Search Results (850)

Grapevine (Vitis vinifera L.) cultivation is an important agricultural sector worldwide. Its expansion into new areas, like Kazakhstan, brings significant phytosanitary risks. Viroids, such as grapevine yellow speckle viroid 1 (GYSVd-1) and hop stunt viroid (HSVd), are RNA pathogens that threaten vineyard productivity. They can cause a progressive decline through latent infections. Traditional diagnostic methods are usually targeted and therefore not suitable for thorough surveillance. In contrast, modern high-throughput sequencing (HTS) methods often face challenges due to their high costs and complicated sample preparation, such as ribosomal RNA (rRNA) depletion. This study introduces a simplified diagnostic workflow that overcomes these barriers. We utilized the latest Oxford Nanopore V14 cDNA chemistry, which is designed to prevent internal priming, by substituting a targeted oligo(dT)VN priming strategy to facilitate the sequencing of non-polyadenylated viroids from total RNA extracts, completely bypassing the rRNA depletion step and use of random oligonucleotides for c DNA synthesis. This method effectively detects and identifies both GYSVd-1 and HSVd. This workflow significantly reduces the time, cost, and complexity of HTS-based diagnostics. It provides a powerful and scalable tool for establishing strong genomic surveillance and phytosanitary certification programs, which are essential for supporting the growing viticulture industry in Kazakhstan. Full article

Botryosphaeria dothidea is the causative agent of Chinese hickory trunk canker, which poses significant threat to the production of Chinese hickory (Carya cathayensis Sarg.). Previous studies reported that endophytic–pathogenic phase transition, also referred to as latent infection, plays an important role in the interaction of Botryosphaeria dothidea with various host plants, including Chinese hickory. However, the mechanism underlying this phase transition is not well understood. Here, we employed RNA-Seq to investigate transcriptional changes in B. dothidea during its phase transition upon interaction with Chinese hickory. A co-expression network was generated based on 6391 differentially expressed genes (DEGs) identified from different infection stages and temperature treatments. One co-expressed module was found that highly correlated with temperature treatments which simulated conditions of B. dothidea latent infection in the field. Subsequently, 53 hub genes were detected, and gene ontology (GO) enrichment analysis revealed three categories of enriched GO terms: transmembrane transport or activity, ion homeostasis or transport, and carbohydrate metabolism. One PacC transcriptional factor (BDLA_00001555, an ambient pH regulator), and one endo-β-1,3-glucanase (BDLA_00010249) were specifically upregulated under temperature treatments that corresponded with the activation stage of B. dothidea’s pathogenic state. The knockout mutant strain of BDLA_00001555 demonstrated defective capability upon the activation of the pathogenic state. This confirmed that BDLA_00001555, the PacC transcriptional factor, plays an important role in the latent infection phase of B. dothidea. Our findings provide insights into the pathogenic mechanism of Chinese hickory trunk canker disease. Full article

Cervical cancer remains a major health burden among women in sub-Saharan Africa, where screening is often limited. Persistent high-risk human papillomavirus (HR-HPV) infection is the principal cause, highlighting the need for accurate molecular diagnostics. This cross-sectional study evaluated the analytical performance of one mRNA assay, APTIMA^® HPV assay (APTIMA mRNA), and two DNA-based assays, the Abbott RealTime High Risk HPV assay (Abbott DNA) and Seegene Allplex™ II HPV28 assay (Seegene DNA), in 527 cervical samples from a South African tertiary hospital, focusing on 14 shared HR-HPV genotypes. Seegene DNA yielded the highest detection rate (53.7%), followed by Abbott DNA (48.2%) and APTIMA mRNA (45.2%). APTIMA mRNA showed a strong agreement with Abbott DNA (87.9%, κ = 0.80), 89.9% sensitivity, 91.2% NPV, and the highest accuracy (AUC = 0.8804 vs. 0.8681). The agreement between APTIMA mRNA and Seegene DNA was moderate (83.4%, κ = 0.70), reflecting target differences. Many DNA-positive/mRNA-negative cases likely represent transient infections, though some may be latent with reactivation potential, warranting a follow-up. In resource-constrained settings, prioritizing transcriptionally active infections through mRNA testing may enhance screening efficiency and reduce burden. Scalable, cost-effective assays with strong clinical utility are essential for broadening access and improving cervical cancer prevention. Further studies should assess the integration of mRNA testing into longitudinal screening algorithms. Full article

This study focuses on analyzing progressive Type-II right censoring competing risks datasets. The latent causes of failures are assumed to follow independent generalized linear exponential distributions. The maximum likelihood and maximum product of spacing methods are employed to estimate the unknown parameters and survival indices. Furthermore, approximate confidence intervals are derived using the asymptotic normality of the maximum likelihood and the maximum product of spacing estimators. Additionally, bootstrap methods are employed to construct confidence intervals. A comprehensive simulation study is carried out to evaluate the effectiveness of these estimation approaches. Finally, real-world datasets are analyzed to illustrate the practical applicability of the proposed model. Full article

Background and Objectives: The causes and clinical outcomes of renal perfusion abnormalities occurring after para-aortic lymphadenectomy (PANDx) for gynecologic malignancies are unknown. We investigated the potential involvement of accessory renal artery (ARA) obstruction in their development by reassessing perioperative contrast-enhanced computed tomography (CECT). Materials and Methods: This retrospective study investigated a clinical database to identify urinary contrast defects using CECT in all patients who had undergone PANDx between January 2020 and December 2024. The perfusion defects in the kidney detected by CECT were extracted by a gynecologic oncologist and evaluated by a radiologist and urologist for suspected obstruction of ARAs. Results: Postoperative renal contrast defects were observed in 3.8% (6/157) of patients. Renal parenchymal fibrosis, cortical atrophy, and parenchymal thinning were observed as universal findings in all patients showing renal contrast defects. In five of the six cases, ARAs supplying the infarcted renal segments were identified on preoperative CECT, and arterial obstruction was confirmed on postoperative imaging. The remaining case was considered to be latent pyelonephritis. All five patients underwent laparotomy, and preoperative CECT failed to detect ARAs. The median resected para-aortic lymph node was 23 nodes (range: 15–33) in five patients, showing no statistically significant difference compared to patients without perfusion abnormalities (p = 0.19). Postoperative serum creatinine levels remained stable. Conclusions: ARA obstruction appears to be a risk factor for segmental renal infarction after para-aortic lymphadenectomy in gynecological malignancies; however, the clinical impact on urinary function may be limited. Awareness of this potential complication is essential for gynecologic oncologists performing PANDx. Full article

Composite laminates are widely used in aerospace, automotive, construction, and luxury industries, owing to their superior mechanical properties and design flexibility. However, detecting manufacturing defects and in-service damage remains a vital challenge for structural safety. While traditional unsupervised machine learning methods have been used in structural health monitoring (SHM), their high false positive rates limit their reliability in real-world applications. This issue is mostly inherited from their limited ability to capture small temporal variations in Lamb wave signals and their dependence on shallow architectures that suffer with complex signal distributions, causing the misclassification of damaged signals as healthy data. To address this, we suggested an unsupervised anomaly detection framework that integrates a self-attention autoencoder with a Gaussian mixture model (SAE-GMM). The model is solely trained on healthy Lamb wave signals, including high-quality synthetic data generated via a generative adversarial network (GAN). Damages are detected through reconstruction errors and probabilistic clustering in the latent space. The self-attention mechanism enhances feature representation by capturing subtle temporal dependencies, while the GMM enables a solid separation among signals. Experimental results demonstrated that the proposed model (SAE-GMM) achieves high detection accuracy, a low false positive rate, and strong generalization under varying noise conditions, outperforming traditional and deep learning baselines. Full article

The increasing complexity of manufacturing processes demands accurate defect prediction and interpretable insights into the causes of quality issues. This study proposes a methodology integrating machine learning, clustering, and Explainable Artificial Intelligence (XAI) to support defect analysis and quality control in industrial environments. Using a dataset based on empirical industrial distributions, we train an XGBoost model to classify high- and low-defect scenarios from multidimensional production and quality metrics. The model demonstrates high predictive performance and is analyzed using five XAI techniques (SHAP, LIME, ELI5, PDP, and ICE) to identify the most influential variables linked to defective outcomes. In parallel, we apply Fuzzy C-Means and K-means to segment production data into latent operational profiles, which are also interpreted using XAI to uncover process-level patterns. This approach provides both global and local interpretability, revealing consistent variables across predictive and structural perspectives. After a thorough review, no prior studies have combined supervised learning, unsupervised clustering, and XAI within a unified framework for manufacturing defect analysis. The results demonstrate that this integration enables a transparent, data-driven understanding of production dynamics. The proposed hybrid approach supports the development of intelligent, explainable Industry 4.0 systems. Full article

The varicella-zoster virus is a human herpesvirus that causes varicella as the primary infection and HZ as the reactivation of a latent infection. Ten to twenty percent of cases of herpes zoster ophthalmicus (HZO) involve the ophthalmic branch of the fifth cranial nerve. Any area of the eye may be affected by the condition. HZ has a lifetime risk of more than 30%. Complications from herpes zoster can significantly lower quality of life. The goal of HZ vaccinations is to stop HZ activation and PHN formation. Despite the uncommon possibility of side effects such as eye problems, the majority of vaccines on the market now are safe. The purpose of this review is to discuss VZV infection and analyze and summarize the ocular complications following VZV vaccination. Full article

The Korean government proposes introducing a transfer-type bus system to reduce urban congestion. Transfer-type buses turn around at the Seoul border, requiring passengers to transfer to other modes to reach downtown. These buses have shorter routes, allowing reduced headways and increased bus supply. While this approach reduces congestion in the downtown area, it may cause transfer resistance, making it essential to analyze willingness to shift (WTS). This study uses a latent class model to categorize potential interregional bus users into three types: transfer avoidance, cost-sensitive, and time-sensitive. Over 50% of users in each group express WTS, showing a positive response to the transfer-type bus introduction. The choice model results indicate that the travel time and cost of direct type buses affect WTS, suggesting that policies should consider these factors for effective implementation. Full article

Background: Alopecia areata (AA), an autoimmune condition causing non-scarring hair loss, often coexists with atopic dermatitis (AD) due to shared T-helper cell type 2 (Th2)-mediated pathways. Dupilumab, a monoclonal antibody inhibiting IL-4 and IL-13 signaling, is a cornerstone treatment for AD but has conflicting reports regarding its impact on AA, with some suggesting therapeutic benefits and others indicating AA induction. Methods: This retrospective study, utilizing the TriNetX Research Network’s de-identified data from over 300 million patient records, investigates the association between dupilumab use and AA risk in AD patients. Results: After propensity score matching, 23,782 dupilumab users were compared with an equal number of controls. Results revealed a statistically significant increased AA risk in dupilumab users (odds ratio: 1.436, 95% CI: 1.066–1.935, p = 0.0167) after 16 weeks. Cases occurring within 16 weeks were excluded. Conclusions: Potential mechanisms include immune rebalancing, with Th2 suppression possibly upregulating Th1/Th17 pathways or unmasking latent AA in predisposed individuals. These findings challenge dupilumab’s potential as an AA treatment and highlight the need for vigilant monitoring, including routine scalp examinations and patient education. Future research should focus on mechanistic pathways, risk stratification, and comparative studies with other biologics to optimize personalized treatment strategies for AD and AA. Full article

Mycobacterium tuberculosis—an acid-fast staining bacterium—is a serious global health challenge that can have both short-term and long-term complications. Although the immune response helps trap the infection, it can also cause necrosis and calcification, leading to lung tissue damage. Calcification is a known outcome of chronic granuloma evolution in TB. Multiple pathways contribute to fibrosis and calcification; some examples are IL-1β, TGF-β, and TNF-α. Current antifibrotic drugs, such as nintedanib and pirfenidone, are effective but may increase the risk of latent tuberculosis reactivation in certain patients. Experimental therapies such as artemisinin derivatives have shown promise in preclinical TB fibrosis models, while cell-based therapies like bone marrow-derived mononuclear cells are also under early investigation for dual antifibrotic and immunomodulatory effects. This literature review will explore recent studies on the pathogenesis of M. tuberculosis, the mechanisms underlying calcification in granuloma formation, and subsequent complications of the disease process. Full article

Background and Aim: Syphilis, caused by Treponema pallidum, classically presents with genital or anal chancres; rectal involvement is rare and frequently misdiagnosed as inflammatory bowel disease or malignancy. We describe an unusually severe case of syphilitic proctitis in the setting of advanced HIV-related immunosuppression (CD4 39 cells/µL), in which targeted immunophenotyping (ERG and CD38) was a valuable adjunctive tool in the differential diagnosis. Case Presentation: A 46-year-old man with a recent history of erosive gastritis and esophageal candidiasis presented after six months of unintentional 20 kg weight loss, profound fatigue, intermittent fevers, profuse diarrhea, and two episodes of hematemesis. Workup revealed a new diagnosis of HIV infection (CD4: 39 cells/µL; viral load: 87,837 copies/mL). Contrast-enhanced CT demonstrated uniform, concentric rectal wall thickening (“target sign”). Colonoscopic biopsy showed exuberant granulation tissue and dense plasma cell infiltrates. Immunohistochemistry revealed a dense infiltrate of CD38-positive plasma cells and ERG-positive endothelial proliferation. These findings, in the context of positive serology, were highly supportive of a spirochetal etiology and helped differentiate it from potential mimics. Serology was positive for latent late syphilis (VDRL 1:64). The patient received three weekly doses of intramuscular benzathine penicillin; lumbar puncture excluded neurosyphilis. Discussion: This is among the first reported cases of syphilitic proctitis in a patient with CD4 < 50 cells/µL, where advanced immunophenotyping differentiated syphilitic inflammation from neoplastic or inflammatory mimics. Profound immunosuppression accelerates disease progression and yields atypical clinical features. Conclusion: In HIV-infected patients with chronic rectal symptoms, especially those with CD4 < 50 cells/µL, syphilitic proctitis must be considered. Integration of radiologic assessment, histopathology with ERG/CD38 staining, and serologic testing permits prompt diagnosis. Early benzathine penicillin therapy and rigorous clinical and serologic follow-up are essential to prevent complications, including neurosyphilis. Full article

The underwater environment severely degrades image quality by absorbing and scattering light. This causes significant challenges, including non-uniform illumination, low contrast, color distortion, and blurring. These degradations compromise the performance of critical underwater applications, including water quality monitoring, object detection, and identification. To address these issues, this study proposes a detail-oriented hybrid framework for underwater image enhancement that synergizes the strengths of traditional image processing with the powerful feature extraction capabilities of unsupervised deep learning. Our framework introduces a novel multi-scale detail enhancement unit to accentuate structural information, followed by a Latent Low-Rank Representation (LatLRR)-based simplification step. This unique combination effectively suppresses common artifacts like oversharpening, spurious edges, and noise by decomposing the image into meaningful subspaces. The principal structural features are then optimally combined with a gamma-corrected luminance channel using an unsupervised MU-Fusion network, achieving a balanced optimization of both global contrast and local details. The experimental results on the challenging Test-C60 and OceanDark datasets demonstrate that our method consistently outperforms state-of-the-art fusion-based approaches, achieving average improvements of 7.5% in UIQM, 6% in IL-NIQE, and 3% in AG. Wilcoxon signed-rank tests confirm that these performance gains are statistically significant (p < 0.01). Consequently, the proposed method significantly mitigates prevalent issues such as color aberration, detail loss, and artificial haze, which are frequently encountered in existing techniques. Full article

Recognizing the interrelationship among variables becomes critical in genetic breeding programs, where the goal is often to optimize selection for multiple traits. Conventional multi-trait models face challenges such as convergence issues, and they fail to account for cause-and-effect relationships. To address these challenges, we conducted a comprehensive analysis involving confirmatory factor analysis (CFA), Bayesian networks (BN), structural equation modeling (SEM), and genome-wide selection (GWS) using data from 195 arabica coffee plants. These plants were genotyped with 21,211 single nucleotide polymorphism markers as part of the Coffea arabica breeding program at UFV/EPAMIG/EMBRAPA. Traits included vegetative vigor (VV), canopy diameter (CD), number of vegetative nodes (NVN), number of reproductive nodes (NRN), leaf length (LL), and yield (Y). CFA established the following latent variables: vigor latent (VL) explaining VV and CD; nodes latent (NL) explaining NVN and NRN; leaf length latent (LLL) explaining LL; and yield latent (YL) explaining Y. These were integrated into the BN model, revealing the following key interrelationships: LLL → VL, LLL → NL, LLL → YL, VL → NL, and NL → YL. SEM estimated structural coefficients, highlighting the biological importance of VL → NL and NL → YL connections. Genomic predictions based on observed and latent variables showed that using VL to predict NVN and NRN traits resulted in similar gains to using NL. Predicting gains in Y using NL increased selection gains by 66.35% compared to YL. The SEM-GWS approach provided insights into selection strategies for traits linked with vegetative vigor, nodes, leaf length, and coffee yield, offering valuable guidance for advancing Arabica coffee breeding programs. Full article

Thermal energy storage plays a vital role in enhancing the efficiency of energy systems, particularly in building applications. Phase change materials (PCMs) have gained significant attention as a passive solution for energy management within building envelopes. This study examines the thermal performance of encapsulated PCMs integrated into bricks as a passive cooling method, taking into account the outdoor climate conditions to enhance indoor thermal comfort throughout summer and winter seasons. A computational fluid dynamics (CFDs) analysis is performed to compare three configurations: a conventional brick, a brick with a single PCM layer, and a brick with three PCM layers. Results indicate that the three-layer PCM configuration provides the most effective thermal regulation, reducing peak indoor temperature fluctuations by up to 4 °C in summer and stabilizing indoor temperature during winter. Also, the second and third PCM layers exhibit minimal latent heat absorption, with their liquid fractions indicating that melting does not occur. As a result, these layers primarily serve as thermal insulation—limiting heat ingress in summer and reducing heat loss in winter. During summer, the absence of the first PCM layer in the single-layer configuration leads to faster thermal penetration, causing the brick to reach peak temperatures approximately two hours earlier in the afternoon and increasing the temperature by about 5 °C. Full article