Search Results (29,845)

The retinal pigment epithelium (RPE) is strongly involved in the pathogenesis of several retinal diseases, such as age-related macular degeneration (AMD). RPE models addressing specific pathological pathways are of high importance for understanding cellular pathomechanisms and pre-clinical screening of potential new therapeutics. The goal of this study is to establish standard operation protocols for single-eye porcine RPE preparation for AMD-relevant models of oxidative stress (RPE-Ox) and inflammation (RPE-Inf). Porcine primary RPE were prepared from one eye and seeded into one well of 12-well plates or, for polar differentiation, in transwell inserts. Different coatings (Poly-ᴅ-Lysine and laminin) and serum content of media (10%, 5%, and 1%) were tested to determine optimal culture parameters. For RPE-Ox, cells were treated with NaIO₃, CoCl₂, or erastin; cell viability (thiazolyl blue tetrazolium bromide, MTT), and gene expression (RT-qPCR) were determined. For RPE-Inf, cells were treated with lipopolysaccharide (LPS), polyinosinic/polycytidylic acid (Poly I:C), or tumor necrosis factor alpha (TNF-α); cell viability (MTT), cytokine secretion (ELISA), and gene expression (RT-qPCR) were determined. For transwell plates in RPE-Inf, cell viability (MTT), polar cytokine secretion (ELISA), gene expression (RT-qPCR), and transepithelial electrical resistance (TEER) for barrier assessment were conducted. For RPE-Ox, effective LD₅₀ could be achieved by using 24 h stimulation with 25 µm erastin, seven days after preparation in 5% serum cultures, without coating. For gene expression assessment, the use of Poly-ᴅ-Lysine is recommended. For RPE-Inf, three days of LPS stimulation (1 µg/mL) showed effective cytokine activation with 5% serum on uncoated 12-well plates. Transwell plates are not recommended for cytokine secretion assessment. It can be used for cell barrier assays in which LPS also showed effective cell barrier decrease and gene expression assays. Two specific best practice protocols for the use of porcine single-eye cultures in AMD research concerning oxidative stress and inflammation with optimized parameters were established and are provided. Full article

The fixation time of alleles is a fundamental concept in population genetics, traditionally studied using the Wright–Fisher model and classical coalescent theory. However, these models often assume homogeneous environments and equal reproductive success among individuals, limiting their applicability to real-world populations where environmental heterogeneity plays a significant role. In this paper, we introduce a new forward-time model for estimating fixation time that incorporates environmental heterogeneity through the use of fractional calculus. By introducing a fractional parameter α, we capture the effects of heterogeneous environments on offspring production. To solve the resulting fractional differential equations, we develop a novel spectral method based on Eta-based functions, which are well-suited for approximating solutions to complex, high-variation systems. The proposed method reduces the problem to an optimization framework via the operational matrix of fractional derivatives. We demonstrate the effectiveness and accuracy of this approach through numerical examples and show that it consistently captures fixation dynamics across various scenarios. This work offers a robust and flexible framework for modeling evolutionary processes in heterogeneous environments. Full article

Regenerative chatter is an unfavorable phenomenon that severely affects machining efficiency and surface finish in milling operations. The prediction of chatter stability is an important way to obtain the stable cutting zone. Based on implicit multistep schemes, this paper presents the third-order and fourth-order implicit exponentially fitted methods (3rd IEM and 4th IEM) for milling stability prediction. To begin with, the delay differential equations (DDEs) with time-periodic coefficients are employed to describe the milling dynamics models, and the principal period of the coefficient matrix is firstly decomposed into two different subintervals according to the cutting state. Subsequently, the fourth-step and fifth-step implicit exponential fitting schemes are applied to more accurately estimate the state term. Two benchmark milling models are utilized to illustrate the effectiveness and advantages of the high-order implicit exponentially fitted methods by making comparisons with the three typical existing methods. Under different radial immersion conditions, the numerical results demonstrate that the 3rd IEM and the 4th IEM exhibit both faster convergence rates and higher prediction accuracy than the other three existing prediction methods, without much loss of computational efficiency. Finally, in order to verify the feasibility of the 3rd IEM and the 4th IEM, a series of experimental verifications are conducted using a computer numerical control machining center. It is clearly visible that the stability boundaries predicted by the 3rd IEM and the 4th IEM are mostly consistent with the cutting test results, which indicates that the proposed high-order exponentially fitted methods achieve significantly better prediction performance for actual milling processes. Full article

Adipose-derived mesenchymal stem cells (ASCs) have great potential in regenerative medicine due to their abundance and innate multi-lineage differentiation potential. However, the therapeutic efficacy of ASCs is often compromised by poor microenvironmental conditions in the damaged tissues after transplantation. In this study, we generated and assessed genetically modified ASCs that expressed granulocyte chemotactic protein-2 (GCP-2) and platelet-derived growth factor-β (PDGF-β). The results revealed that three-dimensional (3D)-cultured ASCs overexpressing GCP-2 and PDGF-β (3D-A/GP) yielded a significant increase in proangiogenic gene expression, cell migration, and endothelial tube formation in vitro. Moreover, the Matrigel plug assay revealed that 3D-A/GP formed functional blood vessels, and 3D-A/GP injection in a hind limb ischemia (HLI) model revealed higher blood flow recovery, limb salvage, and capillary density and lower apoptosis in mice, compared to the controls. Notably, 3D-A/GP exhibited differentiation into endothelial-like cells and upregulated expression of angiogenic factors in ischemic limb tissue. Our results highlight the value of using a combination of genetic engineering and 3D culture systems to improve the therapeutic effect of ASCs in terms of angiogenesis-dependent tissue repair. The dual modulation of GCP-2 and PDGF-β, in combination with 3D culture, presents a new and synergistic opportunity to maximize the use of ASC-based therapies for ischemic diseases and other regenerative medicine applications. Full article

Background: Irradiation (IR) targets cancer cells, but also the tumor microenvironment, including the tumor’s blood vessels. In addition to tumor endothelial cell (TEC) apoptosis, IR can lead to TEC activation, potentially increasing immune cell infiltration. However, the changes underlying the IR-induced activation of endothelial cells (ECs) are poorly understood. This study investigated dose- and time-dependent molecular and functional responses of murine and human EC lines to IR in vitro and TECs in vivo in murine tumor models of colorectal carcinoma. Methods: HUVEC, EA.hy926, and Hulec5a, as well as murine bEND.3, 2H11, and SVEC4-10 EC lines, were irradiated with single doses of 2–10 Gy. EC proliferation and survival after IR were assessed by staining all nuclei (Hoechst 33342) and dead cells (propidium iodide) every 24 h for 5 days using the Cytation 1 Cell Imaging Multi-Mode Reader. RNA sequencing analysis of HUVECs irradiated with 2 Gy and 5 Gy at 24 h and 72 h after IR was conducted, focusing on processes related to EC activation. To validate the RNA sequencing results, immunofluorescence staining for proteins related to EC activation, including Stimulator of Interferon Response cGAMP Interactor 1 (STING), Nuclear factor kappa B (NF-κβ), and Vascular cell adhesion molecule 1 (VCAM-1), was performed. To validate the in vitro results, the response of TEC in vivo was analyzed using publicly available RNA sequencing data of TECs isolated from MC38 colon carcinoma irradiated with a single dose of 15 Gy. Finally, murine CT26 colon carcinoma tumors were immunofluorescently stained for STING and NF-κβ 24 and 48 h after IR with a clinically relevant fractionated regimen of 5 × 5 Gy. Results: Doses of 2, 4, 6, 8, and 10 Gy led to a dose-dependent decrease in proliferation and increased death of ECs. RNA sequencing analysis showed that the effects on the transcriptome of HUVECs were most pronounced 72 h after IR with 5 Gy, with 1014 genes (661 down-regulated and 353 up-regulated) being significantly differentially expressed. Irradiation with 5 Gy resulted in HUVEC activation, with up-regulation of the immune system and extracellular matrix genes, such as STING1 (log₂FC = 0.81) and SELE (log₂FC = 1.09), respectively; and down-regulation of cell cycle markers. Furthermore, IR led to the up-regulation of immune response- and extracellular matrix (ECM)-associated signaling pathways, including NF-κβ signaling and ECM–receptor interaction, which was also observed in the transcriptome of irradiated murine TECs in vivo. This was confirmed at the protein level with higher expressions of the EC activation-associated proteins STING, NF-κβ, and VCAM-1 in irradiated HUVECs and irradiated TECs in vivo. Conclusions: IR induces changes in ECs and TECs, supporting their activation in dose- and time-dependent manners, potentially contributing to the anti-tumor immune response, which may potentially increase the infiltration of immune cells into the tumor and thus, improve the overall efficacy of RT, especially in combination with immune checkpoint inhibitors. Full article

This study investigates the fracture behavior of recycled aggregate concrete by integrating fractal theory and empirical modeling to quantify how recycled coarse aggregates (RCAs) and recycled fine aggregates (RFAs) influence crack complexity and maximum crack width under varying content and loads. The results reveal distinct scale-dependent behaviors between RCA and RFA. For RCA, moderate dosages enhance fractal complexity (a measure of surface roughness) by promoting micro-crack proliferation, while excessive RCA reduces complexity due to matrix homogenization. In contrast, RFA significantly increases both fractal complexity and crack width under equivalent loads, reflecting its susceptibility to micro-scale interfacial transition zone (ITZ) degradation. Non-linear thresholds are identified: RCA’s fractal complexity plateaus at high loads as cracks coalesce into fewer dominant paths, while RFA’s crack width growth decelerates at extreme dosages due to balancing effects like particle packing. Empirical models link aggregate dosage and load to fractal dimension and crack width with high predictive accuracy (R² > 0.85), capturing interaction effects such as RCA’s load-induced complexity reduction and RFA’s load-driven crack width amplification. Secondary analyses further demonstrate that fractal dimension correlates with crack width through non-linear relationships, emphasizing the coupled nature of micro- and macro-scale damage. These findings challenge conventional design assumptions by differentiating the impacts of RCA (macro-crack coalescence) and RFA (micro-crack proliferation), providing actionable thresholds for optimizing mix designs. The study also advances sustainable material design by offering a scientific basis for updating standards to accommodate higher recycled aggregate percentages, supporting circular economy goals through reduced carbon emissions and waste diversion, and laying the groundwork for resilient, low-carbon infrastructure. Full article

Aging of asphalt is a major cause of pavement distress. While regenerators restore aged asphalt, their mechanisms and efficacy differences remain unclear. This study quantified the repair effects of waste bio-oil (WBO) and mineral oil (MO) rejuvenators on aged asphalt binder using a comprehensive characterization approach. Conventional properties (penetration, softening point, ductility), functional groups (FT-IR), thermal stability (TG), differential scanning calorimetry (DSC), and dynamic shear rheology (DSR) were analyzed. Results reveal distinct mechanisms: WBO acts chemically via polar molecules, selectively reducing oxygen-containing groups and significantly improving ductility, while MO acts physically through light components that dilute viscosity, exhibiting weaker chemical repair. WBO-regenerated asphalt showed a lower thermal-oxidative peak temperature, superior low-temperature ductility, and enhanced high-temperature rheological performance (higher rutting factor, optimized viscoelasticity). These mechanistic differences—chemical restoration (WBO) versus physical replenishment (MO)—determine performance outcomes at the binder level. The findings provide a theoretical basis for regenerator selection in pavement engineering, highlighting WBO’s advantages for functional group restoration and balanced thermal rheological properties, supporting sustainable road development. Full article

Stauntonia hexaphylla (Thunb.) Decne (SH), a medicinal plant from the Lardizabalaceae family, holds traditional importance in East Asia for treating rheumatism. Steam treatment is commonly applied to enhance its medicinal properties, but the chemical and biological changes resulting from this process remain unexplored. This study compared steamed and untreated SH fruit (SHF) extracts, analyzing their chemical composition, antioxidant activity, and effects on bone health using in vitro models. Steamed SHF extracts exhibited increased levels of 5-hydroxymethylfurfural (5-HMF), total flavonoids, phenolics, and enhanced antioxidant activity. Bone health assessment using osteoclasts differentiated from RAW 264.7 cells and osteoblasts from MC3T3-E1 cells revealed that steamed extracts promoted alkaline phosphatase activity, calcium nodule formation, and collagen synthesis in osteoblasts while inhibiting tartrate-resistant acid phosphatase (TRAP) activity in osteoclasts. Additionally, steamed SHF extracts effectively modulated gene expression related to osteoclastogenesis and osteoblastogenesis by downregulating TRAP, NFTAc1, RANK, MMP9, c-Fos, and TRAF6 while upregulating ALP, Runx2, BGLAP, Col1a1, and OPG. The component 5-HMF played a pivotal role in promoting alkaline phosphatase and inhibiting TRAP activities. These findings suggest that steamed SHF may offer a promising therapeutic approach for postmenopausal osteoporosis. Full article

The “three rights separation” system plays a vital role in enhancing the economic efficiency of rural residential land use, thereby contributing to land revitalization and rural-urban integration. Using survey data from 456 farmers in Yujiang District and Deqing County, this study employs DEA, Tobit, and threshold regression models to analyze the system’s effects. The results show that the system improves economic efficiency by approximately 8.9%, primarily by incentivizing investment and promoting land transfers. A nonlinear threshold effect exists: investment incentives become significant only when idle land exceeds 35 m², consistent with farmers’ economic decision-making. Land transfers enhance efficiency via marginal return equalization, however, economies of scale are not evident, being constrained by legal and coordination factors. The findings highlight the importance of deepening reform implementation, enhancing farmers’ understanding of property rights, adopting differentiated incentives tailored to land size and farmer capacity, and regulating the land transfer market to ensure transparency and fairness. Furthermore, promoting collective or service-based management models can help overcome natural scale limitations, thereby unlocking the system’s full institutional dividends. Full article

Background: Stereotactic ablative radiotherapy (SABR) is increasingly used in the treatment of localized and metastatic renal cell carcinoma (RCC), a malignancy traditionally considered radioresistant. Beyond direct cytotoxicity, SABR may promote immunogenic cell death and modulate the tumor immune microenvironment, though the underlying mechanisms remain incompletely understood. Objectives and Methods: This study examined the immunomodulatory effects of two high-dose irradiation regimens (8 Gy and 3 × 8 Gy) in an in vitro model using two RCC cell lines (ACHN, Caki-2) and peripheral blood mononuclear cells (PBMCs) from healthy donors. Results: The 3 × 8 Gy regimen more effectively reduced tumor cell viability and proliferation, particularly in ACHN cells, suggesting differential radiosensitivity. Both regimens induced secretion of IL-6, IL-8, TGF-β, and VEGF, with levels varying by cell line and dose. Caki-2 cells exhibited a cytokine profile consistent with a pro-inflammatory and potentially immunosuppressive phenotype. Conditioned media from irradiated cells were used to stimulate PBMCs, revealing divergent responses. Media from 3 × 8 Gy-irradiated ACHN cells enhanced PBMC proliferation and increased CD8⁺ T cells and CD11c⁺ monocytes, along with IFN-γ, IL-2, and TNF-α secretion, suggesting immunostimulatory effects. Conversely, media from Caki-2 cells had minimal impact on PBMC proliferation and increased TGF-β levels. Conclusions: These results indicate that high-dose irradiation can differentially modulate immune responses in RCC cell lines, depending on tumor intrinsic properties and irradiation regimen. Further in vivo studies are warranted to validate these findings and support development of SABR immunotherapy combinations guided by predictive immune biomarkers. Full article

Periodontal therapy remains a complex task in dentistry as current methodologies often tend to induce tissue repair rather than regeneration. Caffeine is an alkaloid found in multiple natural sources, which has been reported to have multiple beneficial effects, such as promoting adipogenic differentiation, a key factor in tissue regeneration. Unfortunately, it has also been reported to decrease cell viability and reduce osteogenic and chondrogenic differentiation, both of which play an important role in regenerative medicine. In this study, we aimed to find a non-cytotoxic dose of purified caffeine over dental pulp stem cells (DPSCs) that could provide its beneficial effects over adipogenesis, while reducing the negative effect upon osteogenesis and chondrogenesis. Additional experiments were conducted to determine its impact upon the expression of pro-inflammatory enzymes, and antibacterial assays to assess a potential antibacterial effect. The results attested that purified caffeine at a dose of 8.03 μM holds no viability reduction effect, nor has any impact on the expression of pro-inflammatory enzymes, promotes adipogenic differentiation, and does not negatively affect osteogenic or chondrogenic differentiation, with any antibacterial effect against Streptococcus mutans, Escherichia coli, and Staphylococcus aureus. These findings suggest that purified caffeine at a dose of 8.03 μM has the potential to aid in the field of regenerative dentistry. Full article

Circular RNAs (circRNAs) are increasingly recognized as regulators of gene expression, although their roles in hematopoietic differentiation remain relatively understudied. This study compares circRNA expression profiles between erythroblasts derived from human fetal liver and bone marrow CD34⁺ hematopoietic stem cells using publicly available RNA-seq datasets (GEO: GSE90878). Twelve samples from each developmental source were analyzed. Differential expression analysis was performed, and circAtlas 3.0 was employed to predict interactions between circRNAs, microRNAs (miRNAs), and RNA-binding proteins. Differentially expressed miRNAs were curated from miRNA-seq data (GEO: GSE110936) profiling the same cell types. Principal component analysis of circRNA expression profiles demonstrated clear separation between erythroblasts from fetal liver and bone marrow, which was statistically confirmed by PERMANOVA (p = 0.001); though this effect size is small (R² = 0.065). One circRNA, circALS2(4).1, was significantly upregulated in bone marrow-derived erythroblasts (adjusted p < 0.05), and ten additional circRNAs showed suggestive evidence for differential expression (adjusted p < 0.1). The resulting interaction networks reveal distinct circRNA landscapes and suggest regulatory circuits that may contribute to developmental differences in human erythropoiesis, indicating that the functions of circRNAs in hematopoietic development remain to be further elucidated. Full article

Triple-negative breast cancer (TNBC) is an aggressive subtype of breast cancer characterized by the absence of estrogen receptor, progesterone receptor, and human epidermal growth factor receptor 2, limiting the efficacy of conventional targeted therapies. As a result, novel therapeutic strategies are urgently needed. Photodynamic therapy (PDT), which relies on the activation of photosensitizers (PSs) by light to induce cytotoxic effects, has emerged as a promising alternative for TNBC treatment. Furthermore, the conjugation of PSs with targeting peptides has demonstrated enhanced selectivity and therapeutic efficacy, particularly for porphyrin-based photosensitizers. In this study, we report the synthesis of novel porphyrin–peptide conjugates designed to selectively target the epidermal growth factor receptor (EGFR), which is frequently overexpressed in TNBC. The conjugates were prepared via thiol displacement of the meso-nitro group in a 5,15-diarylporphyrin scaffold using EGFR-binding peptides. Photodynamic activity was evaluated in two EGFR-overexpressing TNBC cell lines. Cellular uptake of the conjugates correlated with EGFR expression levels, and PDT treatment resulted in differential induction of necrosis, apoptosis, and autophagy. Notably, the conjugates significantly inhibited EGFR-expressing cell line migration, a critical hallmark of metastatic progression. These findings underscore the potential of EGFR-targeted porphyrin–peptide conjugates as promising PDT agents for the treatment of TNBC. Full article

This study introduces a novel approach to correlation-based feature selection and dimensionality reduction in high-dimensional data structures. To this end, a customized scoring function is proposed, designed as a dual-objective structure that simultaneously maximizes the correlation with the target variable while penalizing redundant information among features. The method is built upon three main components: correlation-based preliminary assessment, feature selection via the tailored scoring function, and integration of the selection results into a t-SNE visualization guided by Rel/Red ratios. Initially, features are ranked according to their Pearson correlation with the target, and then redundancy is assessed through pairwise correlations among features. A priority scheme is defined using a scoring function composed of relevance and redundancy components. To enhance the selection process, an optimization framework based on stochastic differential equations (SDEs) is introduced. Throughout this process, feature weights are updated using both gradient information and diffusion dynamics, enabling the identification of subsets that maximize overall correlation. In the final stage, the t-SNE dimensionality reduction technique is applied with weights derived from the Rel/Red scores. In conclusion, this study redefines the feature selection process by integrating correlation-maximizing objectives with stochastic modeling. The proposed approach offers a more comprehensive and effective alternative to conventional methods, particularly in terms of explainability, interpretability, and generalizability. The method demonstrates strong potential for application in advanced machine learning systems, such as credit scoring, and in broader dimensionality reduction tasks. Full article

Background: Ulcerative colitis (UC) is a chronic inflammatory disease of the colon with a rising global incidence. Natural conjugated taurocholic acid (TCA) possesses anti-inflammatory properties and shows potential therapeutic effects against UC, although the underlying mechanisms remain unclear. Methods: This study employed an integrative approach—combining network pharmacology, bioinformatics, machine learning, immune infiltration analysis, and molecular docking—to investigate the therapeutic mechanisms of TCA in UC. UC-related gene expression datasets were obtained from the Gene Expression Omnibus (GEO) database, and potential TCA targets were predicted using the Comparative Toxicogenomics Database (CTD) and TargetNet platforms. Differentially expressed genes (DEGs) were identified and analyzed via GO and KEGG enrichment analyses. Results: Four machine learning algorithms (XGBoost, RF, SVM, and NNet) were used to identify six hub genes (TGM2, MMP9, ABCB1, NOS2, ABCG2, CASP1), which were further validated using an artificial neural network. Immune infiltration analysis with CIBERSORT revealed significant alterations in immune cell populations in UC tissues. Further validation through an artificial neural network model confirmed their predictive ability. The enrichment analysis of the hub genes highlighted their roles in immune-related pathways, while the immune infiltration analysis indicated significant differences in immune cell populations between ulcerative colitis tissues and control tissues. The molecular docking results showed that the binding energies of these six proteins to TCA were lower than −5 kcal/mol, with TGM2 having the strongest binding affinity (−10 kcal/mol). The intervention of TCA on colitis mice could improve the inflammatory response by regulating the expression of the TGM2 gene. Conclusions: In conclusion, this study suggests that taurocholate alleviates ulcerative colitis by targeting key genes such as TGM2 and modulating immune-related pathways, providing a novel basis for future therapeutic exploration. Full article