the branching fraction of Λ+c→nπ+, (6.6±1.2±0.4)×10−4, the ratio of the branching fractions Λ+c→nπ+ and Λ+c→pπ0 is calculated to be 4.2+2.2−1.9; this is an important input for the understanding of the decay mechanisms of charmed baryons. In addition, the absolute branching fraction of Λ+c→pη is measured to be (1.63±0.31stat±0.11syst)×10−3, which is consistent with previous measurements.