Expression characteristics and potential function of non-coding RNA in mouse cortical cells.

Non-coding RNAs (ncRNAs) play essential regulatory functions in various physiological and pathological processes in the brain. To systematically characterize the ncRNA profile in cortical cells, we downloaded single-cell SMART-Seq v4 data of mouse cerebral cortex. Our results revealed that the ncRNAs alone are sufficient to define the identity of most cortical cell types. We identified 1,600 ncRNAs that exhibited cell type specificity, even yielding to distinguish microglia from perivascular macrophages with ncRNA. Moreover, we characterized cortical layer and region specific ncRNAs, in line with the results by spatial transcriptome (ST) data. By constructing a co-expression network of ncRNAs and protein-coding genes, we predicted the function of ncRNAs. By integrating with genome-wide association studies data, we established associations between cell type-specific ncRNAs and traits related to neurological disorders. Collectively, our study identified differentially expressed ncRNAs at multiple levels and provided the valuable resource to explore the functions and dysfunctions of ncRNAs in cortical cells.

Segmentation of retinal vessels based on MRANet.

The segmentation of retinal vessel takes a crucial part in computer-aided diagnosis of diseases and eye disorders. However, the insufficient segmentation of the capillary vessels and weak anti-noise interference ability make such task more difficult. To solve this problem, we proposed a multi-scale residual attention network (MRANet) which is based on U-Net network. Firstly, to collect useful information about the blood vessels more effectively, we proposed a multi-level feature fusion block (MLF block). Then, different weights of each fused feature are learned by using attention blocks, which can retain more useful feature information while reducing the interference of redundant features. Thirdly, multi-scale residual connection block (MSR block) is constructed, which can better extract the image features. Finally, we use the DropBlock layer in the network to reduce the network parameters and alleviate network overfitting. Experiments show that based on DRIVE, the accuracy rate and the AUC performance value of our network are 0.9698 and 0.9899 respectively, and based on CHASE_DB1 dataset, they are 0.9755 and 0.9893 respectively. Our network has a better segmentation effect compared with other methods, which can ensure the continuity and completeness of blood vessel segmentation.

Diagnosis of rectal cancer based on the Xception-MS network.

Objective. Accurate T staging of rectal cancer based on ultrasound images is convenient for doctors to determine the appropriate treatment. To effectively solve the problems of low efficiency and accuracy of traditional methods for T staging diagnosis of rectal cancer, a deep-learning-based Xception-MS diagnostic model is proposed in this paper.Approach. The proposed diagnostic model consists of three steps. First, the model preprocesses rectal cancer images to solve the problem of data imbalance and deficiency of sample size, and reduces the risk of model overfitting. Second, a new Xception-MS network with stronger feature extraction capability, which is a combination of the Xception network and MS module, is proposed. The MS module is a new function module that can more effectively extract multi-scale information from rectal cancer images. In addition, to solve the deficiency of the small sample size of rectal cancer, the proposed network is combined with transfer learning technology. At last, the output layer of the network is modified, in which the global average pooling and a fully connected softmax layer are employed to replace the original ones, and then the rectal cancer 4 classification (T1, T2, T3, T4 staging) is output.Main results. Experiments of rectal cancer T staging are conducted on a dataset of 1078 rectal cancer images in 4 categories collected from the Department of Colorectal Surgery of the Third Affiliated Hospital of Kunming Medical University. The experimental results show that the accuracy, precision, recall andF1 values obtained by the model are 94.66%, 94.70%, 94.65%, and 94.67%, respectively.Significance. The experimental results show that our model is superior to the existing classification models, can effectively and automatically classify ultrasound images of rectal cancer, and can better assist doctors in the diagnosis of rectal cancer.

High-resolution 3D spatiotemporal transcriptomic maps of developing Drosophila embryos and larvae.

Drosophila has long been a successful model organism in multiple biomedical fields. Spatial gene expression patterns are critical for the understanding of complex pathways and interactions, whereas temporal gene expression changes are vital for studying highly dynamic physiological activities. Systematic studies in Drosophila are still impeded by the lack of spatiotemporal transcriptomic information. Here, utilizing spatial enhanced resolution omics-sequencing (Stereo-seq), we dissected the spatiotemporal transcriptomic changes of developing Drosophila with high resolution and sensitivity. We demonstrated that Stereo-seq data can be used for the 3D reconstruction of the spatial transcriptomes of Drosophila embryos and larvae. With these 3D models, we identified functional subregions in embryonic and larval midguts, uncovered spatial cell state dynamics of larval testis, and revealed known and potential regulons of transcription factors within their topographic background. Our data provide the Drosophila research community with useful resources of organism-wide spatiotemporally resolved transcriptomic information across developmental stages.

Cell transcriptomic atlas of the non-human primate Macaca fascicularis.

Studying tissue composition and function in non-human primates (NHPs) is crucial to understand the nature of our own species. Here we present a large-scale cell transcriptomic atlas that encompasses over 1 million cells from 45 tissues of the adult NHP Macaca fascicularis. This dataset provides a vast annotated resource to study a species phylogenetically close to humans. To demonstrate the utility of the atlas, we have reconstructed the cell-cell interaction networks that drive Wnt signalling across the body, mapped the distribution of receptors and co-receptors for viruses causing human infectious diseases, and intersected our data with human genetic disease orthologues to establish potential clinical associations. Our M. fascicularis cell atlas constitutes an essential reference for future studies in humans and NHPs.

[Acupoints selection rules analysis of ancient acupuncture for urinary incontinence based on data mining technology].

Based on ancient literature of acupuncture in Canon of Chinese Medicine (4th edition), the articles regarding acupuncture for urinary incontinence were retrieved and collected to establish a database. By Weka data mining software, the multi-level association rules analysis method was applied to analyze the acupoints selection characteristics and rules of ancient acupuncture for treatment of urinary incontinence. Totally 356 articles of acupuncture for urinary incontinence were collected, involving 41 acupoints with a total frequency of 364. As a result, (1) the acupoints in the yin-meridian of hand and foot were highly valued, as the frequency of acupoints in yin-meridians was 2.6 times than that in yang-meridians, and the frequency of acupoints selected was the most in the liver meridian of foot-jueyin; (2) the acupoints in bladder meridian of foot-taiyang were also highly valued, and among three yang-meridians of foot, the frequency of acupoints in the bladder meridian of foot-taiyang was 54, accounting for 65.85% (54/82); (3) more acupoints selected were located in the lower limbs and abdomen; (4) specific acupoints in above meridians were mostly selected, presenting 73.2% (30/41) to the ratio of number and 79.4% (289/364) to the frequency, respectively; (5) Zhongji (CV 3), the front-mu point of bladder meridian, was seldom selected in the ancient acupuncture literature, which was different from modern literature reports. The results show that urinary incontinence belongs to external genitalia diseases, which should be treated from yin, indicating more yin-meridians be used and special acupoints be focused on. It is essential to focus inheritance and innovation in TCM clinical treatment, and applying data mining technology to ancient literature of acupuncture could provide classic theory basis for TCM clinical treatment.