Search Results (9,074)

The methylation of CpG sites with 5mC mark is a dynamic epigenetic modification. However, the relationship between the methylation and the surrounding genomic sequence context remains poorly explored. Investigation of the allele methylation provides an opportunity to decipher the interplay between differences in the primary DNA sequence and epigenetic variation. Here, we performed high-coverage long-read whole-genome direct DNA sequencing of one individual using Oxford Nanopore technology. We also used Illumina whole-genome sequencing of the parental genomes in order to identify allele-specific methylation sites with a trio-binning approach. We have compared the results of the haplotype-specific methylation detection and revealed that trio binning outperformed other approaches that do not take into account parental information. Also, we analysed the cis-regulatory effects of the genomic variations for influence on CpG methylation. To this end, we have used available Deep Learning models trained on the primary DNA sequence to score the cis-regulatory potential of the genomic loci. We evaluated the functional role of the allele-specific epigenetic changes with respect to gene expression using long-read Nanopore RNA sequencing. Our analysis revealed that the frequency of SNVs near allele-specific methylation positions is approximately four times higher compared to the biallelic methylation positions. In addition, we identified that allele-specific methylation sites are more conserved and enriched at the chromatin states corresponding to bivalent promoters and enhancers. Together, these findings suggest that significant impact on methylation can be encoded in the DNA sequence context. In order to elucidate the effect of the SNVs around sites of allele-specific methylation, we applied the Deep Learning model for detection of the cis-regulatory modules and estimated the impact that a genomic variant brings with respect to changes to the regulatory activity of a DNA loci. We revealed higher cis-regulatory impact variants near differentially methylated sites that we further coupled with transcriptomic long-read sequencing results. Our investigation also highlights technical aspects of allele methylation analysis and the impact of sequencing coverage on the accuracy of genomic phasing. In particular, increasing coverage above 30X does not lead to a significant improvement in allele-specific methylation discovery, and only the addition of trio binning information significantly improves phasing. We investigated genomic variation in a single human individual and coupled computational discovery of cis-regulatory modules with allele-specific methylation (ASM) profiling. In this proof-of-concept analysis, we observed that SNPs located near methylated CpG sites on the same haplotype were enriched for sequence features suggestive of high-impact regulatory potential. This finding—derived from one deeply sequenced genome—illustrates how phased genetic and epigenetic data analyses can jointly put forward a hypotheses about the involvement of regulatory protein machinery in shaping allele-specific epigenetic states. Our investigation provides a methodological framework and candidate loci for future studies of genomic imprinting and cis-mediated epigenetic regulation in humans. Full article

The recent growing adversarial activity against critical systems, such as the power grid, has raised attention on the necessity of appropriate measures to manage the related risks. In this setting, our research focuses on developing tools for early detection of adversarial activities, taking into account the specificities of the energy sector. We developed a framework to design and deploy AI-based detection models, and since one cannot risk disrupting regular operation with on-site tests, we also included a testbed for evaluation and fine-tuning. In the test environment, adversarial activity that produces realistic artifacts can be injected and monitored, and evidence analyzed by the detection models. In this paper we concentrate on the emulation of attacks inside our framework: A tool called SecuriDN is used to define, through a graphical interface, the network in terms of devices, applications, and protection mechanisms. Using this information, SecuriDN produces sequences of attack steps (based on the MITRE ATT&CK project) that are interpreted and executed by software called Netsploit. A case study related to Distributed Energy Resources is presented in order to show the process stages, highlight the possibilities given by our framework, and discuss possible limitations and future improvements. Full article

Respiratory syncytial virus (RSV) remains a leading cause of pneumonia in young children in Mexico and worldwide. To investigate RSV dynamics in Mexico, we conducted a multicenter study from August 2021 to July 2023 in six hospitals across five States, analyzing respiratory samples from children under five years with pneumonia. Multiplex RT-PCR identified 203 RSV-positive cases, of which 123 were RSV-B and 80 RSV-A. Interestingly, 77% of the collected samples showed evidence of coinfection with other respiratory pathogens, with rhinovirus, Haemophilus influenzae, and Streptococcus pneumoniae being the most common. Also, RSV-B dominated in 2021–2022, whereas RSV-A prevailed in 2022–2023, mirroring trends observed in the United States. Sequences of the genes encoding G and F proteins showed that RSV-A lineages were more diverse, with A.D.1, A.D.1.8, and A.D.5.2 being frequently detected. In contrast, nearly all RSV-B sequences belonged to lineage B.D.E.1. Finally, ancestral state inference suggests repeated introductions from the USA and other North American countries, with limited evidence of sustained local circulation. These findings show different trends in RSV circulation between two consecutive seasons and the importance of genomic surveillance to monitor RSV diversity, evaluate vaccine impact, and inform public health strategies in Mexico’s evolving post-pandemic respiratory virus landscape. Full article

In recent years, research in sequential recommendation has primarily refined user intent by constructing sequence-level contrastive learning tasks through data augmentation or by extracting preference information from the latent space of user behavior sequences. However, existing methods suffer from two critical limitations. Firstly, they fail to account for how random data augmentation may introduce unreasonable item associations in contrastive learning samples, thereby perturbing sequential semantic relationships. Secondly, the neglect of temporal dependencies may prevent models from effectively distinguishing between incidental behaviors and stable intentions, ultimately impairing the learning of user intent representations. To address these limitations, we propose TCLRec, a novel temporal-aware and intent contrastive learning framework for sequential recommendation, incorporating symmetry into its architecture. During the data augmentation phase, the model employs a symmetrical contrastive learning architecture and incorporates semantic enhancement operators to integrate user preferences. By introducing user rating information into both branches of the contrastive learning framework, this approach effectively enhances the semantic relevance between positive sample pairs. Furthermore, in the intent contrastive learning phase, TCLRec adaptively attenuates noise information in the frequency domain through learnable filters, while in the pre-training phase of sequence-level contrastive learning, it introduces a temporal-aware network that utilizes additional self-supervised signals to assist the model in capturing both long-term dependencies and short-term interests from user behavior sequences. The model employs a multi-task training strategy that alternately performs intent contrastive learning and sequential recommendation tasks to jointly optimize user intent representations. Comprehensive experiments conducted on the Beauty, Sports, and LastFM datasets demonstrate the soundness and effectiveness of TCLRec, where the incorporation of symmetry enhances the model’s capability to represent user intentions. Full article

Cold stress significantly impairs plant growth and development, making the study of cold resistance mechanisms a critical research focus. Oreorchis patens (Lindl.) exhibits strong cold hardiness, yet its molecular and physiological adaptations to cold stress remain unclear. This study utilized microscopy, physiological assays, and RNA sequencing to comprehensively investigate O. patens’s responses to cold stress. The results reveal that cold stress altered leaf anatomy, leading to irregular mesophyll cells, deformed chloroplasts, and variable epidermal thickness. Physiologically, SOD and POD activities peaked at 5 °C/−10 °C, while CAT activity declined; osmotic regulators (soluble sugars, proline) increased with decreasing temperatures. Compared to the reference plants (e.g., Erigeron canadensis, Allium fistulosum), O. patens exhibited lower SOD and POD but markedly higher CAT activities, alongside reduced MDA, soluble sugars, proline, and proteins, underscoring its distinctive tolerance strategy. Low temperature stress (≤10 °C/5 °C) significantly decreased the SPAD index; the net photosynthetic rate (Pn) initially increased and then approached zero within the temperature range from 30 °C/25 °C to 25 °C/20 °C; transpiration rate (Tr) and stomatal conductance (Gs) changed synchronously, accompanied by an increase in intercellular CO₂ concentration (Ci). RNA sequencing identified 1139 cold-responsive differentially expressed genes, which were primarily enriched in flavonoid/lignin biosynthesis, jasmonic acid synthesis, and ROS scavenging pathways. qRT-PCR analysis revealed the role of secondary metabolites in O. patens response to cold stress. This study was the first to discuss the physiological, biochemical, and molecular regulatory mechanisms of O. patens resistance to cold stress, which provides foundational insights into its overwintering mechanisms and informs breeding strategies for cold-hardy horticultural crops in northern China. Full article

This article presents an innovative methodological approach for the documentation and enhancement of ancient ironworking heritage in the Guéra region of Chad. By combining ethno-historical and archaeological surveys, 3D modeling with Blender, and the generation of images and video sequences through artificial intelligence (AI), we propose an integrated production pipeline enabling the faithful reconstruction of three types of metallurgical furnaces. Our method relies on rigorously collected field data to generate multiple and plausible representations from fragmentary information. A standardized evaluation grid makes it possible to assess the archaeological fidelity, cultural authenticity, and visual quality of the reconstructions, thereby limiting biases inherent to generative models. The results offer strong potential for integration into immersive environments, opening up perspectives in education, digital museology, and the virtual preservation of traditional ironworking knowledge. This work demonstrates the relevance of multimodal approaches in reconciling scientific rigor with engaging visual storytelling. Full article

Background/Objectives: Wilson’s disease (WD) is an autosomal recessive disorder characterized by pathological copper accumulation, primarily in the liver and brain. Severe hepatic involvement can be effectively treated with liver transplantation (LT). Geographic variation in ATP7B mutations suggests the presence of regional patterns that may impact disease presentation and management. This study aims to investigate the genetic basis of WD in patients from a major LT center in Iran. Methods: A retrospective analysis was conducted on clinical, biochemical, and pathological data from patients suspected of WD who underwent evaluation for LT between May 2020 and June 2025 at Shiraz University of Medical Sciences. Genetic testing was carried out on 20 patients at the Shiraz Transplant Research Center (STRC). Direct mutation analysis of ATP7B was performed for all patients, and the results correlated with clinical and demographic information. Results: In total, 20 WD patients who underwent liver transplantation (15 males, 5 females) carried 25 pathogenic or likely pathogenic ATP7B variants, 21 of which were previously unreported. Fifteen patients were homozygous, and five were compound-heterozygous; all heterozygous combinations occurred in the offspring of second-degree consanguineous unions. Recurrent changes included p.L549V, p.V872E, and p.P992S/L, while two nonsense variants (p.E1293X, p.R1319X) predicted truncated proteins. Variants were distributed across copper-binding, transmembrane, phosphorylation, and ATP-binding domains, and in silico AlphaMissense scores indicate damaging effects for most novel substitutions. Post-LT follow-up showed biochemical normalization in the majority of recipients, with five deaths recorded during the study period. Conclusions: This single-center Iranian study reveals a highly heterogeneous ATP7B mutational landscape with a large proportion of novel population-specific variants and underscores the benefit of comprehensive gene sequencing for timely WD diagnosis and family counseling, particularly in regions with prevalent consanguinity. Full article

This article presents a principled framework for selecting and tuning classical computer vision algorithms in the context of optical displacement sensing. By isolating key factors that affect algorithm behavior—such as feed window size and motion step size—the study seeks to move beyond intuition-based practices and provide rigorous, repeatable performance evaluations. Computer vision-based optical odometry sensors offer non-contact, high-precision measurement capabilities essential for modern metrology and robotics applications. This paper presents a systematic comparative analysis of three classical tracking algorithms—phase correlation, template matching, and optical flow—for 2D surface displacement measurement using synthetic image sequences with subpixel-accurate ground truth. A virtual camera system generates controlled test conditions using a multi-circle trajectory pattern, enabling systematic evaluation of tracking performance using 400 × 400 and 200 × 200 pixel feed windows. The systematic characterization enables informed algorithm selection based on specific application requirements rather than empirical trial-and-error approaches. Full article

Microgrids are becoming an innovative piece of modern energy systems as they provide locally sourced and resilient energy opportunities and enable efficient energy sourcing. However, microgrid operations can be greatly affected by sudden environmental changes, deviating demand, and unexpected outages. In particular, extreme climatic events expose the vulnerability of microgrid infrastructure and resilience, often leading to increased risk of system-wide outages. Thus, successful microgrid operation relies on timely and accurate outage predictions. This research proposes a data-driven machine learning framework for the optimized operation of a microgrid and predictive outage detection using a Recurrent Neural Network–Long Short-Term Memory (RNN-LSTM) architecture that reflects inherent temporal modeling methods. A time-aware embedding and masking strategy is employed to handle categorical and sparse temporal features, while mutual information-based feature selection ensures only the most relevant and interpretable inputs are retained for prediction. Moreover, the model addresses the challenges of experiencing rapid power fluctuations by looking at long-term learning dependency aspects within historical and real-time data observation streams. Two datasets are utilized: a locally developed real-time dataset collected from a 5 MW microgrid of Maple Cement Factory in Mianwali and a 15-year national power outage dataset obtained from Kaggle. Both datasets went through intensive preprocessing, normalization, and tokenization to transform raw readings into machine-readable sequences. The suggested approach attained an accuracy of 86.52% on the real-time dataset and 84.19% on the Kaggle dataset, outperforming conventional models in detecting sequential outage patterns. It also achieved a precision of 86%, a recall of 86.20%, and an F1-score of 86.12%, surpassing the performance of other models such as CNN, XGBoost, SVM, and various static classifiers. In contrast to these traditional approaches, the RNN-LSTM’s ability to leverage temporal context makes it a more effective and intelligent choice for real-time outage prediction and microgrid optimization. Full article

The prediction of stock prices is challenging due to their volatility, irregular patterns, and complex time-series structure. Reliably forecasting stock market data plays a crucial role in minimizing financial risk and optimizing investment strategies. However, traditional models often struggle to capture temporal dependencies and extract relevant features from noisy inputs, which limits their predictive performance. To improve this, we developed an enhanced recursive feature elimination (RFE) method that blends the importance of impurity-based features from random forest and gradient boosting models with Kendall tau correlation analysis, and we applied SHapley Additive exPlanations (SHAP) analysis to externally validate the reliability of the selected features. This approach leads to more consistent and reliable feature selection for short-term stock prediction over 1-, 3-, and 7-day intervals. The proposed deep learning (DL) architecture integrates a temporal convolutional network (TCN) for long-term pattern recognition, a gated recurrent unit (GRU) for sequence capture, and multi-head attention (MHA) for focusing on critical information, thereby achieving superior predictive performance. We evaluate the proposed approach using daily stock price data from three leading companies—HDFC Bank, Tata Consultancy Services (TCS), and Tesla—and two major stock indices: Nifty 50 and S&P 500. The performance of our model is compared against five benchmark models: temporal convolutional network (TCN), long short-term memory (LSTM), GRU, Bidirectional GRU, and a hybrid TCN–GRU model. Our method consistently shows lower error rates and higher predictive accuracy across all datasets, as measured by four commonly used performance metrics. Full article

Accurate preoperative staging of bladder cancer on MRI remains challenging because visual reads vary across observers. We investigated a multiparametric MRI (mpMRI) radiomics approach to predict muscle invasion (≥T2) and prospectively tested it on a validation cohort. Eighty-four patients with urothelial carcinoma underwent 1.5-T mpMRI per VI-RADS (T2-weighted imaging and DWI-derived ADC maps). Two blinded radiologists performed 3D tumor segmentation; 37 features per sequence were extracted (LifeX) using absolute resampling. In the training cohort (n = 40), features that differed between non-muscle-invasive and muscle-invasive tumors (Mann–Whitney p < 0.05) underwent ROC analysis with cut-offs defined by the Youden index. A compact descriptor combining GLRLM-LRLGE from T2 and GLRLM-SRLGE from ADC was then fixed and applied without re-selection to a prospective validation cohort (n = 44). Histopathology within 6 weeks—TURBT or cystectomy—served as the reference. Eleven T2-based and fifteen ADC-based features pointed to invasion; DWI texture features were not informative. The descriptor yielded AUCs of 0.934 (training) and 0.871 (validation) with 85.7% sensitivity and 96.2% specificity in validation. Collectively, these findings indicate that combined T2/ADC radiomics can provide high diagnostic accuracy and may serve as a useful decision support tool, after multicenter, multi-vendor validation. Full article

With the rapid development of social media, short-text data have become increasingly important in fields such as public opinion monitoring, user feedback analysis, and intelligent recommendation systems. However, existing short-text sentiment analysis models often suffer from limited cross-domain adaptability and poor generalization performance. To address these challenges, this study proposes a novel short-text sentiment classification model based on the Bidirectional Encoder Representations from Transformers (BERTs) and a dual-stream Transformer gated attention mechanism. This model first employs Bidirectional Encoder Representations from Transformers (BERTs) and the Chinese Robustly Optimized BERT Pretraining Approach (Chinese-RoBERTa) to achieve data augmentation and multilevel semantic mining, thereby expanding the training corpus and enhancing minority class coverage. Second, a dual-stream Transformer gated attention mechanism was developed to dynamically adjust feature fusion weights, enhancing adaptability to heterogeneous texts. Finally, the model integrates a Bidirectional Gated Recurrent Unit (BiGRU) with Multi-Head Self-Attention (MHSA) to strengthen sequence information modeling and global context capture, enabling the precise identification of key sentiment dependencies. The model’s superior performance in handling data imbalance and complex textual sentiment logic scenarios is demonstrated by the experimental results, achieving significant improvements in accuracy and F1 score. The F1 score reached 92.4%, representing an average increase of 8.7% over the baseline models. This provides an effective solution for enhancing the performance and expanding the application scenarios of short-text sentiment analysis models. Full article

Background: Bovine mastitis caused by Prototheca spp. is the most significant animal disease of algal origin, with an increasing number of cases reported worldwide. Currently, there is no effective treatment, so control requires the culling of infected animals. In Chile, information is limited, and a discrepancy remains in the literature regarding the Prototheca species involved in bovine mastitis. Methods: This study aimed to molecularly type and phenotypically characterize Prototheca isolates associated with bovine mastitis in Chile. Sixty-six Prototheca isolates obtained from individual bovine mastitis milk samples and bulk tank milk samples were analyzed through cytochrome b gene (cytb) sequencing, Random Amplified Polymorphic DNA–Polymerase Chain Reaction (RAPD-PCR) analysis, and phenotypic evaluation (morphology, antimicrobial susceptibility, and biofilm formation). Results: Sixty-five isolates were identified as P. bovis and one as P. ciferrii, marking the first report of the latter in bovine mastitis in Chile. RAPD analysis revealed a high genetic diversity in P. bovis. All strains exhibited resistance to the antibiotics tested from the Fluoroquinolone, β-lactam, and sulfonamide groups; however, 100% of the strains showed susceptibility to aminoglycosides, with gentamicin standing out as a potential therapeutic option. Most P. bovis strains formed weak (81.5%, 53/65) or moderate (15.4%, 10/65) biofilms, which could favor the persistence of infection. Conclusions: These findings provide novel insights into the molecular and phenotypic characteristics of Prototheca spp. in Chile, highlighting the predominance of P. bovis, the emergence of P. ciferri, and the implications for antimicrobial management and disease control. Full article

Lunasin is a peptide found in the soybean albumin 2S subunit, which has important bioactivities, such as anticancer and antioxidant. Recently, peptides similar to soybean lunasin have been reported in other cereal and legume seeds; for this reason, it is considered important to carry out a review that compiles this information, whose interest lies mainly in the bioactive properties of these peptides. The peptides reported in the literature contained in barley, wheat, rye, triticale, oat, black nightshade, amaranth, bean, chickpea, grass pea, lentil, and pea are analyzed and described. Isolation methods such as ion exchange chromatography, immunoaffinity column chromatography, Western blot, reversed-phase chromatography coupled to an electrospray ionization source, extraction with water and dialysis, and extraction with PBS, and tests such as internalization, radical scavenging, chelating, cytotoxicity in cancer cell lines essays, and histone acetyltransferase inhibition essays were carried out to identify their anticancer properties. It is worth mentioning that the in silico analyses of proteins in which the lunasin-like peptide is located have been developed in some of these seeds; however, more studies are needed in order to confirm sequence similarity to that of the lunasin peptide. Further work is needed in order to identify the sequence of these lunasin-like peptides and corroborate their similarity to that of the lunasin, such as the development of specific antibodies for each lunasin-like peptide reported in each type of seeds. This document aims to compile the advances in the research on lunasin-like peptides and their bioactivities to have a better understanding of the current advances related to these peptides. Full article

To address the challenge of reduced prediction accuracy caused by capacity regeneration during the use of lithium-ion batteries, this study proposes an RUL (remaining useful life) prediction method based on mode decomposition and an enhanced Informer-LSTM hybrid model. The capacity is selected as the health indicator, and the CEEMDAN (complete ensemble empirical mode decomposition with adaptive noise) algorithm is employed to decompose the capacity sequence into high-frequency and low-frequency components. The high-frequency components are further decomposed and predicted using the Informer model, while the low-frequency components are predicted with an LSTM (long short-term memory) network. Pearson correlation coefficients between each component and the original sequence are calculated to determine fusion weights. The final RUL prediction is obtained through weighted integration of the individual predictions. Experimental validation on publicly available NASA and CALCE (Center for Advanced Life Cycle Engineering) battery datasets demonstrates that the proposed method achieves an average fitting accuracy of approximately 99%, with MAE (mean absolute error) below 0.02. Additionally, both MAPE (mean absolute percentage error) and RMSE (root-mean-square error) remain at low levels, indicating improvements in prediction precision. Full article