Population genetic structure of Marbled Rockfish, Sebastiscus marmoratus (Cuvier, 1829), in the northwestern Pacific Ocean

Sebastiscus marmoratus is an ovoviviparous fish widely distributed in the northwestern Pacific. To examine the gene flow and test larval dispersal strategy of S. marmoratus in Chinese and Japanese coastal waters, 421 specimens were collected from 22 localities across its natural distribution. A 458 base-pair fragment of the mitochondrial DNA (mtDNA) control region was sequenced to examine genetic diversity and population structure. One-hundred-six variable sites defined 166 haplotypes. The populations of S. marmoratus showed high haplotype diversity with a range from 0.8587 to 0.9996, indicating a high level of intrapopulation genetic diversity. Low non-significant genetic differentiation was estimated among populations except those of Hyogo, Behai, and Niiigata, which showed significant genetic differences from the other populations. The demographic history examined by neutrality tests, mismatch distribution analysis, and Bayesian skyline analysis suggested a sudden population expansion dating to the late Pleistocene. Recent population expansion in the last glacial period, wide dispersal of larvae by coastal currents, and the homogeneity of the environment may have important influences on the population genetic pattern. Knowledge of genetic diversity and genetic structure will be crucial to establish appropriate fishery management of S. marmoratus

Acanthopagrus latus migration patterns and habitat use in Wanshan Islands, Pearl River Estuary, determined using otolith microchemical analysis

IntroductionThe waters surrounding the Wanshan Islands are important traditional fishing grounds in China, with rich habitat types. Acanthopagrus latus is an economically important species in this area; however, the distribution of its spawning grounds and habitat use patterns remain unknown.MethodsThus 100 otolith samples of A. latus were collected from three geographic areas (MW: Qi’ao Island Mangrove Water Habitat; OW: Yamen Estuary Oyster Farm Water Habitat; RW: Dong’ao-Guishan Island Reef Water Habitat), and the concentrations of Sr and Ca along the shortest axis of the vertical otolith annual or lunar rings were measured to span the entire life cycle of A. latus, with the core and edge areas corresponding to environmental characteristics at birth and capture, respectively.Results and discussionAnalysis of covariance (ANCOVA) revealed that the ratios of Sr/Ca in otolith edges of RW samples are significantly higher than those of OW and MW samples; however, both the values of Sr/Ca ratio in otolith cores collected from OW and MW are comparable with those of RW samples. Cluster analysis and non-metric multidimensional scaling (nMDS) indicated that at the juvenile stage, RW and MW individuals in the two main clusters belonged to the same cluster. There was no significant difference between the cores of the RW samples and the edges of the MW and OW samples. Therefore, the spawning area of A. latus in the Wanshan Islands is thought to have originated from low to medium-salinity waters with mangroves and oyster farm habitats in the Pearl River Estuary. A. latus from RW was found to have three distinct habitat-use patterns: 1) Marine Resident (7.2% of sampled fish) fish that remain in marine habitats for life; 2) Marine Migrant (16.4% of sampled fish) juveniles inhabit low to moderate salinity habitats and migrate to marine habitats as they grow; 3) Estuarine Visitor (76.4% of sampled fish) repeated migration between low to moderate salinity and marine habitats. This suggests widespread migration between estuarine and marine habitats throughout the ontogeny. The plasticity of this habitat use and the protection of spawning grounds should be considered in future fisheries management because A. Latus in this area has been the victim of the overexploitation of resources

Understanding the impact of unequal utilization of medical services on the consumption of resources in hemophilia

Abstract Objective Unequal utilization of medical services will have a significant impact on the consumption of resources entitled through health insurance claims of patients. With the proposal of the goal of Healthy China, it is essential to achieve the equity of medical service utilization of patients with rare diseases to further promote social equity and justice. To analyze the consumption of medical resources of rare disease patients, so as to explore how different medical insurance types impact patients’ medical resources consumption. This study pioneeringly used medical data from Peking Union Medical College Hospital. By analyzing the consumption data, this paper fills the research gap of existing studies on the analysis of medical service utilization inequality based on the perspective of insurance participation by examining the effects of different types of insurance coverage on medical resource consumption of hemophiliacs. At the same time, rare disease patients as a minority group have long been neglected in the analysis of medical resource consumption, and this paper fills the research gap of medical service utilization of this group to a certain extent by taking hemophiliacs as the object of analysis. Methods Based on the medical data of hemophilia patients in Peking Union Medical College Hospital from 2010 to 2020, we analyze the consumption of medical resources of the patients, and use a multiple regression model to explore how different medical insurance types impact patients’ medical resources consumption. Results The study has three main findings. Firstly, the disparity in medical expenditure among different hemophilia patients is quite obvious, and the drug expense accounts for a large proportion of the total cost. Secondly, the ratio of reimbursement is generally low, and there is a wide difference in the amount of reimbursement for different types of medical insurance. Thirdly, the resource consumption of patients with different medical insurance types differs a lot. Conclusion In order to improve the current medical insurance system and mechanism for providing orphan drugs, we put forward the following suggestions. First of all, the medical security system should expand its coverage to eliminate the medical expenditure gap between different hemophilia patients, therefore better promoting equity under the same insurance type. At the same time, the reimbursement level of medical expenses for patients with rare diseases should be appropriately improved, so as to reduce the financial burden of patients with rare diseases, and promote the realization of economic equity. In addition, society should pay special attention to the disadvantaged groups, reduce the differences between various medical insurance, and improve the level of health and equity of the whole society

CapsNetYY1: identifying YY1-mediated chromatin loops based on a capsule network architecture

Abstract Background Previous studies have identified that chromosome structure plays a very important role in gene control. The transcription factor Yin Yang 1 (YY1), a multifunctional DNA binding protein, could form a dimer to mediate chromatin loops and active enhancer-promoter interactions. The deletion of YY1 or point mutations at the YY1 binding sites significantly inhibit the enhancer-promoter interactions and affect gene expression. To date, only a few computational methods are available for identifying YY1-mediated chromatin loops. Results We proposed a novel model named CapsNetYY1, which was based on capsule network architecture to identify whether a pair of YY1 motifs can form a chromatin loop. Firstly, we encode the DNA sequence using one-hot encoding method. Secondly, multi-scale convolution layer is used to extract local features of the sequence, and bidirectional gated recurrent unit is used to learn the features across time steps. Finally, capsule networks (convolution capsule layer and digital capsule layer) used to extract higher level features and recognize YY1-mediated chromatin loops. Compared with DeepYY1, the only prediction for YY1-mediated chromatin loops, our model CapsNetYY1 achieved the better performance on the independent datasets (AUC $$> 0.99$$ > 0.99 ). Conclusion The results indicate that CapsNetYY1 is an excellent method for identifying YY1-mediated chromatin loops. We believe that the CapsNetYY1 method will be used for predictive classification of other DNA sequences

Divide-and-Attention Network for HE-Stained Pathological Image Classification

Since pathological images have some distinct characteristics that are different from natural images, the direct application of a general convolutional neural network cannot achieve good classification performance, especially for fine-grained classification problems (such as pathological image grading). Inspired by the clinical experience that decomposing a pathological image into different components is beneficial for diagnosis, in this paper, we propose a Divide-and-Attention Network (DANet) for Hematoxylin-and-Eosin (HE)-stained pathological image classification. The DANet utilizes a deep-learning method to decompose a pathological image into nuclei and non-nuclei parts. With such decomposed pathological images, the DANet first performs feature learning independently in each branch, and then focuses on the most important feature representation through the branch selection attention module. In this way, the DANet can learn representative features with respect to different tissue structures and adaptively focus on the most important ones, thereby improving classification performance. In addition, we introduce deep canonical correlation analysis (DCCA) constraints in the feature fusion process of different branches. The DCCA constraints play the role of branch fusion attention, so as to maximize the correlation of different branches and ensure that the fused branches emphasize specific tissue structures. The experimental results of three datasets demonstrate the superiority of the DANet, with an average classification accuracy of 92.5% on breast cancer classification, 95.33% on colorectal cancer grading, and 91.6% on breast cancer grading tasks

MDSCMF: Matrix Decomposition and Similarity-Constrained Matrix Factorization for miRNA–Disease Association Prediction

MicroRNAs (miRNAs) are small non-coding RNAs that are related to a number of complicated biological processes, and numerous studies have demonstrated that miRNAs are closely associated with many human diseases. In this study, we present a matrix decomposition and similarity-constrained matrix factorization (MDSCMF) to predict potential miRNA–disease associations. First of all, we utilized a matrix decomposition (MD) algorithm to get rid of outliers from the miRNA–disease association matrix. Then, miRNA similarity was determined by utilizing similarity kernel fusion (SKF) to integrate miRNA function similarity and Gaussian interaction profile (GIP) kernel similarity, and disease similarity was determined by utilizing SKF to integrate disease semantic similarity and GIP kernel similarity. Furthermore, we added L2 regularization terms and similarity constraint terms to non-negative matrix factorization to form a similarity-constrained matrix factorization (SCMF) algorithm, which was applied to make prediction. MDSCMF achieved AUC values of 0.9488, 0.9540, and 0.8672 based on fivefold cross-validation (5-CV), global leave-one-out cross-validation (global LOOCV), and local leave-one-out cross-validation (local LOOCV), respectively. Case studies on three common human diseases were also implemented to demonstrate the prediction ability of MDSCMF. All experimental results confirmed that MDSCMF was effective in predicting underlying associations between miRNAs and diseases

Distribution Pattern of Coral Reef Fishes in China

Coral reefs are known as “tropical rain forests” in the ocean. Fish diversity is extremely high, accounting for one-third of marine fishes. To better protect and manage coral reef fishes, this study systematically compiled documents and databases published in China. We counted 2855 species of coral reef fishes in China, which belong to 3 classes, 41 orders, 252 families, and 1017 genera. Among these, Perciformes was the dominant order, accounting for 57.31% of the total species. Gobiidae (7.43%), Labridae (5.36%), Pomacentridae (4.52%), and Serranidae (4.38%) were the main families, while other families accounted for less than 4%. Furthermore, 5.56% of coral reef fish species have entered the IUCN Red List. The present study found that coral reef fishes can be divided into nearshore and offshore. This was mainly because the nearshore coral reef fishes were more affected by human disturbance and runoff from the mainland, whereas offshore coral reef fishes were in areas with high salinity and temperature far from the mainland, where human disturbance was less. Coral reef fish species’ diversity had a significant positive correlation with coral species diversity (p < 0.05), mainly because corals provide habitat and shelter. This study is the first systematic compilation and analysis of coral reef fishes in China and provides a basic reference for global protection management and biological geographical analysis

Development Path of Marine Ranching in South China Sea Based on SWOT Analysis

As a modern fishery model to repair the marine ecosystem and realize the proliferation of fishery resources, marine ranching is an important link in promoting the green development of marine economy, promoting the transformation and upgrading of traditional fisheries and building a community of shared future for the sea. However, there are many factors restricting the high-quality development of modern marine ranching in the actual construction. Rational planning of marine ranching and giving full play to its ecological, social and economic benefits are crucial to the sustainable development of marine ranching. This paper summarizes the current situation of the construction, technical development and policy management of marine ranching in the South China Sea, and comprehensively analyzes the development of marine ranching in the South China Sea by using SWOT analysis method, explains the advantages, disadvantages, opportunities and challenges of marine ranching in the South China Sea, and puts forward the path for the development of marine ranching industry in the South China Sea based on the experience and development trend of marine ranching construction at home and abroad, It is expected to provide reference for the high-quality development of marine ranching in China

Figure 5 from: Zhao L, Yi D, Li C, Sun D, Xu H, Gao T (2017) Phylogeography and population structure of - grypotus (Richardson, 1846) as revealed by mitochondrial control region sequences. ZooKeys 705: 143-158. https://doi.org/10.3897/zookeys.705.13001

The 137 individuals of Johnius grypotus were collected from seven localities from the Bohai Sea to the East China Sea. A 549 base pair (bp) fragment of the hypervariable region of the mtDNA control region was sequenced to examine genetic diversity and population structure. The populations of J. grypotus showed high haplotype diversity (h) with a range from 0.7500 to 0.9740 and low nucleotide diversity (π) with a range from 0.0024 to 0.0067. Low and non-significant genetic differentiation was estimated among populations except for North Yellow Sea population, which has a significant genetic difference with other populations. The demographic history examined by mismatch distribution analyses and Bayesian skyline plot (BSP) analyses revealed that a sudden population expansion occurred almost 20 to 40 thousand years before. Relatively recent population expansion in the last glacial period, large dispersal of eggs or larvae carried by coastal current, and the homogeneity of living environment may have an important influence on the population genetic pattern