Human activity recognition (HAR) based on radar has garnered wide interest due to its privacy-friendly and lighting-independent nature. Despite advancements, challenges like response speed and real-world applicability persist. To address these issues, data from different orientations utilizing frequency-modulated continuous-wave (FMCW) radar was collected to better reflect real-world conditions. In terms of data preprocessing, a sliding time-window nonlocal means filter is proposed to effectively remove the noise while retaining the micro-Doppler features. Subsequently, a multiattention enhanced fusion network (MAEF-Net) is proposed for HAR. MAEF-Net, an efficient and lightweight architecture, integrates multiple attention mechanisms to enhance robustness in omnidirectional HAR. It achieves high-accuracy omnidirectional activity recognition by simultaneously focusing on local and global features. Experimental results showcase MAEF-Net achieving 98.3% accuracy in testing, surpassing existing methods, thereby demonstrating its effectiveness in real-world scenarios.

Identification of viruses and further assembly of viral genomes from the next-generation-sequencing data are essential steps in virome studies. This study presented a one-stop tool named VIGA (available at https://github.com/viralInformatics/VIGA) for eukaryotic virus identification and genome assembly from NGS data. It was composed of four modules, namely, identification, taxonomic annotation, assembly and novel virus discovery, which integrated several third-party tools such as BLAST, Trinity, MetaCompass and RagTag. Evaluation on multiple simulated and real virome datasets showed that VIGA assembled more complete virus genomes than its competitors on both the metatranscriptomic and metagenomic data and performed well in assembling virus genomes at the strain level. Finally, VIGA was used to investigate the virome in metatranscriptomic data from the Human Microbiome Project and revealed different composition and positive rate of viromes in diseases of prediabetes, Crohn's disease and ulcerative colitis. Overall, VIGA would help much in identification and characterization of viromes, especially the known viruses, in future studies.

This study introduces a contactless blood pressure monitoring approach that combines conventional radar signal processing with novel deep learning architectures. During the preprocessing phase, datasets suitable for synchronization are created by integrating Kalman filtering, multiscale bandpass filters, and a periodic extraction method in the time domain. These data comprise data on chest micro variations, encapsulating a complex array of physiological and biomedical information reflective of cardiac micromotions. The Radar-based Stacked Deformable convolution Network (RSD-Net) integrates channel and spatial self attention mechanisms within a deformable convolutional framework to enhance feature extraction from radar signals. The network architecture systematically employs deformable convolutions for initial deep feature extraction from individual signals. Subsequently, continuous blood pressure estimation is conducted using self attention mechanisms on feature map from single source coupled with multi-feature map channel attention. The performance of model is corroborated via the open-source dataset procured using a non-invasive 24 GHz six-port continuous wave radar system. The dataset, encompassing readings from 30 healthy individuals subjected to diverse conditions including rest, the Valsalva maneuver, apnea, and tilt-table examinations. It serves to substantiate the validity and resilience of the proposed method in the non-contact assessment of continuous blood pressure. Evaluation metrics reveal Pearson correlation coefficients of 0.838 for systolic and 0.797 for diastolic blood pressure predictions. The Mean Error (ME) and Standard Deviation (SD) for systolic and diastolic blood pressure measurements are -0.32 ±6.14 mmHg and -0.20 ±5.50 mmHg, respectively. The ablation study assesses the contribution of different structural components of the RSD-Net, validating their significance in the overall of model performance.

Lane detection is a special task in autonomous driving. Its most prominent inherent feature is to learn the imagination of severely occluded objects. Traditional CNN-based networks learning the imagination tend to perform poorly. In this work, we propose a novel architecture, called Cycle_accumulation-Transformer (CaT), which is the first structure to handle the lane detection by fusing CNN and Transformer. In particular, Cycle_accumulation structure and Transformer structure complement each other, and they adopt the four-direction cyclic accumulation process of “up to down”, “down to up”, “left to right” and “right to left” in the convolutional mode and the self-attention mechanism of “QKV” to fuse global information respectively. Our method is based on pixel-level semantic segmentation with high detection accuracy while meeting real-time requirements. Moreover, our proposed method achieves state-of-the-art results on the Tusimple and also achieves competitive results on the CULane.

Genomic recombination is an important driving force for viral evolution, and recombination events have been reported for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) during the Coronavirus Disease 2019 pandemic, which significantly alter viral infectivity and transmissibility. However, it is difficult to identify viral recombination, especially for low-divergence viruses such as SARS-CoV-2, since it is hard to distinguish recombination from in situ mutation. Herein, we applied information theory to viral recombination analysis and developed VirusRecom, a program for efficiently screening recombination events on viral genome. In principle, we considered a recombination event as a transmission process of ``information'' and introduced weighted information content (WIC) to quantify the contribution of recombination to a certain region on viral genome; then, we identified the recombination regions by comparing WICs of different regions. In the benchmark using simulated data, VirusRecom showed a good balance between precision and recall compared to two competing tools, RDP5 and 3SEQ. In the detection of SARS-CoV-2 XE, XD and XF recombinants, VirusRecom providing more accurate positions of recombination regions than RDP5 and 3SEQ. In addition, we encapsulated the VirusRecom program into a command-line-interface software for convenient operation by users. In summary, we developed a novel approach based on information theory to identify viral recombination within highly similar sequences, providing a useful tool for monitoring viral evolution and epidemic control.

Virus-encoded small RNAs (vsRNA) have been reported to play an important role in viral infection. Unfortunately, there is still a lack of an effective method for vsRNA identification. Herein, we presented vsRNAfinder, a de novo method for identifying high-confidence vsRNAs from small RNA-Seq (sRNA-Seq) data based on peak calling and Poisson distribution and is publicly available at https://github.com/ZenaCai/vsRNAfinder. vsRNAfinder outperformed two widely used methods namely miRDeep2 and ShortStack in identifying viral miRNAs with a significantly improved sensitivity. It can also be used to identify sRNAs in animals and plants with similar performance to miRDeep2 and ShortStack. vsRNAfinder would greatly facilitate effective identification of vsRNAs from sRNA-Seq data.

MOTIVATION: Viruses continue to threaten human health. Yet, the complete viral species carried by humans and their infection characteristics have not been fully revealed. RESULTS: This study curated an atlas of human viruses from public databases and literature, and built the Human Virus Database (HVD). The HVD contains 1131 virus species of 54 viral families which were more than twice the number of the human-infecting virus species reported in previous studies. These viruses were identified in human samples including 68 human tissues, the excreta and body fluid. The viral diversity in humans was age-dependent with a peak in the infant and a valley in the teenager. The tissue tropism of viruses was found to be associated with several factors including the viral group (DNA, RNA or reverse-transcribing viruses), enveloped or not, viral genome length and GC content, viral receptors and the virus-interacting proteins. Finally, the tissue tropism of DNA viruses was predicted using a random-forest algorithm with a middle performance. Overall, the study not only provides a valuable resource for further studies of human viruses but also deepens our understanding toward the diversity and tissue tropism of human viruses. AVAILABILITY AND IMPLEMENTATION: The HVD is available at http://computationalbiology.cn/humanVirusBase/#/. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

MOTIVATION: Receptors on host cells play a critical role in viral infection. How phages select receptors is still unknown. RESULTS: Here, we manually curated a high-quality database named phageReceptor, including 427 pairs of phage-host receptor interactions, 341 unique viral species or sub-species and 69 bacterial species. Sugars and proteins were most widely used by phages as receptors. The receptor usage of phages in Gram-positive bacteria was different from that in Gram-negative bacteria. Most protein receptors were located on the outer membrane. The phage protein receptors (PPRs) were highly diverse in their structures, and had little sequence identity and no common protein domain with mammalian virus receptors. Further functional characterization of PPRs in Escherichia coli showed that they had larger node degrees and betweennesses in the protein-protein interaction network, and higher expression levels, than other outer membrane proteins, plasma membrane proteins or other intracellular proteins. These findings were consistent with what observed for mammalian virus receptors reported in previous studies, suggesting that viral protein receptors tend to have multiple interaction partners and high expressions. The study deepens our understanding of virus-host interactions. AVAILABILITY AND IMPLEMENTATION: phageReceptor is publicly available from: http://www.computationalbiology.cn/phageReceptor/index.html. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.