Search Results (1,342)

Stem-cell differentiation technologies have traditionally relied on recombinant growth factors, cytokines, and morphogens to initiate and guide lineage specification toward clinically relevant cell types. These approaches have enabled substantial progress in regenerative medicine, as exemplified by recent advances in cell-replacement therapies for Parkinson’s disease, type 1 diabetes, and retinal degeneration. However, protein-based ligands and soluble factors are often limited by short half-lives, pleiotropic signaling, condition-dependent effects, and challenges in achieving precise spatial and temporal control in scalable systems. In this review, we survey differentiation strategies driven by administered substances, organizing the field into five material-centric modules: recombinant growth factors, cytokines, morphogens, exogenous ligands, and agonist antibodies. For each module, we summarize mechanistic principles, representative studies, controllable variables, and translational considerations. While growth factors, cytokines, morphogens, and exogenous ligands remain central tools for directing lineage commitment and maturation, recent studies indicate that agonist antibodies offer an additional and distinct means of controlling differentiation outcomes. These antibodies can function as receptor agonists while also imparting tissue-selective effects, enabling lineage specification with coordinated spatial targeting. By focusing on differentiation methods driven by administered molecules and excluding direct physical stimulation or complex 3D constructs, this review provides a framework that is particularly relevant to immunology and translational practice. We highlight agonist antibody-based induction as an emerging strategy that complements established ligand-based approaches and may broaden the design space for clinically applicable stem-cell differentiation. Full article

The equilibrium shape of a crystal is a fundamental problem in materials science and condensed matter physics. The Wulff construction, a cornerstone of crystal morphology prediction, is traditionally presented and utilized as a powerful geometric algorithm to derive equilibrium shapes from anisotropic surface energy $\gamma \left(\mathbf{n}\right)$. While its application across materials science is vast, the profound mathematical physics underpinning it, specifically its intrinsic identity as a manifestation of the Legendre transform, is often relegated to a passing remark. This work recenters the focus on this fundamental duality. We present a comprehensive, step-by-step derivation of the Wulff shape from the variational principle of surface energy minimization under a constant volume, employing the language of support functions and differential geometry. We then rigorously demonstrate that the equilibrium shape, defined by the support function $h\left(\mathbf{n}\right)$, and the surface energy density $\gamma \left(\mathbf{n}\right)$ are conjugate variables linked by a Legendre transformation; the Wulff shape $\mathcal{W}$ is precisely the zero-sublevel set of the dual function ${\gamma }^{*}\left(\mathbf{x}\right)={sup}_{\mathbf{n}}[\mathbf{x}·\mathbf{n}-\gamma \left(\mathbf{n}\right)]$. This perspective elevates the Wulff construction from a mere graphical tool to a canonical example of convex duality in thermodynamic systems, connecting it to deeper principles in convex analysis and statistical mechanics. To bridge theory and computation, we provide a robust computational algorithm implemented in pseudocode capable of generating Wulff shapes for two-dimensional (2D) crystals with arbitrary N-fold symmetry. Finally, we discuss the relevance and extensions of the classical theory in contemporary research, including non-equilibrium growth, nanoscale effects, and machine learning approaches. Full article

Background/Objectives: Interleukin-17A (IL-17A) is a key pathogenic cytokine in autoimmune arthropathies. Current monoclonal antibody inhibitors targeting the IL-17/IL-17RA axis demonstrate clinical efficacy but face significant limitations, including immunogenicity, the loss of therapeutic response, and cold-chain storage. Our study evaluated oligonucleotide aptamers targeting IL-17A and its receptor as an alternative to monoclonal antibodies to suppress an IL-17A-induced inflammatory response in cell models relevant to immunoinflammatory rheumatic diseases. Methods: We examined three aptamers: 2′-F-RNA aptamers Apt21-2 and Apt3-4 specific to IL-17A and DNA aptamer RA10-6 targeting the receptor of IL-17A. Their ability to suppress IL-17A functional activity was assessed in peripheral blood mononuclear cells (PBMCs) from healthy donors and personalized fibroblast-like synoviocytes (FLSs) from patients with axial spondyloarthritis (axSpA) and rheumatoid arthritis (RA). Inhibition was measured by quantifying IL-6 and MMP-13 secretion using ELISA and flow cytometry, using secukinumab as a reference control. Results: In PBMC, all aptamers suppressed IL-17A-stimulated IL-6 secretion and cell proliferation in a concentration-dependent manner (17–200 nM), with a 65–85% efficacy, comparable to that of secukinumab. In axSpA-derived FLS, we observed time-dependent efficacy: At 4 h, all three aptamers suppressed IL-6 to the same extent as secukinumab; at 24 h, RA10-6 maintained high efficacy while Apt21-2 and Apt3-4 showed reduced activity. A combination of receptor-targeting RA10-6 with anti-IL-17A aptamers resulted in synergistic IL-6 suppression. All aptamers reduced MMP-13 to basal levels. RA-derived FLS showed diminished responses to all inhibitors. Conclusions: Aptamers demonstrate high specificity and sustained efficacy in suppressing IL-17A signaling for an in vitro model of spondyloarthritis, with superior performance over antibodies. Disease-dependent differential efficacy in RA FLS reflects heterogeneity consistent with limited clinical anti-IL-17 efficacy in RA. These findings show the strong potential of the studied aptamers as an alternative to monoclonal antibodies for IL-17-associated inflammatory arthropathies, particularly spondyloarthritis. Full article

Background: Impedance pneumography (IP) is a non-invasive technique for assessing tidal breathing in young children and enables home-based recordings without active patient cooperation. By deriving tidal breathing flow–volume (TBFV) curves and indices such as the expiratory variability index (EVI), IP has been proposed as a tool for identifying obstructive breathing patterns and monitoring airway function in early childhood. However, its clinical role in asthma and wheezing disorders has not been systematically evaluated. This review aimed to assess the evidence of IP in differentiating healthy children from those with asthma or recurrent wheeze, in reflecting treatment-related changes or acute bronchial obstruction, and in relation to other lung function tests. Methods: A systematic literature search of PubMed, Medline, Embase, and the Cochrane Library databases was conducted on 5 January 2026. Original studies using IP in children aged 0–7 years with asthma or wheeze were eligible. Study selection followed PRISMA guidelines, and risk of bias (RoB) was assessed using the Newcastle–Ottawa Scale (NOS). Due to substantial heterogeneity in study design, populations, and outcome measures, results were synthesized narratively. Results: Five studies were included, with a total of 376 participants aged 0.5–7.0 years. Three studies reported significantly lower EVI values and TBFV profile variation in children with asthma or recurrent wheeze compared with healthy controls. Two studies found an association between EVI and markers of airway obstruction. Changes in IP measures following inhaled corticosteroid treatment or medication withdrawal were reported, suggesting sensitivity to treatment-related changes. However, study quality was moderate to low, with small sample sizes, heterogeneous outcome definitions, and limited diagnostic validation. Conclusions: Current evidence suggests that IP-derived indices, particularly EVI, capture clinically relevant features of obstructive breathing patterns in young children and may be useful for longitudinal monitoring of airway function. However, evidence supporting a diagnostic role for IP in childhood asthma remains limited. Larger, independent, and methodologically robust studies are needed before IP can be integrated into routine clinical practice. Full article

Background: Several studies have attempted to identify the initiating drivers of small intestinal neuroendocrine tumor (SI-NET) development and the molecular mechanisms underlying their progression and metastatic spread. Previous gene expression studies have used bulk microarrays or RNA sequencing to compare tumor tissue with normal intestinal mucosa. However, the intestine comprises multiple distinct cell types, and bulk analyses are limited by this cellular heterogeneity, which can confound tumor-specific signals. Methods: We performed single-cell RNA sequencing on primary SI-NETs and paired normal mucosa from two patients to directly compare tumor cells with their cells of origin, the enterochromaffin (EC) cells. To minimize type I errors, we applied a two-step validation strategy by overlapping differentially expressed genes with an external single-cell dataset and cross-referencing candidate genes for enteroendocrine expression in the Human Protein Atlas. Results: For further distinction and characterization, ECs were subdivided into serotonergic and non-serotonergic clusters. This analysis revealed that the SI-NET cells are transcriptionally more similar to serotonergic ECs, consistent with serum metabolite profiles derived from clinical parameters. Our analyses uncovered a loss-of-expression program characterized by regulators of epithelial differentiation and in parallel, a gain-of-expression program displayed neuronal signaling gene induction, implicating functional reprogramming toward neuronal-like properties. Together, these specific losses and gains suggest that our patient-derived SI-NETs undergo adaptation through both loss of enteroendocrine functions and acquisition of neurobiological-promoting signaling pathways. Conclusions: These findings nominate candidate drivers for further functional validation and highlight potential therapeutic strategies in our patient cohort, including restoring suppressed Notch signaling and targeting aberrant neuronal signaling networks. However, even with a two-step validation procedure, the modest cohort size limits statistical power and generalizability, particularly for the proposed association to a serotonergic phenotype. Larger, multi-patient single-cell studies are required to confirm these mechanisms and establish their clinical relevance. Full article

Cadmium (Cd) is an environmental toxicant that poses significant risks to food safety and public health through its bioaccumulation in the food chain. The liver is a primary target for chronic Cd toxicity, yet the system-level mechanisms, particularly in physiologically relevant swine models, remain incompletely understood. This study employed an integrated multi-omics approach to elucidate the mechanisms of Cd-exposed hepatotoxicity in weaned piglets. We combined histopathological examination, transmission electron microscopy, and transcriptome sequencing. Our results revealed severe hepatic damage, characterized by disorganized architecture, vacuolar degeneration, mitochondrial dysfunction, and autophagic activation. Network toxicology predicted 3727 potential targets of Cd-exposed liver injury, while transcriptomics identified 1092 differentially expressed genes (DEGs). Crucially, the convergent analysis of both datasets demonstrated that the PI3K-Akt signaling pathway was the central hub, pinpointing it as a pivotal mechanism in Cd-driven hepatotoxicity. Functional enrichment analyses further highlighted dysregulation in immune-inflammatory responses, lipid metabolism, and oxidative stress. Our findings provide a comprehensive systems-level perspective on chronic Cd hepatotoxicity in a translational swine model. We propose the PI3K-Akt pathway and other identified core targets (EGFR, histones, ribosomal proteins) as critical biomarkers for monitoring Cd contamination in swine production chains, offering valuable insights for environmental risk assessment and agricultural product safety. Full article

Pancreatic β-cell replacement represents a promising therapeutic avenue for insulin-dependent diabetes, yet clinical translation has been limited by donor scarcity, immune rejection, and incomplete engraftment. Three-dimensional (3D) pancreatic organoids derived from human pluripotent stem cells (hPSCs) or primary tissue offer a scalable and physiologically relevant platform, recapitulating native islet architecture, paracrine interactions, and glucose-responsive insulin secretion. Recent advances in differentiation protocols, vascularization strategies, and immune-protective approaches—including encapsulation and hypoimmunogenic engineering—have enhanced β-cell maturation, survival, and functional performance in vitro and in vivo. Despite these developments, challenges remain in achieving fully mature β-cells, durable graft function, and scalable, reproducible production that is suitable for clinical use. This review highlights the promise of pancreatic organoid engineering, emphasizing strategies to optimize β-cell maturation, vascular integration, and immune protection, and outlines key future directions to advance organoid-based β-cell replacement toward safe, effective, and personalized diabetes therapies. Full article

Background/Objectives: Bacterial outer membrane vesicles (OMVs) play a role in bacterial communication, virulence, antimicrobial resistance, and host–pathogen interaction. OMV isolation is a key step for studying these particles’ functions; nevertheless, isolation procedures can greatly influence the yield, purity, and structural integrity of OMVs, thereby affecting downstream biological analyses and functional interpretation. Methods: In this study, we compared the efficacy of two OMV isolation techniques, differential ultracentrifugation (dUC) and size-exclusion chromatography (SEC), in separating and concentrating vesicles produced by two Escherichia coli strains belonging to uropathogenic (UPEC) and Shiga toxin-producing (STEC) pathotypes. The isolated OMVs were characterized using a multi-analytical approach including transmission and scanning electron microscopy (TEM, SEM), nanoparticle tracking analysis (NTA), dynamic light scattering (DLS), ζ-potential measurement, and protein quantification to assess the purity of the preparations. Results: Samples obtained by dUC exhibited higher total protein content, broader particle size distributions, and more pronounced contamination by non-vesicular material. In contrast, SEC yielded morphologically homogeneous and structurally well-preserved vesicles, higher particle-to-protein ratios, and lower total protein content, reflecting reduced co-isolation of protein aggregates. NTA and DLS analyses revealed polydisperse populations in samples obtained with both isolation methods, with DLS measurements highlighting the contribution of larger or transient aggregates. ζ-potential values were close to neutrality for all samples, consistent with limited electrostatic repulsion and with the aggregation tendencies observed in some preparations. Conclusions: This study describes features of OMV produced by two relevant E. coli strains considering two isolation strategies which exert method- and strain-dependent effects on vesicle properties, including size distribution and surface charge, and emphasizes the trade-offs between yield, purity, and vesicle integrity. Full article

This study examines how different programming paradigms are associated with learning experiences and cognitive challenges as encountered by non-computer science novice learners. Using a case-study approach situated within specific instructional contexts, we integrate survey data from undergraduate students with large-scale public question-and-answer data from Stack Overflow to explore paradigm-related difficulty patterns. Four instructional contexts—C, Java, Python, and Prolog—were examined as pedagogical instantiations of imperative, object-oriented, functional-style, and logic-based paradigms using text clustering, word embedding models, and interaction-informed complexity metrics. The analysis identifies distinct patterns of learning challenges across paradigmatic contexts, including difficulties related to low-level memory management in C-based instruction, abstraction and design reasoning in object-oriented contexts, inference-driven reasoning in Prolog-based instruction, and recursion-related challenges in functional-style programming tasks. Survey responses exhibit tendencies that are broadly consistent with patterns observed in public Q&A data, supporting the use of large-scale community-generated content as a complementary source for learner-centered educational analysis. Based on these findings, the study discusses paradigm-aware instructional implications for programming education tailored to non-major learners within comparable educational settings. The results provide empirical support for differentiated instructional approaches and offer evidence-informed insights relevant to curriculum-oriented teaching and future research on adaptive learning systems. Full article

The mechanisms driving the crown-to-root transition in tooth development remain incompletely understood, particularly the functional heterogeneity of dental epithelium. To address this gap and deconstruct this complexity, we aimed to analyze dental epithelial heterogeneity during this critical transition and to identify subpopulation-specific programs relevant to root development. We therefore established a single-cell transcriptomic atlas of the mouse molar at postnatal days 3.5 and 7.5, integrating 30,951 cells to profile the pan-tissue landscape and performing an in-depth analysis of 4323 dental epithelial cells. Our results reveal that the dental epithelium is composed of seven distinct subpopulations with a clear lineage hierarchy, originating from multipotent progenitors and bifurcating into self-renewing and differentiating trajectories. The identified particular functions of each subcluster include the following: structural maintaining progenitor that inhibits mineralization (Cluster 4), proliferation driver (Cluster 0), key signaling center (Cluster 1), terminally differentiated executing enamel formation (Cluster 3 and Cluster 6), and extracellular matrix-organizing hub (Cluster 5), communicating extensively via the Bmp, Tgf-β, and Wnt pathways. Our work defines dental epithelium as a dynamic and heterogeneous orchestrator of root morphogenesis, providing a foundational framework for understanding developmental biology and pioneering future regenerative strategies based on precise epithelial cell functions. Full article

In fish gut microbiome studies, there are no standardized protocols regarding sampling region or post-feeding time, nor clear consensus on whether analyses should target resident (autochthonous) or transient (allochthonous) bacteria. This study examined the dynamics and interactions of both microbial communities in the anterior and posterior intestine of farmed gilthead sea bream and evaluated the resident microbiome at 24 and 48 h post-feeding. Microbial DNA was sequenced using the Oxford Nanopore Technology platform. Data were analyzed through statistical and discriminant approaches, as well as a Bayesian network framework to assess bacterial interactions. Transient communities showed higher richness and diversity, regardless of intestinal section, suggesting a more specialized and stable microbial environment in the mucus layer. The two communities differed markedly in structure and composition. Variations associated with intestinal region were less pronounced, particularly for autochthonous bacteria, and post-feeding fluctuations in the resident microbiome were minimal. Functionally, results indicated relevant synergies between communities. Protein metabolism pathways were enriched in autochthonous bacteria, whereas allochthonous microorganisms contributed mainly to bile acid and carbohydrate metabolism. Overall, resident and transient bacteria constitute distinct communities in the gut of gilthead sea bream, with numerous genera present in both but most being differentially represented and interconnected. Full article

Background/Objectives: Assessing the bioavailability of nutrients and bioactive compounds in vitro commonly relies on coupling standardized gastrointestinal digestion models with intestinal epithelial cell systems. However, digests produced using static digestion protocols such as INFOGEST often impair epithelial barrier integrity, limiting their direct application to intestinal models and reducing reproducibility across studies. Methods: This work systematically compared five commonly used digest conditioning strategies, including acidification, centrifugation, rapid freezing, and ultrafiltration using 10 kDa and 3 kDa molecular weight cut-off membranes, to identify the approach that best preserves intestinal epithelial viability and barrier function while enabling exposure at physiologically relevant concentrations. INFOGEST digests of yogurt were initially evaluated, followed by validation using biscuit and canned mackerel digests. Cell viability and monolayer integrity were assessed in differentiated Caco-2 cells using MTT assay and transepithelial electrical resistance (TEER) measurements. Results: Among the tested approaches, ultrafiltration using 3 kDa membranes consistently preserved epithelial viability and barrier integrity at a 1:10 dilution across all food matrices, whereas other conditioning methods failed to maintain TEER despite acceptable cell viability. At lower dilutions, food-dependent effects emerged, highlighting the importance of matrix-specific evaluation. Conclusions: These findings identify 3 kDa ultrafiltration as an effective and minimally invasive strategy to improve the compatibility of INFOGEST digests with intestinal cell models. By enabling reproducible exposure conditions that preserve epithelial integrity, this approach supports more reliable in vitro assessment of nutrient bioavailability and contributes to methodological standardization in nutrition research. Full article

Rotavirus (RV) is the primary cause of severe gastroenteritis in young children, yet the long noncoding RNA (lncRNA) regulatory landscape governing the host response remains largely unmapped. To address this gap, the present study performed an integrated transcriptomic analysis of mRNA and lncRNA expression profiles in RV-infected MA104 cells at 24 h post-infection. Deep sequencing identified 11,919 high-confidence lncRNAs, revealing a massive transcriptional shift: 3651 mRNAs and 4655 lncRNAs were differentially expressed, with both populations predominantly upregulated. Functional enrichment analysis confirmed the strong activation of key innate immunity pathways, including the RIG-I-like receptor, Toll-like receptor, and TNF signaling pathways. Conversely, fundamental metabolic pathways were found to be suppressed. Crucially, the analysis of lncRNA targets highlighted their involvement in coordinating the host antiviral defense, particularly through transregulation. Experimental validation confirmed the significant upregulation of key immune-related mRNAs (OASL and C3) as well as two novel lncRNAs (lncRNA-6479 and lncRNA-4290) by qRT-PCR. The significant upregulation of OASL and C3 was validated at the protein level, confirming the biological relevance of the transcriptomic data. This study provides a foundational, genome-wide resource, identifying novel lncRNA targets for future mechanistic investigation into host–RV interactions. Full article

Background: Autism spectrum disorder (ASD) is a highly prevalent neurodevelopmental condition influenced by both genetic and non-genetic factors, although the underlying pathomechanisms remain unclear. We systematically analyzed microRNA (miRNA) expression and associated functional pathways in ASD to evaluate their potential as prenatal/postnatal, diagnostic, and prognostic biomarkers. Methods: Peripheral blood mononuclear cells from 12 Sicilian patients with ASD (eight with normal cognitive function) and 15 healthy controls were analyzed using small RNA sequencing. Differential expression analysis was performed with DESeq2 (|fold change| ≥ 1.5; adjusted p ≤ 0.05). Functional enrichment and network analyses were conducted using Ingenuity Pathway Analysis, focusing on Diseases and Biofunctions. Results: 998 miRNAs were differentially expressed in ASD, 424 upregulated and 553 downregulated. Enriched pathways were primarily associated with psychological and neurological disorders. Network analysis highlighted three principal interaction clusters related to inflammation, cell survival and mechanotransduction, synaptic plasticity, and neuronal excitability. Four miRNAs (miR-296-3p, miR-27a, miR-146a-5p, and miR-29b-3p) emerged as key regulatory candidates. Conclusions: The marked divergence in miRNA expression between ASD and controls suggests distinct regulatory patterns, thus reinforcing the central involvement of inflammatory, autoimmune, and infectious mechanisms in ASD, mediated by miRNAs regulating S100 family genes, neuronal migration, and synaptic communication. However, rather than defining a predictive biomarker panel, this study identified candidate miRNAs and regulatory networks that may be relevant to ASD pathophysiology. As such, further validation in appropriately powered cohorts with predictive modeling frameworks are warranted before any biomarker or diagnostic implications can be inferred. Full article

Attention-deficit/hyperactivity disorder (ADHD) is a common neurodevelopmental disorder in childhood, characterized by persistent inattention, hyperactivity, and impulsivity. This narrative review aims to synthesize and critically evaluate recent large-scale magnetic resonance imaging (MRI) studies to clarify the neuroanatomical and functional brain alterations associated with ADHD in children. By addressing current gaps in understanding, this work seeks to identify reliable neurobiological markers that could improve diagnostic accuracy and guide personalized interventions. The literature reveals that large-scale structural MRI studies consistently report abnormal development in total cortical volume and surface area, prefrontal cortex volume, and basal ganglia volume in children with ADHD. Moreover, gray matter alterations show significant age-dependent effects, with the degree of impairment potentially serving as neurobiological markers. Diffusion magnetic resonance imaging studies reveal disrupted white matter microstructures in regions such as the left uncinate fasciculus, superior and inferior longitudinal fasciculi, corpus callosum, cingulum, and internal capsule. Importantly, these white matter abnormalities often persist into adulthood, highlighting their clinical relevance. Functional MRI findings indicate reduced global connectivity within core hubs of the default mode network in children with ADHD. Furthermore, deficits in inhibitory control identified via fMRI may represent one of the neurofunctional signatures that differentiates ADHD from typically developing controls. By consolidating evidence from large-scale multimodal MRI studies, this review provides a comprehensive understanding of the neurodevelopmental alterations in ADHD and underscores their potential utility for improving diagnosis and treatment. Full article