Search Results (383)

Background/Objectives: Schistosomiasis is a neglected tropical disease affecting >200 million people worldwide. Praziquantel is the sole recommended drug against Schistosoma mansoni; however, it lacks activity against juvenile forms and cannot prevent reinfection. Thus, there is an urgent need to identify novel therapeutic targets. Long noncoding RNAs (lncRNAs) are known to regulate various biological processes in S. mansoni, including parasite pairing and fertility; therefore, screening for novel lncRNAs could reveal new potential targets. Methods: We compiled all publicly available RNA-seq data from the Sequence Read Archive (SRA) and performed a hierarchical transcriptome assembly using the multi-sample assembler Ryūtō, combined with version 10 of the S. mansoni genome. We applied HOMER for peak-calling and identification of histone marks and used weighted gene co-expression network analysis (WGCNA) to infer putative functions of lncRNAs in sexual dimorphism. Results: Using a robust pipeline, we identified 10,170 novel lncRNA genes comprising 16,990 novel lncRNA transcripts, including 8783 intergenic, 7918 antisense, and 289 intronic lncRNA transcripts. Most (78.7%) have histone regulatory marks (H3K4me3, H3K27me3, H3K27ac, or H4K20me1) near their transcription start sites, indicating potential expression regulation. Comparing male and female samples, we identified 1991 differentially expressed genes (FDR < 5%, |log₂FC| ≥ 1.5), including 296 known lncRNAs and 339 novel lncRNAs. WGCNA identified hub lncRNAs within co-expression modules, and Gene Ontology enrichment analyses (FDR ≤ 5%) suggest that these lncRNAs are involved in cell differentiation and morphogenesis pathways. Conclusions: We provide a comprehensive catalog of S. mansoni lncRNAs. These findings offer opportunities to discover potential new therapeutic targets, advancing the future development of anti-schistosome therapies. Full article

Alkali-activated materials can significantly reduce carbon dioxide emissions compared with cement. However, their durability remains insufficiently understood. This study investigated the effects of calcium hydroxide (Ca(OH)₂, CH), an expansion agent (calcium sulfoaluminate, CSA), and a shrinkage-reducing agent (SRA) on the compressive strength and length change and determined the optimal content levels for each agent. Experiments were conducted to evaluate the compressive strength and length change of 17 mortar mixtures containing CH, CSA, and SRA. The substitution ratios of CH, CSA, and SRA were fixed at three predefined levels for each factor. The microstructural changes induced by the use of each agent were analyzed using pH measurements, porosity analysis, and X-ray diffraction. In addition, the water desorption behaviors associated with CSA and SRA were assessed. Experimental and statistical analyses demonstrated that the optimal contents of CH, CSA, and SRA for simultaneously improving the compressive strength and length change were 8.54, 10.0, and 0.76 wt.%, respectively. The use of CSA significantly enhanced the compressive strength development and dimensional stability of the mortar. This improvement was associated with a reduction in the porosity, which was attributed to ettringite formation. Furthermore, while the SRA slightly reduced the compressive strength, it significantly improved the dimensional stability. Full article

This paper introduces fairer measures of individual pitcher performance in baseball using the Shapley Value from coalitional game theory. The paper’s key conceptual innovation is a novel two-stage procedure for constructing the coalitionary game value functions for runs allowed and outs recorded by a baseball team’s defense. This procedure enables the Shapley Value calculation to fairly divide credit for runs and out between different pitchers and between pitchers and fielders. It also results in two new statistics—Shapley Pitcher Runs (SPR) and Shapley Pitcher Outs (SPO)—that, unlike traditional pitching statistics, consistently satisfy several mathematical fairness axioms. A third statistic, called Shapley Run Average, provides a fairer measure of pitcher efficiency. I calculate these statistics for the 2022 Major League Baseball regular season and the 1955–2022 World Series championships. Using SPR and SPO as the standard for fairness, empirical analysis reveals that the traditional pitching statistics systematically and unfairly overcredit pitchers by 40–50%, with starting pitchers miscredited more severely than relievers. Analysis of SRA identifies efficient pitchers whose performance is obscured by conventional statistics and enables a reassessment of historic World Series performances. Overall, this work demonstrates another application of the Shapley Value to creating new performance measures in team sports. Full article

Background: Human skin and saliva microbial communities have emerged as promising forensic biomarkers due to their individual specificity. However, existing studies are limited by small sample sizes and methodological inconsistencies. This proof-of-concept study aims to develop a novel framework integrating 2bRAD-M sequencing with a hierarchical attention network (HAN) for forensic individual identification, addressing these limitations through large-scale public data integration and controlled validation. Methods: We utilized 2263 skin and saliva samples from public databases (Qiita, HMP, NCBI SRA) for model development. These public data included longitudinal samples collected over periods up to 180 days. A contemporary validation cohort of 6 volunteers, providing 26 forensic-relevant samples (including simulated touch evidence), was sequenced using 2bRAD-M for validation. Data integration involved batch effect correction (ComBat), normalization (CSS), and cross-database harmonization using GTDB for taxonomic assignment. The HAN model was optimized with triplet margin loss for metric learning. Results: The HAN model achieved 98.7% Rank-1 accuracy for pristine samples, outperforming random forest (70.2%) and CNN (75.8%). Microbial signatures showed high temporal stability (ICC = 0.86 over 180 days) and robustness in mixed samples (87.4% accuracy). Discriminatory biomarkers included Cutibacterium (skin) and Prevotella (saliva). Particulate matter exposure significantly influenced microbial composition (PERMANOVA R² = 0.32, p < 0.001). Conclusions: This study establishes a proof-of-concept pipeline for microbial forensics, demonstrating high accuracy under controlled conditions. Future work must address antibiotic exposure, sample diversity, and cross-laboratory validation before forensic implementation. Full article

Cytochrome P450 monooxygenases (CYPs/P450s) play a key role in organisms’ primary and secondary metabolism in species across all domains of life. Accurate annotation of P450 genes is crucial for identifying their functions, evolution, and, consequently, their biotechnological potential. In this study, we report the identification of an unprecedented one-nucleotide exon required for the correct assembly of CYP621A P450 genes from multiple Fusarium species. Through comparative genomic analysis of 20 orthologous CYP621A genes, supported by an intronless CYP621B1 gene from Aspergillus clavatus, we demonstrate that omission of this single-nucleotide exon disrupts exon phase compatibility and prevents reconstruction of a full-length, functional P450 protein. The micro-exon encodes the central nucleotide of the glycine codon in the highly conserved PKG motif, which is essential for maintaining the structural integrity between the EXXR and PERF motifs, a characteristic of P450 enzymes. Importantly, transcriptomic evidence from sequence read archive (SRA) data confirms accurate splicing of this one-nucleotide exon in Fusarium solani and F. acuminatum under multiple growth conditions. This work presents the second example of the smallest exon reported to date for a gene, and the first for a P450 gene or a fungal gene. The study’s findings have broad implications for genome annotation pipelines, underscoring the need for careful manual curation and improved algorithms to detect ultra-small exons in functionally constrained regions of eukaryotic genes. Full article

Breast cancer entails profound physical, emotional, and relational changes that persist beyond biomedical treatment and may substantially affect women’s body image, sexuality, and engagement in daily occupations. This descriptive phenomenological qualitative study examined the lived experiences of eight Spanish breast cancer survivors through in-depth semi-structured interviews conducted after completion of oncological treatment. Transcripts were analyzed using discourse analysis with iterative interpretation. Three interrelated findings were identified: (1) bodily changes linked to mastectomy and adjuvant therapies disrupted continuity with the previously known body, eliciting estrangement, vulnerability, and grief for the former bodily self; (2) sexuality emerged as a particularly vulnerable domain, shaped by diminished desire, vaginal dryness and pain, shame, altered self-perception, and the need to renegotiate intimacy within the couple; and (3) coping and meaning-making were strengthened by psychological support, efforts to emotionally protect family members, and, notably, peer support and helping other women as key sources of resilience. These findings highlight the need for integrated, culturally sensitive, person-centered survivorship care that explicitly addresses sexuality, body image, and emotional well-being. Occupational therapy may contribute by supporting embodied identity reconstruction, participation in meaningful occupations, and the reconfiguration of intimacy after breast cancer. Full article

Intensive swine production contributes significantly to the global protein supply but generates considerable environmental pressure, particularly through greenhouse gas emissions and surplus slurry management. Anaerobic digestion (AD), especially (co-AD), has been widely investigated as a mitigation strategy to enhance renewable energy generation and nutrient recovery. This systematic review synthesizes life cycle assessment (LCA) studies published between 2019 and 2025 that evaluated AD systems treating swine slurry, following the PRISMA 2020 guidelines. Across diverse methodological approaches and regional contexts, the literature consistently shows that AD can reduce global warming potential compared with conventional slurry management, with stronger environmental benefits when biogas is efficiently valorized and when swine slurry is co-digested with complementary organic substrat. Co-AD emerges as a key mitigation option by improving biogas yields, process stability, and overall environmental performance while also enabling better utilization of external organic waste. However, the results remain highly sensitive to operational factors such as methane leakage, digestate management, energy efficiency, and substrate selection. This review highlights the methodological inconsistencies among LCA studies and underscores the need for harmonized assessment frameworks and improved emission data. Overall, co-AD represents a promising pathway for enhancing the environmental sustainability of swine production systems when integrated into optimized, context-specific management strategies. Full article

The root system provides the interface between the plant and the soil that is responsible for water and nutrient uptake and transport. We hypothesized that almond trees in the commercial production environment could adjust their root acquisitive traits with distance vertically and horizontally from driplines as adaptive responses to within-orchard reductions in irrigation and nitrogen inputs. We compared the responses of root acquisitive traits under four years of treatments ranging from +W+N (15 ML ha⁻¹ water and 300 kg ha⁻¹ nitrogen per season) to −W−N (10.5 ML ha⁻¹ water and 160 kg ha⁻¹ nitrogen per season, with −W involving a 30% reduction in irrigation and −N involving a 46% reduction in nitrogen). Roots (<3 mm) were sampled through soil coring in the winters of 2017, 2018, and 2019. Root sampling was conducted along the vertical gradient and along the horizonal gradient (0 cm, 80 cm, and 240 cm from the dripline). Four years of treatments highlighted that the data variation was driven mainly by the difference between the +W and −W treatments (along PC1). Further, the difference between −W−N (combined resource reduction) and the other three treatments (+W+N, +W−N, and −W+N) contributed to the data variation (along PC2). Also, the temporal dynamics of treatment effects over 2017, 2018, and 2019 suggested a temporally strengthened +W−N effect to increase root biomass, average root diameter, specific root surface area (SRA), and specific root length (SRL) at deeper soil depths and at greater soil distances from driplines. These findings on the spatial and temporal plasticity of traits representing root resource acquisition capabilities highlighted the important role of root systems in maintaining crop productivity under reduced irrigation and nitrogen inputs. Full article

Abdominal aortic aneurysm (AAA) is a serious disease with no effective pharmacological therapy. Although inflammation is recognized as a key regulator of AAA, targeting inflammatory pathways once the disease is established does not improve outcomes. Understanding the earliest molecular indicators could clarify precise biological targets and prognostic markers for AAA. Using ApoE-deficient mice, we performed RNA-Seq on suprarenal abdominal aortas (SRAs) from Ang II- and saline-treated mice 24 h after infusion. We further developed a unique model of hyperlipidemic mice in which the expression of the inhibitor of nuclear factor kappa B kinase subunit beta (IKKβ) can be conditionally suppressed in vascular smooth muscle cells (VSMCs). RNA-Seq data revealed early IKKβ-dependent cellular anabolic processes in SRAs, including activation of the mammalian target of rapamycin complex 1 (mTORC1) pathway. Furthermore, deletion of the Ikbkb gene in VSMCs significantly reduced the rate of aneurysm rupture in mice exposed to Ang II. In situ analysis further confirmed that the absence of IKKβ in VSMCs is associated with a reduced inflammatory response and the preservation of their contractile phenotypes. Our results reinforce the crucial role of VSMCs in rapid adaptation, leading to deleterious inflammation-dependent remodeling of the vascular wall, and define a previously unrecognized anabolic role of IKKβ in AAA pathogenesis. Full article

The blunt snout bream (Megalobrama amblycephala, BSB) is a freshwater economic fish with Chinese characteristics, and its genetic characteristics have unique value for studying fish evolution. The gynogenetic blunt snout bream (GBSB) obtained through distant hybridization between cross-order species, which showed a faster growth rate than the female parent, but its appearance is similar to that of BSB and is difficult to distinguish. Therefore, by comparing the transcriptome sequencing data of BSB and GBSB (SRA number: PRJNA893089, not released yet), we identified 30 SNPs associated with genes related to muscle growth, protein synthesis, and glycolysis that are unique to GBSB. Through multi-sample PCR detection and sequencing analysis, 16 SNPs with stable differences in GBSB and BSB were obtained. The polymorphism analysis of 16 SNP sites showed that 9 SNP sites were polymorphic in GBSB, which could be used to identify GBSB and its female parent, BSB. In addition, the 9 SNP sites are located in the myoz1a (myozenin 1a) gene, which is related to muscle development, and may provide insights for further study of muscle growth regulation. Therefore, this study provides candidate marker resources for GBSB germplasm resource identification and molecular marker-assisted breeding, which is beneficial for improving the efficiency and reliability of selection and breeding work. Full article

This study presents the development and validation of a high-speed optical data acquisition system for detecting and characterizing hydrodynamic cavitation downstream of a triangular nozzle. The system integrates a PIN photodiode, a transimpedance amplifier, and a high-sampling-rate microcontroller. Its performance was first evaluated using controlled sinusoidal signals, and statistical stability was assessed as a function of the number of acquired samples. Experiments were subsequently conducted in a converging–diverging conduit under biphasic flow conditions, where mean irradiance, standard deviation, and frequency spectra were analyzed downstream of the nozzle. The optical signal distributions revealed transitions in flow behavior associated with cavitation development, which were quantified through statistical metrics and spectral features. The Strouhal number was estimated from dominant frequencies extracted from the spectra, exhibiting a non-monotonic dependence on the Reynolds number, consistent with changes in flow structure and turbulence intensity. Spectral analysis further indicated frequency bands associated with energy transfer across turbulent scales and bubble dynamics. Overall, the results demonstrate that the proposed optical system constitutes a viable and non-intrusive methodology for detecting and characterizing cavitation intensity in a way that complements other optical and acoustic methods. Full article

Methicillin-resistant Staphylococcus aureus (MRSA), a major global public health threat due to its broad resistance, urgently requires the development of new antibiotic alternatives. (‒)‒Epigallocatechin-3-gallate (EGCG) is considered a natural bioactive compound with anti-MRSA properties. The L-Lectin module of serine-rich adhesin for platelets (SraP) is considered an important target for blocking MRSA-infected hosts. This study aims to investigate the mechanism of action of EGCG against MRSA. Surface plasmon resonance (SPR), cell adhesion and invasion, biofilm formation, checkerboard assays, RNA sequencing (RNA-seq) and quantitative real-time polymerase chain reaction (qRT-PCR) were performed. The results showed that EGCG bound to SraP L Lectin with high affinity and effectively inhibited MRSA colonization. Additionally, EGCG significantly suppressed pyrimidine metabolism and downregulated related genes, thereby potentially inhibiting bacterial growth. It also markedly reduced the expression of multiple genes associated with β-lactam resistance and inhibited biofilm formation. A strong synergistic effect was observed between EGCG and the bactericidal agent ceftriaxone (CRO). When combined with 10 μg/mL EGCG, CRO required 75% less dosage and exhibited a prolonged antimicrobial effect. In conclusion, EGCG exerts anti-MRSA effects through multiple pathways and represents a promising candidate as an alternative therapeutic agent against MRSA infections. Full article

Hemp (Cannabis sativa L.) is one of the oldest cultivated plants in the world. It is a wind-pollinated and heterozygous species, and diverse phenotypes can occur within population varieties. In our study, three different hemp varieties—(‘Carmagnola Selected’ (CS), ‘Tiborszallasi’ (TS) and ‘Finola selection’ (FS))—were grown. Based on visual characteristics, two, five and four phenotypes were identified within CS, TS and FS, respectively. According to Cannabis sativa L. transcriptome data from the Sequence Read Archive (SRA), 4631 single-nucleotide polymorphism (SNP) positions were identified to develop capture probes. DNA was isolated from 171 plants representing selected phenotypes of three cultivars. Next-generation sequencing (NGS) libraries were constructed and hybridized with capture probes for target enrichment. The population structure of the samples was analyzed using SNP data for each genotype. Based on genotype profiles, CS formed a single cluster, while TS and FS were each grouped into two clusters, with phenotypes randomly distributed among them. The GWAS results were visualized using Manhattan plots. Fourteen significant SNPs surpassing the false discovery rate (FDR) of 0.01 were identified for delta-9-tetrahydrocannabinol (delta-9-THC). For cannabigerol (CBG), 12 significant SNPs were detected, and for myrcene, one SNP exceeded the 0.01 FDR threshold. However, plausible genes located 1000 bp to the left and right of the SNP position were identified for all significant SNPs. Full article

Rootstock selection plays a pivotal role in determining the ecophysiological performance, growth dynamics, and hydraulic functioning of grafted citrus plants. This study evaluated three citrus rootstocks—Trifoliate Orange (TO), Swingle Citrumelo (SC), and Flying Dragon (FD)—grafted with Citrus clementina cv. SRA 63 (CLM), with the aim of elucidating how the rootstock genotype influences morphological traits, dry matter allocation, hydraulic conductance, and xylem anatomical features. Plants were monitored over two years under controlled agronomic conditions, and biometric, physiological, hydraulic, and anatomical traits were assessed. The results revealed distinct rootstock-dependent patterns. CLM/TO and CLM/SC exhibited greater vegetative vigor, higher total biomass, more extensive absorbing root systems, and larger conductive xylem areas, resulting in superior theoretical hydraulic flow. In contrast, CLM/FD demonstrated reduced growth, a smaller trunk diameter, lower biomass accumulation, and elevated hydraulic resistance in both root and graft union sectors, consistent with its known dwarfing behavior. Despite its lower hydraulic efficiency, FD promoted the highest stomatal conductance, suggesting a distinct water use strategy. Overall, the findings demonstrate that the rootstock genotype markedly influences the hydraulic architecture and growth partitioning of grafted Clementine plants. These insights contribute to our understanding of scion–rootstock interactions and support more informed selections of rootstocks in citrus orchards under diverse environmental and management scenarios. Full article

Tyrosine phosphorylation has emerged as a central regulatory mechanism in innate immunity. Building on our recent studies that Syk and EGFR sequentially phosphorylate TLR9 to fully activate it, we discuss how similar mechanisms operate across other Toll-like receptors and the cytosolic DNA sensor STING. Evidence from complementary systems reveals that receptor and nonreceptor tyrosine kinases, including Src-family kinases, Syk, BTK, and EGFR, form an integrated signaling network that triggers receptor activation, trafficking, and downstream gene expression. Scavenger receptors such as SR-A further drive this kinase cascade by coordinating viral recognition to TLR activation. These observations reveal a novel ‘tyrosine kinase axis’ that connects nucleic acid sensing to spatially controlled innate immune signaling and highlight new opportunities to modulate innate immunity through tyrosine kinase regulation. Full article