Search Results (469)

Background/Objectives: Adenomyosis is a common estrogen-dependent gynecological condition with a largely undefined genetic architecture. Ciliary dysfunction has been implicated in its pathogenesis, positioning genes governing ciliary structure and motility as biologically plausible candidates for investigation. The DNAH5 gene encodes a critical component of the outer dynein arms within the ciliary axoneme, and pathogenic variants are among the most common causes of primary ciliary dyskinesia. This study aimed to systematically determine the frequency of a novel synonymous DNAH5 variant, NM_001369.3:c.9258C>T, p.(Leu3086=), in a large, histopathologically confirmed sporadic adenomyosis cohort from Turkiye, and to evaluate its occurrence relative to population-level reference data. Methods: A total of 121 women with histopathologically confirmed adenomyosis following hysterectomy were enrolled. Sanger sequencing was performed under stringent quality control conditions, including primer specificity verification by NCBI BLAST and UCSC In Silico PCR. Variant frequency was compared against gnomAD v4.0 and an in-house Turkish exome database (NGS Cloud; ~30,000 sequences) using Fisher’s exact test. In silico splice site analysis was performed using SpliceAI, and variant classification followed ACMG/AMP guidelines. Results: The variant was detected in 63 of 121 patients (52.1%; 95% CI: 43.1–61.0%), exclusively in the heterozygous state; no homozygous carriers were identified. The variant was absent from both gnomAD v4.0 across all populations and the NGS Cloud Turkish exome database (MAF: 0.0000), yielding a frequency difference (p < 2.2 × 10⁻¹⁶). SpliceAI analysis predicted no significant splice site impact (all delta scores < 0.1). The variant was classified as a variant of uncertain significance (VUS; BP7, PM2_supporting). Conclusions: This study identifies a difference in the frequency of a novel synonymous DNAH5 variant between a histopathologically confirmed adenomyosis cohort from Turkiye and population-level reference datasets, in which the variant was absent. Given the unphenotyped nature of the reference dataset, these findings are hypothesis-generating and do not establish a causal genetic association. Replication in independent cohorts and functional studies are warranted to elucidate the biological significance of this variant in adenomyosis susceptibility. Full article

Background: Circulating cell-free DNA (cfDNA) enables minimally invasive tumour genomic profiling, yet simultaneous interrogation of mutations and DNA methylation remains limited by assay complexity and input constraints. Methods: Here, we evaluate the Agilent Avida Duo system, a single workflow integrating high-sensitivity mutation detection with targeted DNA methylation analysis. We analysed 21 stage III and IV melanoma patient samples. Results: The Avida Duo mutation assay detected mutant allele frequencies (MAFs) down to 0.05% and identified tumour-associated mutations in all melanoma patients, including within GC-rich regions such as the TERT promoter. Optimisation of the Avida Duo mutation workflow, using TapeStation-quantified cfDNA and reduced amplification cycles, improved library consistency without compromising sensitivity. Methylation profiling of the melanoma baseline cohort with the Avida Duo methylation panel showed high concordance with QIAseq targeted methylation results, with the mean cfDNA fraction methylation ranging from 0.051–0.079 in most patients and reaching 0.249 in the patient with the highest ctDNA burden (MAFs up to 35.4%). Conclusions: Our findings demonstrate that the Avida Duo workflow enables simultaneous, high-resolution detection of mutation and methylation profiles from a single cfDNA sample, streamlining processing and enhancing molecular insight for clinical and translational applications. Full article

Nuclear factor erythroid 2-related factor 2 (NRF2) has traditionally been framed as a Kelch-like ECH-associated protein 1 (KEAP1)-regulated stress-response transcription factor, but three observations now require a broader framework: NRF2 turnover is controlled by parallel E3 ligase systems; transcriptional output can be limited by coactivator assembly despite unchanged NRF2 abundance; and NRF2 activation can be beneficial or harmful depending on disease context, as illustrated by lung cancer models in which NRF2 paradoxically promotes metastasis through BTB and CNC homology 1 (BACH1) stabilization. We synthesize these observations into an NRF2 partner-code framework in which NRF2 acts as a context-dependent transcriptional platform assembled through four partly independent modules: a degradation module (KEAP1; β-transducin repeat-containing protein, β-TrCP; HMG-CoA reductase degradation protein 1/synoviolin 1, Hrd1/SYVN1; WD repeat-containing protein 23/DDB1- and CUL4-associated factor 11, WDR23/DCAF11); a cytoplasmic scaffold module (p62/sequestosome 1, p62/SQSTM1; IQ motif-containing GTPase-activating protein 1, IQGAP1; type I phosphatidylinositol 4-phosphate 5-kinase γ/heat shock protein 27, PIPKIγ–HSP27; peptidyl-prolyl cis-trans isomerase NIMA-interacting 1, PIN1; peptidyl-prolyl isomerase A/cyclophilin A, PPIA); a nuclear coactivator module at Neh4/5 (CREB-binding protein/p300, CBP/p300; receptor-associated coactivator 3/steroid receptor coactivator 3, RAC3/SRC-3; protein arginine methyltransferase 1/coactivator-associated arginine methyltransferase 1, PRMT1/CARM1; Mediator complex subunit 16, MED16); and a DNA/chromatin module at Neh1 (small musculoaponeurotic fibrosarcoma [Maf] proteins, BACH1, and chromodomain helicase DNA-binding protein 6, CHD6). Mapping 22 partners onto the Neh-domain architecture identifies approximately 25 pharmacologically addressable interfaces, stratified into four translational tiers. The framework reframes NRF2 pharmacology around one principle: the most actionable target is often a partner rather than NRF2 itself, with disease context dictating the direction of modulation. We close with five testable hypotheses and a partner-code decision matrix linking disease, biomarker, and candidate target. Full article

(1) Background: Centella asiatica (L.) is a long-lived medicinal plant traditionally recognized for its wound-healing and anti-inflammatory properties. Despite the growing demand for diverse C. asiatica species in Korea, studies on genetic diversity remain limited. (2) Methods: Genome assembly data of C. asiatica from the NCBI database were utilized to develop genomic SSR markers. Genetic diversity and population structure were examined in 30 Korean native C. asiatica accessions using 90 SSR markers. (3) Results: Whole-genome sequencing revealed 376,751 SSR loci, from which 127,528 primer pairs were designed. Among 160 randomly selected primers, 90 showed consistent amplification and displayed high levels of polymorphism. Genetic analyses revealed that the MAF ranged from 0.15 to 1.00 (mean 0.55), the NA ranged from 1 to 15 (mean 5.6), the Ho ranged from 0.00 to 1.00 (mean 0.17), and the PIC values ranged from 0.00 to 0.88 (mean 0.52). Clustering analysis with 90 SSR markers revealed three clusters, whereas population structure analysis indicated two populations among the C. asiatica accessions. Furthermore, two minimum marker sets with five marker combinations were identified and proved useful to differentiate all C. asiatica accessions. (4) Conclusions: The newly developed SSR markers for C. asiatica hold promise for facilitating research endeavors pertaining to variety identification, genetic mapping, and marker-assisted selection. Full article

Background: The incidence of inflammatory bowel disease (IBD) is growing in the population. At present, the etiology of inflammatory bowel disease remains unclear, and there is no effective and low-toxic therapeutic drug. This study aimed to investigate the role of Lobenzarit (Lbz) in the treatment of colitis in mice as well as the underlying mechanism. Methods: In this experiment, colitis was induced in mice with dextran sulphate sodium (Dss). Subsequently, the role of Lbz in colitis and its underlying mechanisms were examined using H&E staining, TEM, ELISA, PCR, and other assays. Results: Lbz significantly attenuated the related symptoms of Dss-induced colitis in mice. In addition, Lbz suppressed neutrophil infiltration and restored macrophage polarization towards an anti-inflammatory state. Lbz also inhibited (p < 0.05) the activation of signaling pathways TLR4 and MAPK (51.61% decrease for TLR4 and 56.94% decrease for MAPK), reduced the release of inflammatory factors as it significantly decreased (p < 0.05) colonic IL-1β, TNF-α, IFN-γ, COX2, and VEGF (47.63, 42.49, 53.42, 58.74, and 61.28% decreases respectively) thereby attenuating the inflammatory response in mice. Lbz administration also restored the permeability of the intestinal barrier by increasing (p < 0.05) tight junction-associated proteins (claudin-1, occludin, and ZO-1 with a 5.36- and 2.26-fold increase for claudin-1 and ZO-1, respectively) and decreasing (p < 0.05) MALK levels by 53.51%. In addition, Lbz upregulated colonic Cytochrome C oxidase II, PDH, and ATP synthase levels and upregulated CD163, CD206, c-Maf, and PPAR-γ levels as compared to the DSS-treated group. Conclusions: Lbz has a repairing effect on Dss-induced colitis and may alleviate Dss-induced colitis by targeting the TLR4 pathway and promoting intestinal stem cell proliferation. Full article

Laboratory-based certification cycles systematically underestimate real-world fuel consumption and CO₂ emissions. On-board diagnostics (OBD-II) telemetry offers a low-cost alternative, yet most published approaches rely on mass air flow (MAF) sensors absent from many modern vehicles. This study validates a speed-density air-mass estimation method on a naturally aspirated RON 95 gasoline passenger car (1368 cm³, Euro 6) across seven drive cycles recorded over three measurement days in northwestern Türkiye, covering 609.6 km of highway, urban, and mixed conditions. Instantaneous air mass flow was estimated from four standard OBD-II PIDs—manifold absolute pressure, engine speed, intake air temperature, and fuel trim corrections—using the ideal gas law applied to actual engine displacement. Results were validated against pump-measured fill-up volumes. The speed-density model achieved errors of −3.6% to +4.3% across individual segments (combined error: −0.5%), outperforming the vehicle’s onboard trip computer, which exhibited errors of −10.6% to +14.6%. Derived CO₂ intensities ranged from 125.0 to 166.4 g/km, with a combined average of 147.2 g/km (pump reference: 147.9 g/km). Urban driving produced approximately 15% higher specific emissions than highway driving. These results demonstrate that a physics-based speed-density model can achieve within ±5% trip-level accuracy across diverse real-world conditions without machine learning, bespoke calibration, or a physical MAF sensor. Full article

One of the major obstacles in early cancer detection in dogs is the limited sensitivity in detecting circulating tumor DNAs (ctDNAs) with low abundances. Standard next-generation sequencing (NGS) without error correction typically achieves detection limits around ~1% mutant allele frequency (MAF). We sought to improve the detection sensitivity using a sequential CRISPR-EspCas9 enrichment strategy in which iterative in vitro cleavage (IVC) was combined with PCR amplification to selectively deplete wild-type DNA and enrich rare tumor mutations. Applying the strategy to genomic DNA and cell-free DNA mimics from canine mammary gland tumor cell lines demonstrated that IVC enrichment enabled the detection of cancer-associated PIK3CA H1047R mutations that were undetectable by conventional Sanger sequencing. To evaluate detection sensitivity, we characterized enrichment using synthetic templates for PIK3CA H1047R and other cancer-related mutations, BRAF V596E, and KRAS G12C. We observed that three iterations of sequential IVC achieved ~160, ~15, and ~2.2-fold enrichment for PIK3CA H1047R, BRAF V596E, and KRAS G12C, respectively. Under the present synthetic-template conditions, the analytical LOD reached 0.001% MAF for PIK3CA and 0.01% MAF for BRAF, whereas KRAS showed only modest enrichment and remained practically limited under the current guide design. Together, the results show that the CRISPR-EspCas9 IVC strategy enables selective enrichment of low-frequency single-nucleotide mutant alleles. We anticipate that the finding could be utilized to develop a highly sensitive veterinary liquid biopsy application with further optimization and validation using canine plasma cfDNA. Full article

Background and Objectives: Myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS) is a complex disorder characterized by persistent or relapsing fatigue lasting at least six months, not alleviated by rest and not previously present. It is accompanied by post-exertional symptom exacerbation and non-restorative sleep. Fatigue is often disabling and reduces daily activity by more than 50%. This study aimed to evaluate the long-term frequency of somatic and psychiatric disorders in women previously diagnosed with ME/CFS and to describe the long-term clinical course, laboratory findings, and fatigue-related changes during a 16-year follow-up period. Materials and Methods: Sixteen years ago, 40 women diagnosed with ME/CFS according to then-current CDC criteria were enrolled at the Clinic for Infectious Diseases and the Center for Laboratory Medicine, University Clinical Center of Vojvodina. All participants provided informed consent. After 16 years, 20 women agreed to follow-up evaluation. At both time points, participants underwent structured questionnaires, clinical examination, psychological assessment, and comprehensive laboratory testing, including hematological, biochemical, endocrinological, and virological analyses. Fatigue severity was assessed using the FibroFatigue Scale (FFS) and the Multidimensional Assessment of Fatigue (MAF) scale. Results: During follow-up, 15% of participants were diagnosed with rheumatoid arthritis, 10% with cervical or breast cancer, 5% experienced premature myocardial infarction, 5% developed bronchial asthma, and 20% were diagnosed with clinical depression. Progression of ME/CFS was observed in 15%, while 5% reported infertility. Additionally, 15% developed arterial hypertension. Only 15% of participants did not report symptom worsening or new diagnoses. Conclusions: Over the 16-year follow-up, 85% of women with ME/CFS developed significant somatic or psychiatric conditions. These findings suggest that women diagnosed with ME/CFS may experience substantial long-term somatic and psychiatric disease burden, supporting the need for continued clinical monitoring and individualized follow-up. Full article

Background/Objective: Type 1 diabetes (T1D) is a complex autoimmune disease characterized by the destruction of insulin-producing pancreatic beta cells. The TAB2/SUMO4 locus has been implicated in T1D susceptibility through a biochemical mechanism involving NFκB. Given that alterations in NFκB activity have been linked to the etiology of T1D, this study evaluated the association between single nucleotide polymorphisms (SNPs) in the TAB2/SUMO4 region (rs6942381, rs237027, rs237025, and rs7896) and T1D in a population from southern Brazil. Methods: Two T1D groups, each comprising 150 with childhood-onset (aged ≤14 years) and 150 with adulthood-onset (aged >18 years) were compared with healthy controls (165 children aged ≤14 years and 150 adults aged >18 years, respectively). Genotyping of SNPs in the TAB2/SUMO4 region was performed using real-time PCR. Results: All polymorphisms were in Hardy–Weinberg equilibrium. The genotype and allele frequencies of the studied polymorphisms in the TAB2/SUMO4 region did not differ among groups in either children or adults. The MAF of the children and adults controls are respectively for rs6942381 49.1% (95% CI 44–54%) and 48.0% (95% CI 42–52%), rs237027 12.4% (95% CI 9–16%) and 11.7% (95% CI 8–15%), rs237025 45.5% (95% CI 40–51%) and 46.0% (95% CI 41–52%) and rs7896 18.2% (95% CI 14–22%) and 24.3% (95% CI 19–29%). The haplotype frequencies were also similar between groups. The observed minor allele frequencies were similar to those reported in European populations. Conclusions: TAB2/SUMO4 locus polymorphisms (rs6942381, rs237027, rs237025, and rs7896) were not associated with childhood- or adulthood-onset T1D in the studied population. Full article

Emotion recognition through electroencephalogram (EEG) signals is crucial for brain–computer interfaces (BCIs), yet existing methods often struggle with heterogeneous feature fusion and capturing long-range temporal dependencies. To address these challenges, we propose MAF-TransNet, a novel unified spatiotemporal framework. Specifically, parallel Fully Connected Neural Network (FCNN) modules first non-linearly align heterogeneous differential entropy (DE) and power spectral density (PSD) features. Subsequently, an Adaptive Channel-wise Feature Encoder (ACFE) recalibrates spatial–spectral responses to highlight emotion-relevant cortical activations. Finally, a Transformer encoder dynamically models the global temporal evolution of emotional states. Evaluated on the SEED-IV and DEAP datasets, MAF-TransNet achieves superior subject-dependent (SD) accuracies of 88.80% and 96.58%, respectively, alongside robust subject-independent (SI) performance. Furthermore, Granger causality analysis reveals distinct emotion-dependent prefrontal asymmetry, while t-SNE visualizations confirm the formation of a highly discriminative, linearly separable feature manifold. Ultimately, MAF-TransNet effectively unifies local spatial–spectral extraction with global temporal modeling, providing an accurate and robust approach, while offering preliminary insights into the spatiotemporal dynamics of emotion for future affective BCI applications. Full article

Achieving long-term, continuous, and accurate localization for Unmanned Aerial Vehicles (UAVs) in outdoor GNSS-denied environments where pre-existing reference maps are available is challenging. To this end, this paper proposes a Cross-view Particle Filter Localization (CPFL) framework. Unlike existing particle filter approaches that rely on inertial sensors for state propagation or sparse semantic labels for observation updates, CPFL is a vision-driven solution. This framework introduces specific adaptations into the two core stages of particle filtering: In the motion propagation stage, it achieves visual state transition by calculating a feature-based inter-frame homography mapping to estimate the 2D global relative motion components, eliminating the dependency on inertial priors; in the observation correction stage, a Dual-Granularity Adaptive Gating (DGAG) cross-view network is designed to mitigate perceptual aliasing and generate discriminative absolute position weights for the particles. By fusing these two stages through a filter mechanism, the framework transforms unbounded cumulative drift into bounded absolute localization errors. Furthermore, addressing the measurement deficiencies of traditional single-frame metrics, this paper also proposes a Trajectory Continuity Index (TCI@d) tailored for continuous localization tasks. Experiments on the real-world MAFS dataset confirm that this framework achieves a mean localization error of 5.28 m and a localization success rate of 89.7% under a 10-m threshold. Compared with mainstream vision-only algorithms and IMU-fusion baselines, this framework demonstrates lower mean errors and improved trajectory continuity, validating its effectiveness for long-term robustness. Full article

Surface defects in additively manufactured internal channels limit their practical applications. Conventional post-processing methods suffer from limited accessibility and a tendency toward over-polishing, whereas magnetic abrasive finishing (MAF) offers high adaptability and precise process controllability. This study systematically investigates the material removal mechanisms in magnetic abrasive polishing and clarifies the distinctions and transitions between two-body and three-body wear modes. Based on these findings, a rolling removal model grounded in rough surface contact theory and a sliding removal model incorporating correction factors are established. Experiments were conducted on AlSi10Mg internal channels fabricated via selective laser melting (SLM) using a composite magnetic field polishing apparatus. The results verify the accuracy of the proposed models and demonstrate that the process effectively reduces surface defects and surface roughness. Although some deviations arise from model idealization and non-uniform magnetic field distribution, this study establishes a systematic theoretical framework for material removal in additively manufactured complex internal channels. Full article

Based on SLAF-seq technology, 174 white clover accessions were analyzed using population structure and genetic evolution to develop SNP markers of all accessions. We obtained 2329.4 Mb reads of sequenced data, and the reads of the samples ranged from 4,701,984 to 31,540,232. The sequencing quality value (Q30) uniformly changed from 90.61% to 96.82%, with an average of 93.11%. The GC content of the samples changed from 38.96% to 43.98%, averaging 40.96%, with a control of 34.21%. A total of 320,417 SLAF tags were developed, with an average sequencing depth of 16.42×. There were 202,625 polymorphic SLAF tags, accounting for 63.24% of the total number of SLAF tags. Finally, 2,999,555 polymorphic SNPs were found, and 102,025 high-quality SNPs were selected for downstream analyses after filtering with minor allele frequency (MAF) > 0.05 and completeness > 0.5. Population structure analysis supported K = 2, indicating two major ancestral genetic backgrounds among the accessions. Phylogenetic analysis and principal component analysis further divided the accessions into three genetic subclusters, suggesting finer-scale genetic differentiation. In addition, one-way ANOVA and chi-squared tests revealed a significant association between genetic groups and geographic origin (χ² = 25.78, df = 8, p = 0.0012; F = 3.489, p = 0.032), provided limited evidence for a possible association between genetic grouping and geographic origin. Compared with photosynthetic traits, agronomic traits showed a broader range of variations, with coefficient of variance values for agronomic traits ranging from 24.59% to 139.02% and for photosynthetic traits from 4.29% to 78.57%. This difference suggests that morphological traits were highly differentiated among the 174 accessions. The consistency between phenotypic clustering (based on agronomic traits) and molecular clustering (based on SNP data) suggests that our SNP dataset captures biologically meaningful genetic variation, providing a solid foundation for future genome-wide association studies (GWASs) and marker-assisted selection (MAS) in white clover. Full article

Background: Lymphocyte-activation gene 3 (LAG3) and cytotoxic T-lymphocyte-associated protein 4 (CTLA4) are immune checkpoint receptors and inhibitory regulators of T-cells. Methods: Here, we analyzed the prevalence and potential impact of the LAG3 gene variant rs870849 and the CTLA4 gene variant rs231775 in AML patients eligible for autologous stem cell transplantation. Results: While CTLA4 rs231775 was prevalent at reduced minor allele frequencies (MAF 0.33), LAG3 rs870849 was prevalent at elevated minor allele frequencies (MAF 0.58) in AML patients, compared to the allele frequencies in the European population (MAF 0.37 and MAF 0.39). The gene risk analysis indicated a dose-dependent risk of AML disease associated with LAG3 rs870849, but no risk associated with CTLA4 rs231775. Baseline blood count profiles differed across LAG3 genotypes, suggesting a link between LAG3 rs870849 and disease-associated levels of anemia, thrombocytopenia and peripheral blast percentage. Conslusions: The germline LAG3 variant rs870849 may be associated with AML disease risk and specific hematological disease features. Full article

The Colorado potato beetle, Leptinotarsa decemlineata, is a major insect pest of potatoes. Our previous studies have demonstrated that two cytochrome P450 monooxygenase (P450s) genes, CYP9Z140 and CYP9AY1, and a uridine diphosphate–glycosyltransferase (UGT) gene, UGT321AP1, play important roles in thiamethoxam resistance to L. decemlineata. However, the related upstream regulatory mechanism remains unclear. In this study, we first monitored the resistance of L. decemlineata field populations to thiamethoxam in Xinjiang to determine the resistance ratios. The predicted results demonstrated that four transcription factors (TFs), CncC/Maf, Abd-B, FoxO, and Ptx1, may bind to the core regions of three gene promoters. The qRT-PCR results revealed that the TFs were significantly upregulated by thiamethoxam and exhibited specific spatiotemporal expression patterns. Dual-luciferase reporter assays indicated that the CncC pathway could regulate the expression of three detoxification genes, whereas Abd-B and FoxO only regulate CYP9Z140 and UGT321AP1 expressions, respectively. Ptx1 could regulate the expression of both CYP9AY1 and UGT321AP1. Furthermore, knockdown of several TFs through RNA interference significantly reduced expression of the corresponding detoxification genes, consistent with the dual-luciferase reporter assay results, and increased the thiamethoxam susceptibility of test adults. These findings aid in gaining a deeper understanding of the transcriptional regulation mechanisms of insecticide resistance in insects. Full article