Search Results (2,239)

Jurassic–Cretaceous marine–continental carbonate–evaporitic sequences in the Neuquén Basin of Argentina host numerous stratabound Ba–Sr deposits. Mineralization (Sr–barite, Ba–celestine, and minor Pb–Zn–Cu–Fe sulphides) occurs as bedding parallel lenses and crosscutting veins. The stratiform mineralization is formed by replacements of carbonate and gypsum beds and often exhibits typical zebra textures. Dissolution processes associated with Neogene regional uplift produced karstic cavities where a new generation of barite was deposited. Regionally, W to E distribution of carbonates/evaporites and that of Ba–Sr deposits is coincidental. Lower Cretaceous Sr–Ba deposits are spatially related to large N-S reverse faulting, frequently limited to the eastern limb of the folded structures. Average δ¹⁸O and δ³⁴S of stratiform and crosscutting vetiform mineralization do not differ significantly, suggesting a common source of sulphate and cations. Deposits spatially linked to areas with magmatic activity and those that are not have similar isotopic values, compatible with bacterial and/or thermochemical reduction of contemporaneous seawater sulphate, although sulphides only occur in deposits with evidence of nearby magmatic activity. Thermal convection of basinal brines leached metals from the Mesozoic sedimentary pile; Ba and Sr were extracted from siliciclastic and carbonate rocks, and sulphur from evaporite layers. Fluids related to Tertiary magmatism helped producing an epithermal mineral association composed of barite, quartz, adularia, and minor sulphides/sulphosalts hosted by veins. Arroyo Nuevo mine (Ba) is different, as it seems to be the product of hydrothermal SedEx deposition onto the anoxic seafloor. Full article

We have developed a tool that allows us to easily visualize evolutionary variation via complementary multiple sequence alignments and frequency-based stacked Sequence Logos. This tool, TOTEMS (hisTogram of evOluTionarily consErved aMino acidS), visualizes conserved regions in a multiple sequence alignment within regions of a three-dimensional structure that share similar degrees of evolutionary conservation as revealed in ConSurf output data. Unlike Sequence Logos that illustrate the relative frequency of individual amino acid residues (as in MSAViewer), or moving window averages that focus on properties such as hydrophobicity or electrical charge (as in CATH), TOTEMS can help users discriminate degrees of evolutionary conservation in adjacent positions within a three-dimensional structure. Thus, we offer a tool that serves to complement pre-existing visualization applications such as ConSurf, MSAViewer, and CATH. TOTEMS and its source code are freely available. Full article

Quantum biology is a multidiscipline which analyses possible critical aspects of life that could be based on the macroscopic expression of quantum phenomena. The high efficiency of light energy harvesting in green sulfur bacteria during photosynthesis is associated with entanglement and tunneling effects in the Fenna–Mathew–Olson complex. This has been studied to assess itscontribution, when conducting the light energy captured by the chlorosome, to the reaction center, where it is transformed into chemical energy. This work analyses, in the quantum domain, the coherence and entanglement between those two components associated with a general non-localized absorption spectrum in the pigments serving as input antennas. This study first imposes a more symmetric structure on the absorption spectrum, revealing certain relations which, when it is partially broken and parametrized on the most feasible pigments, displays a characteristic spectrum associated with the nature of the bacteria studied, in terms of their habitat and evolutionary survival. Finally, a brief insight analysis of similarities and differences in the protein sequence of the complex is conducted to trace possible traits relating them to some of the previous quantum features and suggesting some responsible positions within the FMO protein sequence. Full article

Fowl adenoviruses are opportunistic emerging viruses that spread widely in fowls, infecting birds of all ages, including young broiler chicks. This study aims to genotype the current adenovirus strains associated with inclusion body hepatitis hydropericardium syndrome (IBH-HPS) among infected broilers in Upper Egypt and to evaluate their pathogenic features. In 2024, 100 tissue samples were collected across Assiut and Sohag governorates in Upper Egypt for genetic characterization and pathogenicity evaluation. FAdVs were detected in 22% (11/50) of flocks. Typical FAdV lesions of dead embryos were observed after seven days post egg inoculation. Regarding the PCR assay of the hexon gene, only 8 of 30 samples were confirmed positive at 897 bp, yielding a 26.6% positivity rate. The remaining samples were considered negative using established RT-qPCR protocols for other viral pathogens. Partial sequencing of the hexon gene revealed that FAdV isolates (n = 4) clustered within FAdV species-D serotype 2/11, as determined by phylogenetic analysis. The four isolates shared (98–99%) and (94–100%) nucleotide and amino-acid similarities to FAdV-D of Israeli strains (2019–2020) and contemporary Egyptian isolates (2022), respectively, and low genetic divergence (54–81%) in comparison with other documented species. The amino acid sequence alignment and 3D structure indicate that the four immunogenic HVRs are located in the L1 region of the hexon protein, and that the highly conserved ⁹¹GQMTT⁹⁵, a specific region for FAdV-D serotype 2/11, is present. Regarding pathogenicity, the gross and histopathological findings observed clearly demonstrate the systemic pathogenicity of FAdV-2/11 in the infected group, with a final mortality rate of 30% at seven days post-infection (dpi). The FAdV DNA in hepatic tissues and cloacal swabs was confirmed by the PCR method at 3 dpi and 5 dpi. These results emphasize the circulating of FAdV-2/11 species D in Upper Egypt and highlight the significant need for a single inactivated vaccine that effectively targets the relevant FAdV serotypes to achieve broader and more efficient protection. Full article

Trollius chinensis Bunge (TCB), a perennial Ranunculaceae herb, produces Flos Trollii-dried flowers with medicinal properties including heat clearing, detoxification, and relieving oral/throat discomfort, eye pain, and cold-induced fever. TCB is mainly cultivated in northern China, while Trollius ledebouri Rchb. (TLR), distributed in Heilongjiang’s Great Xing’an Mountains, is morphologically similar to TCB. However, their regulatory statuses are inconsistent, and comprehensive comparative studies are lacking. This study adopted morphological assessment, microscopy, DNA barcoding, and physicochemical analysis to explore whether TLR could be a potential alternative source of Flos Trollii. Key differences were identified: TLR’s sepals are shorter than petals, whereas TCB’s sepals and petals are nearly equal in length; TLR has brown secretory structures absent in TCB. Genetic distance analysis showed high conservation in ITS2 and trnL-trnF sequences between the two species, but psbA-trnH sequence divergence exceeded the 0.05 threshold. HPLC quantification revealed that TLR contained slightly higher levels of orientin and vitexin than TCB. HPLC quantification revealed that TLR contained slightly higher levels of orientin (5.370–5.377 mg/g) and vitexin (1.954–2.053 mg/g) compared to TCB (orientin: 4.493–4.620 mg/g; vitexin: 1.361–1.451 mg/g). Collectively, TLR exhibits comparable flavonoid content and holds potential as an alternative Flos Trollii source. Given the limited bioactive compounds analyzed, future research should conduct comprehensive metabolomic profiling to fully evaluate its phytochemical composition and medicinal value. These data establish chemotaxonomic markers for Trollius authentication in herbal medicine. Full article

Recent advances in artificial intelligence have made power efficiency a primary objective in system design. In this context, stochastic computing (SC), which processes probabilistic bitstreams using simple logic, and spiking neural networks (SNNs), a neuromorphic paradigm, have gained prominence as alternative approaches. This study proposes a Stochastic Computing Neural Network (SC-NN) framework that minimizes the intrinsic errors of stochastic computing and leverages the isomorphism between one-count operations on bitstreams and spike-rate computations in spiking neural networks, yielding improvements in accuracy and hardware efficiency. In contrast to earlier studies that utilized independent random number sequences of 10 bits or higher, our study employed a practically implementable 8-bit linear feedback shift Register (LFSR)-based pseudo-random bitstream. Using 4 taps and 255 seeds improves the realism of the hardware. Despite the inherent accuracy ceiling of pseudo-random sequences, the proposed method achieves higher accuracy. Applied to an 8-bit SC-based neural network accelerator, the proposed design improves accuracy by 35% over a conventional FSM baseline, while reducing power and area by 43.8% and 17.2%, respectively, and decreasing delay by 5.5%. These improvements translate to a 2.3× enhancement in the Figure of Merit (FoM), which was further verified through physical layout and FPGA results. Overall, this work introduces a new paradigm that enables simultaneous gains in accuracy and efficiency for low-power AI by suppressing the error sources and embedding the structural similarity between SNNs and SC into the design. Full article

Sex differences in gut microbiota may affect health and aging, but evidence in elderly populations is limited and inconsistent. This study examined sex-specific similarities and differences in gut microbiota diversity and composition among apparently healthy elderly Japanese individuals using shotgun metagenomic sequencing. A cross-sectional study was conducted in 100 community-dwelling adults aged 75–83 years (54 males, 46 females). Fecal samples underwent metagenomic sequencing. Alpha and beta diversity were assessed across six taxonomic levels, and taxonomic differences were evaluated using non-parametric tests. No significant sex differences were observed in alpha diversity indices (Shannon, Simpson, evenness, Chao1) at any taxonomic level. Beta diversity based on Bray–Curtis dissimilarity and PCoA also showed no sex-specific clustering. However, certain taxa differed in relative abundance. Males showed higher abundances of Bacteroidota (phylum), Bacteroidia and Betaproteobacteria (class), and Bacteroidales and Burkholderiales (order) (p < 0.05). No significant differences were detected at the family, genus, or species levels. Overall, gut microbial diversity and community structure were largely similar between elderly males and females, with only modest sex-associated differences at higher taxonomic levels. These findings suggest that biological sex may have a limited influence on gut microbiota composition in advanced age and provide population-level reference data for future longitudinal and interventional studies in elderly cohorts. Full article

Background: The body maintains homeostasis by inflammation, and arthritis is related to autoimmunity or inflammation. Angiogenesis contributes to synovitis through angiogenic factors and proteolytic enzymes, while different inflammatory arthritis conditions, such as osteoarthritis and rheumatoid arthritis, share similar cytokine networks and immune cell populations. Notably, progressive joint damage can occur despite effective systemic immunosuppression, suggesting that local stromal–immune interactions within the joint microenvironment may sustain inflammation and tissue destruction. Methods: We conducted an exploratory single-cell RNA-sequencing analysis using publicly available datasets from the NCBI GEO database, including synovial tissue and synovial fluid samples. Cell–cell communication and transcriptional regulatory networks were inferred using CellChat and SCENIC. Results: Computational analyses suggested that, in RA, macrophage-associated signaling shifts from TNF-related pathways toward SPP1-associated patterns, coinciding with transcriptional features of MMP3⁺ fibroblast-like synoviocytes (FLS). FLS–FLS interactions were associated with FGF-related signaling across disease contexts. ANGPTL-related signaling patterns differed among arthritis subtypes, with ANGPTL4 more prominent in OA and PsA and ANGPTL2 more frequently in RA-related transcriptional programs. Conclusions: These findings provide an exploratory framework for stromal–immune interactions and ANGPTL-associated signaling across inflammatory arthritis. The therapies for PsA may focus on systemic immune modulation and preservation of joint structural integrity. For OA and RA, the highlight may target ANGPTL4 and ANGPTL2 in the early and late stages of disease progression. Given the reliance on computational inference, the results warrant further experimental validation. Full article

Multidrug-resistant Pseudomonas aeruginosa is a major cause of healthcare-associated infections, particularly in high-burden clinical settings where rapid tools to capture clinically relevant resistance and virulence phenotypes are needed. In this study, we applied an integrated whole-genome sequencing (WGS) and Fourier-transform infrared (FTIR) spectroscopy approach to evaluate genotype–phenotype relationships in multidrug-resistant P. aeruginosa isolates collected during the COVID-19 pandemic. High-quality WGS data were used to characterize antimicrobial resistance determinants, mobile genetic elements, and virulence gene repertoires, while FTIR spectroscopy provided culture-based phenotypic fingerprints reflecting cell envelope composition. Genomic analyses revealed a conserved efflux-centered intrinsic resistance backbone, variably supplemented by acquired β-lactamases and aminoglycoside-modifying enzymes, alongside a largely conserved core virulome with heterogeneity driven primarily by type III secretion system effector profiles. Comparison of FTIR- and WGS-derived distance matrices revealed a weak but statistically significant global association, indicating a non-linear relationship between genomic relatedness and phenotypic similarity. Cluster-level concordance was strongly scale-dependent, with high agreement emerging only at finer clustering resolutions, consistent with FTIR capturing phenotypic variation linked to regulatory, metabolic, and cell envelope adaptations rather than deep phylogenetic structure. Together, these findings show that multidrug resistance and virulence in P. aeruginosa are shaped by a modular genomic architecture that manifests as distinct, measurable phenotypic states. The observed scale-dependent concordance supports FTIR spectroscopy as a rapid, cost-effective phenotypic screening tool for outbreak-oriented surveillance, complementing WGS in integrated antimicrobial resistance monitoring workflows. Full article

The protein kinase N family belongs to the AGC kinase group and contains three isozymes: PKN1, PKN2, and PKN3. Catalytic domains of PKNs share high sequence similarity, yet the proteins differ in tissue distribution, functions, and involvement in pathological processes. In particular, PKN3 has been implicated in tumor growth and metastatic progression, highlighting the need for isozyme-selective inhibitors as both research tools and therapeutic leads. Here, we report the rational design of selective PKN3 inhibitors based on distinctive structural features of this kinase. Two strategies were applied. First, the smaller threonine gatekeeper residue unique to PKN3 within the AGC group was exploited by derivatization of N-(2-aminoethyl)isoquinoline-5-sulfonamide (H-9) at position C8. Among the resulting compounds, a phenylamino-substituted derivative displayed the highest affinity, with a dissociation constant (K_D) of 23 nM and more than 1000-fold selectivity over protein kinase A. Second, bisubstrate-analog design was employed to enhance binding to basophilic AGC kinases through covalent attachment of a (d-Arg)₃-containing chain to H-9 derivatives. This approach yielded ARC-2603, which bound PKN3 with a K_D value of 0.2 nM and showed 5500-fold selectivity over PKAcα. The selectivity of ARC-2603 was further evaluated in a commercial panel of 397 protein kinases, which supported its utility as a highly selective PKN3 inhibitor. Full article

Identifying structurally similar ligand-binding sites in unrelated proteins can facilitate drug repurposing, reveal off-target effects, and deepen our understanding of protein function. A number of tools were developed for structural screening, but many of them suffer from limited sensitivity and scalability. Using a data bank of crystallized protein structures, we aimed to discover novel protein targets for a ligand by leveraging a known ligand-binding query protein with a resolved structure. Here, we present SLAM (Spacio-Linear Alignment of Macromolecules), a novel alignment-based algorithm that detects local 3D similarities between ligand-binding cavities or protein-exposed surfaces of query and target proteins. SLAM encodes spatial substructure neighborhoods into short linear sequences of physicochemically annotated atoms, then applies pairwise sequence alignment combined with distance-correlation scoring to identify high-fidelity structural matches. Benchmarking using the Kahraman-36 dataset demonstrated that SLAM outperforms the state-of-the-art ProBiS algorithm in true-positive rate for predicting ligand-docking compatibility. Furthermore, SLAM identifies candidate ligands that may inhibit functionally critical domains of CRISPR-Cas proteins and predicts novel binding partners of toxic per- and polyfluoroalkyl Substance (PFAS) compounds (PFOA, PFOS) with plausible mechanistic links to toxicity. In conclusion, SLAM is a robust computationally efficient and flexible structural screening tool capable of detecting subtle physicochemical compatibilities between protein surfaces, promising to accelerate target discovery in pharmacology and elucidate protein–ligand interactions in environmental toxicology. Full article

Radar image extrapolation serves as a fundamental methodology in meteorological forecasting, facilitating precise short-term weather prediction through spatiotemporal sequence analysis. Conventional approaches remain constrained by progressive image degradation and artifacts, substantially limiting operational forecasting reliability. This research introduces E-HEOA—an enhanced deep learning architecture with integrated hyperparameter optimization. Our framework incorporates two fundamental innovations: (a) a hybrid metaheuristic optimizer merging a Gaussian-mutated ESOA and Cauchy-mutated HEOA for autonomous learning rate and dropout optimization and (b) embedded ConvLSTM2D modules for enhanced spatiotemporal feature preservation. Experimental validation on 170,000 radar echo samples demonstrates superior performance, demonstrating considerable enhancement in almost all aspects relative to the baseline model while establishing new state-of-the-art benchmarks in prediction fidelity, convergence efficiency, and structural similarity metrics. Full article

The yak represents a distinct domestic animal species that predominantly inhabits the Qinghai–Tibet Plateau and adjacent areas, possessing considerable value in both scientific and economic contexts. Compared to animals that mainly dwell on plains, such as cattle, the sperm maturation process in yak exhibits a certain degree of species specificity to adapt to their unique reproductive needs in high-altitude environments. Serving as the main storage site for functionally competent sperm, the cauda epididymis plays an integral role in mediating their post-testicular maturation. MiRNAs are vital regulatory molecules in the epididymis, influencing sperm maturation by modulating gene expression after transcription. To investigate the unique regulatory mechanisms of sperm maturation in yak, this study compared the miRNA expression profiles in the cauda epididymis of yak and cattle using high-throughput small RNA (sRNA) sequencing. The comparative analysis identified and characterized sRNA populations in the cauda epididymis of yak and cattle, revealing a similar length distribution that peaked at 22 nt and a predominance of known miRNAs. Notably, eight miRNAs were found to be highly expressed in both species. Furthermore, the first-nucleotide bias differed significantly between known and novel miRNAs within each species. A total of 31 differentially expressed (DE) miRNAs were identified, with 11 upregulated and 20 downregulated in yak compared to cattle. Among these, bta-miR-1298 exhibited the most significant upregulation, while bta-miR-2344 displayed the most pronounced downregulation. Bioinformatic analysis linked the predicted target genes of these miRNAs to numerous critical signaling pathways, including calcium signaling, the mitogen-activated protein kinase (MAPK) signaling pathway, the Ras-associated protein 1 (Rap1) signaling pathway, and the cyclic guanosine monophosphate-protein kinase G (cGMP-PKG) signaling pathway. Furthermore, eight significantly DE miRNAs, including bta-miR-2443, bta-miR-503-3p, bta-miR-6517, bta-miR-2440, bta-miR-2431-3p, bta-miR-2436-3p, bta-miR-6523a, and bta-miR-6775, were predicted to target genes involved in various aspects of sperm structural and functional maturation. These aspects include flagellum formation, sperm motility, chromatin remodeling, acrosome reaction, acrosome structure, sperm capacitation, chemotaxis, and nuclear chromatin condensation. Multiple miRNAs and their corresponding predicted target genes were analyzed by quantitative real-time PCR (qPCR), demonstrating an inverse correlation between miRNA expression and target gene levels. These findings reveal a distinct, species-specific miRNA signature in the yak cauda epididymis, which suggests a potential contribution to regulating the epididymal luminal environment and the process of sperm maturation. This study provides preliminary foundational data for elucidating the differences in sperm maturation mechanisms between yak and cattle, and offers potential novel targets for improving reproductive efficiency in plateau livestock. Full article

Illumina sequencing of segment 2, which encodes the polymerase basic subunit 2 (PB2) of the RNA-dependent RNA polymerase of a divergent amnoonvirus recently detected in tissues of Nile tilapia farmed in Egypt, revealed the presence of two genetic variants of the same virus: AmnoonvirusEGY1F and -H. The phylogenetic and genetic analyses presented in this study support the inclusion of both variants in the genus Tilapinevirus, family Amnoonviridae, order Articulavirales. The Egyptian strains formed distinct, well-supported clades in both nucleotide- and amino acid-based trees, showing a notable divergence from unclassified amnoonviruses and clustered with members of the genus Tilapinevirus. Within the genus Tilapinevirus, both Egyptian strains were divergent from all tilapia lake virus (TiLV) strains, whose full RNA segment 2 sequences are available in public databases, as well as the newly isolated Tilapinevirus poikilos from the fancy-tailed guppy. The Egyptian strains were also divergent from TiLV strains identified in Israel and Lake Victoria. Although the PB2 proteins of AmnoonvirusEGY1F and -H exhibited striking similarity, several mutations were detected that altered the sequence of their antigenic cell epitopes. Some of these mutations in the AmnoonvirusEGY1H strain were predicted to affect PB2-encoded functions. Collectively, findings of this study aid in the growing understanding of viral diversity and PB2 evolution in emerging amnoonviruses, particularly the role of amino acid substitutions in affecting the encoded protein structure, function, and immunogenicity. Full article

Primula beesiana is a perennial herbaceous plant predominantly distributed in the alpine wetland regions of Yunnan Province, China. This species faces dual threats from habitat fragmentation and climate change, but research into its genetic background is severely lacking. Consequently, systematic analysis of the genetic diversity and population structure of Primula beesiana is crucial in formulating scientific conservation strategies. In this study, 86 individuals from six natural populations in Lijiang City, Yunnan Province, were collected and genotyped using double-digest restriction site-associated DNA sequencing (ddRAD-seq). A total of 1537 high-quality SNP loci were identified and used for genetic diversity, principal component (PCA), population structure (STRUCTURE), and gene flow analyses. Analysis of base substitutions revealed twelve mutation types, with transversions accounting for 67.9% and a transition/transversion ratio (Ti/Tv) of 0.47, potentially indicating strong environmental selection pressure. Although high overall genetic diversity was observed, significant genetic differentiation may exist among populations (Fst = 0.0056-0.0407), with heterozygote deficiency detected across all populations. Genetic structure analyses consistently grouped the six populations into four distinct clusters. Populations MDJ, WH, and HS each formed independent clusters, exhibiting clear genetic isolation, whereas XHC2, XHC1, and NX clustered together, showing high genetic similarity and frequent gene flow. Mantel tests demonstrated a significant positive correlation between genetic and geographical distances (r = 0.854, p < 0.01), supporting an isolation-by-distance model. Gene flow estimates varied considerably among populations (5.90-44.69) and decreased with increasing geographical distance. This study provides the first genomic-level evidence of significant genetic differentiation and isolation based on distance in Primula beesiana populations, offering crucial scientific support in identifying evolutionarily significant units and developing zoned conservation management strategies for this species. Full article