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This work aims to differentiate strangeness produced from hard processes (jet-like) and softer processes (underlying event) by measuring the angular correlation between a high-momentum trigger hadron (h) acting as a jet-proxy and a produced strange hadron (φ(1020) meson). Measuring h–φ correlations at midrapidity in p–Pb collisions at √sNN = 5.02 TeV as a function of event multiplicity provides insight into the microscopic origin of strangeness enhancement in small collision systems. The jet-like and the underlying-event-like strangeness production are investigated as a function of event multiplicity. They are also compared between a lower and higher momentum region. The evolution of the per-trigger yields within the near-side (aligned with the trigger hadron) and away-side (in the opposite direction of the trigger hadron) jet is studied separately, allowing for the characterization of two distinct jet-like production regimes. Furthermore, the h–φ correlations within the underlying event give access to a production regime dominated by soft production processes, which can be compared directly to the in-jet production. Comparisons between h–φ and dihadron correlations show that the observed strangeness enhancement is largely driven by the underlying event, where the φ/h ratio is significantly larger than within the jet regions. As multiplicity increases, the fraction of the total φ(1020) yield coming from jets decreases compared to the underlying event production, leading to high-multiplicity events being dominated by the increased strangeness production from the underlying event
Mitochondria are dynamic organelles exhibiting diverse shapes. While the variation of shapes, ranging from spheres to elongated tubules, and the transition between them, are clearly seen in many cell types, the molecular mechanisms governing this morphological variability remain poorly understood. Here, we propose a novel shaping mechanism based on the interplay between the inner and outer mitochondrial membranes. Our biophysical model suggests that the difference in surface area, arising from the pulling of the inner membrane into cristae, correlates with mitochondrial elongation. Analysis of live cell super-resolution microscopy data supports this correlation, linking elongated shapes to the extent of cristae in the inner membrane. Knocking down cristae shaping proteins further confirms the impact on mitochondrial shape, demonstrating that defects in cristae formation correlate with mitochondrial sphericity. Our results suggest that the dynamics of the inner mitochondrial membrane are important not only for simply creating surface area required for respiratory capacity, but go beyond that to affect the whole organelle morphology. This work explores the biophysical foundations of individual mitochondrial shape, suggesting potential links between mitochondrial structure and function. This should be of profound significance, particularly in the context of disrupted cristae shaping proteins and their implications in mitochondrial diseases.
We measure the Born cross section for the reaction e+e−→ηhc from s√=4.129 to 4.600~GeV using data sets collected by the BESIII detector running at the BEPCII collider. A resonant structure in the cross section line shape near 4.200~GeV is observed with a statistical significance of 7σ. The parameters of this resonance are measured to be \MeasMass\ and \MeasWidth, where the first uncertainties are statistical and the second systematic.
We prove that the projectivized strata of differentials are not contained in pointed Brill-Noether divisors, with only a few exceptions. For a generic element in a stratum of differentials, we show that many of the associated pointed Brill-Noether loci are of expected dimension. We use our results to study the Auel-Haburcak Conjecture: We obtain new non-containments between maximal Brill-Noether loci in Mg. Our results regarding quadratic differentials imply that the quadratic strata in genus 6 are uniruled.
Interacting with the environment to process sensory information, generate perceptions, and shape behavior engages neural networks in brain areas with highly varied representations, ranging from unimodal sensory cortices to higher-order association areas. Recent work suggests a much greater degree of commonality across areas, with distributed and modular networks present in both sensory and non-sensory areas during early development. However, it is currently unknown whether this initially common modular structure undergoes an equally common developmental trajectory, or whether such a modular functional organization persists in some areas—such as primary visual cortex—but not others. Here we examine the development of network organization across diverse cortical regions in ferrets of both sexes using in vivo widefield calcium imaging of spontaneous activity. We find that all regions examined, including both primary sensory cortices (visual, auditory, and somatosensory—V1, A1, and S1, respectively) and higher order association areas (prefrontal and posterior parietal cortices) exhibit a largely similar pattern of changes over an approximately 3 week developmental period spanning eye opening and the transition to predominantly externally-driven sensory activity. We find that both a modular functional organization and millimeter-scale correlated networks remain present across all cortical areas examined. These networks weakened over development in most cortical areas, but strengthened in V1. Overall, the conserved maintenance of modular organization across different cortical areas suggests a common pathway of network refinement, and suggests that a modular organization—known to encode functional representations in visual areas—may be similarly engaged in highly diverse brain areas.
Significance Different areas of the mature brain encode vastly different representations of the world. This study shows that a modular functional organization where nearby neurons participate in similar functional networks is shared across different brain areas not only during early development, but also as the brain matures where it remains a shared feature that shapes neural activity. The largely conserved trajectory of developmental changes across brain areas suggests that similar circuit mechanisms may drive this maturation. This implies that the large literature on developing cortical circuits, which is largely focused on sensory areas, may also apply more broadly, and that perturbations during development that impinge on any such shared mechanisms may produce deficits that extend across multiple brain systems.
Observation of η_(c)(1S, 2S) and χ_(cJ) decays to 2(π⁺π^(−))η via ψ(3686) radiative transitions
(2024)
Based on 2.7×109 ψ(3686) decays collected with the BESIII detector, the radiative decay ψ(3686)→γ2(π+π−)η is investigated to measure properties of S- and P-wave charmonium states. The branching fraction of the decay ηc(1S)→2(π+π−)η, which is found to have a strong dependence on the interference pattern between ηc(1S) and non-ηc(1S) processes, is measured in both destructive and constructive interference scenarios for the first time. The mass and width of the ηc(1S) are measured to be M=(2984.14±0.13±0.38) MeV/c2 and Γ=(28.82±0.11±0.82) MeV, respectively. Clear signals for the decays of the χcJ(J=0,1,2) and the ηc(2S) to 2(π+π−)η are also observed for the first time, and the corresponding branching fractions are measured. The ratio of the branching fractions between the ηc(2S) and ηc(1S) decays is significantly lower than the theoretical prediction, which might suggest different dynamics in their decays.
Based on (2712.4±14.3)×106 ψ(3686) events, we investigate four hadronic decay modes of the P-wave charmonium spin-singlet state hc(1P1)→h+h−π0/η (h=π or K) via the process ψ(3686)→π0hc at BESIII. The hc→π+π−π0 decay is observed with a significance of 9.6σ after taking into account systematic uncertainties. Evidences for hc→K+K−π0 and hc→K+K−η are found with significances of 3.5σ and 3.3σ, respectively, after considering the systematic uncertainties. The branching fractions of these decays are measured to be B(hc→π+π−π0)=(1.36±0.16±0.14)×10−3, B(hc→K+K−π0)=(3.26±0.84±0.36)×10−4, and B(hc→K+K−η)=(3.13±1.08±0.38)×10−4, where the first uncertainties are statistical and the second are systematic. No significant signal of hc→π+π−η is found, and the upper limit of its decay branching fraction is determined to be B(hc→π+π−η)<4.0×10−4 at 90% confidence level.
Using 9.0 fb−1 of e+e− collision data collected at center-of-mass energies from 4.178 to 4.278 GeV with the BESIII detector at the BEPCII collider, we perform the first search for the radiative transition χc1(3872)→γψ2(3823). No χc1(3872)→γψ2(3823) signal is observed. The upper limit on the ratio of branching fractions B(χc1(3872)→γψ2(3823),ψ2(3823)→γχc1)/B(χc1(3872)→π+π−J/ψ) is set as 0.075 at the 90\% confidence level. Our result contradicts theoretical predictions under the assumption that the χc1(3872) is the pure charmonium state χc1(2P).
We report the first amplitude analysis of the decays D0→π+π−η and D+→π+π0η using a data sample taken with the BESIII detector at the center-of-mass energy of 3.773 GeV, corresponding to an integrated luminosity of 7.9 fb−1. The contribution from the process D0(+)→a0(980)+π−(0) is significantly larger than the D0(+)→a0(980)−(0)π+ contribution. The ratios B(D0→a0(980)+π−)/B(D0→a0(980)−π+) and B(D+→a0(980)+π0)/B(D+→a0(980)0π+) are measured to be 7.5+2.5−0.8stat.±1.7syst. and 2.6±0.6stat.±0.3syst., respectively. The measured D0 ratio disagrees with the theoretical predictions by orders of magnitudes, thus implying a substantial contribution from final-state interactions.
The process e+e−→pp¯π0 is studied at 20 center-of-mass energies ranging from 2.1000 to 3.0800 GeV using 636.8 pb−1 of data collected with the BESIII detector operating at the BEPCII collider. The Born cross sections for e+e−→pp¯π0 are measured with high precision. Since the lowest center-of-mass energy, 2.1000 GeV, is less than 90 MeV above the pp¯π0 energy threshold, we can probe the threshold behavior for this reaction. However, no anomalous threshold enhancement is found in the cross sections for e+e−→pp¯π0.
We search for the di-photon decay of a light pseudoscalar axion-like particle, a, in radiative decays of the J/ψ, using 10 billion J/ψ events collected with the BESIII detector. We find no evidence of a narrow resonance and set upper limits at the 95% confidence level on the product branching fraction B(J/ψ→γa)×B(a→γγ) and the axion-like particle photon coupling constant gaγγ in the ranges of (3.6−49.8)×10−8 and (2.2−103.8)×10−4 GeV−1, respectively, for 0.18≤ma≤2.85 GeV/c2. These are the most stringent limits to date in this mass region.
Based on (2.712±0.014)×109 ψ(3686) events collected by the BESIII collaboration, evidence of the hadronic decay hc→K0SK+π−+c.c. is found with a significance of 4.3σ in the ψ(3686)→π0hc process. The branching fraction of hc→K0SK+π−+c.c. is measured to be (7.3±0.8±1.8)×10−4, where the first and second uncertainties are statistical and systematic, respectively. Combining with the exclusive decay width of ηc→KK¯π, our result indicates inconsistencies with both pQCD and NRQCD predictions.
We present the first observation of the singly Cabibbo-suppressed decay Λ+c→ΛK+π0 with a significance of 5.7σ and the first evidence of Λ+c→ΛK+π+π− decay with a significance of 3.1σ, based on e+e− annihilation data recorded by the BESIII detector at the BEPCII collider. The data correspond to an integrated luminosity of 6.4 fb−1, in the center-of-mass energy range from 4.600 GeV to 4.950 GeV. We determine the branching fractions of Λ+c→ΛK+π0 and Λ+c→ΛK+π+π− relative to their Cabibbo-favored counterparts to be B(Λ+c→ΛK+π0)B(Λ+c→Λπ+π0)=(2.09±0.39stat.±0.07syst.)×10−2 and B(Λ+c→ΛK+π+π−)B(Λ+c→Λπ+π+π−)=(1.13±0.41stat.±0.06syst.)×10−2, respectively. Moreover, by combining our measured result with the world average of B(Λ+c→Λπ+π0), we obtain the branching fraction B(Λ+c→ΛK+π0)=(1.49±0.27stat.±0.05syst.±0.08ref.)×10−3. This result significantly departs from theoretical predictions based on quark SU(3) flavor symmetry, which is underpinned by the presumption of meson pair S-wave amplitude dominance.
A light scalar X0 or vector X1 particles have been introduced as a possible explanation for the (g−2)μ anomaly and dark matter phenomena.
Using (8.998±0.039)×109 $\jpsi$ events collected by the BESIII detector, we search for a light muon philic scalar X0 or vector X1 in the processes J/ψ→μ+μ−X0,1 with X0,1 invisible decays. No obvious signal is found, and the upper limits on the coupling g′0,1 between the muon and the X0,1 particles are set to be between 1.1×10−3 and 1.0×10−2 for the X0,1 mass in the range of 1<M(X0,1)<1000 MeV/c2 at 90% confidence level.
The Cabbibo-favored decay Λ+c→Ξ0K+π0 is studied for the first time using 6.1 fb−1 of e+e− collision data at center-of-mass energies between 4.600 and 4.840 GeV, collected with the BESIII detector at the BEPCII collider. With a double-tag method, the branching fraction of the three-body decay Λ+c→Ξ0K+π0 is measured to be (7.79±1.46±0.71)×10−3, where the first and second uncertainties are statistical and systematic, respectively. The branching fraction of the two-body decay Λ+c→Ξ(1530)0K+ is (5.99±1.04±0.29)×10−3, which is consistent with the previous result of (5.02±0.99±0.31)×10−3. In addition, the upper limit on the branching fraction of the doubly Cabbibo-suppressed decay Λ+c→nK+π0 is 7.1×10−4 at the 90% confidence level. The upper limits on the branching fractions of Λ+c→Σ0K+π0 and ΛK+π0 are also determined to be 1.8×10−3 and 2.0×10−3, respectively.
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.
Based on 4.5 fb−1 of e+e− collision data accumulated at center-of-mass energies between 4599.53 MeV and 4698.82 MeV with the BESIII detector, the decay Λ+c→nK0Sπ+π0 is observed for the first time with a significance of 9.2σ. The branching fraction is measured to be (0.85±0.13±0.03)%, where the first uncertainty is statistical and the second systematic, which differs from the theoretical prediction based on isospin by 4.4σ. This indicates that there may be resonant contributions or some unknown dynamics in this decay.
Based on 4.5 fb−1 of e+e− collision data accumulated at center-of-mass energies between 4599.53 MeV and 4698.82 MeV with the BESIII detector, the decay Λ+c→nK0Sπ+π0 is observed for the first time with a significance of 9.2σ. The branching fraction is measured to be (0.85±0.13±0.03)%, where the first uncertainty is statistical and the second systematic, which differs from the theoretical prediction based on isospin by 4.4σ. This indicates that there may be resonant contributions or some unknown dynamics in this decay.
Using 2.93 fb−1 of e+e− collision data collected with the BESIII detector at the center-of-mass energy of 3.773 GeV, we investigate the semileptonic decays D+→π+π−ℓ+νℓ (ℓ=e and μ). The D+→f0(500)μ+νμ decay is observed for the first time. By analyzing simultaneously the differential decay rates of D+→f0(500)μ+νμ and D+→f0(500)e+νe in different ℓ+νℓ four-momentum transfer intervals, the product of the relevant hadronic form factor ff0+(0) and the magnitude of the c→d Cabibbo-Kobayashi-Maskawa matrix element |Vcd| is determined to be ff0+(0)|Vcd|=0.0787±0.0060stat±0.0033syst for the first time. With the input of |Vcd| from the global fit in the standard model, we determine ff0+(0)=0.350±0.027stat±0.015syst. The absolute branching fractions of D+→f0(500)(π+π−)μ+νμ and D+→ρ0(π+π−)μ+νμ are determined as (0.72±0.13stat±0.10syst)×10−3 and (1.64±0.13stat±0.11syst)×10−3. Combining these results with those of previous BESIII measurements on their semielectronic counterparts from the same data sample, we test lepton flavor universality by measuring the branching fraction ratios BD+→ρ0μ+νμ/BD+→ρ0e+νe = 0.88±0.10 and BD+→f0(500)μ+νμ/BD+→f0(500)e+νe = 1.14±0.28, which are compatible with the standard model expectation.
Using 2.93 fb−1 of e+e− collision data collected with the BESIII detector at the center-of-mass energy of 3.773 GeV, we investigate the semileptonic decays D+→π+π−ℓ+νℓ (ℓ=e and μ). The D+→f0(500)μ+νμ decay is observed for the first time. By analyzing simultaneously the differential decay rates of D+→f0(500)μ+νμ and D+→f0(500)e+νe in different ℓ+νℓ four-momentum transfer intervals, the product of the relevant hadronic form factor ff0+(0) and the magnitude of the c→d Cabibbo-Kobayashi-Maskawa matrix element |Vcd| is determined to be ff0+(0)|Vcd|=0.0787±0.0060stat±0.0033syst for the first time. With the input of |Vcd| from the global fit in the standard model, we determine ff0+(0)=0.350±0.027stat±0.015syst. The absolute branching fractions of D+→f0(500)(π+π−)μ+νμ and D+→ρ0(π+π−)μ+νμ are determined as (0.72±0.13stat±0.10syst)×10−3 and (1.64±0.13stat±0.11syst)×10−3. Combining these results with those of previous BESIII measurements on their semielectronic counterparts from the same data sample, we test lepton flavor universality by measuring the branching fraction ratios BD+→ρ0μ+νμ/BD+→ρ0e+νe=0.88±0.10 and BD+→f0(500)μ+νμ/BD+→f0(500)e+νe = 1.14±0.28, which are compatible with the standard model expectation.
The absolute branching fraction of the decay Λc(2625)+→Λ+cπ+π− is measured for the first time to be (50.7±5.0stat.±4.9syst.)% with 368.48 pb−1 of e+e− collision data collected by the BESIII detector at the center-of-mass energies of s√=4.918 and 4.950 GeV. This result is lower than the naive prediction of 67\%, obtained from isospin symmetry, by more than 2σ, thereby indicating that the novel mechanism referred to as the \textit{threshold effect}, proposed for the strong decays of Λc(2595)+, also applies to Λc(2625)+. This measurement is necessary to obtain the coupling constants for the transitions between s-wave and p-wave charmed baryons in heavy hadron chiral perturbation theory. In addition, we search for the decay Λc(2595)+→Λ+cπ+π−. No significant signal is observed, and the upper limit on its branching fraction is determined to be 80.8\% at the 90\% confidence level.
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, which distinctly exceeds the upper limit measured by Belle experiment. Combining with the branching fraction of Λ+c→nπ+, (6.6±1.3)×10−4, the ratio of the branching fractions of Λ+c→nπ+ and Λ+c→pπ0 is calculated to be 3.2+2.2−1.2. As an important input for the theoretical models describing the decay mechanisms of charmed baryons, our result indicates that the non-factorizable contributions play an essential role and their interference with the factorizable contributions should not be significant. 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.
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, which distinctly exceeds the upper limit measured by Belle experiment. Combining with the branching fraction of Λ+c→nπ+, (6.6±1.3)×10−4, the ratio of the branching fractions of Λ+c→nπ+ and Λ+c→pπ0 is calculated to be 3.2+2.2−1.2. As an important input for the theoretical models describing the decay mechanisms of charmed baryons, our result indicates that the non-factorizable contributions play an essential role and their interference with the factorizable contributions should not be significant. 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.
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±1.3)×10−4, the ratio of the branching fractions of Λ+c→nπ+ and Λ+c→pπ0 is calculated to be 3.2+2.2−1.2. As an important input for the theoretical models describing the decay mechanisms of charmed baryons, our result indicates that the non-factorizable contributions play an essential role and their interference with the factorizable contributions should not be significant. In addition, the absolute branching fraction of Λ+c→pη is measured to be (1.63±0.31stat±0.11syst)×10−3.
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±1.3)×10−4, the ratio of the branching fractions of Λ+c→nπ+ and Λ+c→pπ0 is calculated to be 3.2+2.2−1.2. As an important input for the theoretical models describing the decay mechanisms of charmed baryons, our result indicates that the non-factorizable contributions play an essential role and their interference with the factorizable contributions should not be significant. In addition, the absolute branching fraction of Λ+c→pη is measured to be (1.63±0.31stat±0.11syst)×10−3.
Using 7.33~fb−1 of e+e− collision data collected by the BESIII detector at center-of-mass energies in the range of s√=4.128−4.226~GeV, we search for the rare decays D+s→h+(h0)e+e−, where h represents a kaon or pion. By requiring the e+e− invariant mass to be consistent with a ϕ(1020), 0.98<M(e+e−)<1.04 ~GeV/c2, the decay D+s→π+ϕ,ϕ→e+e− is observed with a statistical significance of 7.8σ, and evidence for the decay D+s→ρ+ϕ,ϕ→e+e− is found for the first time with a statistical significance of 4.4σ. The decay branching fractions are measured to be B(D+s→π+ϕ,ϕ→e+e−)=(1.17+0.23−0.21±0.03)×10−5, and B(D+s→ρ+ϕ,ϕ→e+e−)=(2.44+0.67−0.62±0.16)×10−5, where the first uncertainties are statistical and the second systematic. No significant signal for the three four-body decays of D+s→π+π0e+e−, D+s→K+π0e+e−, and D+s→K0Sπ+e+e− is observed. For D+s→π+π0e+e−, the ϕ mass region is vetoed to minimize the long-distance effects. The 90% confidence level upper limits set on the branching fractions of these decays are in the range of (7.0−8.1)×10−5.
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 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 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.
Upon infection, human immunodeficiency virus (HIV-1) releases its cone-shaped capsid into the cytoplasm of infected T-cells and macrophages. As its largest known cargo, the capsid enters the nuclear pore complex (NPC), driven by interactions with numerous FG-repeat nucleoporins (FG-Nups). Whether NPCs structurally adapt to capsid passage and whether capsids are modified during passage remains unknown, however. Here, we combined super-resolution and correlative microscopy with cryo electron tomography and molecular simulations to study nuclear entry of HIV-1 capsids in primary human macrophages. We found that cytosolically bound cyclophilin A is stripped off capsids entering the NPC, and the capsid hexagonal lattice remains largely intact inside and beyond the central channel. Strikingly, the NPC scaffold rings frequently crack during capsid passage, consistent with computer simulations indicating the need for NPC widening. The unique cone shape of the HIV-1 capsid facilitates its entry into NPCs and helps to crack their rings.
Tree-related microhabitats (TreMs) describe the microhabitats that a tree can provide for a multitude of other taxonomic groups and have been proposed as an important indicator for forest biodiversity (Asbeck et al., 2021). So far, the focus of TreM studies has been on temperate forests, although many trees in the tropics harbour exceptionally high numbers of TreMs. In this study, TreMs in the lowland tropical forests of the Choco (Ecuador) and in the mountain tropical forests of Mount Kilimanjaro (Tanzania) were surveyed. Our results extend the existing typology of TreMs of Larrieu et al. (2018) to include tropical forests and enabled a comparison of the relative recordings and diversity of TreMs between tropical and temperate forests. A new TreM form, Root formations, and three new TreM groups, concavities build by fruits or leaves, dendrotelms, and root formations, were established. In total, 15 new TreM types in five different TreM groups were specified. The relative recordings of most TreMs were similar between tropical and temperate forests. However, ivy and lianas, and ferns were more common in the lowland rainforest than in temperate forests, and bark microsoil, limb breakage, and foliose and fruticose lichens in tropical montane forest than in lowland rainforest. Mountain tropical forests hosted the highest diversity for common and dominant TreM types, and lowland tropical forest the highest diversity for rare TreMs. Our extended typology of tree-related microhabitats can support studies of forest-dwelling biodiversity in tropical forests. Specifically, given the ongoing threat to tropical forests, TreMs can serve as an additional tool allowing rapid assessments of biodiversity in these hyperdiverse ecosystems.
MicroRNAs (miRNAs) are critical post-transcriptional regulators in many biological processes. They act by guiding RNA-induced silencing complexes to miRNA response elements (MREs) in target mRNAs, inducing translational inhibition and/or mRNA degradation. Functional MREs are expected to predominantly occur in the 3' untranslated region and involve perfect base-pairing of the miRNA seed. Here, we generate a high-resolution map of miR-181a/b-1 (miR-181) MREs to define the targeting rules of miR-181 in developing murine T-cells. By combining a multi-omics approach with computational high-resolution analyses, we uncover novel miR-181 targets and demonstrate that miR-181 acts predominantly through RNA destabilization. Importantly, we discover an alternative seed match and identify a distinct set of targets with repeat elements in the coding sequence which are targeted by miR-181 and mediate translational inhibition. In conclusion, deep profiling of MREs in primary cells is critical to expand physiologically relevant targetomes and establish context-dependent miRNA targeting rules.
This Letter presents the first measurement of event-by-event fluctuations of the net number (difference between the particle and antiparticle multiplicities) of multistrange hadrons Ξ− and Ξ¯¯¯¯+ and its correlation with the net-kaon number using the data collected by the ALICE Collaboration in pp, p−Pb, and Pb−Pb collisions at a center-of-mass energy per nucleon pair sNN−−−√=5.02 TeV. The statistical hadronization model with a correlation over three units of rapidity between hadrons having the same and opposite strangeness content successfully describes the results. On the other hand, string-fragmentation models that mainly correlate strange hadrons with opposite strange quark content over a small rapidity range fail to describe the data.
Using e+e− annihilation data corresponding to an integrated luminosity of 2.93 fb−1 taken at the center-of-mass energy s√=3.773~GeV with the BESIII detector, a joint amplitude analysis is performed on the decays D0→π+π−π+π− and D0→π+π−π0π0(non-η). The fit fractions of individual components are obtained, and large interferences among the dominant components of D0→a1(1260)π, D0→π(1300)π, D0→ρ(770)ρ(770) and D0→2(ππ)S are found in both channels. With the obtained amplitude model, the CP-even fractions of D0→π+π−π+π− and D0→π+π−π0π0(non-η) are determined to be (75.2±1.1stat.±1.5syst.)% and (68.9±1.5stat.±2.4syst.)%, respectively. The branching fractions of D0→π+π−π+π− and D0→π+π−π0π0(non-η) are measured to be (0.688±0.010stat.±0.010syst.)% and (0.951±0.025stat.±0.021syst.)%, respectively. The amplitude analysis provides an important model for binning strategy in the measurements of the strong phase parameters of D0→4π when used to determine the CKM angle γ(ϕ3) via the B−→DK− decay.
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.
Using a sample of (10087±44)×106 J/ψ events, which is about 45 times larger than that was previously analyzed, a further investigation on the J/ψ→γ3(π+π−) decay is performed. A significant distortion at 1.84 GeV/c2 in the line-shape of the 3(π+π−) invariant mass spectrum is observed for the first time, which could be resolved by two overlapping resonant structures, X(1840) and X(1880). The new state X(1880) is observed with a statistical significance larger than 10σ. The mass and width of X(1880) are determined to be 1882.1±1.7±0.7 MeV/c2 and 30.7±5.5±2.4 MeV, respectively, which indicates the existence of a pp¯ bound state.
Using data samples with an integrated luminosity of 4.67 fb−1 collected by the BESIII detector operating at the BEPCII collider, we search for the process e+e−→η′ψ(2S) at center-of-mass energies from 4.66 to 4.95 GeV. No significant signal is observed, and upper limits for the Born cross sections σB(e+e−→η′ψ(2S)) at the 90\% confidence level are determined.
First measurements of hadron(h)−Λ azimuthal angular correlations in p−Pb collisions at sNN−−−√ = 5.02 TeV using the ALICE detector at the LHC are presented. These correlations are used to separate the production of associated Λ baryons into three different kinematic regions, namely those produced in the direction of the trigger particle (near-side), those produced in the opposite direction (away-side), and those whose production is uncorrelated with the jet-axis (underlying event). The per-trigger associated Λ yields in these regions are extracted, along with the near- and away-side azimuthal peak widths, and the results are studied as a function of associated particle pT and event multiplicity. Comparisons with the DPMJET event generator and previous measurements of the ϕ(1020) meson are also made. The final results indicate that strangeness production in the highest multiplicity p−Pb collisions is enhanced relative to low multiplicity collisions in the jet-like regions, as well as the underlying event. The production of Λ relative to charged hadrons is also enhanced in the underlying event when compared to the jet-like regions. Additionally, the results hint that strange quark production in the away-side of the jet is modified by soft interactions with the underlying event.
Measurements of (anti)deuteron and (anti)3He production in the rapidity range |y|< 0.5 as a function of the transverse momentum and event multiplicity in Xe−Xe collisions at a center-of-mass energy per nucleon−nucleon pair of sNN−−−√ = 5.44 TeV are presented. The coalescence parameters B2 and B3 are measured as a function of the transverse momentum per nucleon. The ratios between (anti)deuteron and (anti)3He yields and those of (anti)protons and pions are reported as a function of the mean charged-particle multiplicity density, and compared with two implementations of the statistical hadronization model (SHM) and with coalescence predictions. The elliptic flow of (anti)deuterons is measured for the first time in Xe−Xe collisions and shows features similar to those already observed in Pb−Pb collisions, i.e., the mass ordering at low transverse momentum and the meson−baryon grouping at intermediate transverse momentum. The production of nuclei is particularly sensitive to the chemical freeze-out temperature of the system created in the collision, which is extracted from a grand-canonical-ensemble-based thermal fit, performed for the first time including light nuclei along with light-flavor hadrons in Xe−Xe collisions. The extracted chemical freeze-out temperature Tchem = (154.2 ± 1.1) MeV in Xe−Xe collisions is similar to that observed in Pb−Pb collisions and close to the crossover temperature predicted by lattice QCD calculations.
The transverse momentum (pT) differential production cross section of the promptly-produced charm-strange baryon Ξ0c (and its charge conjugate Ξ0c¯¯¯¯¯¯) is measured at midrapidity via its hadronic decay into π+Ξ− in p−Pb collisions at a centre-of-mass energy per nucleon−nucleon collision sNN−−−√ = 5.02 TeV with the ALICE detector at the LHC. The Ξ0c nuclear modification factor (RpPb), calculated from the cross sections in pp and p−Pb collisions, is presented and compared with the RpPb of Λ+c baryons. The ratios between the pT-differential production cross section of Ξ0c baryons and those of D0 mesons and Λ+c baryons are also reported and compared with results at forward and backward rapidity from the LHCb Collaboration. The measurements of the production cross section of prompt Ξ0c baryons are compared with a model based on perturbative QCD calculations of charm-quark production cross sections, which includes only cold nuclear matter effects in p−Pb collisions, and underestimates the measurement by a factor of about 50. This discrepancy is reduced when the data is compared with a model in which hadronisation is implemented via quark coalescence. The pT-integrated cross section of prompt Ξ0c-baryon production at midrapidity extrapolated down to pT = 0 is also reported. These measurements offer insights and constraints for theoretical calculations of the hadronisation process. Additionally, they provide inputs for the calculation of the charm production cross section in p−Pb collisions at midrapidity.
Investigating strangeness enhancement with multiplicity in pp collisions using angular correlations
(2024)
A study of strange hadron production associated with hard scattering processes and with the underlying event is conducted to investigate the origin of the enhanced production of strange hadrons in small collision systems characterised by large charged-particle multiplicities. For this purpose, the production of the single-strange meson K0S and the double-strange baryon Ξ± is measured, in each event, in the azimuthal direction of the highest-pT particle (``trigger" particle), related to hard scattering processes, and in the direction transverse to it in azimuth, associated with the underlying event, in pp collisions at s√=5.02 TeV and s√=13 TeV using the ALICE detector at the LHC. The per-trigger yields of K0S and Ξ± are dominated by the transverse-to-leading production (i.e., in the direction transverse to the trigger particle), whose contribution relative to the toward-leading production is observed to increase with the event charged-particle multiplicity. The transverse-to-leading and the toward-leading Ξ±/K0S yield ratios increase with the multiplicity of charged particles, suggesting that strangeness enhancement with multiplicity is associated with both hard scattering processes and the underlying event. The relative production of Ξ± with respect to K0S is higher in transverse-to-leading processes over the whole multiplicity interval covered by the measurement. The K0S and Ξ± per-trigger yields and yield ratios are compared with predictions of three different phenomenological models, namely PYTHIA 8.2 with the Monash tune, PYTHIA 8.2 with ropes and EPOS LHC. The comparison shows that none of them can quantitatively describe either the transverse-to-leading or the toward-leading yields of K0S and Ξ±.
The first measurement of the impact-parameter dependent angular anisotropy in the decay of coherently photoproduced ρ0 mesons is presented. The ρ0 mesons are reconstructed through their decay into a pion pair. The measured anisotropy corresponds to the amplitude of the cos(2ϕ) modulation, where ϕ is the angle between the two vectors formed by the sum and the difference of the transverse momenta of the pions, respectively. The measurement was performed by the ALICE Collaboration at the LHC using data from ultraperipheral Pb−Pb collisions at a center-of-mass energy of sNN−−−√ = 5.02 TeV per nucleon pair. Different impact-parameter regions are selected by classifying the events in nuclear-breakup classes. The amplitude of the cos(2ϕ) modulation is found to increase by about one order of magnitude from large to small impact parameters. Theoretical calculations, which describe the measurement, explain the cos(2ϕ) anisotropy as the result of a quantum interference effect at the femtometer scale that arises from the ambiguity as to which of the nuclei is the source of the photon in the interaction.
he first measurement of 3ΛH and 3Λ¯¯¯¯H¯¯¯¯ differential production with respect to transverse momentum and centrality in Pb−Pb collisions at sNN−−−√=5.02~TeV is presented. The 3ΛH has been reconstructed via its two-charged-body decay channel, i.e., 3ΛH→3He+π−. A Blast-Wave model fit of the pT-differential spectra of all nuclear species measured by the ALICE collaboration suggests that the 3ΛH kinetic freeze-out surface is consistent with that of other nuclei. The ratio between the integrated yields of 3ΛH and 3He is compared to predictions from the statistical hadronisation model and the coalescence model, with the latter being favoured by the presented measurements.
Six C-even states, denoted as X, with quantum numbers JPC=0−+, 1±+, or 2±+, are searched for via the e+e−→γD±sD∗∓s process using (1667.39±8.84) pb−1 of e+e− collision data collected with the BESIII detector operating at the BEPCII storage ring at center-of-mass energy of s√=(4681.92±0.30) MeV. No statistically significant signal is observed in the mass range from 4.08 to 4.32 GeV/c2. The upper limits of σ[e+e−→γX]⋅B[X→D±sD∗∓s] at a 90% confidence level are determined.
Isothermal titration calorimetry (ITC) is a widely used technique for the characterization of protein-protein and protein-ligand interactions. It provides information on the stoichiometry, affinity, and the thermodynamic driving forces of interactions. This chapter exemplifies the use of ITC to investigate interactions between human autophagy modifiers (LC3/GABARAP proteins) and their interaction partners, the LIR motif containing sequences. The purpose of this report is to present a detailed protocol for the production of LC3/GABARAP-interacting LIR peptides using E. coli expression systems. In addition, we outline the design of ITC experiments using the LC3/GABARAP:peptide interactions as an example. Comprehensive troubleshooting notes are provided to facilitate the adaptation of these protocols to different ligand-receptor systems. The methodology outlined for studying protein-ligand interactions will help to avoid common errors and misinterpretations of experimental results.
The total charm-quark production cross section per unit of rapidity dσ(cc)/dy, and the fragmentation fractions of charm quarks to different charm-hadron species f(c → hc), are measured for the first time in p–Pb collisions at √sNN = 5.02 TeV at midrapidity (−0.96 < y < 0.04 in the centre-ofmass frame) using data collected by ALICE at the CERN LHC. The results are obtained based on all the available measurements of prompt production of ground-state charm-hadron species: D0, D+,D+s, and J/ψ mesons, and Λ+cand Ξ0cbaryons. The resulting cross section is dσ(cc)/dy = 219.6±6.3 (stat.)+10.5−11.8(syst.)+7.6−2.9(extr.)±5.4 (BR)±4.6 (lumi.)±19.5 (rapidity shape) +15.0 (Ω0c) mb, which is consistent with a binary scaling of pQCD calculations from pp ollisions. The measured fragmentation fractions are compatible with those measured in pp collisions at √s = 5.02 and 13 TeV, showing an increase in the relative production rates of charm baryons with respect to charm mesons in pp and p–Pb collisions compared with e+e − and e−p collisions. The pT-integrated nuclear modification factor of charm quarks, RpPb(cc) = 0.91±0.04 (stat.) +0.08 −0.09 (syst.) +0.04 −0.03 (extr.)±0.03 (lumi.), is found to be consistent with unity and with theoretical predictions including nuclear modifications of the parton distribution functions.
The e+e−→D+sDs1(2536)− and e+e−→D+sD∗s2(2573)− processes are studied using data samples collected with the BESIII detector at center-of-mass energies from 4.530 to 4.946~GeV. The absolute branching fractions of Ds1(2536)−→D¯∗0K− and D∗s2(2573)−→D¯0K− are measured for the first time to be (35.9±4.8±3.5)% and (37.4±3.1±4.6)%, respectively. The measurements are in tension with predictions based on the assumption that the Ds1(2536) and D∗s2(2573) are dominated by a bare cs¯ component. The e+e−→D+sDs1(2536)− and e+e−→D+sD∗s2(2573)− cross sections are measured, and a resonant structure at around 4.6~GeV with a width of 50~MeV is observed for the first time with a statistical significance of 15σ in the e+e−→D+sD∗s2(2573)− process. It could be the Y(4626) found by the Belle collaboration in the D+sDs1(2536)− final state, since they have similar masses and widths. There is also evidence for a structure at around 4.75~GeV in both processes.
The family of cubic noncentrosymmetric 3-4-3 compounds has become a fertile ground for the discovery of novel correlated metallic and insulating phases. Here, we report the synthesis of a new heavy fermion compound, Ce3Bi4Ni3. It is an isoelectronic analog of the prototypical Kondo insulator Ce3Bi4Pt3 and of the recently discovered Weyl-Kondo semimetal Ce3Bi4Pd3. In contrast to the volume-preserving Pt-Pd substitution, structural and chemical analyses reveal a positive chemical pressure effect in Ce3Bi4Ni3 relative to its heavier counterparts. Based on the results of electrical resistivity, Hall effect, magnetic susceptibility, and specific heat measurements, we identify an energy gap of 65-70 meV, about eight times larger than that in Ce3Bi4Pt3 and about 45 times larger than that of the Kondo-insulating background hosting the Weyl nodes in Ce3Bi4Pd3. We show that this gap as well as other physical properties do not evolve monotonically with increasing atomic number, i.e., in the sequence Ce3Bi4Ni3-Ce3Bi4Pd3-Ce3Bi4Pt3, but instead with increasing partial electronic density of states of the d orbitals at the Fermi energy. To understand under which condition topological states form in these materials is a topic for future studies.
Heterostructures of graphene in proximity to magnetic insulators open the possibility to investigate exotic states emerging from the interplay of magnetism, strain and charge transfer between the layers. Recent reports on the growth of self-integrated atomic wires of β-RuCl3 on graphite suggest these materials as versatile candidates to investigate these effects. Here we present detailed first principles calculations on the charge transfer and electronic structure of β-RuCl3/heterostructures and provide a comparison with the work function analysis of the related honeycomb family members α-RuX3 (X = Cl,Br,I). We find that proximity of the two layers leads to a hole-doped graphene and electron-doped RuX3 in all cases, which is sensitively dependent on the distance between the two layers. Furthermore, strain effects due to lattice mismatch control the magnetization which itself has a strong effect on the charge transfer. Charge accumulation in β-RuCl3 strongly drops away from the chain making such heterostructures suitable candidates for sharp interfacial junctions in graphene-based devices.
canning tunneling microscopy (STM) is perhaps the most promising way to detect the superconducting gap size and structure in the canonical unconventional superconductor Sr2RuO4 directly. However, in many cases, researchers have reported being unable to detect the gap at all in simple STM conductance measurements. Recently, an investigation of this issue on various local topographic structures on a Sr-terminated surface found that superconducting spectra appeared only in the region of small nanoscale canyons, corresponding to the removal of one RuO surface layer. Here, we analyze the electronic structure of various possible surface structures using first principles methods, and argue that bulk conditions favorable for superconductivity can be achieved when removal of the RuO layer suppresses the RuO4 octahedral rotation locally. We further propose alternative terminations to the most frequently reported Sr termination where superconductivity surfaces should be observed.
Motivated by recently reported magnetic-field induced topological phases in ultracold atoms and correlated Moiré materials, we investigate topological phase transitions in a minimal model consisting of interacting spinless fermions described by the Hofstadter model on a square lattice. For interacting lattice Hamiltonians in the presence of a commensurate magnetic flux it has been demonstrated that the quantized Hall conductivity is constrained by a Lieb-Schultz-Mattis (LSM)-type theorem due to magnetic translation symmetry. In this work, we revisit the validity of the theorem for such models and establish that a topological phase transition from a topological to a trivial insulating phase can be realized but must be accompanied by spontaneous magnetic translation symmetry breaking caused by charge ordering of the spinless fermions. To support our findings, the topological phase diagram for varying interaction strength is mapped out numerically with exact diagonalization for different flux quantum ratios and band fillings using symmetry indicators. We discuss our results in the context of the LSM-type theorem.
On the potential for GWAS with phenotypic population means and allele-frequency data (popGWAS)
(2024)
This study explores the potential of a novel genome-wide association study (GWAS) approach for identifying loci underlying quantitative polygenic traits in natural populations. Extensive population genetic forward simulations demonstrate that the approach is generally effective for oligogenic and moderately polygenic traits and relatively insensitive to low heritability, but applicability is limited for highly polygenic architectures and pronounced population structure. The required sample size is moderate with very good results being obtained already for a few dozen populations scored. The method performs well in predicting population means even with a moderate false positive rate. When combined with machine learning for feature selection, this rate can be further reduced. The data efficiency of the method, particularly when using pooled sequencing, makes GWAS studies more accessible for research in biodiversity genomics. Overall, this study highlights the promise of this popGWAS approach for dissecting the genetic basis of complex traits in natural populations.
Motivated by the on-going discussion on the nature of magnetism in the quantum Ising chain CoNb2O6, we present a first-principles-based analysis of its exchange interactions by applying an \textit{ab initio} approach with additional modelling that accounts for various drawbacks of a purely density functional theory ansatz. With this method we are able to extract and understand the origin of the magnetic couplings under inclusion of all symmetry-allowed terms, and to resolve the conflicting model descriptions in CoNb2O6. We find that the twisted Kitaev chain and the transverse-field ferromagnetic Ising chain views are mutually compatible, although additional off-diagonal exchanges are necessary to provide a complete picture. We show that the dominant exchange interaction is a ligand-centered exchange process - involving the eg electrons -, which is rendered anisotropic by the low-symmetry crystal fields environments in CoNb2O6, giving rise to the dominant Ising exchange, while the smaller bond-dependent anisotropies are found to originate from d−d kinetic exchange processes involving the t2g electrons. We demonstrate the validity of our approach by comparing the predictions of the obtained low-energy model to measured THz and inelastic neutron scattering spectra.
Abstract
Seed harvesting from wild plant populations is key for ecological restoration, but may threaten the persistence of source populations. Consequently, several countries have set guidelines limiting the proportions of harvestable seeds. However, these guidelines are so far inconsistent, and they lack a solid empirical basis. Here, we use high-resolution data from 298 plant species to model the demographic consequences of seed harvesting. We find that the current guidelines do not protect populations of annuals and short-lived perennials, while they are overly restrictive for long-lived plants. We show that the maximum possible fraction of seed production – what can be harvested without compromising the long-term persistence of populations – is strongly related to the generation time of the target species. When harvesting every year, this safe seed fraction ranges from 80% in long-lived species to 2% in most annuals. Less frequent seed harvesting substantially increases the safe seed fraction: In the most vulnerable annual species, it is safe to harvest 5%, 10% or 30% of population seed production when harvesting every two, five or ten years, respectively. Our results provide a quantitative basis for seed harvesting legislations worldwide, based on species’ generation time and harvesting regime.
Significance The UN Decade on Ecosystem Restoration, 2021-2030, foresees upscaling restoration, and the demand for native seed is skyrocketing. Seeds for restoring native vegetation are often harvested in wild, but too intensive harvest can threaten the donor populations. Existing guidelines that set limits to wild seed harvest are mostly based on expert opinions, yet they commonly lack empirical basis and vary among regions in one order of magnitude. We show that the current guidelines urgently need to be reformulated, because they are overly restrictive in long-lived species, while they do not protect annual plants from extinction. Using matrix population models of nearly 300 plant species, we provide a quantitative basis for a new seed harvesting legislation world-wide.
Dynamic imaging of landmark organelles, such as nuclei, cell membrane, nuclear envelope, and lipid droplets enables image-based phenotyping of functional states of cells. Multispectral fluorescent imaging of landmark organelles requires labor-intensive labeling, limits throughput, and compromises cell health. Virtual staining of label-free images with deep neural networks is an emerging solution for this problem. Multiplexed imaging of cellular landmarks from scattered light and subsequent demultiplexing with virtual staining saves the light spectrum for imaging additional molecular reporters, photomanipulation, or other tasks. Published approaches for virtual staining of landmark organelles are fragile in the presence of nuisance variations in imaging, culture conditions, and cell types. This paper reports model training protocols for virtual staining of nuclei and membranes robust to label-free imaging parameters, cell states, and cell types. We developed a flexible and scalable convolutional architecture, named UNeXt2, for supervised training and self-supervised pre-training. The strategies we report here enable robust virtual staining of nuclei and cell membranes in multiple cell types, including neuromasts of zebrafish, across a range of imaging conditions. We assess the models by comparing the intensity, segmentations, and application-specific measurements obtained from virtually stained and experimentally stained nuclei and membranes. The models rescue the missing label, non-uniform expression of labels, and photobleaching. We share three pre-trained models, named VSCyto3D, VSCyto2D, and VSNeuromast, as well as VisCy, a PyTorch-based pipeline for training, inference, and deployment that leverages the modern OME-Zarr format.
Cyclin CLB2 mRNA localization and protein synthesis link cell cycle progression to bud growth
(2024)
Clb2 is a conserved mitotic B-type cyclin, the levels of which are finely controlled to drive progression through the cell cycle. While it is known that CLB2 transcription and Clb2 protein degradation are important for precise control of its expression, it remains unclear whether the synthesis of Clb2 is also regulated. To address whether and how Clb2 expression levels respond to cell growth changes and adapt cell cycle progression, we combined single-cell and single-molecule imaging methods to measure CLB2 mRNA and protein expression throughout the Saccharomyces cerevisiae cell cycle. We found that the CLB2 mRNA was efficiently localized to the yeast bud as soon as this compartment was formed, but strikingly the Clb2 protein accumulated in the mother nucleus. The CLB2 mRNA localization in the yeast bud by the She2-3 complex did not control protein localization but rather promoted CLB2 translation. Moreover, CLB2 mRNA bud localization and protein synthesis were coupled and dependent on a single secondary structure -a ZIP code-located in the coding sequence. In a CLB2 ZIP code mutant, mRNA localization was impaired and Clb2 protein synthesis decreased, resulting in changes in cell cycle distribution and increased size of daughter cells at birth. Finally, while in WT cells the Clb2 protein concentration followed bud growth, this relationship was impaired in the ZIP code mutant. We propose that S. cerevisiae couples the control of CLB2 mRNA bud localization and protein synthesis to coordinate cell growth and cell cycle progression. This mechanism extends our knowledge of CLB2 expression regulation, and constitutes a novel function for mRNA localization.
Antimatter is a research topic of fundamental interest. Sufficient matter-antimatter asymmetry in the early Universe created the matter-dominated world today. The origin of this asymmetry is not completely understood to date. High-energy nuclear collisions create conditions similar to the Universe microseconds after the Big Bang, with comparable amounts of matter and antimatter. Much of the antimatter created escapes the rapidly expanding fireball without annihilation, making such collisions an effective experimental tool to create heavy antimatter nuclear objects and study their properties. In this paper, we report the first observation of the antimatter hypernucleus 4Λ¯H¯¯¯¯, composed of an Λ¯, an antiproton and two antineutrons. The discovery was made through its two-body decay after production in ultrarelativistic heavy-ion collisions by the STAR experiment at the Relativistic Heavy Ion Collider. In total, 15.6 candidate 4Λ¯H¯¯¯¯ antimatter hypernuclei are obtained with an estimated background count of 6.4. Lifetimes of the antihypernuclei 3Λ¯H¯¯¯¯ and 4Λ¯H¯¯¯¯ are measured and compared with the lifetimes of their corresponding hypernuclei, testing the symmetry between matter and antimatter. Various production yield ratios among (anti)hypernuclei and (anti)nuclei are also measured and compared with theoretical model predictions, shedding light on their production mechanism.
We report results on an elastic cross section measurement in proton-proton collisions at a center-of-mass energy s√=510 GeV, obtained with the Roman Pot setup of the STAR experiment at the Relativistic Heavy Ion Collider (RHIC). The elastic differential cross section is measured in the four-momentum transfer squared range 0.23≤−t≤0.67 GeV2. We find that a constant slope B does not fit the data in the aforementioned t range, and we obtain a much better fit using a second-order polynomial for B(t). The t dependence of B is determined using six subintervals of t in the STAR measured t range, and is in good agreement with the phenomenological models. The measured elastic differential cross section dσ/dt agrees well with the results obtained at s√=546 GeV for proton--antiproton collisions by the UA4 experiment. We also determine that the integrated elastic cross section within the STAR t-range is σfidel=462.1±0.9(stat.)±1.1(syst.)±11.6(scale) μb.
We report results on an elastic cross section measurement in proton-proton collisions at a center-of-mass energy s√=510 GeV, obtained with the Roman Pot setup of the STAR experiment at the Relativistic Heavy Ion Collider (RHIC). The elastic differential cross section is measured in the four-momentum transfer squared range 0.23≤−t≤0.67 GeV2. We find that a constant slope B does not fit the data in the aforementioned t range, and we obtain a much better fit using a second-order polynomial for B(t). The t dependence of B is determined using six subintervals of t in the STAR measured t range, and is in good agreement with the phenomenological models. The measured elastic differential cross section dσ/dt agrees well with the results obtained at s√=546 GeV for proton--antiproton collisions by the UA4 experiment. We also determine that the integrated elastic cross section within the STAR t-range is σfidel=462.1±0.9(stat.)±1.1(syst.)±11.6(scale) μb.
We report results on an elastic cross section measurement in proton-proton collisions at a center-of-mass energy s√=510 GeV, obtained with the Roman Pot setup of the STAR experiment at the Relativistic Heavy Ion Collider (RHIC). The elastic differential cross section is measured in the four-momentum transfer squared range 0.23≤−t≤0.67 GeV2. We find that a constant slope B does not fit the data in the aforementioned t range, and we obtain a much better fit using a second-order polynomial for B(t). The t dependence of B is determined using six subintervals of t in the STAR measured t range, and is in good agreement with the phenomenological models. The measured elastic differential cross section dσ/dt agrees well with the results obtained at s√=546~GeV for proton--antiproton collisions by the UA4 experiment. We also determine that the integrated elastic cross section within the STAR t-range is σfidel=462.1±0.9(stat.)±1.1(syst.)±11.6(scale) μb.
We measure triangular flow relative to the reaction plane at 3 GeV center-of-mass energy in Au+Au collisions at the BNL Relativistic Heavy Ion Collider. A significant v3 signal for protons is observed, which increases for higher rapidity, higher transverse momentum, and more peripheral collisions. The triangular flow is essentially rapidity-odd with a slope at mid-rapidity, dv3/dy|(y=0), opposite in sign compared to the slope for directed flow. No significant v3 signal is observed for charged pions and kaons. Comparisons with models suggest that a mean field potential is required to describe these results, and that the triangular shape of the participant nucleons is the result of stopping and nuclear geometry.
We report the first measurements of cumulants, up to 4th order, of deuteron number distributions and proton-deuteron correlations in Au+Au collisions recorded by the STAR experiment in phase-I of Beam Energy Scan (BES) program at the Relativistic Heavy Ion Collider. Deuteron cumulants, their ratios, and proton-deuteron mixed cumulants are presented for different collision centralities covering a range of center-of-mass energy per nucleon pair sNN−−−−√~=~7.7 to 200~GeV. It is found that the cumulant ratios at lower collision energies favor a canonical ensemble over a grand canonical ensemble in thermal models. An anti-correlation between proton and deuteron multiplicity is observed across all collision energies and centralities, consistent with the expectation from global baryon number conservation. The UrQMD model coupled with a phase-space coalescence mechanism qualitatively reproduces the collision-energy dependence of cumulant ratios and proton-deuteron correlations.
In heavy-ion collision experiments, the global collectivity of final-state particles can be quantified by anisotropic flow coefficients (vn). The first-order flow coefficient, also referred to as the directed flow (v1), describes the collective sideward motion of produced particles and nuclear fragments in heavy-ion collisions. It carries information on the very early stage of the collision, especially at large pseudorapidity (η), where it is believed to be generated during the nuclear passage time. Directed flow therefore probes the onset of bulk collective dynamics during thermalization, providing valuable experimental guidance to models of the pre-equilibrium stage. In 2018, the Event Plane Detector (EPD) was installed in STAR and used for the Beam Energy Scan phase-II (BES-II) data taking. The combination of EPD (2.1<|η|<5.1) and high-statistics BES-II data enables us to extend the v1 measurement to the forward and backward η regions. In this paper, we present the measurement of v1 over a wide η range in Au+Au collisions at √sNN= 19.6 and 27 GeV using the STAR EPD. The results of the analysis at √sNN=19.6 GeV exhibit excellent consistency with the previous PHOBOS measurement, while elevating the precision of the overall measurement. The increased precision of the measurement also revealed finer structures in heavy-ion collisions, including a potential observation of the first-order event-plane decorrelation. Multiple physics models were compared to the experimental results. Only a transport model and a three-fluid hybrid model can reproduce a sizable v1 at large η as was observed experimentally. The model comparison also indicates v1 at large η might be sensitive to the QGP phase transition.
In a Quark-Gluon Plasma (QGP), the fundamental building blocks of matter, quarks and gluons, are under extreme conditions of temperature and density. A QGP could exist in the early stages of the Universe, and in various objects and events in the cosmos. The thermodynamic and hydrodynamic properties of the QGP are described by Quantum Chromodynamics (QCD) and can be studied in heavy-ion collisions. Despite being a key thermodynamic parameter, the QGP temperature is still poorly known. Thermal lepton pairs (e+e− and μ+μ−) are ideal penetrating probes of the true temperature of the emitting source, since their invariant-mass spectra suffer neither from strong final-state interactions nor from blue-shift effects due to rapid expansion. Here we measure the QGP temperature using thermal e+e− production at the Relativistic Heavy Ion Collider (RHIC). The average temperature from the low-mass region (in-medium ρ0 vector-meson dominant) is (1.99±0.24)×1012 K, consistent with the chemical freeze-out temperature from statistical models and the phase transition temperature from LQCD. The average temperature from the intermediate mass region (above the ρ0 mass, QGP dominant) is significantly higher at (3.40±0.55)×1012 K. This work provides essential experimental thermodynamic measurements to map out the QCD phase diagram and understand the properties of matter under extreme conditions.
With the STAR experiment at RHIC, we characterize √sNN = 200 GeV p+Au collisions by event activity (EA) measured within the pseudorapidity range η∈[−5,−3.4] in the Au-going direction and report correlations between this EA and hard- and soft-scale particle production at mid-rapidity (η∈[−1,1]). At the soft scale, charged particle production in low-EA p+Au collisions is comparable to that in \pp collisions and increases monotonically with increasing EA. At the hard scale, we report measurements of high transverse momentum (pT) jets in events of different EAs. In contrast to the soft particle production, high-pT particle production and EA are found to be inversely related. To investigate whether this is a signal of jet quenching in high-EA events, we also report ratios of pT imbalance and azimuthal separation of dijets in high- and low-EA events. Within our measurement precision, no significant differences are observed, disfavoring the presence of jet quenching in the highest 30% EA p+Au collisions at √sNN = 200 GeV.
Atomic nuclei are self-organized, many-body quantum systems bound by strong nuclear forces within femtometer-scale space. These complex systems manifest a diverse set of shapes~, traditionally explored via non-invasive spectroscopic techniques at low energies. Their instantaneous shapes, obscured by long-timescale quantum fluctuations, are considered not directly observable at low energy. We introduce a complementary method, collective flow assisted nuclear shape imaging, to image the nuclear global shape by colliding them at ultrarelativistic speeds and analyzing the collective response of outgoing debris. This technique captures a collision-specific snapshot of the spatial matter distribution in the nuclei, which, through the hydrodynamic expansion, leaves imprints on the particle momentum distribution patterns observed in detectors. We benchmark this method in collisions of ground state Uranium-238 nuclei, known for its elongated, axial-symmetric shape. Our findings, while confirming an overall deformation broadly consistent with prior low-energy experiments, also indicate a small deviation from axial symmetry in the nuclear ground state. This approach marks a new way of imaging nuclei, especially those with uncertain shape characteristics, and refines initial conditions in high-energy nuclear collisions. It tackles the important issue of nuclear structure evolution across various energy scales.
We report a new measurement of transverse single-spin asymmetries for dijet production in collisions of polarized protons at s√ = 200 GeV. Correlations between the proton spin and the transverse momenta of its partons, each perpendicular to the proton momentum direction, are probed at high Q2 ≈160 GeV2. The associated Sivers observable ⟨kT⟩, the average parton transverse momentum, is extracted using simple kinematics. Nonzero Sivers effects are observed for the first time in dijets from proton-proton collisions, but only when the jets are sorted by their net charge, which enhances the u- or d-quark contributions to separate data samples. This also enables a simple kinematic approach for determination of the individual partonic contributions to the observed asymmetries.
Using data samples collected with the BESIII detector operating at the BEPCII storage ring, the cross section of the inclusive process e+e−→η+X, normalized by the total cross section of e+e−→hadrons, is measured at eight center-of-mass energy points from 2.0000 GeV to 3.6710 GeV. These are the first measurements with momentum dependence in this energy region. Our measurement shows a significant discrepancy from calculations with the existing fragmentation functions. To address this discrepancy, a new QCD analysis is performed at the next-to-next-to-leading order with hadron mass corrections and higher twist effects, which can explain both the established high-energy data and our measurements reasonably well.
Muller's ratchet, in its prototype version, models a haploid, asexual population whose size~N is constant over the generations. Slightly deleterious mutations are acquired along the lineages at a constant rate, and individuals carrying less mutations have a selective advantage. The classical variant considers {\it fitness proportional} selection, but other fitness schemes are conceivable as well. Inspired by the work of Etheridge et al. ([EPW09]) we propose a parameter scaling which fits well to the ``near-critical'' regime that was in the focus of [EPW09] (and in which the mutation-selection ratio diverges logarithmically as N→∞). Using a Moran model, we investigate the``rule of thumb'' given in [EPW09] for the click rate of the ``classical ratchet'' by putting it into the context of new results on the long-time evolution of the size of the best class of the ratchet with (binary) tournament selection, which (other than that of the classical ratchet) follows an autonomous dynamics up to the time of its extinction. In [GSW23] it was discovered that the tournament ratchet has a hierarchy of dual processes which can be constructed on top of an Ancestral Selection graph with a Poisson decoration. For a regime in which the mutation/selection-ratio remains bounded away from 1, this was used in [GSW23] to reveal the asymptotics of the click rates as well as that of the type frequency profile between clicks. We will describe how these ideas can be extended to the near-critical regime in which the mutation-selection ratio of the tournament ratchet converges to 1 as N→∞.
Bounding Dark Energy from the SPARC rotation curves: Data driven probe for galaxy virialization
(2024)
Dark Energy (DE) acts as a repulsive force that opposes gravitational attraction. Assuming galaxies maintain a steady state over extended periods, the estimated upper bound on DE studies its resistance to the attractive gravitational force from dark matter. Using the SPARC dataset, we fit the Navarro-Frenk-White (NFW) and Hernquist models to identify the most suitable galaxies for these models. Introducing the presence of DE in these galaxies helps establish the upper limit on its repulsive force. This upper bound on DE sits around ρ(<Λ)∼10−25~kg/m3, only two orders of magnitude higher than the one measured by Planck. We discuss the conditions for detecting DE in different systems and show the consistency of the upper bound from galaxies to other systems. The upper bound is of the same order of magnitude as ρ200=200ρc for both dark matter profiles. We also address the implications for future measurements on that upper bound and the condition for detecting the impact of Λ on galactic scales.
The production cross section of inclusive isolated photons has been measured by the ALICE experiment at the CERN LHC in pp collisions at centre-of-momentum energy of s√=13 TeV collected during the LHC Run 2 data-taking period. The measurement is performed by combining the measurements of the electromagnetic calorimeter EMCal and the central tracking detectors ITS and TPC, covering a pseudorapidity range of |ηγ|<0.67 and a transverse momentum range of 7<pγT<200 GeV/c. The result extends to lower pγT and xγT=2pγT/s√ ranges, the lowest xγT of any isolated photon measurements to date, extending significantly those measured by the ATLAS and CMS experiments towards lower pγT at the same collision energy with a small overlap between the measurements. The measurement is compared with next-to-leading order perturbative QCD calculations and the results from the ATLAS and CMS experiments as well as with measurements at other collision energies. The measurement and theory prediction are in agreement with each other within the experimental and theoretical uncertainties.
Experimental data from the NA49 collaboration show an unexpectedly steep rise of the rapidity width of the ϕ meson as function of beam energy, which was suggested as possible interesting signal for novel physics. In this work we show that the Ultra-relativistic Quantum-Molecular-Dynamics (UrQMD) model is able to reproduce the shapes of the rapidity distributions of most measured hadrons and predicts a common linear increase of the width for all hadrons. Only when following the exact same analysis technique and experimental acceptance of the NA49 and NA61/SHINE collaborations, we find that the extracted value of the rapidity width of the ϕ increases drastically for the highest beam energy. We conclude that the observed steep increase of the ϕ rapidity width is a problem of limited detector acceptance and the simplified Gaussian fit approximation.