Node localization, which is formulated as an unconstrained NP-hard optimization problem, is considered as one of the most significant issues of wireless sensor networks (WSNs). Recently, many swarm intelligent algorithms (SIAs) were applied to solve this problem. This study aimed to determine node location with high precision by SIA and presented a new localization algorithm named LMQPDV-hop. In LMQPDV-hop, an improved DV-Hop was employed as an underground mechanism to gather the estimation distance, in which the average hop distance was modified by a defined weight to reduce the distance errors among nodes. Furthermore, an efficient quantum-behaved particle swarm optimization algorithm (QPSO), named LMQPSO, was developed to find the best coordinates of unknown nodes. In LMQPSO, the memetic algorithm (MA) and Lévy flight were introduced into QPSO to enhance the global searching ability and a new fast local search rule was designed to speed up the convergence. Extensive simulations were conducted on different WSN deployment scenarios to evaluate the performance of the new algorithm and the results show that the new algorithm can effectively improve position precision.

Mobile sinks can achieve load-balancing and energy-consumption balancing across the wireless sensor networks (WSNs). However, the frequent change of the paths between source nodes and the sinks caused by sink mobility introduces significant overhead in terms of energy and packet delays. To enhance network performance of WSNs with mobile sinks (MWSNs), we present an efficient routing strategy, which is formulated as an optimization problem and employs the particle swarm optimization algorithm (PSO) to build the optimal routing paths. However, the conventional PSO is insufficient to solve discrete routing optimization problems. Therefore, a novel greedy discrete particle swarm optimization with memory (GMDPSO) is put forward to address this problem. In the GMDPSO, particle’s position and velocity of traditional PSO are redefined under discrete MWSNs scenario. Particle updating rule is also reconsidered based on the subnetwork topology of MWSNs. Besides, by improving the greedy forwarding routing, a greedy search strategy is designed to drive particles to find a better position quickly. Furthermore, searching history is memorized to accelerate convergence. Simulation results demonstrate that our new protocol significantly improves the robustness and adapts to rapid topological changes with multiple mobile sinks, while efficiently reducing the communication overhead and the energy consumption.

Shuffled frog leaping algorithm, a novel heuristic method, is inspired by the foraging behavior of the frog population, which has been designed by the shuffled process and the PSO framework. To increase the convergence speed and effectiveness, the currently improved versions are focused on the local search ability in PSO framework, which limited the development of SFLA. Therefore, we first propose a new scheme based on evolutionary strategy, which is accomplished by quantum evolution and eigenvector evolution. In this scheme, the frog leaping rule based on quantum evolution is achieved by two potential wells with the historical information for the local search, and eigenvector evolution is achieved by the eigenvector evolutionary operator for the global search. To test the performance of the proposed approach, the basic benchmark suites, CEC2013 and CEC2014, and a parameter optimization problem of SVM are used to compare 15 well‐known algorithms. Experimental results demonstrate that the performance of the proposed algorithm is better than that of the other heuristic algorithms.

Existing studies have demonstrated that the integration analysis of transcriptomic and epigenomic data can be used to better understand the onset and progression of many diseases, as well as identify new diagnostic and prognostic biomarkers. However, such investigations on large-scale sequencing data remain challenging for researchers or clinicians with limited bioinformatics knowledge. To facilitate the interpretation of the gene regulatory landscape, we developed an R Shiny application [Linking of atac-seq to gene expression data (Linkage)] for exploring and visualizing potential cis-regulatory elements (CREs) of genes based on ATAC-seq and RNA-seq data. Linkage offers six modules to identify, annotate, and interpret potential gene regulatory elements from the whole genome step by step. Linkage currently supports the analysis of human and mouse datasets. Linkage can provide interactive visualization for the correlation between chromatin accessibility and gene expression. More than that, Linkage identifies transcription factors (TFs) that potentially drive the chromatin changes through identifying TF binding motifs within the CREs and constructing trans-regulatory networks of the target gene set. This powerful tool enables researchers to conduct extensive multi-omics integration analysis and generate visually appealing visualizations that effectively highlight the relationship between genes and corresponding regulatory elements. With Linkage, users can obtain publishable results and gain deeper insights into the gene regulatory landscape. ‘Linkage’ is freely available as a Shiny web application https://xulabgdpu.org.cn/linkage . The source code and instructions for Linkage can be accessed via Github https://github.com/luoyyyy/Linkage .

Aberrant alternative splicing and abnormal alternative splicing events (ASEs) in glioblastoma multiforme (GBM) remain largely elusive. The prognostic-associated ASEs in GBM were identified and summarized into 123 genes using GBM and LGG datasets from ASCancer Atlas and TCGA. The eleven genes (C2, COL3A1, CTSL, EIF3L, FKBP9, FN1, HPCAL1, HSPB1, IGFBP4, MANBA, PRKAR1B) were screened to develop an alternative splicing prognostic risk score (ASRS) model through machine learning algorithms. The model was trained on the TCGA-GBM cohort and validated with four external datasets from CGGA and GEO, achieving AUC values of 0.808, 0.814, 0.763, 0.859, and 0.836 for 3-year survival rates, respectively. ASRS could be an independent prognostic factor for GBM patients (HR > 1.8 across three datasets) through multivariate Cox regression analysis. The high-risk group demonstrated poorer prognosis, elevated immune scores, increased levels of immune cell infiltration, and greater differences in drug sensitivity. We found that FN1, used for model construction, contained 4 abnormal ASEs resulting in high expression of non-canonical transcripts and the presence of premature termination codon. These abnormal ASEs may be regulated by tumour-related splicing factors according to the PPI network. Furthermore, both mRNA and protein levels of FN1 were highly expressed in GBM compared to LGG, correlating with poor prognosis in GBM. In conclusion, our findings highlight the role of ASEs in affecting the progression of GBM, and the model showed a potential application for prognostic risk of patients. FN1 may serve as a promising splicing biomarker for GBM, and mechanisms of processes of aberrant splicing need to be revealed in the future.