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Comprehensive benchmarking of metagenomic binning tools reveals key factors for improved genome recovery
Abstract Metagenomic binning is essential for reconstructing prokaryotic genomes from metagenomic samples. We benchmarked various binning tools using Critical Assessment of Metagenome Interpretation (CAMI)-simulated, custom-simulated, and real metagenomic datasets, primarily focusing on short-read sequencing data. Our analysis highlights critical factors influencing binning efficacy: (i) Sequencing depth and taxonomic complexity strongly impact binning performance, while CAMI-simulated benchmarking datasets exhibit substantially lower complexity than human gut and environmental metagenomes, (ii) Chimeric genome rates vary widely across tools, (iii) Multi-sample binning is most effective with about 20 samples, as using too few or too many samples can reduce its benefits, and (iv) Binning efficacy was lower for single-end sequencing samples due to reduced contig quality and assembly fragmentation. Neural network-based tools consistently outperformed others in genome recovery from both real samples and simulated samples with realistic taxonomic complexity, though at higher computational cost. By integrating and refining genome bins from the top three binning tools, we recovered >30% more high-quality genomes than previous methods. This study provides practical guidance for improving metagenomic binning to facilitate the reconstruction of prokaryotic genomes.
Zn1−xMgxO/Eu-doped Zn1−yMgyO (x>y) multi-quantum well structures toward maximizing Eu3+ luminescence in oxide-based light sources
Europium-doped wide-bandgap semiconductors are promising materials for red light-emitting devices. Here, we present a europium-doped Zn(Mg)O-based multi-quantum well (MQW) structure design consisting of undoped Zn1−xMgxO barrier layers and Eu-doped Zn1−yMgyO (x > y ≥ 0), quantum wells. A gradient in the Mg content between the layers provides the potential barrier necessary to confine Eu dopants. A reference structure consisting of 20 pairs of Zn0.9Mg0.1O/ZnO:Eu was grown on the c-ZnO substrate. The structural and luminescence properties of these MQWs grown using plasma-assisted molecular beam epitaxy technique are investigated. A systematic comparison of the luminescence intensity and decay dynamics of Zn1−xMgxO/Zn1−yMgyO:Eu MQWs with ZnMgO:Eu epilayers reveals the clear superiority of MQWs over epilayers. The photoluminescence of Eu ions in the MQWs is two orders of magnitude stronger than that of ZnMgO:Eu epilayers, when the Mg content in the Eu-doped QW layer and epilayer is comparable. This can be explained by the increased carrier density around the Eu ions, as a result of their localization in QWs. The results suggest that the Zn1−xMgxO/Zn1−yMgyO:Eu MQWs enhance Eu emission via exciton generation in both the barriers and QW layers, followed by carrier relaxation into the QWs and subsequent energy transfer to the Eu dopants.
Post-acute organ complications within one year following COVID-19 hospitalization and related socioeconomic inequalities
Donor band formation in Si quantum dots using hot P+-ion implantation
We demonstrated the formation of a donor band even in Si quantum dots (Si-QDs) with fewer than ten donors. Hot P+-ions were implanted at 800 °C into Si-QDs fabricated by implanting hot Si+ ions into a SiO2 layer. After post-N2 annealing at 1000 °C, the P+-doped Si-QDs with a diameter of 2.5 nm were embedded into the SiO2 layer. The P+-ion dose (DP) varied from 1 × 1015 to 9 × 1015 cm−2. Energy-dispersive x-ray spectroscopy revealed that the implanted P atoms clustered in the Si-QDs, which led to the experimental verification of the co-clustering of hot Si+/P+-ion implantation. Thus, the DP dependence of the P-atom concentration (NP-EDX) in Si-QDs was accurately determined. Additionally, the P 1s spectrum obtained by hard x-ray photoelectron spectroscopy revealed that the P–Si bond of the P-doped Si-QDs, including substantial P atoms, directly verifies donor formation in the Si-QDs. The upper limit of activation rate RACTUP of the implanted P atoms in the Si-QDs was obtained by the P–Si bond ratio. Therefore, the upper limit of donor concentration in the Si-QDs (NDUP) was determined by NDUP =NP-EDX × RACTUP, resulting in 1.4 × 1020 ≤ NDUP ≤ 1.3 × 1021 cm−3. The upper limit of number of donors in the Si-QDs (nDUP) was overestimated to be between 1 and 12. Additionally, the photoluminescence revealed the bandgap EG narrowing (ΔEG), even in the Si-QDs with nDUP < 12 caused by donor band tailing. ΔEG was much lower than those of two- and three-dimensional Si.
Signaling cascades shape functional subpopulations of cortical astrocytes in male wild-type mice and APP/PS1dE9 Alzheimer’s disease model
Abstract Astrocytes are key partners for neurons and can impact diseases such as Alzheimer’s disease (AD), as they exhibit multiple reactive changes. Recent single cell/nucleus genomics analyses evidence astrocyte subpopulations coexisting in normal and AD brains. However, the signaling cascades controlling them, their functional characteristics and roles in AD are still unknown. Here, thanks to astrocyte-specific reporters for STAT3 and NF-kB signaling pathways, two regulators of astrocyte reactivity, we report the presence of three astrocyte subpopulations defined by their signaling activity, in the prefrontal cortex of male APP/PS1dE9 mice. These subpopulations are not triggered by amyloid deposition and are also observed in wild-type mice. They show distinct morphologies, molecular signatures and functional profiles. While NF-kB+ astrocytes have larger territories and higher lysosomal activity, STAT3+ astrocytes display enhanced hemichannel activity. Specific inhibition of these subpopulations reduces amyloid plaque size and impacts anxiety, social preference and social memory in AD but not wild-type mice. Our results show how innate signaling shapes astrocyte subpopulations in the mouse cortex, with distinct functions in health and disease.
Non-Hermiticity induced thermal entanglement phase transition
Theoretical analysis of a prototypical two-qubit effective non-Hermitian system characterized by asymmetric Heisenberg XY interactions in the absence of external magnetic fields demonstrates that maximal bipartite entanglement and quantum phase transitions can be induced exclusively through non-Hermiticity. At thermal equilibrium as T→0, the system attains maximal entanglement C=1 for values of the non-Hermiticity parameter greater than a critical value γ>γc=J1−δ2, where J denotes the exchange interaction and δ represents the anisotropy of the system; conversely, for γ<γc, entanglement is nonmaximal and given by C=1−(γ/J)2. The entanglement undergoes a discontinuous transition to zero precisely at γ=γc. This phase transition originates from the closing of the energy gap at a non-Hermiticity-driven ground state degeneracy, which is fundamentally different from an exceptional point.
Medullary cavity expansion is mediated by distinct cell populations during fetal bone development
Research on acoustic wave manipulation based on subwavelength fence structure
Acoustic metamaterials have been the focus of research in recent years. By designing the unit structure of materials at the sub-wavelength scale, materials have unprecedented special properties, such as the realization of acoustic beam collimation. However, in previous studies, these collimated acoustic beams either have strong sidelobes, or the structure of the metamaterials is complex and difficult to verify experimentally. In this paper, we propose a simple fence-structured unit that, after periodic arrangement, excites collective surface oscillations in a specific frequency band to achieve an acoustic beam collimation with almost no sidelobe, which is verified by numerical simulations and experiments. This structural unit provides an effective means for directional sound propagation in air.
Machine learning driven discovery of low modulus biomedical titanium alloys for additive manufacturing
Mechanical toughening in BaTiO3–Au composite thin films
Ceramic films possess inherently high stiffness; however, their brittleness and limited hardness constrain their use in practical applications. In this study, we demonstrate a strategy to concurrently enhance the mechanical and tribological performance of BaTiO3 (BTO) films by incorporating Au nanostructures at controlled molar ratios (BTO:Au = 5:1, 5:3, 5:5 refer to B5A1, B5A3, B5A5). Nanoindentation tests reveal substantial increases in nanohardness and toughness for the B5A1 and B5A3 films. Complementary tribological testing shows notable reductions in both friction coefficient and wear rate, with the B5A1 film exhibiting the most pronounced improvement, which is attributed to the favorable dispersion state of the Au phase. This work highlights an effective pathway for engineering hard yet damage-tolerant ceramic films through metal incorporation and microstructural tailoring.
Global impact of germline structural variation on the cancer proteome
Theoretical ion sputtering yields from loose powders using a multiscale Monte Carlo approach
Ion sputtering from loose powders remains poorly understood despite its relevance to planetary science and industry. We developed a multiscale Monte Carlo model to simulate sputtering from powders, using a higher-fidelity approach for the target geometry compared to voxel-based methods. Simulating Kr+ ions impacting Cu powders and flat slabs, we show that sputtering from loose powders differs markedly from that of flat slabs or rough surfaces. The main differences are: (1) for incident angles α > 0° relative to the bulk normal, the escaping sputtering yield is dominated by backward-directed ejecta for all ion energies; (2) for α ≤ 60°, the yield peaks toward the ion-beam origin, similar to the opposition effect seen in optical observations of airless bodies; (3) the angular distribution peak is half or less than that of a flat slab; (4) as ion energy increases, no evolution occurs from primary to secondary knock-on sputtering in the ejecta angular distribution. We attribute these behaviors to the powder's interconnected voids. Ions penetrate these voids and sputter underlying grains; the ejecta then preferentially escape toward the ion-beam origin, where shadowing is minimal. We derive two fitting functions: (1) relating the escaping sputtering yield of a powder to that of a flat surface, depending only on porosity, incident angle, mean local incidence angle, and the corresponding flat slab yield; (2) providing the double-differential angular distribution of the escaping ejecta for porosities ≥0.49. These provide a potentially universal fitting function of the absolute doubly differential escaping sputtering yield from loose powders.
Restorative macrophage-derived RNAseT2 stimulates muscle stem cell fusion via an SLK/N-WASP/actin bundling dependent axis
Loss mechanisms in low-fiber H-shaped absorbers and multi-angle microwave absorption control via array density
To overcome the bottlenecks in achieving broadband absorption and thin-profile design for high-temperature absorber-load-bearing integrated fiber composites, this paper presents an in-depth study on H-shaped fiber array structures composed of carbon fibers and silicon carbide fibers. By integrating the minimal aperture method with equivalent medium theory, an accurate extraction model for the equivalent electromagnetic parameters of non-uniform structures was established, resolving the challenge of electromagnetic parameter inversion for traditional all-metal backplane structures. Using nonlinear fitting methods, the contributions of conduction loss and relaxation polarization loss to dielectric loss were quantitatively analyzed. Results indicate that in the X and Ku bands, relaxation polarization loss is dominant, accounting for 63.73% of the total loss. The carbon fiber skeleton primarily dissipates energy through eddy current effects and ohmic losses induced by high conductivity, while silicon carbide fibers contribute to relaxation polarization loss via interfacial dipole reorientation polarization. Furthermore, constructing a 2.5 mm uniform-thickness multilayer gradient stack structure effectively mitigates impedance mismatch and significantly broadens the absorption bandwidth. Notably, under 20° oblique incidence, absorption performance improved by 1.8 times, reaching −32.5 dB from −17.8 dB. The effective absorption bandwidth increased by 1.7 times, broadening from 4.66 to 7.83 GHz. With a fiber content of only 4.536%, this structure achieves high-efficiency broadband absorption within a 2.5 mm thickness.
Sphingosine-1-Phosphate-derived 2-Hexadecenal is a central mediator of ocular neovascularization by inhibiting Sphingosine-1-Phosphate receptor 5
Abstract Sphingosine-1-phosphate (S1P) is a crucial sphingolipid mediator in vasculature and neovascular eye diseases by controlling angiogenesis, inflammation and fibrosis. Five S1P receptors (S1PRs) are key therapeutic targets, with several S1PR-targeted drugs already in clinical use or trials. However, the vascular function of its major metabolic product, the reactive lipid aldehyde 2-hexadecenal (2-HD), remains unexplored. Here, we show that loss of the aldehyde dehydrogenase ALDH3B1 impairs 2-HD detoxification and leads to retinal vascular abnormalities in zebrafish, without affecting the trunk vasculature. Mechanistically, multi-omics analyses reveal that 2-HD accumulation disrupts iron homeostasis and induces ferroptosis by directly interacting with S1PR5. This finding is supported by integrative analyses of single-cell RNA sequencing and RNA sequencing from human neovascular retinal samples, identifying S1PR5 as a clinically relevant target. These findings uncover a previously unrecognized role of S1P derived 2-HD in vasculature and retinal vascular homeostasis, suggesting that targeting S1PR5 could offer a therapeutic strategy for diabetic retinopathy.
NO-driven etching behavior of SiO2 and Si3N4 in cryogenic NF3/NO plasmas
Gas composition and substrate temperature play key roles in governing surface reaction pathways and the etching behavior of dielectric films. In this study, the temperature- and composition-dependent etching characteristics of silicon dioxide and silicon nitride films were investigated in cryogenic NF3/NO plasmas, with the aim of clarifying how NO modulates material-dependent surface reactions. A range of observations revealed systematic variations in NO-, F-, and NOF-related species as functions of substrate temperature and gas composition. When the substrate temperature was reduced below 0 °C, the dominant reaction pathway of NO shifted from gas-phase reactions to processes dominated by surface reactions. Surface chemical analysis using x-ray photoelectron spectroscopy revealed distinct material-dependent responses under cryogenic conditions. For SiO2, lowering the substrate temperature promoted fluorine transfer reactions at the surface, consistent with enhanced chemical etching. In contrast, SiN exhibited increased surface trapping of NO- and NOF-related species, which suppressed the overall etching reaction under otherwise identical plasma conditions. These results demonstrate that NO acts as a reaction moderator whose influence depends on both the material type and the processing conditions. By correlating plasma diagnostics with surface chemical analysis, this work provides insight into non-polymer-based selective etching mechanisms in cryogenic NF3/NO plasmas and contributes to the understanding of process control strategies for high-aspect-ratio dielectric structures.
Experimental study on cavitation-induced micro-spallation in Sn under double explosively driven shock
The micro-spallation damage behavior of low-melting-point metals under double shock is a critical concern in advanced equipment design. However, there is currently a lack of detailed spatial distribution information on micro-spallation after the second shock. In this study, two experiments on tin under different loading paths were conducted using a double-shock apparatus with adjusted backing plates. In addition, the loading histories were accurately measured using photonic Doppler velocimetry and Asay window diagnostics. To overcome the limitation in conventional approaches for extracting spatial information from the Asay window, an innovative inversion method for the micro-spallation material impacting Asay windows in vacuum was proposed. A dedicated post-processing procedure was further implemented to reconstruct the corresponding spatial volume density distribution. Comparison of the reconstructed volume density distributions under different loading paths reveals a consistent increasing trend from the free surface toward the rear interface. However, the slopes of these trends differ, particularly in the region near the free surface. Further analysis indicated that the shorter time interval between the first and second shock and the stronger secondary loading affect the damage microstructure of the porous, cavitated regions, leading to a more extensive porous zone adjacent to the free surface. This study provides insights into the micro-spallation distribution under double-shock and serves as a foundation for further investigations.
Enhancement of high-frequency bulk acoustic wave resonator performance via rapid thermal annealing
The Mo electrode thickness in AlScN-based bulk acoustic wave (BAW) resonators is constrained to sub-100 nm to satisfy high-frequency operational requirements, leading to degraded electrical conductivity and increased electrical losses. In this work, the electrical properties of the Mo electrode were enhanced through rapid thermal annealing (RTA). The Mo films showed a 102.5% enhancement in electrical conductivity, attributed to improved crystalline quality and suppressed surface scattering. Furthermore, thermal annealing reduced the residual stress in the film and promoted in-plane atomic rearrangement, thereby enhancing the effective electromechanical coupling coefficient (keff2) and reducing acoustic losses in the resonators. As a result, the figure of merit of the device increased by approximately 46.5%, reaching 152 after the annealing process. Moreover, the influence of electrode conductivity on resonator performance was analyzed using finite-element analysis. This work presented a promising strategy—the RTA process—for enhancing the electrical properties of the Mo electrode and improving the performance of BAW filters at high operating frequencies.