Search Results (2,384)

Recent developments in next-generation sequencing technology have led to the creation of extensive, open-source protein databases consisting of hundreds of millions of sequences. To render these sequences applicable in biomedical applications, they must be meticulously annotated by wet lab testing or extracting them from existing literature. Over the last few years, researchers have developed numerous automatic annotation systems, particularly deep learning models based on machine learning and artificial intelligence, to address this issue. In this work, we propose a transformer-based fusion model capable of predicting Gene Ontology (GO) terms from full-scale protein sequences, achieving state-of-the-art accuracy compared to other contemporary machine learning annotation systems. The approach performs particularly well on clustered split datasets, which comprise training and testing samples originating from distinct distributions that are structurally diverse. This demonstrates that the model is able to understand both short and long term dependencies within the protein’s structure and can capture sequence features that are predictive of the various GO terms. Furthermore, the technique is lightweight and less computationally expensive compared to the benchmark methods, while at the same time unaffected by sequence length, rendering it appropriate for diverse applications with varying sequence lengths. Full article

Unmanned surface vehicles (USVs) rely on multi-sensor perception, such as radar, LiDAR, GPS, and vision, to ensure safe and efficient navigation in complex maritime environments. Traditional ant colony optimization (ACO) for path planning, however, suffers from premature convergence, slow adaptation, and poor smoothness in cluttered waters, while the dynamic window approach (DWA) without global guidance can become trapped in local obstacle configurations. This paper presents a sensor-oriented hybrid method that couples an improved ACO for global route planning with an enhanced DWA for local, real-time obstacle avoidance. In the global stage, the ACO state–transition rule integrates path length, obstacle clearance, and trajectory smoothness heuristics, while a cosine-annealed schedule adaptively balances exploration and exploitation. Pheromone updating combines local and global mechanisms under bounded limits, with a stagnation detector to restore diversity. In the local stage, the DWA cost function is redesigned under USV kinematics to integrate velocity adaptability, trajectory smoothness, and goal-deviation, using obstacle data that would typically originate from onboard sensors. Simulation studies, where obstacle maps emulate sensor-detected environments, show that the proposed method achieves shorter paths, faster convergence, smoother trajectories, larger safety margins, and higher success rates against dynamic obstacles compared with standalone ACO or DWA. These results demonstrate the method’s potential for sensor-based, real-time USV navigation and collision avoidance in complex maritime scenarios. Full article

Schizochytrium is often added to feed to enhance the growth and health of farmed animals, yet research on its effects on amphibians remains relatively scarce. Here, this study investigated the effects of dietary Schizochytrium meal on growth, metamorphosis, intermediate metabolism, and intestinal health of bullfrogs. Six compound feeds (S0–S5) containing different gradients of Schizochytrium meal (0.00, 2.00, 5.00, 10.00, 15.00, and 20.00 g/kg diets) were formulated. After 90 days, the S4 group (15.00 g/kg) exhibited significantly superior growth performance, with the weight gain rate (WGR) increasing by up to 23.78% compared to the control (S0). Metamorphosis rate (MR) peaked at 23.33% in the S4 group. The enzyme activities of digestion (amylase (AMS), lipase (LPS), protease), brush border membrane (Na⁺, K⁺-ATPase, alkaline phosphatase (AKP), γ-glutamyl transferase (γ-GT), creatine kinase (CK), and antioxidation (superoxide dismutase (SOD), catalase (CAT)), as well as microvilli length and mucosal epithelial cell height in the intestine were the highest in the S4 group. Intestinal microbial diversity (Ace index) significantly increased by 41.28% in the S4 group, which also promoted beneficial bacteria. Key genes related to the GH-IGF-1 axis, metabolism, and intestinal barrier function were significantly upregulated with increasing Schizochytrium levels up to 15.00 g/kg, whereas pro-inflammatory genes showed an opposite trend. Overall, dietary supplementation with Schizochytrium meal at 15.00 g/kg promotes growth, metamorphosis, and intestinal health in bullfrog tadpoles by modulating the GH-IGF-1 axis, enhancing digestion and absorption, and improving intestinal integrity. Optimal Schizochytrium meal levels were identified as 13.27 g/kg. Full article

Acute respiratory infections (ARIs) continue to pose a major global health threat, particularly among vulnerable populations. These infections often present with similar clinical symptoms, complicating accurate diagnosis and facilitating unmonitored transmissions. Genomic surveillance has emerged as an invaluable tool for pathogen identification and monitoring of such infectious pathogens; however, its implementation is frequently limited by high costs. The widespread use of high-throughput sequencing during the COVID-19 pandemic has created an opportunity to repurpose existing genomic platforms for broader respiratory virus surveillance. In this study, we evaluated the feasibility of adapting the Illumina COVIDSeq assay—initially designed for SARS-CoV-2 whole-genome sequencing—for use with Influenza A/B, Respiratory Syncytial Virus (RSV), and Rhinovirus. Positive control samples were processed using two approaches for library preparation: four virus-specific multiple workflows and a combined rapid workflow. Both workflows incorporated pathogen-specific primers for amplification and followed the Illumina COVIDSeq protocol for library preparation and sequencing. Sequencing quality metrics were analysed, including Phred scores, read length distribution, and coverage depth. The study did not identify significant differences in genome coverage and genetic diversity metrics between workflows. Genome Detective consistently identified the correct species across both methods. The findings of this study demonstrate that the COVIDSeq assay can be effectively adapted for multi-pathogen genomic surveillance and that the combined rapid workflow can offer a cost- and labour-efficient alternative with minimal compromise to data quality. Full article

Structural variation (SV) serves as a fundamental driver of phenotypic diversity and environmental adaptation in plants and animals, significantly influencing key agronomic traits in crops. Common wheat (Triticum aestivum L.), an allohexaploid species, harbors extensive chromosomal SVs and distant hybridization-induced recombination events that provide critical resources for genetic improvement. This study utilizes non-denaturing fluorescence in situ hybridization (ND-FISH) and oligonucleotide multiplex probe-based FISH (ONPM-FISH) to analyze the karyotypes of 153 BC₁F₄–BC₁F₆ lines derived from the hybrid line Xiaoyan 7430 and common wheat Yannong 1212. The results revealed that Xiaoyan 7430 carries 8 alien chromosome pairs and 20 wheat chromosome pairs (lacking 6B), and Yannong 1212 contains 21 pairs of wheat chromosomes. The parental lines exhibited presence/absence variations (PAVs) on chromosomes 2A, 6A, 5B, 1D, and 2D. Chromosomal variations, including numerical chromosomal variation (NCV), structural chromosomal variation (SCV), and complex chromosomal variation (CCV), were detected in the progeny lines through ONPM-FISH analysis. The tracking of alien chromosomes over three consecutive generations revealed a significant decrease in transmission frequency, declining from 61.82% in BC₁F₄ to 26.83% in BC₁F₆. Telosomes were also lost during transmission, declining from 21.82% in BC₁F₄ to 9.76% in BC₁F₆. Alien chromosome 1J^S, 4J, and 6J exhibited the highest transmission stability and were detected across all three generations. Association analysis showed that YN-PAV.2A significantly affected the length/width ratio (LWR) and grain diameter (GD); YN-PAV.6A, XY-PAV.6A, and PAV.5B increased six grain traits (+2.25%~15.36%); YN-PAV.1D negatively affected grain length (GL) and grain circumference (GC); and XY-PAV.2D exerted positive effects on thousand-grain weight (TGW). Alien chromosomes differentially modulated grain characteristics: 1J^S and 6J both reduced grain length and grain circumference; 1J^S increased LWR; and 4J negatively impacted TGW, grain width (GW), GD, and grain area (GA). Meanwhile, increasing alien chromosome numbers correlated with progressively stronger negative effects on grain traits. These findings elucidate the genetic mechanisms underlying wheat chromosomal variations induced by distant hybridization and their impact on wheat grain traits, and provide critical intermediate materials for genome design breeding and marker-assisted selection in wheat improvement. Full article

Pubertal molting represents a pivotal transition in the life cycle of crustaceans, marking the shift from somatic growth to reproductive development. In mud crabs, mating is known to facilitate this process, yet the molecular mechanisms remain poorly understood. Here, we applied full-length transcriptome sequencing to characterize changes in gene expression and alternative splicing (AS) across post-mating ovarian development. AS analysis revealed extensive transcript diversity, predominantly alternative first exon (AF) and alternative 5′ splice site (A5) events, enriched in genes linked to chromatin remodeling, protein regulation, and metabolism, underscoring AS as a fine-tuning mechanism in ovarian development. Comparative analyses revealed profound molecular reprogramming after mating. In the UM vs. M1 comparison, pathways related to serotonin and catecholamine signaling were enriched, suggesting early neuroendocrine regulation. Serotonin likely promoted, while dopamine inhibited, oocyte maturation, indicating a potential “inhibition–activation” switch. In the UM vs. M3 comparison, pathways associated with oxidative phosphorylation, ATP biosynthesis, and lipid metabolism were upregulated, reflecting heightened energy demands during vitellogenesis. ECM-receptor interaction, HIF-1, and IL-17 signaling pathways further pointed to structural remodeling and tissue regulation. Enhanced antioxidant defenses, including upregulation of SOD2, CAT, GPX4, and GSTO1, highlighted the importance of redox homeostasis. Together, these findings provide the first comprehensive view of transcriptional and splicing dynamics underlying post-mating ovarian maturation in Scylla paramamosain, offering novel insights into the molecular basis of crustacean reproduction. Full article

Dioscorea polystachya (Chinese yam) is a crop valued for both medicinal and edible purposes, and exhibits rich genetic diversity. However, research into its germplasm resources remains understudied, and molecular breeding efforts lag behind. To bridge this gap, this study employed an integrated approach, combining the analysis of 23 phenotypic traits (17 qualitative and 6 quantitative) with genotyping using 19 polymorphic SSR markers. This combined strategy was applied to 53 accessions collected across 16 Chinese provinces to assess genetic diversity, population structure, and marker–trait associations. Phenotypic analysis revealed high diversity, with the Shannon diversity index (I) ranging from 0.09 to 1.15 for qualitative traits and from 1.45 to 1.79 for quantitative traits. Tuber traits exhibited the highest variability (with a CV up to 71.45%), indicating significant potential for yield improvement. Principal component analysis distilled phenotypic variation into eight principal components (accounting for 73.13% of the cumulative variance), and elite germplasm (e.g., DP24, DP52) was selected for breeding based on this analysis. Stepwise regression prioritized eight core evaluation traits (e.g., flowering rate, tuber length). SSR markers amplified 80 alleles (mean 4.211/locus), showing moderate genetic diversity (He = 0.529, PIC = 0.585). Population structure analysis divided accessions into two subpopulations, correlated with geographic origins: Group 1 (northern/southwestern China) and Group 2 (central/eastern China), reflecting adaptation to local climates and human selection. Association analysis identified 10 SSR loci significantly linked (p < 0.01) to key traits, including YM07_2 (flowering, R² = 13.94%), YM37_2 (leaf margin color, R² = 19.03%), and YM19_3 (leaf width, R² = 19.34%). This study establishes a comprehensive genetic framework for Chinese yam, offering molecular tools for marker-assisted breeding and strategies to conserve high-diversity germplasm, thereby enhancing the utilization of this orphan crop. Full article

The microbial community in a recirculating aquaculture system (RAS) is pivotal in fish health, contributing significantly to the productive performance during the growing-out phase. Classical and molecular methods using PCR for species-specific amplifications have traditionally been used for bacterial community surveillance. Unfortunately, these approaches mask the real bacterial diversity and abundance, population dynamics, and prevalence of pathogenic bacteria. In this study, we explored the use of Oxford Nanopore Technology to characterize the microbiota and functional metagenomics in a commercial freshwater RAS. Intestine samples from Atlantic salmon (Salmo salar (85 ± 5.7 g)) and water samples from the inlet/outlet water, settling tank, and biofilters were collected. The full-length 16S rRNA gene was sequenced to reconstruct the microbial community, and bioinformatic tools were applied to estimate the functional potential in the RAS and fish microbiota. The analysis showed that bacteria involved in denitrification processes were found in water samples, as well as metabolic pathways related to hydrogen sulfide metabolism. Observations suggested that fish classified as sick exhibited decreased microbial diversity compared with fish without clinical symptomatology (p < 0.05). Proteobacteria were predominant in ill fish, and pathogens of the genera Aeromonas, Aliivibrio, and Vibrio were detected in all intestinal samples. Notably, Aliivibrio wodanis was detected in fish showing abnormal clinical conditions. Healthy salmon showed higher contributions of pathways related to amino acid metabolism and short-chain fatty acid fermentation (p < 0.05), which may indicate more favorable fish conditions. These findings suggest the utility of nanopore sequencing methods in assessing the microbial community in RASs for salmon aquaculture. Full article

With the proliferation of multimedia data, controllable summarization generation has become a key focus in Artificial Intelligence Content Generation. However, many traditional methods lack precise control over output length, often resulting in summaries that are either too verbose or too brief, thus failing to meet diverse user needs. In this paper, we propose a length-customizable approach for multimodal image-text summarization. Our method integrates combinatorial optimization with deep learning to address the length-control challenge. Specifically, we formulate the summarization task as a knapsack optimization problem, enhanced by a greedy algorithm to strictly adhere to user-defined length constraints. Additionally, we introduce a multimodal attention mechanism to ensure balanced and coherent integration of textual and visual information. To further enhance semantic alignment, we employ a cross-modal matching strategy for image selection based on pre-trained vision-language models. Experimental evaluations on the MSMO dataset and validate against baselines like LEAD-3, Seq2Seq, Attention, and Transformer that our method achieves a ROUGE-1 score of 40.52, ROUGE-2 of 16.07, and ROUGE-L of 35.15, outperforming existing length-controllable baselines. Moreover, our approach attains the lowest length variance, confirming its precise adherence to target summary lengths. These results validate the effectiveness of our method in generating high-quality, length-constrained multimodal summaries. Full article

Myelin oligodendrocyte glycoprotein antibody–associated disease (MOGAD) is an inflammatory demyelinating disorder of the central nervous system characterised by heterogeneous clinical and radiological presentations. Accurate interpretation of serum anti–myelin oligodendrocyte glycoprotein (anti-MOG) antibody titres is critical to improve diagnostic precision and prognostic assessment. This single-centre retrospective study evaluated 19 patients diagnosed with MOGAD in 2023, all of whom were seropositive for anti-MOG IgG, as confirmed by live cell-based assays (CBAs) using full-length human MOG and IgG1-specific secondary antibodies. Antibody quantification combined a ratiometric semi-quantitative fluorescence index with classical endpoint dilution titres, enabling classification into low, medium, and high titre groups. Stratification revealed titre-dependent phenotypic heterogeneity: high-titre patients were older at onset and predominantly presented with optic neuritis, often bilateral, and encephalic involvement, whereas low-titre patients more frequently exhibited spinal cord syndromes, cerebellar or brainstem symptoms, and a higher prevalence of cerebrospinal fluid-restricted oligoclonal bands. Semi-quantitative fluorescence ratios correlated consistently with endpoint titres, and exponential decay analysis demonstrated slower signal loss in high-titre sera, confirming assay reliability. No significant association emerged between titre level and monophasic versus relapsing disease course. Anti-MOG antibody titres could serve not only as a diagnostic biomarker but also to capture clinically relevant immunopathological diversity, supporting a titre-stratified approach to diagnosis and early prognostication. Incorporating semi-quantitative metrics alongside clinical and imaging features may refine the diagnostic algorithm and prevent misclassification of atypical presentations. Full article

T cell receptor (TCR) profiling using next-generation sequencing (NGS) enables high-throughput, in-depth analysis of repertoire diversity, offering numerous clinical applications. We developed a DNA-based strategy to analyse the TCRβ-chain using NGS and established reference values for T cell repertoire characteristics in 74 healthy donors, including 44 adults, 20 paediatrics, and 10 cord blood units (CBUs). Additionally, four paediatric patients with combined immunodeficiency (CID) or severe CID (SCID) due to deleterious mutations in recombination activating genes (RAG) were analysed. The developed strategy demonstrated high specificity, reproducibility, and sensitivity, and all functional variable and joining genes were detected with minimal PCR bias. All donors had a Gaussian-like distribution of complementary-determining region 3 length, with lower presence of non-templated nucleotides and higher proportion of non-functional clonotypes in CBUs. Both CBUs and paediatrics showed greater convergence and TCRβ diversity was significantly lower in adults and donors with cytomegalovirus-positive serostatus. Finally, an analysis of paediatric patients with RAG-SCID/CID showed significantly shorter CDR3 region length and lower repertoire diversity compared to healthy paediatrics. In summary, we developed a reliable and feasible TCRβ sequencing strategy for application in the clinical setting, and established reference values that could assist in the diagnosis and monitoring of pathological conditions affecting the T cell repertoire. Full article

The size and mass of fish are crucial parameters in aquaculture management. However, existing research primarily focuses on conducting fish size and mass estimation under ideal conditions, which limits its application in actual aquaculture scenarios with complex water quality and fluctuating lighting. A non-contact size and mass measurement framework is proposed for complex underwater environments, which integrates the improved FishKP-YOLOv11 module based on YOLOv11, stereo vision technology, and a Random Forest model. This framework fuses the detected 2D key points with binocular stereo technology to reconstruct the 3D key point coordinates. Fish size is computed based on these 3D key points, and a Random Forest model establishes a mapping relationship between size and mass. For validating the performance of the framework, a self-constructed grass carp dataset for key point detection is established. The experimental results indicate that the mean average precision (mAP) of FishKP-YOLOv11 surpasses that of diverse versions of YOLOv5–YOLOv12. The mean absolute errors (MAEs) for length and width estimations are 0.35 cm and 0.10 cm, respectively. The MAE for mass estimations is 2.7 g. Therefore, the proposed framework is well suited for application in actual breeding environments. Full article

Flow dynamics were characterized and stable zones in diversions were quantified using physical modeling, in situ experiments, and 3D numerical simulations. ADV (1 cm spatial resolution) and water-level probes (0.01 cm spatial resolution) were used in the physical experiments in a rectangular channel. ADCP (resolution of 50 cm) was employed for in situ validation at a northern China hub. Numerical simulations using ANSYS 2022R2 Fluent software with RNG k-ε and VOF showed little error (<15%) compared to the experiments. The results quantified the diversion zone into four sub-regions: acceleration (length 0.8–1.2 h); stabilization (1.2–3.5 h); diffusion deceleration (3.5–5.0 h); and stagnation (localized eddies, diameter 0.3–0.8 d). The stable zone length was dominantly controlled by the nonlinear coupling of geometric (B_s/B_m, 42%) and hydraulic (Fr, 28%) parameters. Upstream and downstream stable zone empirical models showed high accuracy (R² = 0.83 and 0.76, p < 0.01), with an average relative error <15%. Based on the proposed zoning principles and flow characteristics, measurement facilities in the irrigation area are presented. These tools enhance irrigation diversion design and management for improved water efficiency. Full article

Ensete ventricosum is a morphologically gigantic, monocot, diploid sister to the banana plant species. It is commercially cultivated as a starch source, only in Ethiopia, where it feeds twenty million people. Here, the complete chloroplast (CP) genomes of 15 diverse landraces of E. ventricosum were assembled and annotated, for comparative genomics, genetic diversity analysis, and molecular marker development. The assembled E. ventricosum CP genomes ranged between 168,388 and 168,806 bp. The sampled CP genomes were quadripartite in structure and had two single-copy regions, a large single-copy region (LSC, average length 88,657 bp), and a small single-copy region (SSC, average length 11,098 bp) separated by inverted repeat regions (IR, average length 34,437 bp). The total number of annotated genes varies between 135 and 138, including 89–92 protein-coding genes, 38 tRNA genes, and 4 rRNA genes. All CP genes, including non-functional ones and intergenic regions, were transcribed with the transcriptome, covering almost 92% of the E. ventricosum CP genome. Codon usage, amino acid frequency, GC contents, and repeat nucleotides were similar among the 15 landraces. Mono- and tetranucleotide simple sequence repeats (SSRs) were found more frequently than other SSRs. An average of 71% of these SSRs were located in the LSC region, and the majority of the SSR motifs were composed of A/T nucleotides. A phylogenetic analysis of the 15 Ensete landraces indicated a common evolutionary origin, while the China sample was positioned separately, suggesting notable genetic differences. This study presents a comparative analysis of the chloroplast genomes of 15 E. ventricosum landraces, providing valuable insights into their genetic diversity and evolution. The identified SSR markers and conserved genomic features offer essential resources for future research and an improvement in Ensete conservation and breeding. Full article

Lipopolysaccharides (LPS) from Gram-negative bacteria represent a significant challenge across various industries due to their prevalence and pathogenicity and the limitations of existing detection methods. Traditional approaches, such as the rabbit pyrogen test (RPT) and the Limulus Amebocyte Lysate (LAL) assay, have served as gold standards for endotoxin detection. However, these methods are constrained by high costs, lengthy processing times, environmental concerns, and the need for significant reagent volumes, which limit their scalability and application in resource-limited settings. In this study, we introduce an innovative microfluidic platform that integrates the LAL assay within microdroplets, addressing the critical limitations of traditional techniques. By leveraging the precise fluid control and reaction isolation offered by microdroplet technology, the system reduces reagent consumption, enhances sensitivity, and enables high-throughput analysis. Calibration tests were performed to validate the platform’s ability to detect LPS, using colorimetric measurements. Results demonstrated comparable or improved performance relative to traditional systems, achieving lower detection limits and greater accuracy. This work demonstrates a proof-of-concept miniaturisation of the pharmacopoeial LAL assay. The method yielded low intra-assay variability (σ ≈ 0.002 OD; CV ≈ 0.9% over n = 50 droplets per point) and a LOD estimated from calibration statistics after path-length normalisation. Broader adoption will require additional comparative validation and standardisation. This scalable, cost-effective, and environmentally sustainable approach offers a practical solution for endotoxin detection in clinical diagnostics, biopharmaceutical production, and environmental monitoring. The proposed technology paves the way for advanced LPS detection methods that meet stringent safety standards while improving efficiency, affordability, and adaptability for diverse applications. Full article