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The epitranscriptome embodies many new and largely unexplored functions of RNA. A major roadblock in the epitranscriptomics field is the lack of transcriptome-wide methods to detect more than a single RNA modification type at a time, identify RNA modifications in individual molecules, and estimate modification stoichiometry accurately. We address these issues with CHEUI (CH3 (methylation) Estimation Using Ionic current), a new method that concurrently detects N6-methyladenosine (m6A) and 5-methylcytidine (m5C) in individual RNA molecules from the same sample, as well as differential methylation between any two conditions. CHEUI processes observed and expected nanopore direct RNA sequencing signals with convolutional neural networks to achieve high single-molecule accuracy and outperforms other methods in detecting m6A and m5C sites and quantifying their stoichiometry. CHEUI’s unique capability to identify two modification types in the same sample reveals a non-random co-occurrence of m6A and m5C in mRNA transcripts in cell lines and tissues. CHEUI unlocks an unprecedented potential to study RNA modification configurations and discover new epitranscriptome functions.
The expanding field of epitranscriptomics might rival the epigenome in the diversity of the biological processes impacted. However, the identification of modifications in individual RNA molecules remains challenging. We present CHEUI, a new method that detects N6-methyladenosine (m6A) and 5-methylcytidine (m5C) at single-nucleotide and single-molecule resolution from Nanopore signals. CHEUI predicts methylation in Nanopore reads and transcriptomic sites in a single condition, and differential m6A and m5C methylation between any two conditions. Using extensive benchmarking with Nanopore data derived from synthetic and natural RNA, CHEUI showed higher accuracy than other existing methods in detecting m6A and m5C sites and quantifying the site stoichiometry levels, while maintaining a lower proportion of false positives. CHEUI provides a new capability to detect RNA modifications with high accuracy and resolution that can be cost-effectively expanded to other modifications to unveil the full span of the epitranscriptome in normal and disease conditions.
Anhand eines Datensatzes von 1.708 Vegetationsaufnahmen aus 154 bayerischen Naturwaldreservaten wurde die realisierte ökologische Nische von 25 Baumarten hinsichtlich Lichtbedarf bzw. Schattentoleranz untersucht. Für jede Baumart wurde die Stetigkeit des Vorkommens in Baumschicht und Verjüngung berechnet. Für jede Aufnahme wurde die dem Bestandesunterwuchs zur Verfügung stehende Lichtmenge durch Berechnung des mittleren ungewichteten Licht-Zeigerwertes (mL) aller vorkommenden Arten (ohne Baumschicht) auf einer Relativskala geschätzt. Für jede 0,5-Einheiten-Stufe von mL wurde die Präferenz jeder Baumart, getrennt nach Baum- (> 5m) und Verjüngungsschicht (< 5m), als Differenz zwischen relativer Häufigkeit der jeweiligen Art und der relativen Häufigkeit aller Aufnahmen in der mL-Stufe im gesamten Datensatz berechnet. Die Präferenzprofile von Baumschicht und Verjüngungsschicht bildeten die Grundlage einer numerischen Klassifikation von 6 lichtökologischen Nischen typen. Diese Typen werden hinsichtlich ihrer Bindung an bestimmte Entwicklungsphasen und Strukturen der natürlichen Walddynamik diskutiert, mit geläufigen Einteilungen der Baumarten verglichen und im Hinblick auf eine Prognose des Verhaltens unter sich ändernden Umweltbedingungen ausgewertet. – Während sich Edellaubbäume des Tilio-Acerion in den Reservaten sehr ähnlich wie Fagus und Abies verhalten, bilden die Baumarten der Eichenmischwälder eine lichtökologische Gruppe mit rückläufiger Verjüngungstendenz. Unter den übrigen Halbschattbaumarten hebt sich eine Gruppe heraus, welche sich in geschlossenen Beständen vorausverjüngt und nach Störung in die Baumschicht vordringt. Pionierbaumarten bleiben in Naturwaldreservaten weitestgehend auf Sonderstandorte, wo ihre Verjüngung viel Licht vorfindet, beschränkt.
Observation of directed flow of hypernuclei Λ³H and Λ⁴H in √sNN = 3 GeV Au+Au collisions at RHIC
(2023)
We report here the first observation of directed flow (v1) of the hypernuclei 3ΛH and 4ΛH in mid-central Au+Au collisions at sNN−−−√ = 3 GeV at RHIC. These data are taken as part of the beam energy scan program carried out by the STAR experiment. From 165 × 106 events in 5%-40% centrality, about 8400 3ΛH and 5200 4ΛH candidates are reconstructed through two- and three-body decay channels. We observe that these hypernuclei exhibit significant directed flow. Comparing to that of light nuclei, it is found that the midrapidity v1 slopes of 3ΛH and 4ΛH follow baryon number scaling, implying that the coalescence is the dominant mechanism for these hypernuclei production in such collisions.
The linear and mode-coupled contributions to higher-order anisotropic flow are presented for Au+Au collisions at sNN−−−√ = 27, 39, 54.4, and 200 GeV and compared to similar measurements for Pb+Pb collisions at the Large Hadron Collider (LHC). The coefficients and the flow harmonics' correlations, which characterize the linear and mode-coupled response to the lower-order anisotropies, indicate a beam energy dependence consistent with an influence from the specific shear viscosity (η/s). In contrast, the dimensionless coefficients, mode-coupled response coefficients, and normalized symmetric cumulants are approximately beam-energy independent, consistent with a significant role from initial-state effects. These measurements could provide unique supplemental constraints to (i) distinguish between different initial-state models and (ii) delineate the temperature (T) and baryon chemical potential (μB) dependence of the specific shear viscosity ηs(T,μB).
We report the beam energy and collision centrality dependence of fifth and sixth order cumulants (C5, C6) and factorial cumulants (κ5, κ6) of net-proton and proton distributions, from sNN−−−−√=3−200 GeV Au+Au collisions at RHIC. The net-proton cumulant ratios generally follow the hierarchy expected from QCD thermodynamics, except for the case of collisions at sNN−−−−√ = 3 GeV. C6/C2 for 0-40\% centrality collisions is increasingly negative with decreasing sNN−−−−√, while it is positive for the lowest sNN−−−−√ studied. These observed negative signs are consistent with QCD calculations (at baryon chemical potential, μB≤ 110 MeV) that include a crossover quark-hadron transition. In addition, for sNN−−−−√≥ 11.5 GeV, the measured proton κn, within uncertainties, does not support the two-component shape of proton distributions that would be expected from a first-order phase transition. Taken in combination, the hyper-order proton number fluctuations suggest that the structure of QCD matter at high baryon density, μB∼750 MeV (sNN−−−−√ = 3 GeV) is starkly different from those at vanishing μB∼20MeV (sNN−−−−√ = 200 GeV and higher).
A decisive experimental test of the Chiral Magnetic Effect (CME) is considered one of the major scientific goals at the Relativistic Heavy-Ion Collider (RHIC) towards understanding the nontrivial topological fluctuations of the Quantum Chromodynamics vacuum. In heavy-ion collisions, the CME is expected to result in a charge separation phenomenon across the reaction plane, whose strength could be strongly energy dependent. The previous CME searches have been focused on top RHIC energy collisions. In this Letter, we present a low energy search for the CME in Au+Au collisions at sNN−−−√=27 GeV. We measure elliptic flow scaled charge-dependent correlators relative to the event planes that are defined at both mid-rapidity |η|<1.0 and at forward rapidity 2.1<|η|<5.1. We compare the results based on the directed flow plane (Ψ1) at forward rapidity and the elliptic flow plane (Ψ2) at both central and forward rapidity. The CME scenario is expected to result in a larger correlation relative to Ψ1 than to Ψ2, while a flow driven background scenario would lead to a consistent result for both event planes. In 10-50\% centrality, results using three different event planes are found to be consistent within experimental uncertainties, suggesting a flow driven background scenario dominating the measurement. We obtain an upper limit on the deviation from a flow driven background scenario at the 95\% confidence level. This work opens up a possible road map towards future CME search with the high statistics data from the RHIC Beam Energy Scan Phase-II.
A decisive experimental test of the Chiral Magnetic Effect (CME) is considered one of the major scientific goals at the Relativistic Heavy-Ion Collider (RHIC) towards understanding the nontrivial topological fluctuations of the Quantum Chromodynamics vacuum. In heavy-ion collisions, the CME is expected to result in a charge separation phenomenon across the reaction plane, whose strength could be strongly energy dependent. The previous CME searches have been focused on top RHIC energy collisions. In this Letter, we present a low energy search for the CME in Au+Au collisions at sNN−−−√=27 GeV. We measure elliptic flow scaled charge-dependent correlators relative to the event planes that are defined at both mid-rapidity |η|<1.0 and at forward rapidity 2.1<|η|<5.1. We compare the results based on the directed flow plane (Ψ1) at forward rapidity and the elliptic flow plane (Ψ2) at both central and forward rapidity. The CME scenario is expected to result in a larger correlation relative to Ψ1 than to Ψ2, while a flow driven background scenario would lead to a consistent result for both event planes. In 10-50\% centrality, results using three different event planes are found to be consistent within experimental uncertainties, suggesting a flow driven background scenario dominating the measurement. We obtain an upper limit on the deviation from a flow driven background scenario at the 95\% confidence level. This work opens up a possible road map towards future CME search with the high statistics data from the RHIC Beam Energy Scan Phase-II.
We report on measurements of sequential Υ suppression in Au+Au collisions at sNN−−−√ = 200 GeV with the STAR detector at the Relativistic Heavy Ion Collider (RHIC) through both the dielectron and dimuon decay channels. In the 0-60% centrality class, the nuclear modification factors (RAA), which quantify the level of yield suppression in heavy-ion collisions compared to p+p collisions, for Υ(1S) and Υ(2S) are 0.40±0.03 (stat.)±0.03 (sys.)±0.09 (norm.) and 0.26±0.08 (stat.)±0.02 (sys.)±0.06 (norm.), respectively, while the upper limit of the Υ(3S) RAA is 0.17 at a 95% confidence level. This provides experimental evidence that the Υ(3S) is significantly more suppressed than the Υ(1S) at RHIC. The level of suppression for Υ(1S) is comparable to that observed at the much higher collision energy at the Large Hadron Collider. These results point to the creation of a medium at RHIC whose temperature is sufficiently high to strongly suppress excited Υ states.
Using 16 energy points of e+e− annihilation data collected in the vicinity of the J/ψ resonance with the BESIII detector and with a total integrated luminosity of around 100 pb−1, we study the relative phase between the strong and electromagnetic amplitudes of J/ψ decays. The relative phase between J/ψ electromagnetic decay and the continuum process (e+e− annihilation without the J/ψ resonance) is confirmed to be zero by studying the cross section lineshape of μ+μ− production. The relative phase between J/ψ strong and electromagnetic decays is then measured to be (84.9 ± 3.6)◦ or (−84.7 ± 3.1)◦ for the 2(π+π−)π0 final state by investigating the interference pattern between the J/ψ decay and the continuum process. This is the first measurement of the relative phase between J/ψ strong and electromagnetic decays into a multihadron final state using the lineshape of the production cross section. We also study the production lineshape of the multihadron final state ηπ+π− with η → π+π−π0, which provides additional information about the phase between the J/ψ electromagnetic decay amplitude and the continuum process. Additionally, the branching fraction of J/ψ → 2(π+π−)π0 is measured to be (4.73 ± 0.44)% or (4.85 ± 0.45)%, and the branching fraction of J/ψ → ηπ+π− is measured to be (3.78 ± 0.68) × 10−4. Both of them are consistent with the world average values. The quoted uncertainties include both statistical and systematic uncertainties, which are mainly caused by the low statistics.
Using a data sample of 448.1×106 ψ(3686) events collected at s√= 3.686 GeV with the BESIII detector at the BEPCII, we search for the rare decay J/ψ→ϕe+e− via ψ(3686)→π+π−J/ψ. No signal events are observed and the upper limit on the branching fraction is set to be B(J/ψ→ϕe+e−)<1.2×10−7 at the 90\% confidence level, which is still about one order of magnitude higher than the Standard Model prediction.
The decays of χc2→K+K−π0, KSK±π∓ and π+π−π0 are studied with the ψ(3686) data samples collected with the Beijing Spectrometer (BESIII). For the first time, the branching fractions of χc2→K∗K¯¯¯¯¯, χc2→a±2(1320)π∓/a02(1320)π0 and χc2→ρ(770)±π∓ are measured. Here K∗K¯¯¯¯¯ denotes both K∗±K∓ and K∗0K¯¯¯¯¯0+c.c., and K∗ denotes the resonances K∗(892), K∗2(1430) and K∗3(1780). The observations indicate a strong violation of the helicity selection rule in χc2 decays into vector and pseudoscalar meson pairs. The measured branching fractions of χc2→K∗(892)K¯¯¯¯¯ are more than 20 times larger than that of χc2→ρ(770)±π∓, which implies the effects are largely due to U-spin symmetry breaking, rather than just isospin symmetry breaking in charmonium decays.
The decays of χc2→K+K−π0, KSK±π∓ and π+π−π0 are studied with the ψ(3686) data samples collected with the Beijing Spectrometer (BESIII). For the first time, the branching fractions of χc2→K∗K¯¯¯¯¯, χc2→a±2(1320)π∓/a02(1320)π0 and χc2→ρ(770)±π∓ are measured. Here K∗K¯¯¯¯¯ denotes both K∗±K∓ and K∗0K¯¯¯¯¯0+c.c., and K∗ denotes the resonances K∗(892), K∗2(1430) and K∗3(1780). The observations indicate a strong violation of the helicity selection rule in χc2 decays into vector and pseudoscalar meson pairs. The measured branching fractions of χc2→K∗(892)K¯¯¯¯¯ are more than 20 times larger than that of χc2→ρ(770)±π∓, which implies the effects are largely due to U-spin symmetry breaking, rather than just isospin symmetry breaking in charmonium decays.
The decays of χc2→K+K−π0, KSK±π∓ and π+π−π0 are studied with the ψ(3686) data samples collected with the Beijing Spectrometer (BESIII). For the first time, the branching fractions of χc2→K∗K¯¯¯¯¯, χc2→a±2(1320)π∓/a02(1320)π0 and χc2→ρ(770)±π∓ are measured. Here K∗K¯¯¯¯¯ denotes both K∗±K∓ and K∗0K¯¯¯¯¯0+c.c., and K∗ denotes the resonances K∗(892), K∗2(1430) and K∗3(1780). The observations indicate a strong violation of the helicity selection rule in χc2 decays into vector and pseudoscalar meson pairs. The measured branching fractions of χc2→K∗(892)K¯¯¯¯¯ are more than 10 times larger than the upper limit of χc2→ρ(770)±π∓, which is so far the first direct observation of a significant U-spin symmetry breaking effect in charmonium decays.
The decays of χc2→K+K−π0, KSK±π∓ and π+π−π0 are studied with the ψ(3686) data samples collected with the Beijing Spectrometer (BESIII). For the first time, the branching fractions of χc2→K∗K¯¯¯¯¯, χc2→a±2(1320)π∓/a02(1320)π0 and χc2→ρ(770)±π∓ are measured. Here K∗K¯¯¯¯¯ denotes both K∗±K∓ and K∗0K¯¯¯¯¯0+c.c., and K∗ denotes the resonances K∗(892), K∗2(1430) and K∗3(1780). The observations indicate a strong violation of the helicity selection rule in χc2 decays into vector and pseudoscalar meson pairs. The measured branching fractions of χc2→K∗(892)K¯¯¯¯¯ are more than 10 times larger than the upper limit of χc2→ρ(770)±π∓, which is so far the first direct observation of a significant U-spin symmetry breaking effect in charmonium decays.
Using (10087±44)×106 J/ψ events collected with the BESIII detector, the radiative hyperon decay Σ→pγ is studied at an electron-positron collider experiment for the first time. The absolute branching fraction is measured to be (0.996±0.021stat.±0.018syst.)×10−3, which is lower than its world average value by 4.2 standard deviations. Its decay asymmetry parameter is determined to be −0.652±0.056stat.±0.020syst.. The branching fraction and decay asymmetry parameter are the most precise to date, and the accuracies are improved by 78% and 34%, respectively.
Using (10087±44)×106 J/ψ events collected with the BESIII detector, the radiative hyperon decay Σ→pγ is studied at an electron-positron collider experiment for the first time. The absolute branching fraction is measured to be (0.996±0.021stat.±0.018syst.)×10−3, which is lower than its world average value by 4.2 standard deviations. Its decay asymmetry parameter is determined to be −0.652±0.056stat.±0.020syst.. The branching fraction and decay asymmetry parameter are the most precise to date, and the accuracies are improved by 78% and 34%, respectively.
The Born cross sections of the process e+e−→D∗0D∗−π+ at center-of-mass energies from 4.189 to 4.951 GeV are measured for the first time. The data samples used correspond to an integrated luminosity of 17.9fb−1 and were collected by the BESIII detector operating at the BEPCII storage ring. Three enhancements around 4.20, 4.47 and 4.67 GeV are visible. The resonances have masses of 4209.6±4.7±5.9MeV/c2, 4469.1±26.2±3.6MeV/c2 and 4675.3±29.5±3.5MeV/c2 and widths of 81.6±17.8±9.0MeV, 246.3±36.7±9.4MeV, and 218.3±72.9±9.3MeV, respectively, where the first uncertainties are statistical and the second systematic. The first and third resonances are consistent with the ψ(4230) and ψ(4660) states, respectively, while the second one is compatible with the ψ(4500) observed in the e+e−→K+K−J/ψ process. These three charmoniumlike ψ states are observed in e+e−→D∗0D∗−π+ process for the first time.
Observation of three charmonium-like states with JPC = 1⁻⁻ in e⁺e⁻− → D*⁰D*⁻π⁺ + c.c. process
(2023)
The Born cross sections of the process e+e−→D∗0D∗−π++c.c. at center-of-mass energies from 4.189 to 4.951 GeV are measured for the first time. The data samples used correspond to an integrated luminosity of 17.9fb−1 and were collected by the BESIII detector operating at the BEPCII storage ring. Three enhancements around 4.20, 4.47 and 4.67 GeV are visible. The resonances have masses of 4209.6±4.7±5.9MeV/c2, 4469.1±26.2±3.6MeV/c2 and 4675.3±29.5±3.5MeV/c2 and widths of 81.6±17.8±9.0MeV, 246.3±36.7±9.4MeV and 218.3±72.9±9.3MeV, respectively, where the first uncertainties are statistical and the second systematic. The first and third resonances are consistent with the Y(4230) and Y(4660) states, respectively, while the second one is compatible with the Y(4500) observed in the e+e−→K+K−J/ψ process. These three Y states are observed in e+e−→D∗0D∗−π++c.c. process for the first time.
We search for an axion-like particle (ALP) a through the process ψ(3686)→π+π−J/ψ, J/ψ→γa, a→γγ in a data sample of (2.71±0.01)×109 ψ(3686) events collected by the BESIII detector. No significant ALP signal is observed over the expected background, and the upper limits on the branching fraction of the decay J/ψ→γa and the ALP-photon coupling constant gaγγ are set at 95% confidence level in the mass range of 0.165≤ma≤2.84GeV/c2. The limits on B(J/ψ→γa) range from 8.3×10−8 to 1.8×10−6 over the search region, and the constraints on the ALP-photon coupling are the most stringent to date for 0.165≤ma≤1.468GeV/c2.