In order to ensure the safety of transmission lines, the use of unmanned aerial vehicle (UAV) images for automatic object detection has important application prospects, such as the detection of birds’ nests. The traditional bird’s nest detection methods mainly include the study of morphological characteristics of the bird’s nest. These methods have poor applicability and low accuracy. In this work, we propose a deep learning-based birds’ nests automatic detection framework—region of interest (ROI) mining faster region-based convolutional neural networks (RCNN). First, the prior dimensions of anchors are obtained by using k-means clustering to improve the accuracy of coordinate boxes generation. Second, in order to balance the number of foreground and background samples in the training process, the focal loss function is introduced in the region proposal network (RPN) classification stage. Finally, the ROI mining module is added to solve the class imbalance problem in the classification stage, combined with the characteristics of difficult-to-classify bird’s nest samples in the UAV images. After parameter optimization and experimental verification, the deep learning-based bird’s nest automatic detection framework proposed in this work achieves high detection accuracy. In addition, the mean average precision (mAP) and formula 1 (F1) score of the proposed method are higher than the original faster RCNN and cascade RCNN. Our comparative analysis verifies the effectiveness of the proposed method.

The ability of a transcription factor to regulate its targets is modulated by a variety of genetic and epigenetic mechanisms. Alternative splicing can modulate gene function by adding or removing certain protein domains, and therefore affect the activity of protein. Reverse engineering of gene regulatory networks using gene expression profiles has proven valuable in dissecting the logical relationships among multiple proteins during the transcriptional regulation. However, it is unclear whether alternative splicing of certain proteins affects the activity of other transcription factors. In order to investigate the roles of alternative splicing during transcriptional regulation, we constructed a statistical model to infer whether the alternative splicing events of modulator proteins can affect the ability of key transcription factors in regulating the expression levels of their transcriptional targets. We tested our strategy in KIRC (Kidney Renal Clear Cell Carcinoma) using the RNA-seq data downloaded from TCGA (the Cancer Genomic Atlas). We identified 828of modulation relationships between the splicing levels of modulator proteins and activity levels of transcription factors. For instance, we found that the activity levels of GR (glucocorticoid receptor) protein, a key transcription factor in kidney, can be influenced by the splicing status of multiple proteins, including TP53, MDM2 (mouse double minute 2 homolog), RBM14 (RNA-binding protein 14) and SLK (STE20 like kinase). The influenced GR-targets are enriched by key cancer-related pathways, including p53 signaling pathway, TR/RXR activation, CAR/RXR activation, G1/S checkpoint regulation pathway, and G2/M DNA damage checkpoint regulation pathway. Our analysis suggests, for the first time, that exon inclusion levels of certain regulatory proteins can affect the activities of many transcription factors. Such analysis can potentially unravel a novel mechanism of how splicing variation influences the cellular function and provide important insights for how dysregulation of splicing outcome can lead to various diseases.

Accurate assessment of N staging in patients with non-small cell lung cancer (NSCLC) is critical for the development of effective treatment plans, the optimization of therapeutic strategies, and the enhancement of patient survival rates. This study proposes a hybrid model based on 3D convolutional neural networks (CNNs) and transformers for predicting the N-staging and survival rates of NSCLC patients within the NSCLC radiogenomics and Nsclc-radiomics datasets. The model achieved accuracies of 0.805, 0.828, and 0.819 for the training, validation, and testing sets, respectively. By leveraging the strengths of CNNs in local feature extraction and the superior performance of transformers in global information modeling, the model significantly enhances predictive accuracy and efficacy. A comparative analysis with traditional CNN and transformer architectures demonstrates that the CNN-transformer hybrid model outperforms N-staging predictions. Furthermore, this study extracts the one-year survival rate as a feature and employs the Lasso–Cox model for survival predictions at various time intervals (1, 3, 5, and 7 years), with all survival prediction p-values being less than 0.05, illustrating the time-dependent nature of survival analysis. The application of time-dependent ROC curves further validates the model’s accuracy and reliability for survival predictions. Overall, this research provides innovative methodologies and new insights for the early diagnosis and prognostic evaluation of NSCLC.

The cerebrospinal fluid (CSF) levels of total tau (t-tau) and Aβ1–42 are potential early diagnostic markers for probable Alzheimer’s disease (AD). The influence of genetic variation on these CSF biomarkers has been investigated in candidate or genome-wide association studies (GWAS). However, the investigation of statistically modest associations in GWAS in the context of biological networks is still an under-explored topic in AD studies. The main objective of this study is to gain further biological insights via the integration of statistical gene associations in AD with physical protein interaction networks. The CSF and genotyping data of 843 study subjects (199 CN, 85 SMC, 239 EMCI, 207 LMCI, 113 AD) from the Alzheimer’s Disease Neuroimaging Initiative (ADNI) were analyzed. PLINK was used to perform GWAS on the t-tau/Aβ1–42 ratio using quality controlled genotype data, including 563,980 single nucleotide polymorphisms (SNPs), with age, sex and diagnosis as covariates. Gene-level p-values were obtained by VEGAS2. Genes with p-value ≤ 0.05 were mapped on to a protein-protein interaction (PPI) network (9,617 nodes, 39,240 edges, from the HPRD Database). We integrated a consensus model strategy into the iPINBPA network analysis framework, and named it as CM-iPINBPA. Four consensus modules (CMs) were discovered by CM-iPINBPA, and were functionally annotated using the pathway analysis tool Enrichr. The intersection of four CMs forms a common subnetwork of 29 genes, including those related to tau phosphorylation (GSK3B, SUMO1, AKAP5, CALM1 and DLG4), amyloid beta production (CASP8, PIK3R1, PPA1, PARP1, CSNK2A1, NGFR, and RHOA), and AD (BCL3, CFLAR, SMAD1, and HIF1A). This study coupled a consensus module (CM) strategy with the iPINBPA network analysis framework, and applied it to the GWAS of CSF t-tau/Aβ1-42 ratio in an AD study. The genome-wide network analysis yielded 4 enriched CMs that share not only genes related to tau phosphorylation or amyloid beta production but also multiple genes enriching several KEGG pathways such as Alzheimer’s disease, colorectal cancer, gliomas, renal cell carcinoma, Huntington’s disease, and others. This study demonstrated that integration of gene-level associations with CMs could yield statistically significant findings to offer valuable biological insights (e.g., functional interaction among the protein products of these genes) and suggest high confidence candidates for subsequent analyses.