Search Results (32)

Background/Objectives: Diabetic retinopathy is a leading cause of vision impairment worldwide, and the development of reliable automated classification systems is crucial for early diagnosis and clinical decision-making. This study presents a comprehensive comparative evaluation of two state-of-the-art deep learning families for the task of classifying diabetic retinopathy using retinal fundus images. Methods: The models were trained and tested in both binary and multi-class settings. The experimental design involved partitioning the data into training (70%), validation (20%), and testing (10%) sets. Model performance was assessed using standard metrics, including precision, sensitivity, specificity, F1-score, and the area under the receiver operating characteristic curve. Results: In binary classification, the ResNeXt101-64x4d model and RegNetY32GT model demonstrated outstanding performance, each achieving high sensitivity and precision. For multi-class classification, ResNeXt101-32x8d exhibited strong performance in early stages, while RegNetY16GT showed better balance across all stages, particularly in advanced diabetic retinopathy cases. To enhance transparency, SHapley Additive exPlanations were employed to visualize the pixel-level contributions for each model’s predictions. Conclusions: The findings suggest that while ResNeXt models are effective in detecting early signs, RegNet models offer more consistent performance in distinguishing between multiple stages of diabetic retinopathy severity. This dual approach combining quantitative evaluation and model interpretability supports the development of more robust and clinically trustworthy decision support systems for diabetic retinopathy screening. Full article

REG3A, a prominent member of the human regenerating islet-derived (REG) lectin family, plays a pivotal and multifaceted role in immune defense, inflammation, and cancer biology. Primarily expressed in gastrointestinal epithelial cells, REG3A reinforces barrier integrity, orchestrates mucosal immune responses, and regulates host–microbiota interactions. It also functions as a potent non-enzymatic antioxidant, protecting tissues from oxidative stress. REG3A expression is tightly regulated by inflammatory stimuli and is robustly induced during immune activation, where it limits microbial invasion, dampens tissue injury, and promotes epithelial repair. Beyond its antimicrobial and immunomodulatory properties, REG3A contributes to the resolution of inflammation and the maintenance of tissue homeostasis. However, its role in cancer is highly context-dependent. In some tumor types, REG3A fosters malignant progression by enhancing cell survival, proliferation, and invasiveness. In others, it acts as a tumor suppressor, inhibiting growth and metastatic potential. These opposing effects are likely dictated by a combination of factors, including the tissue of origin, the composition and dynamics of the tumor microenvironment, and the stage of disease progression. Additionally, the secreted nature of REG3A implies both local and systemic effects, further modulated by organ-specific physiology. Experimental variability may also reflect differences in methodologies, analytical tools, and model systems used. This review synthesizes current knowledge on the pleiotropic functions of REG3A, emphasizing its roles in epithelial defense, immune regulation, redox homeostasis, and oncogenesis. A deeper understanding of REG3A’s pleiotropic effects could open up new therapeutic avenues in both inflammatory disorders and cancer. Full article

The Malvaceae family contains a variety of medicinal plants, including those of the mallow (Malva) genus. This study investigated the phytochemical composition, antioxidant activity, and morphometry of fruit from three Malva species (common mallow M. sylvestris, cheeseweed mallow M. parviflora, and Cornish mallow M. multiflora. The phytochemical analysis and antioxidant potentials were conducted on dry and powdered fruits. The morphometry and texture were performed using the software imagery tools. Results showed that the principal component analysis based on phytochemical content, antioxidant activity, and morphometric and texture traits showed a group structure according to species. The M. multiflora fruits were distinguished by high values of morphometric and texture traits, oil content (17.96%), total flavonoid content (1.70 mg RE/g DM), total antioxidant activity, and high FRAP value. The M. parviflora fruits were smaller than the M. multiflora and were rich in proteins (17.70%), starch (94.41 mg/g DW), and soluble sugar contents (57.74 mg/g DW). However, the M. sylvestris fruits have an intermediate position within the two other species and are rich in total polyphenols (2.34 mg GAE/g DM) and flavonoid contents (0.75 mg RE/g DM). The combined data, including phytochemical characterization, antioxidant activity, and morphometry, could be used as an alternative tool to molecular analysis to distinguish between Malva species and to select future application of Malva fruits based on their metabolite’s composition. Full article

Background: Over the past 40 years since the discovery of regenerating family proteins (Reg proteins), numerous studies have highlighted their biological functions in promoting cell proliferation and resisting cell apoptosis, particularly in the regeneration and repair of pancreatic islets and exocrine glands. Successively, short peptides derived from Reg3δ and Reg3α have been employed in clinical trials, showing favorable therapeutic effects in patients with type I and type II diabetes. However, continued reports have been limited, presumably attributed to the potential side effects. Methods: This review summarizes extensive research on Reg proteins over the past decade, combined with our own related studies, proposing that Reg proteins exhibit dimorphic effects. Results: The activity of Reg proteins is not as simplistic as previously perceived but shows auto-immunogenicity depending on different pathophysiological microenvironments. The immunogenicity of Reg proteins could recruit immune cells leading to an anti-tumor effect. Such functional diversity is correlated with their structural characteristics: the N-terminal region contributes to autoantigenicity, while the C-type lectin fragment near the C-terminal determines the trophic action. It should be noted that B-cell masking antigens might also reside within the C-type lectin domain. Conclusions: Reg proteins have dual functional roles under various physiological and pathological conditions. These theoretical foundations facilitate the subsequent development of diagnostic reagents and therapeutic drugs targeting Reg proteins. Full article

Regenerating Family Member 3 Alpha (REG3A) is an antimicrobial protein secreted by the intestine and pancreas with additional immunomodulatory properties. Previously, we published that REG3A expression in ischemic stroke patient systemic blood, during mechanical thrombectomy (MT), is significantly associated with inflammatory cytokines and patient function on admission. This paper, however, did not investigate post-acute death rates. Therefore, we investigated plasma REG3A protein expression, during MT, in patients (n = 141) that survived or died within the end of the follow-up after MT. Subjects who died had significantly higher systemic plasma REG3A levels at the time of MT compared to survivors (p = 0.001). Age, sex, time from last known normal, and admission NIHSS were included as predictors to control for confounding variables and were all examined to determine their association in patient mortality. Logistic regression was used to demonstrate that higher odds of death were associated with increased REG3A levels (p = 0.002). REG3A demonstrated acceptable discrimination (AUC (95% CI): 0.669 (0.566–0.772) in predicting mortality. The overall model with age, sex, time from last known normal, and admission NIHSS discriminated well between survivors and those who died (AUC (95% CI): 0.784 (0.703–0.864)). In conclusion, REG3A could be promising as a biomarker to prognosticate stroke outcomes and stratify high-risk groups following acute ischemic stroke. Full article

The present study was performed to determine the chemical constituents, cytotoxicity, antioxidant and enzyme inhibition activities of the aerial parts of Glaucium acutidentatum Hausskn. and Bornm. (family Papaveraceae). Methanolic and aqueous extracts were prepared by maceration, homogenizer-assisted extraction (HAE) and infusion. Results showed that the highest total phenolic and flavonoids contents were obtained from the methanol extracts obtained by HAE (53.22 ± 0.10 mg GAE/g) and maceration (30.28 ± 0.51 mg RE/g), respectively. The aporphine, beznyltetrahydroisoquinoline, and protopine types of Glaucium alkaloids have been tentatively identified. Among them, glaucine was identified in all extracts. Flavonoids, phenolic acids, coumarins, organic acids and fatty acids were also detected. Methanolic extract obtained using the HAE method displayed the highest anti-DPPH (41.42 ± 0.62 mg TE/g), total antioxidant (1.20 ± 0.17 mmol TE/g), Cu²⁺ (113.55 ± 6.44 mg TE/g), and Fe³⁺ (74.52 ± 4.74 mg TE/g) reducing properties. The aqueous extracts obtained by infusion and HAE methods exerted the best anti-ABTS (103.59 ± 1.49 mg TE/g) and chelating (19.81 ± 0.05 mg EDTAE/g) activities, respectively. Methanolic extract from HAE recorded the highest acetylcholinesterase (2.55 ± 0.10 mg GALAE/g) and α-amylase (0.51 ± 0.02 mmol ACAE/g) inhibition activities, while that obtained by maceration showed the best butyrylcholinesterase (3.76 ± 0.31 mg GALAE/g) inhibition activity. Both extracts revealed the best tyrosinase inhibitory activity (25.15 ± 1.00 and 26.79 ± 2.36 mg KAE/g, p ≥ 0.05). G. acutidentatum maceration-derived aqueous extract showed selective anticancer activity against cells originating from human hypopharyngeal carcinoma. In conclusion, these findings indicated that G. acutidentatum is a promising source of alkaloids and phenolic compounds for variable pharmaceutical formulations. Full article

Asthma is a multifactorial condition that can be associated with obesity. The phenotypes of asthma in lean and obese patients are different, with proinflammatory signatures being further elevated in the latter. Both obesity and asthma are associated with alterations in intestinal barrier function and immunity, and with the composition of the intestinal microbiota and food consumption. In this study, we aimed to establish an organoid model to test the hypothesis that the intestinal content of lean and obese, allergic, asthmatic children differentially regulates epithelial intestinal gene expression. A model of mouse jejunum intestinal organoids was used. A group of healthy, normal-weight children was used as a control. The intestinal content of asthmatic obese children differentially induced the expression of inflammatory and mitochondrial response genes (Tnf-tumor necrosis factor, Cd14, Muc13-mucin 13, Tff2-Trefoil factor 2 and Tff3, Cldn1-claudin 1 and 5, Reg3g-regenerating family member 3 gamma, mt-Nd1-NADH dehydrogenase 1 and 6, and mt-Cyb-mitochondrial cytochrome b) via the RAGE-advanced glycosylation end product-specific receptor, NF-κB-nuclear factor kappa b and AKT kinase signal transduction pathways. Fecal homogenates from asthmatic normal-weight and obese children induce a differential phenotype in intestinal organoids, in which the presence of obesity plays a major role. Full article

The present study was designed to determine the phenolic constituents, antioxidant, and enzyme inhibition activities of aerial parts and bulbs of Allium lycaonicum (family Amaryllidaceae). Extracts were prepared by maceration and Soxhlet/infusion using hexane, methanol, and water as extraction solvents. Generally, extracts from the aerial parts showed higher total phenolic and individual components and antioxidant activity than their respective bulb extracts. Maceration with water was the best to extract total phenolic content from the aerial parts (29.00 mg gallic acid equivalents (GAE)/g), while the Soxhlet extraction with hexane (22.29 mg GAE/g) was the best for the bulb. Maceration with methanol recovered the highest total flavonoid content from both the aerial parts (41.95 mg (rutin equivalents (RE)/g) and bulb (1.83 mg RE/g). Polar extracts of aerial parts were characterized by higher abundance of kaempferol-3-glucoside (≤20,624.27 µg/mg), hyperoside (≤19,722.76 µg/g), isoquercitrin (≤17,270.70 µg/g), delphindin-3,5-diglucoside (≤14,625.21 µg/g), and rutin (≤10,901.61 µg/g) than the bulb. Aerial parts’ aqueous extract, prepared by maceration, exerted the highest anti-ABTS (2,2′-azino-bis(3-ethylbenzothiazoline-6-sulfonic acid) radical activity (64.09 mg trolox equivalents (TE)/g), Cu⁺⁺ (83.03 mg TE/g) and Fe⁺⁺⁺ (63.03 mg TE/g) reducing capacity while that prepared by infusion recorded the highest anti-DPPH (2,2-diphenyl-1-picrylhydrazyl) radical (31.70 mg TE/g) and metal chelating (27.66 mg EDTAE/g) activities. The highest total antioxidant activity (1.46 mmol TE/g) was obtained by maceration of the bulb with water. Extracts obtained by organic solvents showed remarkable enzyme inhibition properties against the tested enzymes. Soxhlet extraction of the bulb with hexane and methanol recorded the highest acetylcholinesterase inhibition (4.75 mg galanthamine equivalents (GALAE)/g) and tyrosinase inhibition (139.95 mg kojic acid equivalents/g) activities, respectively. Extracts obtained by maceration of the bulb with methanol and the aerial parts with hexane exerted the highest glucosidase inhibition (3.25 mmol acarbose equivalents/g) and butyrylcholinesterase inhibition (20.99 mg GALAE/g) activities, respectively. These data indicated that A. lycaonicum is a source of bioactive molecules with potential antioxidant and enzyme inhibition properties. Nonetheless, the extracts obtained through various solvents and extraction techniques showed variations in their phytoconstituent composition and biological properties. Full article

Plant tissue regeneration is a key process for genetic transformation and genome editing. The exploration of regulatory mechanisms in plant regeneration would improve regeneration efficiency. In comparison to some model plants, the genomic heterozygosity is much higher in forest trees, increasing the complexity of transcriptional regulation. Here, we report the allele-specific transcriptional analysis in hybrid poplar 84K (Populus alba × P. tremula var. glandulosa cv. 84K) during the shoot regeneration process. Firstly, 180 regeneration-related genes (REGs) and 2446 REG-homologous genes (REGHs) were identified in hybrid poplar. The expression patterns of REGs exhibited that about half of them were positively correlated between poplar and Arabidopsis at the locus level. The expression levels of REGHs vary among the gene family at different stages during callus and shoot induction. Among the gene clusters with similar expression patterns, the distribution of gene families in poplar and Arabidopsis also exhibits large variations. At the allele level, most of the allele pairs of REGs were positively correlated in expression. The expression patterns of genes in auxin synthesis, transport, and signaling pathways agree with the general patterns. Due to the presence/absence of variations between two subgenomes, two YUC alleles and two IAA alleles are present only in one subgenome, and the expression patterns of the two alleles are greatly different. Our analysis indicates the conservativeness and diversity of transcriptional regulation during shoot regeneration in poplar and Arabidopsis. The complexity in allele expression contributed by heterozygosity suggests the importance of genotyping in the screening of explants for plant regeneration. Full article

Antibodies play a crucial role in activating protective immunity against malaria by interacting with Fc-gamma receptors (FcγRs). Genetic variations in genes encoding FcγRs can affect immune cell responses to the parasite. In this study, our aim was to investigate whether non-coding variants that regulate FcγR expression could influence the prevalence of Plasmodium falciparum infection. Through bioinformatics approaches, we selected expression quantitative trait loci (eQTL) for FCGR2A, FCGR2B, FCGR2C, FCGR3A, and FCGR3B genes encoding FcγRs (FCGR), in whole blood. We prioritized two regulatory variants, rs2099684 and rs1771575, located in open genomic regions. These variants were identified using RegVar, ImmuNexUT, and transcription factor annotations specific to immune cells. In addition to these, we genotyped the coding variants FCGR2A/rs1801274 and FCGR2B/rs1050501 in 234 individuals from a malaria-endemic area in Burkina Faso. We conducted age and family-based analyses to evaluate associations with the prevalence of malarial infection in both children and adults. The analysis revealed that the regulatory rs1771575-CC genotype was predicted to influence FCGR2B/FCGR2C/FCGR3A transcripts in immune cells and was the sole variant associated with a higher prevalence of malarial infection in children. In conclusion, this study identifies the rs1771575 cis-regulatory variant affecting several FcγRs in myeloid and neutrophil cells and associates it with the inter-individual capacity of children living in Burkina Faso to control malarial infection. Full article

The proteasome, a complex multi-catalytic protease machinery, orchestrates the protein degradation essential for maintaining cellular homeostasis, and its dysregulation also underlies many different types of diseases. Its function is regulated by many different mechanisms that encompass various factors such as proteasome activators (PAs), adaptor proteins, and post-translational modifications. This review highlights the unique characteristics of proteasomal regulation through the lens of a distinct family of regulators, the 11S, REGs, or PA26/PA28. This ATP-independent family, spanning from amoebas to mammals, exhibits a common architectural structure; yet, their cellular biology and criteria for protein degradation remain mostly elusive. We delve into their evolution and cellular biology, and contrast their structure and function comprehensively, emphasizing the unanswered questions regarding their regulatory mechanisms and broader roles in proteostasis. A deeper understanding of these processes will illuminate the roles of this regulatory family in biology and disease, thus contributing to the advancement of therapeutic strategies. Full article

During the last few decades, bat lyssaviruses have become the topic of intensive molecular and epidemiological investigations. Since ancient times, rhabdoviruses have caused fatal encephalitis in humans which has led to research into effective strategies for their eradication. Modelling of potential future cross-species virus transmissions forms a substantial component of the recent infection biology of rabies. In this article, we summarise the available data on the phylogeography of both bats and lyssaviruses in Europe and the adjacent reg ions, especially in the contact zone between the Palearctic and Ethiopian realms. Within these zones, three bat families are present with high potential for cross-species transmission and the spread of lyssaviruses in Phylogroup II to Europe (part of the western Palearctic). The lack of effective therapies for rabies viruses in Phylogroup II and the most divergent lyssaviruses generates impetus for additional phylogenetic and virological research within this geographical region. Full article

Congenital hepatic fibrosis/Autosomal recessive polycystic kidney disease (CHF/ARPKD) is an inherited neonatal disease induced by mutations in the PKHD1 gene and characterized by cysts and robust pericystic fibrosis in the liver and kidneys. The PCK rat is an excellent animal model that carries a Pkhd1 mutation and exhibits similar pathophysiology. We performed RNA-Seq analysis on liver samples from PCK rats over a time course of postnatal day (PND) 15, 20, 30, and 90 using age-matched Sprague Dawley (SD) rats as controls to characterize molecular mechanisms of CHF/ARPKD pathogenesis. A comprehensive gene expression analysis identified 1298 differentially expressed genes (DEGs) between PCK and SD rats. The genes overexpressed in the PCK rats at PND30 and 90 were involved cell migration (e.g., Lamc2, Tgfb2, and Plet1), cell adhesion (e.g., Spp1, Adgrg1, and Cd44), and wound healing (e.g., Plat, Celsr1, Tpm1). Connective tissue growth factor (Ctgf) and platelet-derived growth factor (Pdgfb), two genes associated with fibrosis, were upregulated in PCK rats at all time points. Genes associated with MHC class I molecules (e.g., RT1-A2) or involved in ribosome assembly (e.g., Pes1) were significantly downregulated in PCK rats. Upstream regulator analysis showed activation of proteins involved tissue growth (MTPN) inflammation (STAT family members), chromatin remodeling (BRG1), reduction in fibrosis (SMAD7), and inhibition of proteins involved in hepatic differentiation (HNF4α). Immunofluorescence staining revealed that cyst wall epithelium cells also express hepatic progenitor cell markers. The increase in mRNAs of four top upregulated genes, including Reg3b, Aoc1, Tm4sf20, and Cdx2, was confirmed at the protein level using immunohistochemistry. In conclusion, these studies indicate that a combination of increased inflammation, cell migration, wound healing, decreased antifibrotic gene expression, and inhibition of hepatic function are the major underlying pathogenic mechanisms in CHF/ARPKD. Full article

Light-harvesting chlorophyll a/b binding (Lhc) proteins play a key role in the efficiency of the photosynthetic system of plants and participate in the regulation of plant growth, development, and the response to abiotic stress. In this study, 28 PbrLhc genes of the family were identified in the pear Pyrus bretschneideri genome database, which were distributed on 25 of the 27 chromosomes. Phylogenetic relationship analysis demonstrated that PbrLhc proteins could be divided into five subfamilies. Using MEME Suite, PlantRegMap, and Softberry, the conserved motifs, transcription binding sites, and predicated location of all PbrLhc proteins, respectively, were determined. A collinearity relationship using MCScanX software showed that there was a collinearity relationship between different PbrLhc genes. Using the hierarchical clustering method to develop a heat map of gene expression, five genes were found to be down-regulated under irrigation treatment and up-regulated under drought treatment; seven genes were up-regulated under irrigation treatment and down-regulated under drought treatment. Finally, the results of these analyses will provide theoretical basis for future study on the function and differential expression of PbrLhc genes in response to drought stress. Full article

The evolutionary transition from single-celled to multicellular individuality requires organismal fitness to shift from the cell level to a cell group. This reorganization of fitness occurs by re-allocating the two components of fitness, survival and reproduction, between two specialized cell types in the multicellular group: soma and germ, respectively. How does the genetic basis for such fitness reorganization evolve? One possible mechanism is the co-option of life history genes present in the unicellular ancestors of a multicellular lineage. For instance, single-celled organisms must regulate their investment in survival and reproduction in response to environmental changes, particularly decreasing reproduction to ensure survival under stress. Such stress response life history genes can provide the genetic basis for the evolution of cellular differentiation in multicellular lineages. The regA-like gene family in the volvocine green algal lineage provides an excellent model system to study how this co-option can occur. We discuss the origin and evolution of the volvocine regA-like gene family, including regA—the gene that controls somatic cell development in the model organism Volvox carteri. We hypothesize that the co-option of life history trade-off genes is a general mechanism involved in the transition to multicellular individuality, making volvocine algae and the regA-like family a useful template for similar investigations in other lineages. Full article