Using artificial intelligence to document the hidden RNA virosphere.

Current metagenomic tools can fail to identify highly divergent RNA viruses. We developed a deep learning algorithm, termed LucaProt, to discover highly divergent RNA-dependent RNA polymerase (RdRP) sequences in 10,487 metatranscriptomes generated from diverse global ecosystems. LucaProt integrates both sequence and predicted structural information, enabling the accurate detection of RdRP sequences. Using this approach, we identified 161,979 potential RNA virus species and 180 RNA virus supergroups, including many previously poorly studied groups, as well as RNA virus genomes of exceptional length (up to 47,250 nucleotides) and genomic complexity. A subset of these novel RNA viruses was confirmed by RT-PCR and RNA/DNA sequencing. Newly discovered RNA viruses were present in diverse environments, including air, hot springs, and hydrothermal vents, with virus diversity and abundance varying substantially among ecosystems. This study advances virus discovery, highlights the scale of the virosphere, and provides computational tools to better document the global RNA virome.

Selenium-GPX4 axis protects follicular helper T cells from ferroptosis.

Follicular helper T (TFH) cells are a specialized subset of CD4+ T cells that essentially support germinal center responses where high-affinity and long-lived humoral immunity is generated. The regulation of TFH cell survival remains unclear. Here we report that TFH cells show intensified lipid peroxidation and altered mitochondrial morphology, resembling the features of ferroptosis, a form of programmed cell death that is driven by iron-dependent accumulation of lipid peroxidation. Glutathione peroxidase 4 (GPX4) is the major lipid peroxidation scavenger and is necessary for TFH cell survival. The deletion of GPX4 in T cells selectively abrogated TFH cells and germinal center responses in immunized mice. Selenium supplementation enhanced GPX4 expression in T cells, increased TFH cell numbers and promoted antibody responses in immunized mice and young adults after influenza vaccination. Our findings reveal the central role of the selenium-GPX4-ferroptosis axis in regulating TFH homeostasis, which can be targeted to enhance TFH cell function in infection and following vaccination.

Centrosome anchoring regulates progenitor properties and cortical formation.

Radial glial progenitor cells (RGPs) are the major neural progenitor cells that generate neurons and glia in the developing mammalian cerebral cortex1-4. In RGPs, the centrosome is positioned away from the nucleus at the apical surface of the ventricular zone of the cerebral cortex5-8. However, the molecular basis and precise function of this distinctive subcellular organization of the centrosome are largely unknown. Here we show in mice that anchoring of the centrosome to the apical membrane controls the mechanical properties of cortical RGPs, and consequently their mitotic behaviour and the size and formation of the cortex. The mother centriole in RGPs develops distal appendages that anchor it to the apical membrane. Selective removal of centrosomal protein 83 (CEP83) eliminates these distal appendages and disrupts the anchorage of the centrosome to the apical membrane, resulting in the disorganization of microtubules and stretching and stiffening of the apical membrane. The elimination of CEP83 also activates the mechanically sensitive yes-associated protein (YAP) and promotes the excessive proliferation of RGPs, together with a subsequent overproduction of intermediate progenitor cells, which leads to the formation of an enlarged cortex with abnormal folding. Simultaneous elimination of YAP suppresses the cortical enlargement and folding that is induced by the removal of CEP83. Together, these results indicate a previously unknown role of the centrosome in regulating the mechanical features of neural progenitor cells and the size and configuration of the mammalian cerebral cortex.

A dominant autoinflammatory disease caused by non-cleavable variants of RIPK1.

Activation of RIPK1 controls TNF-mediated apoptosis, necroptosis and inflammatory pathways1. Cleavage of human and mouse RIPK1 after residues D324 and D325, respectively, by caspase-8 separates the RIPK1 kinase domain from the intermediate and death domains. The D325A mutation in mouse RIPK1 leads to embryonic lethality during mouse development2,3. However, the functional importance of blocking caspase-8-mediated cleavage of RIPK1 on RIPK1 activation in humans is unknown. Here we identify two families with variants in RIPK1 (D324V and D324H) that lead to distinct symptoms of recurrent fevers and lymphadenopathy in an autosomal-dominant manner. Impaired cleavage of RIPK1 D324 variants by caspase-8 sensitized patients' peripheral blood mononuclear cells to RIPK1 activation, apoptosis and necroptosis induced by TNF. The patients showed strong RIPK1-dependent activation of inflammatory signalling pathways and overproduction of inflammatory cytokines and chemokines compared with unaffected controls. Furthermore, we show that expression of the RIPK1 mutants D325V or D325H in mouse embryonic fibroblasts confers not only increased sensitivity to RIPK1 activation-mediated apoptosis and necroptosis, but also induction of pro-inflammatory cytokines such as IL-6 and TNF. By contrast, patient-derived fibroblasts showed reduced expression of RIPK1 and downregulated production of reactive oxygen species, resulting in resistance to necroptosis and ferroptosis. Together, these data suggest that human non-cleavable RIPK1 variants promote activation of RIPK1, and lead to an autoinflammatory disease characterized by hypersensitivity to apoptosis and necroptosis and increased inflammatory response in peripheral blood mononuclear cells, as well as a compensatory mechanism to protect against several pro-death stimuli in fibroblasts.

Genetic adaptation of skin pigmentation in highland Tibetans.

Strong ultraviolet (UV) radiation at high altitude imposes a serious selective pressure, which may induce skin pigmentation adaptation of indigenous populations. We conducted skin pigmentation phenotyping and genome-wide analysis of Tibetans in order to understand the underlying mechanism of adaptation to UV radiation. We observe that Tibetans have darker baseline skin color compared with lowland Han Chinese, as well as an improved tanning ability, suggesting a two-level adaptation to boost their melanin production. A genome-wide search for the responsible genes identifies GNPAT showing strong signals of positive selection in Tibetans. An enhancer mutation (rs75356281) located in GNPAT intron 2 is enriched in Tibetans (58%) but rare in other world populations (0 to 18%). The adaptive allele of rs75356281 is associated with darker skin in Tibetans and, under UVB treatment, it displays higher enhancer activities compared with the wild-type allele in in vitro luciferase assays. Transcriptome analyses of gene-edited cells clearly show that with UVB treatment, the adaptive variant of GNPAT promotes melanin synthesis, likely through the interactions of CAT and ACAA1 in peroxisomes with other pigmentation genes, and they act synergistically, leading to an improved tanning ability in Tibetans for UV protection.

Selective Generation of V2 Silicon Vacancy Centers in 4H-Silicon Carbide.

The deterministic generation of individual color centers with defined orientations or types in solid-state systems is paramount for advancements in quantum technologies. Silicon vacancies in 4H-silicon carbide (4H-SiC) can be formed in V1 and V2 types. However, silicon vacancies are typically generated randomly between V1 and V2 types with similar probabilities. Here, we show that the preferred V2 centers can be selectively generated by focused ion beam (FIB) implantation on the m-plane in 4H-SiC. When implantation is on the m-plane (a-plane), the generation probability ratio between V1 and V2 centers increase exponentially (remains constant) with decreasing FIB fluences. With a fluence of 10 ions/spot, the probability to generate V2 centers is seven times higher than V1 centers. Our results represent a critical step toward the deterministic creation of specific defect types.

Fluorine Induced In Situ Formation of High Valent Nickel Species for Ultra Low Potential Electrooxidation of 5-Hydroxymethylfurfural.

The Nickel-based catalysts have a good catalytic effect on the 5-hydroxymethylfurfural electrooxidation reaction (HMFOR), but limited by the conversion potential of Ni2+ /Ni3+ , 1.35 V versus RHE, the HMF electrooxidation potential of nickel-based catalysts is generally greater than 1.35 V versus RHE. Considering fluorine has the highest Pauling electronegativity and similar atomic radius of oxygen, the introduction of fluorine into the lattice of metal oxides might promote the adsorption of intermediate species, thus improving the catalytic performance. F is successfully doped into the lattice structure of NiCo2 O4 spinel oxide by the strategy of hydrothermal reaction and low-temperature fluorination. As is confirmed by in situ electrochemical impedance spectroscopy and Raman spectroscopy, the introduction of F weakens the interaction force of metal-oxygen covalent bonds of the asymmetric MT -O-MO backbone and improves the valence of Ni in tetrahedra structure, which makes it easier to be oxidized to higher valence active Ni3+ under the action of electric field and promotes the adsorption of OH- , while the decrease of Co valence enhances the adsorption of HMF with the catalyst. Combining the above reasons, F-NiCo2 O4 shows superb electrocatalytic performance with a potential of only 1.297 V versus RHE at a current density of 20 mA cm-2 , which is lower than the most catalyst.

The miR-15b-5p/miR-379-3p-FOXO axis regulates cell cycle and apoptosis in scleral remodeling during experimental myopia.

BACKGROUND: Myopia is one of the most common eye diseases in children and adolescents worldwide, and scleral remodeling plays a role in myopia progression. However, the identity of the initiating factors and signaling pathways that induce myopia-associated scleral remodeling is still unclear. This study aimed to identify biomarkers of scleral remodeling to elucidate the pathogenesis of myopia. METHODS: The gene expression omnibus (GEO) and comparative toxicogenomics database (CTD) mining were used to identify the miRNA-mRNA regulatory network related to scleral remodeling in myopia. Real-time quantitative PCR (RT-qPCR), Western blot, immunofluorescence, H&E staining, Masson staining, and flow cytometry were used to detect the changes in the FOXO signaling pathway, fibrosis, apoptosis, cell cycle, and other related factors in scleral remodeling. RESULTS: miR-15b-5p/miR-379-3p can regulate the FOXO signaling pathway. Confirmatory studies confirmed that the axial length of the eye was significantly increased, the scleral thickness was thinner, the levels of miR-15b-5p, miR-379-3p, PTEN, p-PTEN, FOXO3a, cyclin-dependent kinase (CDK) inhibitor 1B (CDKN1B) were increased, and the levels of IGF1R were decreased in Len-induced myopia (LIM) group. CDK2, cyclin D1 (CCND1), and cell cycle block assessed by flow cytometry indicated G1/S cell cycle arrest in myopic sclera. The increase in BAX level and the decrease in BCL-2 level indicated enhanced apoptosis of the myopic sclera. In addition, we found that the levels of transforming growth factor-ß1 (TGF-ß1), collagen type 1 (COL-1), and α-smooth muscle actin (α-SMA) were decreased, suggesting scleral remodeling occurred in myopia. CONCLUSIONS: miR-15b-5p/miR-379-3p can regulate the scleral cell cycle and apoptosis through the IGF1R/PTEN/FOXO signaling pathway, thereby promoting scleral remodeling in myopia progression.

miR-92b-3p protects retinal tissues against DNA damage and apoptosis by targeting BTG2 in experimental myopia.

BACKGROUND: Myopia is one of the eye diseases that can damage the vision of young people. This study aimed to explore the protective role of miR-92b-3p against DNA damage and apoptosis in retinal tissues of negative lens-induced myopic (LIM) guinea pigs by targeting BTG2. METHODS: Biometric measurements of ocular parameters, flash electroretinogram (FERG), and retinal thickness (RT) were performed after miR-92b-3p intravitreal injection in LIM guinea pigs. The apoptotic rate was detected by Annexin V-FITC/PI double staining, and the change in mitochondrial membrane potential was measured by JC-1 staining. Retinal apoptosis and expression of p53, BTG2, and CDK2 were explored by TdT-mediated dUTP-biotin nick labeling (TUNEL) and immunofluorescence staining assays, respectively. BTG2 and its upstream and downstream molecules at gene and protein levels in retinal tissues were measured by real-time quantitative PCR (qPCR) and Western blotting. RESULTS: Compared with normal controls (NC), the ocular axial length of LIM guinea pig significantly increased, whereas refraction decreased. Meanwhile, dMax-a and -b wave amplitudes of ERG declined, retinal thickness was decreased, the number of apoptotic cells and apoptotic rate in LIM eyes was exaggerated, and the mitochondrial membrane potential significantly decreased. In addition, results of qPCR and Western blot assays showed that the expression levels of p53, BTG2, CDK2, and BAX in LIM guinea pigs were higher than the levels of the NC group, whereas the BCL-2 expression level was decreased. By contrast, the miR-92b-3p intravitreal injection in LIM guinea pigs could significantly inhibit axial elongation, alleviate DNA damage and apoptosis, and thus protect guinea pigs against myopia. CONCLUSION: In conclusion, p53 and BTG2 were activated in the retinal tissue of myopic guinea pigs, and the activated BTG2 could elevate the expression of CDK2 and BAX, and attenuate the expression of BCL-2, which in turn promote apoptosis and eventually lead to retinal thinning and impaired visual function in myopic guinea pigs. The miR-92b-3p intravitreal injection can attenuate the elongation of ocular length and retinal thickness, and inhibit the CDK2, BAX, and p53 expression by targeting BTG2, thereby ameliorating DNA damage and apoptosis in LIM guinea pigs and protecting ocular tissues.

Skin colour: A window into human phenotypic evolution and environmental adaptation.

As modern humans ventured out of Africa and dispersed around the world, they faced novel environmental challenges that led to geographic adaptations including skin colour. Over the long history of human evolution, skin colour has changed dramatically, showing tremendous diversity across different geographical regions, for example, the majority of individuals from the expansive lands of Africa have darker skin, whereas the majority of people from Eurasia exhibit lighter skin. What adaptations did lighter skin confer upon modern humans as they migrated from Africa to Eurasia? What genetic mechanisms underlie the diversity of skin colour observed in different populations? In recent years, scientists have gradually gained a deeper understanding of the interactions between pigmentation gene and skin colour through population-based genomic studies of different groups around the world, particularly in East Asia and Africa. In this review, we summarize our current understanding of 26 skin colour-related pigmentation genes and 48 SNPs that influence skin colour. Important pigmentation genes across three major populations are described in detail: MFSD12, SLC24A5, PDPK1 and DDB1/CYB561A3/TMEM138 influence skin colour in African populations; OCA2, KITLG, SLC24A2, GNPAT and PAH are key to the evolution of skin pigmentation in East Asian populations; and SLC24A5, SLC45A2, TYR, TYRP1, ASIP, MC1R and IRF4 significantly contribute to the lightening of skin colour in European populations. We summarized recent findings in genomic studies of skin colour in populations that implicate diverse geographic environments, local adaptation among populations, gene flow and multi-gene interactions as factors influencing skin colour diversity.

A Solar Evaporator Based on Polypyrrole Coated 3D Carbon Nanotube Materials for Efficient Solar-Driven Vapor Generation.

Highly porous light absorbers are fabricated based on polypyrrole (PPy)-coated carbon nanotube (CNT). Carbon nanotube sponge (CNTS) or carbon nanotube array (CNTA) with three-dimensional (3D) network structure is the framework of porous light absorbers. Both PPy@CNTS and PPy@CNTA composites exhibit excellent light absorption of the full solar spectrum. The CNTS and CNTA with porous structures have extremely large effective surface area for light absorption and for water evaporation that has great practical benefit to the solar-driven vapor generation. The PPy layer on CNT sidewalls significantly improves the hydrophilicity of porous CNTS and CNTA. The good wettability of water on CNT sidewalls makes water transport in porous CNT materials highly efficient. The PPy@CNTS and PPy@CNTA light absorbers achieve high water evaporation rates of 3.35 and 3.41 kg m-2 h-1, respectively, under 1-sun radiation. The orientation of nano channels in CNTA-based light absorbers also plays an important role in the solar-driven vapor generation. The water transport and vapor escape are more efficient in CNTA-based light absorbers as compared to the CNTS-based light absorbers due to the relatively short path for the water transport and the vapor escape in CNTA-based light absorbers.

Clinical Implications of a New DDX58 Pathogenic Variant That Causes Lupus Nephritis due to RIG-I Hyperactivation.

BACKGROUND: Lupus nephritis (LN) is one of the most severe complications of systemic lupus erythematosus, with heterogeneous phenotypes and different responses to therapy. Identifying genetic causes of LN can facilitate more individual treatment strategies. METHODS: We performed whole-exome sequencing in a cohort of Chinese patients with LN and identified variants of a disease-causing gene. Extensive biochemical, immunologic, and functional analyses assessed the effect of the variant on type I IFN signaling. We further investigated the effectiveness of targeted therapy using single-cell RNA sequencing. RESULTS: We identified a novel DDX58 pathogenic variant, R109C, in five unrelated families with LN. The DDX58 R109C variant is a gain-of-function mutation, elevating type I IFN signaling due to reduced autoinhibition, which leads to RIG-I hyperactivation, increased RIG-I K63 ubiquitination, and MAVS aggregation. Transcriptome analysis revealed an increased IFN signature in patient monocytes. Initiation of JAK inhibitor therapy (baricitinib 2 mg/d) effectively suppressed the IFN signal in one patient. CONCLUSIONS: A novel DDX58 R109C variant that can cause LN connects IFNopathy and LN, suggesting targeted therapy on the basis of pathogenicity. PODCAST: This article contains a podcast at.

Integrated Communication, Sensing, and Computation Framework for 6G Networks.

In the sixth generation (6G) era, intelligent machine network (IMN) applications, such as intelligent transportation, require collaborative machines with communication, sensing, and computation (CSC) capabilities. This article proposes an integrated communication, sensing, and computation (ICSAC) framework for 6G to achieve the reciprocity among CSC functions to enhance the reliability and latency of communication, accuracy and timeliness of sensing information acquisition, and privacy and security of computing to realize the IMN applications. Specifically, the sensing and communication functions can merge into unified platforms using the same transmit signals, and the acquired real-time sensing information can be exploited as prior information for intelligent algorithms to enhance the performance of communication networks. This is called the computing-empowered integrated sensing and communications (ISAC) reciprocity. Such reciprocity can further improve the performance of distributed computation with the assistance of networked sensing capability, which is named the sensing-empowered integrated communications and computation (ICAC) reciprocity. The above ISAC and ICAC reciprocities can enhance each other iteratively and finally lead to the ICSAC reciprocity. To achieve these reciprocities, we explore the potential enabling technologies for the ICSAC framework. Finally, we present the evaluation results of crucial enabling technologies to show the feasibility of the ICSAC framework.

An energy-efficient solution to sludge drying and combustion process through Camellia oleifera shells amended foaming.

Foaming pretreatment has been proven effective in promoting sludge drying, however, the variation in sludge properties significantly influences the foaming efficiency. Inspired by foam stabilizer of solid particles, Camellia oleifera shells (COS) was screened out from various biomasses as an additive incorporated with the CaO for promoting the sludge foaming. For the introduction of COS, this study analyzed the drying behaviors of foamed sludge, quantified the surface cracks information, characterized the combustion performance, and evaluated the energy consumption. The results indicated that 46.72-50.10% of time could be saved in foaming the sludge to 0.70 g/mL by addition of 3.0 wt% COS. Compared with the original sludge (OS), the 0.70 g/mL foamed sludge saved 47.43% of time for sludge drying at 80 °C, and this value further increased to 53.14% with 3.0 wt% COS addition. Combining the multifractal spectra and drying kinetics analysis, the foaming promoted the formation of complex surface cracks in the warm-up period, while COS further improved the complexity of cracks in the constant rate period, and the shrinkage of isolated sludge blocks in the falling rate period, thus enhanced the moisture diffusion and heat transfer. Furthermore, the appropriate porous structure and additional volatile matters promoted the combustion performance. The 0.90 g/mL foamed sludge with COS presented the lowest activation energy of 180.362 kJ/mol in combustion. Overall, compared with OS, the 0.70 g/mL foamed sludge with COS saved 40.65% energy consumption during the foaming, drying and combustion processes, providing an energy-efficient solution for the sludge treatment and disposal.

A Joint Communication and Computation Design for Probabilistic Semantic Communications.

In this paper, the problem of joint transmission and computation resource allocation for a multi-user probabilistic semantic communication (PSC) network is investigated. In the considered model, users employ semantic information extraction techniques to compress their large-sized data before transmitting them to a multi-antenna base station (BS). Our model represents large-sized data through substantial knowledge graphs, utilizing shared probability graphs between the users and the BS for efficient semantic compression. The resource allocation problem is formulated as an optimization problem with the objective of maximizing the sum of the equivalent rate of all users, considering the total power budget and semantic resource limit constraints. The computation load considered in the PSC network is formulated as a non-smooth piecewise function with respect to the semantic compression ratio. To tackle this non-convex non-smooth optimization challenge, a three-stage algorithm is proposed, where the solutions for the received beamforming matrix of the BS, the transmit power of each user, and the semantic compression ratio of each user are obtained stage by stage. The numerical results validate the effectiveness of our proposed scheme.

Intermolecular Hydrogen Bonding Networks Stabilized Organic Supramolecular Cathode for Ultra-High Capacity and Ultra-Long Cycle Life Rechargeable Aluminum Batteries.

Rechargeable aluminum batteries (RABs) are a promising candidate for large-scale energy storage, attributing to the abundant reserves, low cost, intrinsic safety, and high theoretical capacity of Al. However, the cathode materials reported thus far still face challenges such as limited capacity, sluggish kinetics, and undesirable cycle life. Herein, we propose an organic cathode benzo[i] benzo[6,7] quinoxalino [2,3-a] benzo [6,7] quinoxalino [2,3-c] phenazine-5,8,13,16,21,24-hexaone (BQQPH) for RABs. The six C=O and six C=N redox active sites in each molecule enable BQQPH to deliver a record ultra-high capacity of 413 mAh g-1 at 0.2 A g-1. Encouragingly, the intermolecular hydrogen bonding network and π-π stacking interactions endow BQQPH with robust structural stability and minimal solubility, enabling an ultra-long lifetime of 100,000 cycles. Moreover, the electron-withdrawing carbonyl group induces a reduction in the energy level of the lowest unoccupied molecular orbital and expands the π-conjugated system, which considerably enhances both the discharge voltage and redox kinetics of BQQPH. In situ and ex situ characterizations combined with theoretical calculations unveil that the charge storage mechanism is reversible coordination/dissociation of AlCl2 + with the N and O sites in BQQPH accompanied by 12-electron transfer. This work provides valuable insights into the design of high-performance organic cathode materials for RABs.

Operando Forming of Lattice Vacancy Defect in Ultrathin Crumpled NiVW-Layered Metal Hydroxides Nanosheets for Valorization of Biomass.

The 2D layered metal hydroxides (LMHs) have been developed for electrooxidation of 5-hydroxymethylfurfural (HMF). In this work, an effective strategy is proposed to tailor the electronic structure of active sites at the atomic level, which is by introducing defects into the lattice structure. As an example, a series of ultrathin crumpled ternary NiVW-LMH electrocatalysts with abundant lattice vacancies (denoted as NiVWv -LMH) are prepared in this way. The introduction of tungsten (W) endows the catalyst with a special crumpled structure, which promotes the generation of lattice vacancies and thus exposes more unsaturated Ni activity sites. The NiVWv -LMH displays superb performance in the electrooxidation of HMF. The Tafel slope for electrodehydrogenation of Ni2+ OH bond to Ni(OH)O species is 12.04 mV dec-1 . The current density at 1.43 V versus reversible hydrogen electrode (RHE) toward the oxidation reaction of HMF reaches about 193 mA cm-2 , which is better than most of the common electrocatalysts, with an 5.37-fold improvement compared with Ni(OH)2 electrode. The preparation strategy demonstrates in this work can be useful for developing highly efficient electrocatalysts.

Orbital angular momentum spectra of twisted Laguerre-Gaussian Schell-model beams propagating in weak-to-strong Kolmogorov atmospheric turbulence.

The presence of atmospheric turbulence in a beam propagation path results in the spread of orbital angular momentum (OAM) modes of laser beams, limiting the performance of free-space optical communications with the utility of vortex beams. The knowledge of the effects of turbulence on the OAM spectrum (also named as spiral spectrum) is thus of utmost importance. However, most of the existing studies considering this effect are limited to the weak turbulence that is modeled as a random complex "screen" in the receiver plane. In this paper, the behavior of the OAM spectra of twisted Laguerre-Gaussian Schell-model (TLGSM) beams propagation through anisotropic Kolmogorov atmospheric turbulence is examined based on the extended Huygens-Fresnel integral which is considered to be applicable in weak-to-strong turbulence. The discrepancies of the OAM spectra between weak and strong turbulence are studied comparatively. The influences of the twist phase and the anisotropy of turbulence on the OAM spectra during propagation are investigated through numerical examples. Our results reveal that the twist phase plays a crucial role in determining the OAM spectra in turbulence, resisting the degeneration of the detection mode weight by appropriately choosing the twist factor, while the effects of the anisotropic factors of turbulence on the OAM spectra seem to be not obvious. Our findings can be applied to the analysis of OAM spectra of laser beams both in weak and strong turbulence.