Search Results (645)

Transposable elements (TEs) account for nearly half of the human genome and shape chromatin organization, gene regulation, and genome evolution. However, their contributions to human physiology and disease remain incompletely understood. The most active elements in humans, LINE-1 (L1), Alu, and SVA, retain some copies with the ability to evade epigenetic repression and mobilize via target-primed reverse transcription (TPRT), whereas copies become inactive through various fragmentations and mutations. TE activity contributes to genomic instability and has been implicated in aging, cancer, neurological disorders, chromatin organization, and epigenetic regulation. Studying TE is challenging due to their repetitive and polymorphic nature. Recent advances in sequencing technologies and short- and long-read sequencing platforms, combined with specialized bioinformatic pipelines, currently enable more comprehensive characterization of TE insertions, deletions, expression, and epigenetic status. Computational approaches vary in sensitivity, specificity, and resource requirements, and their performance is influenced by sequencing modality, coverage, and the reference genome used. Assembly-based and read-based methods, as well as integrating methylation data or single-cell data, provide complementary insights into TE biology. This review summarizes the biology of active human TE, surveys state-of-the-art short- and long-read pipelines for TE analysis, and highlights their applications in studies of aging, cancer, and other complex diseases. We also provide practical guidance for selecting appropriate sequencing strategies and tools for TE-focused projects, and discuss emerging approaches and open questions in the field. Full article

This paper comprehensively investigates the ultraviolet (UV) nanosecond laser fabrication of micro-groove textures on planar PEEK surfaces, as well as their surface performance in terms of wettability and frictional properties. Firstly, a three-dimensional finite element model, incorporating a moving Gaussian heat source, solid heat transfer and deformed geometry, was established to simulate the transient temperature field and ablation profile of PEEK during UV laser ablation. The predicted groove depth agreed with the experimental value with a low deviation of 11.19%. Based on the simulation and single-factor experiments, the optimized single-track laser parameters were determined as a laser power of 1.2 W, a scanning speed of 100 mm/s and a repetitive frequency of 100 kHz. Secondly, systematic single-factor and multi-pass laser ablation experiments of PEEK surfaces were conducted to fabricate micro-groove textures with precisely tailored geometric parameters. Furthermore, ablated surface characterization showed that the laser-textured surfaces exhibited increased roughness, apparent crystallinity up to 22.13%, and pronounced anisotropic wettability, with improved liquid spreading along the groove direction and restricted spreading across the grooves. Finally, fretting wear tests under simulated body fluid lubrication were carried out. The research findings reported in this paper provide a systematic theoretical and experimental basis for the application of UV nanosecond laser surface texturing in the fabrication of PEEK-based components. Full article

The development of effective conservation and management strategies for wild Ribes populations requires a comprehensive understanding of genetic diversity and population structure of these taxa, but only a few genetic studies exist, and these have focused on cultivated material in the genus. We evaluated the use of MobiSeq as a reduced representation sequencing approach to detect genetic variation in three Ribes species, and we used the data to characterize the genetic diversity and population structure in the Netherlands and the relationships between the wild Ribes populations, the ex situ genebank collection, and cultivars. MobiSeq with a single primer designed for repetitive elements that occur in the three species produced 17,000–31,000 SNPs per species after filtering against markers with minor allele frequency (MAF) < 0.01 and markers deviating from Hardy-Weinberg equilibrium (HWE). The SNPs were called against consensus sequences, producing separate sets of markers for each of the species. All three species had moderate genetic diversity (H_S = 0.141–0.239) and relatively low differentiation (F_ST = 0.049–0.083) with no evidence of inbreeding, consistent with their predominantly outcrossing life-history traits. This suggests that Dutch wild populations have largely retained their genetic diversity despite the current habitat fragmentation. Several putatively wild individuals showed evidence of cultivated ancestry, possibly indicating historical introgression or naturalized escapes from cultivation, particularly in R. rubrum and R. uva-crispa. Low differentiation between in situ and ex situ material (F_ST = 0.004–0.026) suggests that the genebank collections already capture most of the genetic diversity present in wild populations. Full article

Plant genomes exhibit extensive structural diversity generated by large-scale genomic alterations, collectively known as structural variations (SVs). Unlike single nucleotide polymorphisms (SNPs) and small insertions/deletions (indels), SVs can reshape genome architecture through changes in sequence content, gene dosage, regulatory landscapes, and chromosome organization. Recent advances in long-read sequencing (LRS), pan-genome construction, and multi-omics technologies have greatly expanded our ability to identify and interpret SVs across plant species. In this review, we summarize recent progress in understanding the formation mechanisms, classification, and functional consequences of plant SVs. We discuss major sources of SV generation, including transposable element activity, non-allelic homologous recombination (NAHR), horizontal gene transfer (HGT), and genome restructuring following polyploidization. We further highlight how LRS and graph-based pan-genomes overcome limitations of traditional linear reference genomes and enable more comprehensive characterization of genetic diversity. Beyond variant discovery, we emphasize the importance of integrating genomic, transcriptomic, epigenomic, proteomic, metabolomic, and spatial omics datasets to decipher how SVs influence gene regulation and complex agronomic traits. We also discuss current challenges, including repetitive genomes, polyploidy, computational complexity, and translation of SV knowledge into practical breeding applications. Together, these advances establish SV-centered genomics as a critical framework for understanding plant genome evolution and accelerating precision crop improvement. Full article

Fragile X syndrome (FRAX) is caused by CGG repeat expansion in the FMR1 gene, which triggers aberrant DNA hypermethylation, chromatin condensation, and transcriptional gene silencing. However, the mechanism that underlies this repeat-induced epigenetic defect remains poorly understood. SMCHD1 is a chromatin regulator that promotes de novo DNA methylation and heterochromatin formation at long repetitive elements, including the D4Z4 macrosatellite repeat implicated in facioscapulohumeral muscular dystrophy (FSHD). Given the mechanistic parallels between FSHD and FRAX, we hypothesized that SMCHD1 contributes to repeat-induced FMR1 hypermethylation. To test this, we disrupted SMCHD1 in an XY FRAX human embryonic stem cell (hESC) line carrying a heavily methylated CGG-expanded FMR1 allele. Despite efficient loss of SMCHD1, FMR1 hypermethylation remained unchanged, indicating that SMCHD1 is dispensable for FMR1 gene silencing. We next combined SMCHD1 knockout with CRISPR-mediated CGG repeat contraction to determine whether removal of the pathogenic mutation could restore the aberrant methylation. Nevertheless, FMR1 hypermethylation was preserved in all edited clones. These findings demonstrate that, unlike D4Z4 silencing in FSHD, FMR1 repeat-induced hypermethylation does not depend on SMCHD1 activity. Moreover, correction of the underlying CGG expansion through repeat contraction is insufficient to restore the normal hypomethylated state of the FMR1 locus in pluripotent stem cells. Full article

Rising temperatures pose daunting challenges for sustainable yield and nutritional quality of rice (Oryza sativa L.), thus putting food security at risk. Limited information exists regarding cis-acting regulatory elements and candidate genes controlling the heat shock transcription factor (HSF) gene family in rice. Therefore, the present study identified HSF genes in the japonica (Nipponbare) and indica (9311) rice cultivars through in silico repositories. Three candidate genes (HSFC2B, HSFB1, and HSFC2A) were selected for qRT-PCR analysis to validate their expression patterns under heat stress (HS). The present findings reported a total of 25 OsHSF genes through in silico genome-wide identification. Comparative analysis illustrated that the OsHSF genes had structural similarities but different expression and transcriptional regulation between the two cultivars. HSF genes were unevenly distributed across the 12 rice chromosomes, suggesting that tandem duplication and gene repetition may have contributed to the evolution of novel genes. Phylogenetic analysis revealed that all OsHSF gene family members have shared common ancestry, but several genes lack introns, potentially facilitating swift stress responses as indicated by gene structure analysis. Expression analysis revealed that candidate genes were active, with HSFC2A exhibiting the highest level of expression in the japonica cultivar compared to indica under heat-stressed conditions. HSFC2B gene showed a higher statistical difference in its response between cultivars, time points, and cultivar vs. time points interactions compared to HSFC2A and HSFB1. These findings offer valuable insights into the function of OsHSF genes that will contribute to the development of climate-resilient rice cultivars. Full article

In this work, LiF was introduced as a flux additive to overcome the high viscosity challenge of the self-flux system, which successfully grew a large-scale cesium lithium borate (CLBO) single crystal with dimensions of 136 × 132 × 68 mm³ and a weight of 1275 g via the top-seeded solution growth (TSSG) method. The as-grown crystal showed an optical transmittance of over 90% in the spectral range of 230–1880 nm and an extremely low absorption coefficient of 2.8 ppm/cm at 1064 nm. Notably, under 120 W pumping at a high repetition rate of 2 MHz, the fabricated CLBO optical element achieved a record-high 266 nm output power of 26.1 W with an optical conversion efficiency of 21.75%. Moreover, the laser system maintained stable continuous operation at >23 W for over 120 h. Full article

The increasing adoption of light electric vehicles (LEVs) has intensified demand for efficient, high-performance electric drive systems. Brushless direct-current motors (BLDCMs) in outer-rotor configurations are the predominant drive solution for L7e-class LEVs owing to their high torque density, compact structure, and low maintenance requirements. However, electromagnetic design and performance analysis of outer-rotor BLDCMs involve complex, multi-parameter calculations and time-consuming finite element simulations. To the best of the authors’ knowledge, no prior study has simultaneously addressed multi-output performance prediction of outer-rotor BLDCMs across multiple slot–pole combinations and supply voltage levels using an ANN-based surrogate model. This study proposes such a model, capable of predicting six rated performance parameters (no-load speed, nominal speed, torque, phase current, input current, and output power) directly from design inputs, without requiring repetitive finite element analyses. Three outer-rotor BLDCMs were analytically designed and simulated for L7e-class LEVs operating at different voltage levels, and the resulting FEA dataset was used to train a feedforward backpropagation ANN. The model takes key geometric and electrical design parameters as inputs and delivers multi-output performance predictions with high accuracy. Validation against a physically manufactured motor confirmed prediction accuracy exceeding 92%, demonstrating the model’s reliability on real-world unseen configurations. The proposed model reduces electromagnetic analysis time from several hours to mere seconds, offering a practical and scalable AI-assisted framework for BLDCM design in sustainable transportation applications. Full article

Homologous regions (hrs) are repetitive DNA sequences widely distributed in baculovirus genomes, and are known to function as transcriptional enhancers. In this study, we systematically characterized the seven hrs (hr1, hr2L, hr2R, hr3, hr4L, hr4R, and hr5) from a novel isolate of Bombyx mori nucleopolyhedrovirus (strain BmNPV-YT). The seven hrs range from 390 to 880 bp in length and consist of 1–7 repeat units of approximately 72 bp, each containing a 30 bp palindrome with an EcoRI site. Structural diversity among the hrs includes variable numbers of stem–loop motifs, major late transcription factor (MLTF) sites, cAMP response elements (CRE-like), and 12-O-tetradecanoylphorbol 13-acetate (TPA)-response elements (TRE-like). Functional assays using luciferase reporter plasmids revealed that all seven hrs function as potent transcriptional enhancers for both homologous and heterologous promoters in vitro and in vivo. In BmN cells and fifth-instar silkworm larvae, the hrs enhanced the homologous ie1 promoter 11–1258-fold and 43–1545-fold, respectively, with hr2L showing the strongest activity (counts per minute: 4.82 × 10⁸ in cells; 7.08 × 10⁷ in larvae) and hr4R the weakest. Similarly, when driving the heterologous AcMNPV ie1 promoter in Sf21 cells and larvae, enhancement ranged from 19- to 1023-fold and 13- to 449-fold, respectively, again with hr2L and hr3 showing maximal effects and hr4R minimal enhancement. Notably, all the hrs, except hr4R, also stimulated the homologous late p10 promoter, with activation levels of up to 37.7-fold in vitro and 79.2-fold in vivo, significantly above baseline. However, hr4R showed negligible or no enhancement (0.84–1.05-fold). Among all the active hrs, hr5 emerged as the most potent enhancer of the p10 promoter. Spearman’s correlation analyses demonstrated that enhancer efficiency for all three promoters (homologous ie1, heterologous ie1, and homologous p10) correlated significantly with the number of palindromic sequences, the combined count of CRE and TRE motifs, and the total number of characteristic sequences (r = 0.873–0.982, p < 0.05 or p < 0.01). Collectively, our findings clarify the structural features of hrs from the newly isolated strain BmNPV-YT, systematically identify their promoter preferences and host adaptability as transcriptional enhancers, and establish their structure–function relationships. These findings provide novel insights into the transcriptional regulation of baculoviruses and offer valuable tools for optimizing baculovirus expression vector systems. Full article

As a paradigm-shifting hypervelocity propulsion technology, electromagnetic rail launch (EMRL) is fundamentally constrained by armature/rail (A/R) interface degradation, which directly erodes its service longevity and operational reliability. Small-caliber circular bore electromagnetic launchers (SCCB-EMRL) offer superior structural integration and ballistic stability over traditional rectangular bores. Their inherently lower self-centering capability imposes strict requirements on interfacial contact stability. This study investigates the physicochemical evolution of the A/R interface at extreme loading. Consecutive repetitive launch experiments were conducted, and samples were prepared by typical areas of rail according to the current curve. Characterization was performed using scanning electron microscopy (SEM), energy-dispersive X-ray spectroscopy (EDS), and Raman spectroscopy. Results revealed a bimodal non-uniform thickness distribution of the deposition layer along the launch direction. The maximum deposition thickness reached 60.6 μm within the acceleration-startup zone. The deposited material comprises transferred Al, oxidized phases (Al₂O₃), Al-Cu intermetallic, and a mixed carbonaceous system containing amorphous and graphitized carbon. Initial launches triggered rapid material accumulation and increased start-up times, after which the interface reached a dynamic equilibrium. This work reveals the evolution patterns of elemental composition and thickness distribution of the deposition layer at the armature/rail interface in small-caliber circular-bore electromagnetic launching and provides experimental reference for the design of anti-deposition coatings to extend the service lifespan of SCCB-EMRL systems. Full article

Accurate channel estimation in frequency-selective multiple-input multiple-output orthogonal frequency division multiplexing (MIMO-OFDM) systems requires balancing pilot overhead, reconstruction accuracy, and computational cost. This paper presents a reproducible compressed sensing benchmark for sparse delay-domain channel estimation with reduced pilot observations. Its novelty is not the invention of Orthogonal Matching Pursuit (OMP), Compressive Sampling Matching Pursuit (CoSaMP), or Subspace Pursuit (SP), but the construction of a transparent and auditable evaluation protocol in which all estimators operate on the same channel realizations, sensing matrices, pilot budgets, signal-to-noise ratios (SNRs), stopping rules, and Monte Carlo trials. The framework explicitly defines the underdetermined observation model, the per-link 4 × 4 MIMO interpretation, the minimum-norm least-squares (LS) baseline, the identity-prior linear minimum mean-square error (LMMSE) baseline, the oracle-known sparsity assumption, uncertainty reporting, runtime protocol, and the mapping from delay-domain estimates to link- and subcarrier-domain quantities. OMP, CoSaMP, SP, LS, and LMMSE are evaluated for a 128-element delay dictionary, five active taps, sampling ratios from 0.10 to 0.70, SNRs from 0 to 30 dB, and 80 independent trials per operating point. The results show that sparse recovery exploits the assumed delay-domain sparsity more effectively than non-sparse baselines in the underdetermined regime, while pilot density remains a dominant factor in support identification and reconstruction error. The accompanying Python human–machine interface (HMI) produces confidence-aware metrics and publication-ready figures, enabling exact repetition of the benchmark and controlled extension to more realistic channel models. The conclusions are limited to simulation-based algorithmic evidence and define a direct pathway toward standardized-channel, software-defined radio (SDR), and measured radio-frequency (RF) validation. Full article

Type IV composite hydrogen storage vessels must ensure structural safety under high internal pressure, and determining the optimal laminate configuration typically requires repetitive finite element analysis (FEA), leading to significant computational cost during the early design stage. To address this limitation, this study proposes a machine learning (ML)-based design-assistance framework for predicting the minimum laminate configuration required to satisfy structural safety based on the Tsai–Wu failure criterion. Three geometric design variables—liner radius, liner length, and polar hole radius—were used as inputs, and a dataset was generated using ANSYS Workbench-based FEA. Five ML models—SVR, GPR, RF, XGBoost, and MLP—were applied and evaluated using leave-one-out cross-validation (LOOCV) and an independent test set. All models achieved high predictive accuracy, with LOOCV R² values ranging from 0.9801 to 0.9907 and test-set R² values from 0.9866 to 0.9949, while maintaining MAPE below 6%. The consistent performance between LOOCV and the independent test set indicates stable predictive behavior. Learning curve analysis demonstrated stable convergence and a small performance gap between training and validation, suggesting stable predictive behavior within the considered design space. Feature importance analysis using the RF model identified the liner radius as the dominant parameter, while the influence of liner length was relatively minor. These results demonstrate that the proposed ML-based surrogate model can serve as an efficient tool for rapid design decision-making, reducing reliance on repetitive FEA in the early design stage. Full article

The Arabian leopard (Panthera pardus nimr), native to the Arabian Peninsula, is critically endangered and faces acute threats from habitat fragmentation, low population size, and genetic erosion. As a continuation of our previous study on the complete mitochondrial genome of this subspecies, we now report the first nuclear genome assembly of P. p. nimr, generated from the same wild-born male individual sampled in the Oman. Using PacBio HiFi long-read sequencing, we produced 162.9 gigabases (Gb) of high-fidelity data and assembled a haplotype-aware draft genome with HiFiasm. The assembly spans approximately 2.43 Gb across 94 contigs, achieving a contig N50 of 62.4 Mb and zero gap content, with BUSCO completeness of 99.4%. Genome annotation predicted 23,459 protein-coding genes with annotation BUSCO completeness of 95.0%, and 84.1% of proteins were classified as consistent with the Panthera lineage by OMArk. Repetitive elements occupy 34.01% of the assembly, with retroelements dominating and L1/CIN4 LINEs (15.44%) and SINEs (9.61%) representing the two largest subclasses. Comparative simple sequence repeat (SSR) analysis across six Panthera genomes confirmed a conserved repeat motif architecture, with no lineage-specific expansions detected in P. p. nimr. This nuclear genome complements the mitochondrial reference and provides a foundational resource for future studies on genetic diversity, demographic history, inbreeding load, and conservation planning for the Arabian leopard and other Panthera lineages. Full article

Shared bikes are frequently parked in disorder, resulting in low efficiency of manual collection and transfer and heavy workload for maintenance staff. Random parking across various areas forces shared bikes to occupy sidewalks and fire exits, damaging urban landscapes and disrupting traffic order. To tackle these industrial pain points, this paper develops an integrated intelligent robot system equipped with functions of multi-pose grasping, automatic transfer and fixed-point delivery of shared bikes, which can effectively address the drawbacks of low efficiency and high labor costs in traditional manual maintenance. This paper focuses on the completion of the robot’s overall mechanical structure design, stiffness–precision collaborative optimization model construction, finite-element static simulation verification, 1:7 scaled prototype development and performance testing. Firstly, the overall layout design of the multi-posture adaptive floating clamping mechanism, transfer-bearing frame, and Mecanum wheel omnidirectional mobile chassis is completed, and the structural parameters and assembly benchmarks of the core components are clarified. Secondly, a stiffness–precision coupling optimization model is established, and the static analysis under extreme load conditions is carried out through Abaqus finite-element software, which verifies the rationality of 45# carbon steel material selection and the safety of structural strength. Subsequently, a 1:7 scaled principle prototype is developed, and repetitive grabbing and transfer tests are carried out to verify the system operation feasibility, stability and grabbing accuracy. Finally, the statistical analysis of the test data and the horizontal comparison of similar schemes are completed. The test and simulation results show that the maximum stress of the system under extreme working conditions is 131.21 MPa, which is far lower than the allowable stress of 355 MPa of 45# steel, and the safety factor reaches 2.71. The maximum total deformation is 4.0552 mm, which is concentrated at the end of the front-end clamping mechanism, and is within the allowable stiffness deviation range of the transfer system. The average value of the single clamping positioning error of the scaled prototype is 0.476 mm, with a 95% confidence interval of 0.457–0.495 mm, which is converted to a positioning error of ≤3.4 mm for the full-scale prototype, which is far better than similar industry solutions. The average time of a single complete grabbing and transfer operation is 12.38 s, which is more than 45% higher than the traditional manual mode. The structural design, grabbing accuracy and operation stability of the robot designed in this paper all meet the requirements of actual working conditions of urban sidewalks, which can effectively reduce the intensity of manual labor and improve the operation and maintenance efficiency of shared bicycles. It has strong engineering application value and can provide reference for the design and manufacturing of intelligent collection and transfer systems for shared two-wheelers. Full article

Dybowski’s frog (Rana dybowskii) supports a multi-billion-dollar aquaculture sector in northern China and plays a critical ecological role in forest ecosystems. Despite its immense economic value, germplasm degradation and the mystery surrounding its homomorphic sex-determination system present major bottlenecks for the industry. Here, we integrated PacBio HiFi long-read sequencing, Illumina short-read sequencing, and High-Throughput Chromosome Conformation Capture (Hi-C) technologies to assemble the first chromosome-level reference genome of R. dybowskii. The final assembled genome size is 3.77 Gb, with a contig N50 of 16.27 Mb and a scaffold N50 of 41.54 Mb. A total of 97.82% of the sequences were successfully anchored onto 12 definitive pseudochromosomes corresponding to haploid chromosome number. Repetitive elements account for 65.61% of the genome, characterized by an unusual dominance of DNA transposons (37.19%) over retrotransposons, suggesting a genomic landscape shaped by extreme cold adaptation. Combining multi-tissue transcriptomic evidence, we structurally predicted 26,862 protein-coding genes, and the predicted gene set showed a BUSCO completeness of 96.1%. Functional annotation successfully categorized 96.55% of the total genes. This genomic resource successfully fills a crucial phylogenetic gap in the Rana genus, driving high-efficiency molecular breeding and sustainable conservation of this economic amphibian. Full article