Improved Combinatorial Assembly and Barcode Sequencing for Gene-Sized DNA Constructs
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Microbes play a critical role in plant litter decomposition and influence the fate of carbon in rivers and riparian zones. When decomposing low-nutrient plant litter, microbes acquire nitrogen (N) and phosphorus (P) from the environment (i.e., nutrient immobilization), and this process is potentially sensitive to nutrient loading and changing climate. Nonetheless, environmental controls on immobilization are poorly understood because rates are also influenced by plant litter chemistry, which is coupled to the same environmental factors. Here we used a standardized, low-nutrient organic matter substrate (cotton strips) to quantify nutrient immobilization at 100 paired stream and riparian sites representing 11 biomes worldwide. Immobilization rates varied by three orders of magnitude, were greater in rivers than riparian zones, and were strongly correlated to decomposition rates. In rivers, P immobilization rates were controlled by surface water phosphate concentrations, but N immobilization rates were not related to inorganic N. The N:P of immobilized nutrients was tightly constrained to a molar ratio of 10:1 despite wide variation in surface water N:P. Immobilization rates were temperature-dependent in riparian zones but not related to temperature in rivers. However, in rivers nutrient supply ultimately controlled whether microbes could achieve the maximum expected decomposition rate at a given temperature. Collectively, we demonstrated that exogenous nutrient supply and immobilization are critical control points for decomposition of organic matter.
It has become common knowledge that phonons can generate thermal Hall effect in a wide variety of materials, although the underlying mechanism is still controversial. We study longitudinal κ xx and transverse κ xy thermal conductivity in Pr 2 Ir 2 O 7 , which is a metallic analog of spin ice. Despite the presence of mobile charge carriers, we find that both κ xx and κ xy are dominated by phonons. A T/H scaling of κ xx unambiguously reveals that longitudinal heat current is substantially impeded by resonant scattering of phonons on paramagnetic spins. Upon cooling, the resonant scattering is strongly affected by a development of spin ice correlation and κ xx deviates from the scaling in an anisotropic way with respect to field directions. Strikingly, a set of the κ xx and κ xy data clearly shows that κ xy correlates with κ xx in its response to magnetic field including a success of the T/H scaling and its failure at low temperature. This remarkable correlation provides solid evidence that an indispensable role is played by spin-phonon scattering not only for hindering the longitudinal heat conduction, but also for generating the transverse response.
Mouse and human brains have different functions that depend on their neuronal networks. We analyzed nanometer-scale three-dimensional structures of brain tissues of the mouse medial prefrontal cortex and compared them with structures of the human anterior cingulate cortex. The obtained results indicated that mouse neuronal somata are smaller and neurites are thinner than those of human neurons. We implemented these characteristics of mouse neurons in convolutional layers of a generative adversarial network (GAN) and a denoising diffusion implicit model (DDIM), which were then subjected to image generation tasks using photo datasets of cat faces, cheese, human faces, birds, and automobiles. The mouse-mimetic GAN outperformed a standard GAN in the image generation task using the cat faces and cheese photo datasets, but underperformed for human faces and birds. The mouse-mimetic DDIM gave similar results, suggesting that the nature of the datasets affected the results. Analyses of the five datasets indicated differences in their image entropy, which should influence the number of parameters required for image generation. The preferences of the mouse-mimetic AIs coincided with the impressions commonly associated with mice. The relationship between the neuronal network and brain function should be investigated by implementing other biological findings in artificial neural networks.
Recent measurements of 𝐽/𝜓 production as a function of event charged-particle multiplicity at the collision energies of both the Large Hadron Collider (LHC) and the Relativistic Heavy Ion Collider (RHIC) show enhanced 𝐽/𝜓 production yields with increasing multiplicity. One potential explanation for this type of dependence is multiparton interactions (MPI). We present the first study of potential autocorrelations at RHIC energies and forward and backward rapidity of self-normalized 𝐽/𝜓 yields and 𝜓(2𝑆) to 𝐽/𝜓 ratio, as a function of self-normalized multiplicity in 𝑝 + 𝑝 collisions. In addition, detailed pythia studies tuned to RHIC energies were performed to investigate the MPI impacts. We find that the PHENIX data at RHIC are consistent with recent LHC measurements and can only be described by pythia calculations that include MPI effects. The forward and backward 𝜓(2𝑆) to 𝐽/𝜓 ratio is found to be less dependent on the charged-particle multiplicity.
The jet cross section and jet-substructure observables in 𝑝 + 𝑝 collisions at $\sqrt{s}$ =200 GeV were measured by the PHENIX Collaboration at the Relativistic Heavy Ion Collider (RHIC). Jets are reconstructed from charged-particle tracks and electromagnetic-calorimeter clusters using the anti-𝑘 𝑡 algorithm with a jet radius of 𝑅 = 0.3 for jets with transverse momentum within 8.0 < 𝑝 𝑇 < 40.0 GeV/𝑐 and pseudorapidity |𝜂| < 0.15. Measurements include the jet cross section, as well as distributions of SoftDrop-groomed momentum fraction (𝑧 𝑔 ), charged-particle transverse momentum with respect to jet axis (𝑗 𝑇 ), and radial distributions of charged particles within jets (𝑟). Also measured was the distribution of 𝜉 = −ln(𝑧), where 𝑧 is the fraction of the jet momentum carried by the charged particle. The measurements are compared to theoretical next-to and next-to-next-to-leading-order calculations, the PYTHIA and H erwig event generators, and to other existing experimental results. Indicated from these measurements is a lower particle multiplicity in jets at RHIC energies when compared to models. Also noted are implications for future jet measurements with sPHENIX at RHIC as well as at the future Electron-Ion Collider.
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In this work, the effective interactions between two nuclear clusters, d + d, t + t, and α + α, are investigated within a cluster model using local nucleon-nucleon (NN) forces. It is shown that the interaction in the spin-aligned d + d system is repulsive for all intercluster distances, whereas the α + α and spin-aligned t + t systems are attractive at intermediate distances. The Pauli blocking between identical-nucleon pairs is responsible for the cluster-cluster repulsion and becomes dominant in the shallow binding limit. We demonstrate that two d clusters could be bound if the NN force has nonzero range and is strong enough to form a deeply bound d cluster, or if the NN force has both even-parity and odd-parity attraction. Effective dimer-dimer interactions for general quantum systems of two-component fermions are also discussed in heavy-light mass limit, where one component is much heavier than the other, and their relation to intercluster interactions in nuclear systems are discussed. Our findings provide a conceptual foundation for conclusions obtained numerically in the literature, that increasing the range or strength of the local part of the attractive nucleon-nucleon interaction results in a more attractive cluster-cluster interaction.
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Suppression of the J/ψ nuclear-modification factor has been seen as a trademark signature of final-state effects in large collision systems for decades. In small systems, the nuclear modification was attributed to cold-nuclear-matter effects until the observation of strong differential suppression of the ψ(2S) state in p+A and d+A collisions suggested the presence of final-state effects. Results of J/ψ and ψ(2S) measurements in the dimuon decay channel are presented here for p+p, p+Al, and p+Au collision systems at $\sqrt{^{S}NN}$ = 200 GeV. The results are predominantly shown in the form of the nuclear-modification factor, R pA , the ratio of the ψ(2S) invariant yield per nucleon-nucleon collision in collisions of proton on target nucleus to that in p+p collisions. Finally, measurements of the J/ψ and ψ(2S) nuclear-modification factor are compared with shadowing and transport-model predictions, as well as to complementary measurements at Large-Hadron-Collider energies.
We report small nuclear collisions are mainly sensitive to cold-nuclear-matter effects; however, the collective behavior observed in these collisions shows a hint of hot-nuclear-matter effects. The identified-particle spectra, especially the φ mesons which contain strange and antistrange quarks and have a relatively small hadronic-interaction cross section, are a good tool to study these effects. The PHENIX experiment has measured φ mesons in a specific set of small collision systems p+Al, p+Au, and 3 He+Au, as well as d+Au at $\sqrt{s_{NN}}$=200 GeV. The transverse-momentum spectra and nuclear-modification factors are presented and compared to theoretical-model predictions. The comparisons with different calculations suggest that quark-gluon plasma may be formed in these small collision systems at $\sqrt{s_{NN}}$=200 GeV. However, the volume and the lifetime of the produced medium may be insufficient for observing strangeness-enhancement and jet-quenching effects. The comparison with calculations suggests that the main production mechanisms of φ mesons at midrapidity may be different in p+Al versus p/d/ 3 He+Au collisions at $\sqrt{s_{NN}}$=200 GeV. While thermal quark recombination seems to dominate in p/d/ 3 He+Au collisions, fragmentation seems to be the main production mechanism in p+Al collisions.
Recently, the PHENIX Collaboration has published second- and third-harmonic Fourier coefficients v 2 and v 3 for midrapidity (|η|< 0.35 ) charged hadrons in 0%–5% central p+Au, d+Au, and 3 He+Au collisions at $\sqrt{s_{NN}}$= 200 GeV, utilizing three sets of two-particle correlations for two detector combinations with different pseudorapidity acceptance [Acharya et al., Phys. Rev. C 105, 024901 (2022)]. Here, this paper extends these measurements of v 2 to all centralities in p+Au, d+Au, and 3 He+Au collisions, as well as p+p collisions, as a function of transverse momentum (p T ) and event multiplicity. The kinematic dependence of v 2 is quantified as the ratio R of v 2 between the two detector combinations as a function of event multiplicity for 0.5 < p T <1 and 2 T < 2.5 GeV/c. A multiphase-transport (AMPT) model can reproduce the observed v 2 in most-central to midcentral d Au and 3 He+Au collisions. However, the AMPT model systematically overestimates the measurements in p+p, p+Au, and peripheral d+Au and 3 He+Au collisions, indicating a higher nonflow contribution in the AMPT model than in the experimental data. The AMPT model fails to describe the observed R for 0.5 < p T < 1 GeV/c , but there is qualitative agreement with the measurements for 2 < p T < 2.5 GeV/c.
The PHENIX experiment has performed a systematic study of identified charged-hadron (𝜋 ± , 𝐾 ± , 𝑝, $\bar{𝑝}$) production at midrapidity in 𝑝 + Al, 3 He + Au, and Cu + Au collisions at $\sqrt{s_{NN}}$ = 200 GeV and U + U collisions at $\sqrt{s_{NN}}$ = 193 GeV. Identified charged-hadron invariant transverse-momentum (𝑝 𝑇 ) and transverse-mass (𝑚 𝑇 ) spectra are presented and interpreted in terms of radially expanding thermalized systems. The particle ratios of 𝐾/𝜋 and 𝑝/𝜋 have been measured in different centrality ranges of large (Cu + Au and U + U) and small (𝑝 + Al and 3 He + Au) collision systems. The values of 𝐾/𝜋 ratios measured in all considered collision systems were found to be consistent with those measured in 𝑝+𝑝 collisions. However, the values of 𝑝/𝜋 ratios measured in large collision systems reach the values of ≈0.6, which is a factor of ≈2 larger than in 𝑝 + 𝑝 collisions. These results can be qualitatively understood in terms of the baryon enhancement expected from hadronization by recombination. Identified charged-hadron nuclear-modification factors (𝑅 𝐴𝐵 ) are also presented. Enhancement of proton 𝑅 𝐴𝐵 values over meson 𝑅 𝐴𝐵 values was observed in central 3 He + Au, Cu + Au, and U + U collisions. Finally, the proton 𝑅 𝐴𝐵 values measured in the 𝑝 + Al collision system were found to be consistent with 𝑅 𝐴𝐵 values of 𝜙, 𝜋 ± , 𝐾 ± , and 𝜋 0 mesons, which may indicate that the size of the system produced in 𝑝 + Al collisions is too small for recombination to cause a noticeable increase in proton production.
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The cross section of bottom quark-antiquark ( b b ¯ ) production in p + p collisions at s = 510 GeV is measured with the PHENIX detector at the Relativistic Heavy Ion Collider. The results are based on the yield of high mass, like-sign muon pairs measured within the PHENIX muon arm acceptance ( 1.2 < | y | < 2.2 ). The b b ¯ signal is extracted from like-sign dimuons by utilizing the unique properties of neutral B meson oscillation. We report a differential cross section of d σ b b ¯ → μ ± μ ± / d y = 0.16 ± 0.01 ( stat ) ± 0.02 ( syst ) ± 0.02 ( global ) nb for like-sign muons in the rapidity and p T ranges 1.2 < | y | < 2.2 and p T > 1 GeV / c , and dimuon mass of 5 – 10 GeV / c 2 . The extrapolated total cross section at this energy for b b ¯ production is 13.1 ± 0.6 ( stat ) ± 1.5 ( syst ) ± 2.7 ( global ) μ b . The total cross section is compared to a perturbative quantum chromodynamics calculation and is consistent within uncertainties. The azimuthal opening angle between muon pairs from b b ¯ decays and their p T distributions are compared to distributions generated using ps pythia 6, which includes next-to-leading order processes. The azimuthal correlations and pair p T distribution are not very well described by pythia calculations, but are still consistent within uncertainties. Flavor creation and flavor excitation subprocesses are favored over gluon splitting.