Search Results (955)

The Epstein–Barr virus (EBV) is a prevalent virus linked to various diseases, including infectious mononucleosis (IM), nasopharyngeal carcinoma, and Hodgkin’s lymphoma. Over the past few decades, EBV diagnostic strategies have evolved significantly—progressing from traditional serological assays and histopathology to more sensitive and specific molecular techniques such as nucleic acid amplification and high-throughput sequencing (HTS). While conventional methods remain valuable for their accessibility and established clinical use, they are often limited by sensitivity, speed, and multiplexing capability. In contrast, emerging technologies, including isothermal amplification, Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)-based diagnostics, multi-omics integration, and AI-assisted analysis, have demonstrated great promise in improving diagnostic accuracy, speed, and applicability in diverse clinical settings, including point-of-care testing (POCT). This review systematically explores the historical development of EBV diagnostic technologies, highlighting key milestones and future trends in precision medicine and global health readiness. Full article

H. pylori infects over half of the global population and is associated with various gastric and extra-gastric diseases. Other species, such as zoonotic non-Helicobacter pylori Helicobacters (NHPHs), have shown similar associations with gastritis and MALT lymphoma and H. pylori-negative cases with gastric disease have been identified, including gastric MALT lymphoma, chronic gastritis, and gastroduodenal ulcers. Accurate identification of these species is of great relevance but remains challenging using conventional diagnostic methods. This cross-sectional study aimed to determine the prevalence of H. pylori and NHPH infections, comparing standard histological protocols with molecular techniques. Between December 2024 and February 2025, 54 adult patients undergoing upper gastrointestinal endoscopy (UGE) with gastric biopsy in three hospitals in Algarve, Portugal were recruited. Endoscopic assessment was performed, and gastric biopsies were collected for histological and molecular analysis. DNA was extracted from antral biopsies and analyzed by conventional PCR to detect H. pylori and NHPH. H. pylori diagnostic techniques were compared, descriptive plus statistical analysis was performed, and p-values < 0.05 were considered to be statistically significant. Fifty-four patients were included in the study, with 51.9% of them presenting symptoms. Endoscopic gastritis was observed in 66.7% of patients, while histological gastritis was present in 88.9%, with statistically significant differences between the two diagnostic techniques (p = 0.004). Helicobacter spp. were identified in 44.4% (24/54) of the patients. H. pylori was detected in 42.6% of the patients by Modified Giemsa stain and in 33.3% by PCR. H. bizzozeronii was found in 35.9% of the patients, with 22.2% showing mixed infections. This study reveals a significant prevalence of Helicobacter spp. in patients from the Algarve region, with both H. pylori and zoonotic H. bizzozeronii detected. This is the first report of H. bizzozeronii DNA detection in gastric biopsies via PCR from patients undergoing UGE in Portugal, highlighting the need to consider NHPH in clinical diagnosis. It is important to include molecular methods in routine diagnostics and the need for broader studies to assess regional and national trends in Helicobacter infections besides H. pylori. Full article

Rare genetic diseases are often caused by structural variants (SVs), such as insertions, deletions, duplications, inversions, and complex rearrangements. However, due to the technical limitations of short-read sequencing, these variants remain underdiagnosed. Long-read sequencing technologies, including Oxford Nanopore and Pacific Biosciences high-fidelity (HiFi), have recently advanced to the point that they can accurately find SVs throughout the genome, including in previously unreachable areas like repetitive sequences and segmental duplications. This study underscores the transformative role of long-read sequencing in diagnosing rare diseases, emphasizing the bioinformatics tools designed for detecting and interpreting structural variants (SVs). Comprehensive methods are reviewed, including methylation profiling, RNA-seq, phasing analysis, and long-read sequencing. The effectiveness and applications of well-known tools like Sniffles2, SVIM, and cuteSV are also assessed. Case studies illustrate how this technique has revealed new pathogenic pathways and solved cases that were previously undetected. Along with outlining potential future paths like telomere-to-telomere assemblies and pan-genome integration, we also address existing issues, including cost, clinical validation, and computational complexity. For uncommon genetic illnesses, long-read sequencing has the potential to completely change the molecular diagnostic picture as it approaches clinical adoption. Full article

Background/Objectives: Gastric cancer (GC) remains a significant global health burden due to its high mortality rate and frequent diagnosis at advanced stages. This study aimed to identify reliable diagnostic biomarkers and elucidate molecular mechanisms underlying GC by integrating transcriptomic data from independent platforms and applying machine learning techniques. Methods: Two transcriptomic datasets from the Gene Expression Omnibus were analyzed: GSE26899 (microarray, n = 108) as the discovery dataset and GSE248612 (RNA-seq, n = 12) for validation. Differential expression analysis was conducted using limma and DESeq2, selecting genes with |log2FC| > 1 and adjusted p < 0.05. The top 200 differentially expressed genes (DEGs) were used to develop machine learning models (random forest, logistic regression, neural networks). Functional enrichment analyses (GO, KEGG, Hallmark) were applied to explore relevant biological pathways. Results: In GSE26899, 627 DEGs were identified (201 upregulated, 426 downregulated), with key genes including CST1, KIAA1199, TIMP1, MSLN, and ATP4A. The random forest model demonstrated excellent classification performance (AUC = 0.952). GSE248612 validation yielded 738 DEGs. Cross-platform comparison confirmed 55.6% concordance among core genes, highlighting CST1, TIMP1, KRT17, ATP4A, CHIA, KRT16, and CRABP2. Enrichment analyses revealed involvement in ECM–receptor interaction, PI3K-Akt signaling, EMT, and cell cycle. Conclusions: This integrative transcriptomic and machine learning framework effectively identified high-confidence biomarkers for GC. Notably, CST1, TIMP1, KRT16, and ATP4A emerged as consistent, biologically relevant candidates with strong diagnostic performance and potential clinical utility. These findings may aid early detection strategies and guide future therapeutic developments in gastric cancer. Full article

The advent of immune checkpoint inhibitors (ICIs) has revolutionized cancer treatment, significantly improving patient outcomes across multiple malignancies. Nonetheless, these therapies are associated with immune-related adverse effects, including cardiotoxicity, which remains a critical concern. This review provides a comprehensive analysis of ICI-related cardiotoxicity, encompassing its pathophysiological mechanisms, risk factors, diagnostic modalities, and management strategies. The onset of cardiotoxicity varies widely, ranging from acute myocarditis to long-term cardiovascular complications. Early identification through clinical assessment, biomarkers, and advanced imaging techniques is crucial for timely intervention. Management strategies include high-dose corticosteroids, other immunosuppressive agents, and supportive therapies, with a focus on balancing oncologic efficacy and cardiovascular safety. Additionally, rechallenging patients with ICIs following cardiotoxic events remains a complex clinical decision requiring multidisciplinary evaluation. As immunotherapy indications expand to include high-risk populations in a curative setting too, optimizing screening, prevention, and treatment strategies is essential to mitigate cardiovascular risks. A deep understanding of the molecular and clinical aspects of ICI-related cardiotoxicity will enhance patient safety and therapeutic decision-making, underscoring the need for ongoing research in this rapidly evolving field. Full article

Microbiological contamination of food remains a critical global public health concern, contributing to millions of foodborne illness cases each year. Traditional diagnostic methods, particularly culture-based techniques, have been widely employed but are often limited by low sensitivity, insufficient specificity, and lengthy turnaround times. Recent advances in molecular biology, biosensor technology, and analytical chemistry have enabled the development of more rapid and precise diagnostic tools. Among these, Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry (MALDI-TOF MS) has emerged as a transformative method for microbial identification. This review provides a comprehensive overview of the current applications of MALDI-TOF MS in the diagnosis of microbiological contamination in food. The method offers rapid, accurate, and cost-effective identification of microorganisms and is increasingly used in food safety laboratories for the detection of foodborne pathogens, ensuring the safety and quality of food products. We highlight the fundamental principles of MALDI-TOF MS, discuss its methodologies, and examine its advantages, limitations, and future prospects in food microbiology and quality assurance. Full article

Background/Objectives: Degenerative joint diseases (DJDs) involve intricate molecular disruptions within bone, cartilage, and synovial tissues, often preceding overt radiographic changes. These tissues exhibit complex biomolecular architectures and their degeneration leads to microstructural disorganization and inflammation that are challenging to detect with conventional imaging techniques. This review aims to synthesize recent advances in imaging, computational modeling, and sequencing technologies that enable high-resolution, non-invasive characterization of joint tissue health. Methods: We examined advanced modalities including high-resolution MRI (e.g., T1ρ, sodium MRI), quantitative and dual-energy CT (qCT, DECT), and ultrasound elastography, integrating them with radiomics, deep learning, and multi-scale modeling approaches. We also evaluated RNA-seq, spatial transcriptomics, and mass spectrometry-based proteomics for omics-guided imaging biomarker discovery. Results: Emerging technologies now permit detailed visualization of proteoglycan content, collagen integrity, mineralization patterns, and inflammatory microenvironments. Computational frameworks ranging from convolutional neural networks to finite element and agent-based models enhance diagnostic granularity. Multi-omics integration links imaging phenotypes to gene and protein expression, enabling predictive modeling of tissue remodeling, risk stratification, and personalized therapy planning. Conclusions: The convergence of imaging, AI, and molecular profiling is transforming musculoskeletal diagnostics. These synergistic platforms enable early detection, multi-parametric tissue assessment, and targeted intervention. Widespread clinical integration requires robust data infrastructure, regulatory compliance, and physician education, but offers a pathway toward precision musculoskeletal care. Full article

Nitric oxide (NO) predominantly regulates endometrial receptivity, angiogenesis, immunological tolerance, and trophoblast invasion throughout the implantation period. Both insufficient and excessive nitric oxide production have been linked to suboptimal embryo implantation and infertility. The primary enzymatic source of uterine nitric oxide, along with hormonal, metabolic, and immunological variables and genetic variations in the endothelial nitric oxide synthase gene (NOS3), affects endothelial nitric oxide synthase (eNOS). Despite its considerable importance, there is limited knowledge regarding the practical implementation of nitric oxide-related diagnoses and therapies in reproductive medicine. A comprehensive assessment was performed in accordance with the PRISMA principles. Electronic searches were carried out in PubMed, Scopus, and Embase, and we analyzed the literature published from 2000 to 2024 regarding the association between NO, its metabolites (NO₂⁻ and NO₃⁻), eNOS expression, NOS3 gene variants, and reproductive outcomes. Relevant studies encompassed clinical trials, observational studies, and experimental research using either human or animal subjects. We collected data about therapeutic interventions, hormonal and immunological associations, nitric oxide measurement techniques, and in vitro fertilization success rates. A total of thirty-four studies were included. Dysregulated nitric oxide signaling, characterized by modified eNOS expression, oxidative stress, or NOS3 polymorphisms (e.g., Glu298Asp and intron 4 VNTR), was linked to diminished endometrial receptivity and an elevated risk of implantation failure and miscarriage. The dynamics of local uterine NO are essential as elevated and diminished systemic levels of NO₂⁻/NO₃⁻ corresponded with enhanced and decreased implantation rates, respectively. Among many therapeutic approaches, targeted hormone treatments, antioxidant therapy, and dietary nitrate supplements have demonstrated potential in restoring nitric oxide balance and enhancing reproductive outcomes. In animal models, the modification of nitric oxide significantly impacted decidualization, angiogenesis, and embryo viability. Nitric oxide is a multifaceted molecular mediator with considerable ramifications for successful implantation. Its therapeutic and diagnostic efficacy increases with its sensitivity to environmental, hormonal, and genetic alterations. Integrating targeted nitric oxide modulation, oxidative stress assessment, and NOS3 genotyping with personalized reproductive therapy will enhance endometrial receptivity and improve IVF outcomes. Future translational research should incorporate nitric oxide signaling into personalized treatment protocols for patients with unexplained infertility or recurrent implantation failure. Full article

Aflatoxins, toxic secondary metabolites produced primarily by Aspergillus flavus and Aspergillus parasiticus, pose a significant global health concern due to their frequent presence in crops, food, and feed—especially under climate change conditions. This review addresses the growing threat of aflatoxins by analyzing recent advances in detection and mitigation. A comprehensive literature review was conducted, focusing on bioremediation, physical and chemical detoxification, and fungal growth inhibition strategies. The occurrence of aflatoxins in water systems was also examined, along with current detection techniques, removal processes, and regulatory frameworks. Emerging technologies such as molecular diagnostics, immunoassays, biosensors, and chromatographic methods are discussed for their potential to improve monitoring and control. Key findings highlight the increasing efficacy of integrative approaches combining biological and technological solutions and the potential of AI-based tools and portable devices for on-site detection. Intelligent packaging and transgenic crops are also explored for their role in minimizing contamination at the source. Overall, this review emphasizes the importance of continued interdisciplinary research and the development of sustainable, adaptive strategies to mitigate aflatoxin risks, thereby supporting food safety and public health in the face of environmental challenges. Full article

Equine piroplasmosis (EP), caused by Theileria equi and Babesia caballi, is a worldwide tick-borne disease with severe economic, commercial, and sanitary implications for equids. Although diagnosis is based on direct (blood smear or PCR) or indirect (serology) methods, these techniques are expensive, laborious, and false-negative and false-positive results can be yielded. Biochemistry blood profiles are routinely performed in horses. Biochemical parameters and ratios could be a reliable complementary diagnostic tool to assist clinicians in EP diagnosis, mainly in endemic areas, or for discarding similar disorders (piro-like diseases) and prioritizing specific diagnostic testing. This study describes the changes induced by EP infection in blood biochemical parameters and common and novel biochemical ratios in horses. EP-infected horses showed increased serum total and indirect bilirubin, triglycerides, and GLDH concentrations and decreased sodium concentrations compared to non-infected animals. These findings could be linked to hemolysis, diminution of athletic performance, and liver inflammation due to oxidative stress damage. While molecular methods remain the gold standard for EP diagnosis, a complete biochemical profile and ratios could provide valuable complementary information to enhance the diagnostic accuracy of piroplasmosis in horses. Full article

Accurate, rapid and inexpensive diagnosis of poultry respiratory pathogens remains a challenge, especially in many developing countries. Meanwhile, poultry respiratory pathogens are a major threat to poultry production worldwide, accounting for billions of dollars in economic loss to the sector. Early and accurate diagnosis of these diseases is critical for economic poultry production. Molecular diagnostic methods, including PCR-based techniques, have been developed and used to fill this gap, but unfortunately, these techniques require skilled technicians, relatively costly equipment and reagents and can only be performed in a laboratory setting. This warrants the development of other diagnostic tools, which can be used in the field even by unskilled personnel. In this review, we discussed the genesis, challenges, advances and prospects of loop-mediated isothermal amplification (LAMP) for the detection of poultry respiratory pathogens at the flock side, especially in resource-constrained countries. We highlighted the application of LAMP in routine poultry disease surveillance and early outbreak detection, underscoring its value as a transformative diagnostic tool in poultry production. The development and use of a point-of-care (POC) LAMP assay that can be used to screen for these poultry respiratory pathogens simultaneously enhance disease surveillance and diagnosis. Full article

Background: Trichophyton indotineae, a new emerging pathogen according to the WHO, is known to cause severe forms of tinea. Given that traditional identification methods rely on morphological characteristics, and the morphological distinctions among T. indotineae, T. mentagrophytes, and T. interdigitale are minimal, the adoption of alternative diagnostic techniques, such as RT-PCR or gene sequencing, has become critically important to prevent misidentification. The purpose of this study was firstly to analyze the local epidemiology of dermatophytes isolated and secondly to investigate the presence of T. indotineae among the isolated strains. Methods: Between January 2021 and June 2024, 1096 samples of skin adnexa were analysed. The isolated strains belonging to the genus Trichophyton were submitted to molecular identification by ITS sequencing, and T. indotineae strains were subjected to squalene epoxidase (SQLE) sequencing analysis. Results: Trichophyton rubrum and Trichophyton interdigitale appear to be the most prevalent pathogenic species. Molecular identification reveals four T. indotineae strains (4/87; 4.61%) from Asian patients, which were also characterized by gene mutations associated with terbinafine resistance. Conclusions: This study has made it clear that there is a need to implement basic mycological diagnostics with molecular methods to avoid misidentifications, ensure the correct identification, and evaluate the presence of mutations associated with antifungal drug resistance. Full article

The global prevalence of hepatocellular carcinoma (HCC) is getting worse, leading to an urgent need for improved diagnostic and prognostic strategies. Liquid biopsy, which analyzes circulating tumor cells (CTCs), cell-free DNA (cfDNA), cell-free RNA (cfRNA), and extracellular vesicles (EVs), has emerged as a minimally invasive and promising alternative to traditional tissue biopsy. These biomarkers can be detected using sensitive molecular techniques such as digital PCR, quantitative PCR, methylation-specific assays, immunoaffinity-based CTC isolation, nanoparticle tracking analysis, ELISA, next-generation sequencing, whole-genome sequencing, and whole-exome sequencing. Despite several advantages, liquid biopsy still has challenges like sensitivity, cost-effectiveness, and clinical accessibility. Reports highlight the significance of multi-analyte liquid biopsy panels in enhancing diagnostic sensitivity and specificity. This approach offers a more comprehensive molecular profile of HCC, early detection, and tracking therapeutic treatment, particularly in those cases where single-analyte assays and imaging fail. The technological advancement in the isolation and analysis of CTC, cell-free nucleic acids, and EVs is increasing our understanding of extracting genetic information from HCC tumors and discovering mechanisms of therapeutic resistance. Furthermore, crucial information on tumor-specific transcriptomic and genomic changes can be obtained using cfRNA and cfDNA released into the peripheral blood by tumor cells. This review provides an overview of current liquid biopsy strategies in HCC and their use for early detection, prognosis, and monitoring the effectiveness of HCC therapy. Full article

Background and Objectives: Thyroid cancer is the prevailing endocrine malignancy, with incidence growing over the last decades in the world. The current diagnostic techniques often yield inconclusive results, emphasizing the need for more effective diagnostic approaches. Molecular profiling emerges as a promising avenue for carcinoma differentiation, offering precise insights to guide patient selection for surgical intervention. This study aimed to identify molecular markers in thyroid cancer through the expression analysis of genes within the MAPK pathway, aiming to enhance the sensitivity and specificity of carcinoma diagnosis. Methods: Through a comparative analysis of malignant and benign thyroid samples, we identified 46 genes of the MAPK pathway that exhibited differential expression by PCR array analysis. Results: Validation through RT-qPCR and in silico analysis using TCGA confirmed significant results for CCNA1, CDKN1C, CREB1, FOS, HSPA5, JUN, MAP2K6, and SFN genes identified in our cohort, reinforcing the relevance of these biomarkers. Specifically, noteworthy are our findings regarding the potential diagnostic value of CCNA1 and SFN genes in papillary thyroid carcinoma, while the reduced expression of CDKN1C, FOS, and JUN genes in follicular carcinoma suggests their value in distinguishing the thyroid pathologies. Conclusions: This study identifies promising diagnostic markers, namely CCNA1, CDKN1C, FOS, JUN, and SFN genes, which have the potential to enhance clinical decision-making in thyroid cancer. Full article

Background/Objectives: T2 mapping is a quantitative magnetic resonance imaging (MRI) technique that provides information about tissue water content and molecular mobility. This study aimed to evaluate the diagnostic utility of T2 mapping in assessing sacroiliitis associated with spondyloarthropathy (SpA). Methods: A prospective study examined a total of 56 participants, comprising 31 SpA patients (n = 31) and 25 healthy controls (n = 25), who underwent sacroiliac joint MRI between August 2018 and August 2020. T2 mapping images were generated using multi-echo turbo spin echo (TSE) sequence, and quantitative T2 relaxation times were measured from bone and cartilage regions. Statistical analysis employed appropriate parametric and non-parametric tests with significance set at p < 0.05. Results: The mean T2 relaxation time measured from the areas with osteitis of SpA patients (100.23 ± 7.41 ms; 95% CI: 97.51–102.95) was significantly higher than that of the control group in normal bone (69.44 ± 4.37 ms; 95% CI: 67.64–71.24), and this difference was found to be statistically significant (p < 0.001). No significant difference was observed between cartilage T2 relaxation times in SpA patients and controls (p > 0.05). Conclusions: T2 mapping serves as a valuable quantitative imaging biomarker for diagnosing sacroiliitis associated with SpA, particularly by detecting bone marrow edema. The technique shows promise for objective disease assessment, though larger studies are needed to establish standardized reference values for T2 relaxation times in osteitis to enhance diagnostic accuracy and facilitate treatment monitoring. Full article