Explore the vast range of titles available.

In bioinformatics, alignment is an essential technique for finding similarities between biological sequences. Usually, the alignment is performed with the Smith-Waterman (SW) algorithm, a well-known sequence alignment technique of high-level precision based on dynamic programming. However, given the massive data volume in biological databases and their continuous exponential increase, high-speed data processing is necessary. Therefore, this work proposes a parallel hardware design for the SW algorithm with a systolic array structure to accelerate the forward and backtracking steps. For this purpose, the architecture calculates and stores the paths in the forward stage for pre-organizing the alignment, which reduces the complexity of the backtracking stage. The backtracking starts from the maximum score position in the matrix and generates the optimal SW sequence alignment path. The architecture was validated on Field-Programmable Gate Array (FPGA), and synthesis analyses have shown that the proposed design reaches up to 79.5 Giga Cell Updates per Second (GCPUS).

This work proposes an implementation of the SHA-256, the most common blockchain hash algorithm, on a field-programmable gate array (FPGA) to improve processing capacity and power saving in Internet of Things (IoT) devices to solve security and privacy issues. This implementation presents a different approach than other papers in the literature, using clustered cores executing the SHA-256 algorithm in parallel. Details about the proposed architecture and an analysis of the resources used by the FPGA are presented. The implementation achieved a throughput of approximately 1.4 Gbps for 16 cores on a single FPGA. Furthermore, it saved dynamic power, using almost 1000 times less compared to previous works in the literature, making this proposal suitable for practical problems for IoT devices in blockchain environments. The target FPGA used was the Xilinx Virtex 6 xc6vlx240t-1ff1156.

Purpose In this study, we present DeepVirusClassifier, a tool capable of accurately classifying Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) viral sequences among other subtypes of the coronaviridae family. This classification is achieved through a deep neural network model that relies on convolutional neural networks (CNNs). Since viruses within the same family share similar genetic and structural characteristics, the classification process becomes more challenging, necessitating more robust models. With the rapid evolution of viral genomes and the increasing need for timely classification, we aimed to provide a robust and efficient tool that could increase the accuracy of viral identification and classification processes. Contribute to advancing research in viral genomics and assist in surveilling emerging viral strains. Methods Based on a one-dimensional deep CNN, the proposed tool is capable of training and testing on the Coronaviridae family, including SARS-CoV-2. Our model’s performance was assessed using various metrics, including F1-score and AUROC. Additionally, artificial mutation tests were conducted to evaluate the model’s generalization ability across sequence variations. We also used the BLAST algorithm and conducted comprehensive processing time analyses for comparison. Results DeepVirusClassifier demonstrated exceptional performance across several evaluation metrics in the training and testing phases. Indicating its robust learning capacity. Notably, during testing on more than 10,000 viral sequences, the model exhibited a more than 99% sensitivity for sequences with fewer than 2000 mutations. The tool achieves superior accuracy and significantly reduced processing times compared to the Basic Local Alignment Search Tool algorithm. Furthermore, the results appear more reliable than the work discussed in the text, indicating that the tool has great potential to revolutionize viral genomic research. Conclusion DeepVirusClassifier is a powerful tool for accurately classifying viral sequences, specifically focusing on SARS-CoV-2 and other subtypes within the Coronaviridae family. The superiority of our model becomes evident through rigorous evaluation and comparison with existing methods. Introducing artificial mutations into the sequences demonstrates the tool’s ability to identify variations and significantly contributes to viral classification and genomic research. As viral surveillance becomes increasingly critical, our model holds promise in aiding rapid and accurate identification of emerging viral strains.

Background In December 2019, the first case of COVID-19 was described in Wuhan, China, and by July 2022, there were already 540 million confirmed cases. Due to the rapid spread of the virus, the scientific community has made efforts to develop techniques for the viral classification of SARS-CoV-2. Results In this context, we developed a new proposal for gene sequence representation with Genomic Signal Processing techniques for the work presented in this paper. First, we applied the mapping approach to samples of six viral species of the Coronaviridae family, which belongs SARS-CoV-2 Virus. We then used the sequence downsized obtained by the method proposed in a deep learning architecture for viral classification, achieving an accuracy of 98.35%, 99.08%, and 99.69% for the 64, 128, and 256 sizes of the viral signatures, respectively, and obtaining 99.95% precision for the vectors with size 256. Conclusions The classification results obtained, in comparison to the results produced using other state-of-the-art representation techniques, demonstrate that the proposed mapping can provide a satisfactory performance result with low computational memory and processing time costs.

This work aimed to develop a real-time test platform for systems associated with the tactile internet area. The proposal comprises a master device, a communication channel and a slave device. The master device is a tactile glove (wearable technology) that works as a tactile interface based on vibratory feedback. The master device can interact with virtual elements (local or remote). The Matlab/Simulink environment and a robotics toolbox form the communication channel and the slave device. The communication channel introduces a bidirectional connection of variable latency, and the slave device is defined as a robotic phantom omni manipulator emulated in Matlab/Simulink. The virtual robotic manipulator, the slave device, can generate different types of tactile sensations in the tactile glove, that is, in the master device. The platform can model tactile sensations such as coarse roughness, fine roughness, smoothness, dripping and softness. The proposed platform presented adequate results and can be used to test various algorithms and methods correlated to the tactile internet.

Tactile internet applications allow robotic devices to be remotely controlled over a communication medium with an unnoticeable time delay. In bilateral communication, the acceptable round trip latency is usually 1 ms up to 10 ms, depending on the application requirements. The communication network is estimated to generate 70% of the total latency, and master and slave devices produce the remaining 30%. Thus, this paper proposes a strategy to reduce 30% of the total latency produced by such devices. The strategy is to use FPGAs to minimize the execution time of device-associated algorithms. With this in mind, this work presents a new hardware reference model for modules that implement nonlinear positioning and force calculations and a tactile system formed by two robotic manipulators. In addition to presenting the implementation details, simulations and experimental tests are performed in order to validate the hardware proposed model. Results associated with the FPGA sampling rate, throughput, latency, and post-synthesis occupancy area are analyzed.

This study investigates the use of machine learning (ML) models combined with explainable artificial intelligence (XAI) techniques to identify the most influential genes in the classification of five recurrent cancer types in women: breast cancer (BRCA), lung adenocarcinoma (LUAD), thyroid cancer (THCA), ovarian cancer (OV), and colon adenocarcinoma (COAD). Gene expression data from RNA-seq, extracted from The Cancer Genome Atlas (TCGA), were used to train ML models, including decision trees (DTs), random forest (RF), and XGBoost (XGB), which achieved accuracies of 98.69%, 99.82%, and 99.37%, respectively. However, the challenges in this analysis included the high dimensionality of the dataset and the lack of transparency in the ML models. To mitigate these challenges, the SHAP (Shapley Additive Explanations) method was applied to generate a list of features, aiming to understand which characteristics influenced the models’ decision-making processes and, consequently, the prediction results for the five tumor types. The SHAP analysis identified 119, 80, and 10 genes for the RF, XGB, and DT models, respectively, totaling 209 genes, resulting in 172 unique genes. The new list, representing 0.8% of the original input features, is coherent and fully explainable, increasing confidence in the applied models. Additionally, the results suggest that the SHAP method can be effectively used as a feature selector in gene expression data. This approach not only enhances model transparency but also maintains high classification performance, highlighting its potential in identifying biologically relevant features that may serve as biomarkers for cancer diagnostics and treatment planning.

This paper presents a fuzzy logic-based approach for replica scaling in a Kubernetes environment, focusing on integrating Edge Computing. The proposed FHS (Fuzzy-based Horizontal Scaling) system was compared to the standard Kubernetes scaling mechanism, HPA (Horizontal Pod Autoscaler). The comparison considered resource consumption, the number of replicas used, and adherence to latency Service-Level Agreements (SLAs). The experiments were conducted in an environment simulating Edge Computing infrastructure, with virtual machines used to represent edge nodes and traffic generated via JMeter. The results demonstrate that FHS achieves a reduction in CPU consumption, uses fewer replicas under the same stress conditions, and exhibits more distributed SLA latency violation rates compared to HPA. These results indicate that FHS offers a more efficient and customizable solution for replica scaling in Kubernetes within Edge Computing environments, contributing to both operational efficiency and service quality.

Changes in epigenetic processes such as histone acetylation are proposed as key events influencing cancer cell function and the initiation and progression of pediatric brain tumors. Valproic acid (VPA) is an antiepileptic drug that acts partially by inhibiting histone deacetylases (HDACs) and could be repurposed as an epigenetic anticancer therapy. Here, we show that VPA reduced medulloblastoma (MB) cell viability and led to cell cycle arrest. These effects were accompanied by enhanced H3K9 histone acetylation (H3K9ac) and decreased expression of the MYC oncogene. VPA impaired the expansion of MB neurospheres enriched in stemness markers and reduced MYC while increasing TP53 expression in these neurospheres. In addition, VPA induced morphological changes consistent with neuronal differentiation and the increased expression of differentiation marker genes TUBB3 and ENO2. The expression of stemness genes SOX2, NES, and PRTG was differentially affected by VPA in MB cells with different TP53 status. VPA increased H3K9 occupancy of the promoter region of TP53. Among the genes regulated by VPA, the stemness regulators MYC and NES showed an association with patient survival in specific MB subgroups. Our results indicate that VPA may exert antitumor effects in MB by influencing histone acetylation, which may result in the modulation of stemness, neuronal differentiation, and the expression of genes associated with patient prognosis in specific molecular subgroups. Importantly, the actions of VPA in MB cells and neurospheres include a reduction in the expression of MYC and an increase in TP53.

The literature on ECG delineation algorithms has seen significant growth in recent decades. However, several challenges still need to be addressed. This work aims to propose a lightweight R-peak-detection algorithm that does not require pre-setting and performs classification on a sample-by-sample basis. The novelty of the proposed approach lies in the utilization of the typicality eccentricity detection anomaly (TEDA) algorithm for R-peak detection. The proposed method for R-peak detection consists of three phases. Firstly, the ECG signal is preprocessed by calculating the signal’s slope and applying filtering techniques. Next, the preprocessed signal is inputted into the TEDA algorithm for R-peak estimation. Finally, in the third and last step, the R-peak identification is carried out. To evaluate the effectiveness of the proposed technique, experiments were conducted on the MIT-BIH arrhythmia database (MIT-AD) for R-peak detection and validation. The results of the study demonstrated that the proposed evolutive algorithm achieved a sensitivity (Se in %), positive predictivity (+P in %), and accuracy (ACC in %) of 95.45%, 99.61%, and 95.09%, respectively, with a tolerance (TOL) of 100 milliseconds. One key advantage of the proposed technique is its low computational complexity, as it is based on a statistical framework calculated recursively. It employs the concepts of typicity and eccentricity to determine whether a given sample is normal or abnormal within the dataset. Unlike most traditional methods, it does not require signal buffering or windowing. Furthermore, the proposed technique employs simple decision rules rather than heuristic approaches, further contributing to its computational efficiency.