Article
Fisheries
ChangHong Cheng, HongLing Ma, GuangXin Liu, YiQing Deng, JianJun Jiang, Juan Feng, ZhiXun Guo
Summary: This study investigated the physiological, transcriptomic, and metabolomic responses after MCRV infection. The results showed that MCRV infection caused changes in enzyme activities, oxidative stress, and tissue damage. Transcriptome analysis identified genes related to detoxification, immune response, and metabolic processes. Two key pathways, phagocytosis and apoptosis, played important roles in response to MCRV infection.
FISH & SHELLFISH IMMUNOLOGY
(2022)
Article
Fisheries
Hengwei Deng, Danrong Xian, Taixin Lian, Mingyu He, Jingjing Li, Xiaopeng Xu, Zhixun Guo, Jianguo He, Shaoping Weng
Summary: A Dicer2 gene named SpDicer2 from Scylla paramamosain was cloned and characterized. SpDicer2 plays an important role in defending against MCRV in mud crab by activating the JAK/STAT signaling pathways, influencing multiple immune pathways and the expression of immune effector genes.
DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Yu-Kun Jie, Chang-Hong Cheng, Li-Cang Wang, Hong-Ling Ma, Yi-Qin Deng, Guang-Xin Liu, Juan Feng, Zhi-Xun Guo, Ling-Tong Ye
Summary: The mud crab is an economically important cultured species in China, and hypoxia is a major environmental stressor during its culture. The study found that the activities of SOD, T-AOC, and LDH in the gills of mud crab increased significantly after hypoxia stress, while MDA concentration also increased. Transcriptomic analysis revealed that genes related to glycolysis and tricarboxylic acid cycle play crucial roles in regulating the adaptation of mud crab to hypoxia stress.
COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY C-TOXICOLOGY & PHARMACOLOGY
(2021)
Article
Microbiology
Ming Zhang, Xinxu Zhang, Ngoc Tuan Tran, Zaiqiao Sun, Xusheng Zhang, Haihui Ye, Yueling Zhang, Hongyu Ma, Jude Juventus Aweya, Shengkang Li
Summary: This study found that molting in mud crabs leads to significant changes in microbial communities, particularly in the gills and midgut, and is closely associated with the expression of antimicrobial peptide genes and the relative abundance of microbes in the hemolymph. Additionally, digestive enzymes play a role in regulating the microbiota in the hepatopancreas and midgut, facilitating the restoration and reconstruction of host-microbiome homeostasis during molting.
Article
Fisheries
Zhanning Xu, Yujie Wei, Guizhong Wang, Haihui Ye
Summary: B-type allatostatins (AST-B) are neuropeptides that may act as pleiotropic neuropeptides in mud crabs, involved in regulating immune responses. This study confirmed that AST-B induces innate immunity in mud crabs by modulating immune-related genes and enhancing hemocyte activity.
DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY
(2021)
Article
Fisheries
Yuanhao Ren, Wei Wang, Yin Fu, Zhiqiang Liu, Ming Zhao, Likun Xu, Tianyong Zhan, Ting Huang, Minghao Luo, Wei Chen, Chunyan Ma, Fengying Zhang, Keji Jiang, Lingbo Ma
Summary: This study conducted a comparative transcriptome analysis of the ovaries of mud crabs at various stages of ovarian maturation, and found that MAPK signaling pathway plays a critical role in lipid metabolism during vitellogenesis. Genes involved in carbohydrate, amino acid, and lipid metabolism were found to be highly expressed during vitellogenesis. Additionally, two genes in the PPAR signaling pathway were identified to be associated with lipid metabolism in the ovary, and MAPK signaling pathway might regulate lipid metabolism through PPAR signaling pathway based on Protein-Protein Interaction (PPI) network. These findings provide new insights into the mechanism of lipid accumulation during ovarian maturation in mud crabs.
Article
Environmental Sciences
Wen -Bin Xu, Yan-Mei Zhang, Bang-Ze Li, Chen -Yang Lin, Da -Yong Chen, Yuan-Xin Cheng, Xiao-Ling Guo, Wei-Ren Dong, Miao-An Shu
Summary: Two populations of mud crab from Hangzhou Bay and Zhangzhou Bay in China have different osmoregulatory capacities under low salinity stress, with the population from Hangzhou Bay showing stronger ion transport, energy supply, and osmolyte regulation. Additionally, epigenetic modification may contribute to the rapid response to salinity fluctuation in the Hangzhou Bay population.
SCIENCE OF THE TOTAL ENVIRONMENT
(2023)
Article
Genetics & Heredity
Haifu Wan, Jinying Zhong, Ziping Zhang, Pengfei Zou, Xianyuan Zeng, Yilei Wang
Summary: This study identified 7 members of the Dmrt gene family in the mud crab Scylla paramamosain, with differential expression patterns in gonads. Spdmrt-like and Spdmrt1a showed higher expression in testis, while Spdmrt-3 and Spidmrt-2 exhibited higher levels in the testis as well. These findings highlight the important roles of Dmrt genes in sex determination and gonad development.
Article
Multidisciplinary Sciences
Xiao Yu, Yun Wang, Xiaoyi Shi, Zhihui Wang, Peihao Wen, Yuting He, Wenzhi Guo
Summary: This study identified differentially expressed protein-coding genes (PCGs) and constructed a risk model using different statistical methods. They also constructed a 9-gene prognostic risk model based on epigenetic PCGs. The risk score was found to be significantly related to survival and an independent risk factor for pancreatic cancer patients.
SCIENTIFIC REPORTS
(2023)
Article
Fisheries
Yu-Kun Jie, Zhi-Ping Luo, Jia-Wei Xie, Chang-Hong Cheng, Hong-Ling Ma, Guang-Xin Liu, Jian-Jun Jiang, Yi-Qin Deng, Juan Feng, Zhi-Xun Guo
Summary: In this study, a PFK gene from the mud crab Scylla paramamosain, named SpPFK, was cloned and characterized. Knocking down SpPFK using RNA interference significantly reduced lactate dehydrogenase expression after MCDV-1 infection and increased the survival rate of mud crabs. These results suggest that SpPFK plays an important role in the proliferation of MCDV-1 in mud crabs.
FISH & SHELLFISH IMMUNOLOGY
(2022)
Article
Biochemistry & Molecular Biology
David S. Wishart, Ray Kruger, Aadhavya Sivakumaran, Karxena Harford, Selena Sanford, Rahil Doshi, Nitya Kehrtarpal, Omolola Fatokun, Daphnee Doucet, Ashley Zubkowski, Hayley Jackson, Gina Sykes, Miguel Ramirez-Gaona, Ana Marcu, Carin Li, Kristen Yee, Christiana Garros, Dorsa Yahya Rayat, Jeanne Coleongco, Tharuni Nandyala, Vasuk Gautam, Eponine Oler
Summary: PathBank is a database that provides comprehensive metabolite pathway information. With the latest update of PathBank 2.0, there have been significant improvements in the number, quality, and functionality of pathways, making it more useful for interpreting metabolomics data.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Food Science & Technology
Ming Zhang, Ngoc Tuan Tran, Peina Ji, Yongsheng Zhang, Daimeng Zhang, Huaiping Zheng, Shengkang Li
Summary: Yellow oil mud crab (YOC) is a new variant of mud crab with high nutrition value. This study aimed to investigate the nutrient compositions, gene differences, and fatty acid synthesis ability of YOC compared to normal mud crabs. The results showed that YOC has higher nutritional value and better fatty acid synthesis ability.
FOOD RESEARCH INTERNATIONAL
(2023)
Article
Environmental Sciences
Wenxiao Cui, Qin Yang, Yin Zhang, Ardavan Farhadi, Huan Fang, Huaiping Zheng, Shengkang Li, Yueling Zhang, Mhd Ikhwanuddin, Hongyu Ma
Summary: This study utilized single-molecule long-read technology combined with RNA sequencing to construct a full-length transcriptome for the gonads of Scylla paramamosain, identifying a significant number of novel transcripts and genes associated with reproductive development and maturation.
FRONTIERS IN MARINE SCIENCE
(2021)
Article
Fisheries
ChangHong Cheng, HongLing Ma, GuangXin Liu, SiGang Fan, YiQin Deng, JianJun Jiang, Juan Feng, ZhiXun Guo
Summary: In this study, a novel Nrf2 gene was identified in the mud crab, which plays important roles in detoxification and antioxidant enzymes against oxidative stress. The Nrf2 signaling pathway was found to be involved in the response to bacterial infection. Over-expression of Nrf2 improved cell viability under oxidative stress, while silencing Nrf2 increased mortality in response to bacterial infection.
FISH & SHELLFISH IMMUNOLOGY
(2023)
Article
Agronomy
Jing Guo, Xiuli Song, Shiqi Sun, Baihui Shao, Bo Tao, Lili Zhang
Summary: This study focused on selecting potato varieties with tolerance and sensitivity to bentazone, determining key genes involved in tolerance, and providing a theoretical basis for selecting stress-resistant resources in the future. The research found that tolerant potato plants showed a significantly higher photosynthetic rate and experienced faster degradation of bentazone compared to sensitive plants, with specific genes such as PPO, AOMT3, RBCS-C, and CHS2 identified as contributing to bentazone tolerance.
Article
Economics
Kun Wang, Jianqiang Chen
Summary: This paper examines the impact of fraud deterrence on firms' innovation outputs. The study finds that fraud deterrence is positively related to firms' innovation outputs, especially when there is high information asymmetry or employee turnover.
APPLIED ECONOMICS LETTERS
(2023)
Review
Chemistry, Physical
Yang Zhao, Jiazhao Huang, Jianqiang Chen, Youwen Liu, Tianyou Zhai
Summary: Two-dimensional transition metal dichalcogenides (TMDs) have shown excellent catalytic performance for hydrogen evolution and are considered suitable substitutes for commercial Pt-based catalysts. Chemical vapor deposition (CVD) is an important technique for synthesizing controllable and high-purity TMDs for electrocatalysis and electronic devices. Recent research progress in CVD-grown TMDs nanosheets for electrocatalytic hydrogen evolution, including synthesis factors and engineering strategies, has been presented in this review.
Article
Computer Science, Artificial Intelligence
Xuedong He, Calvin Yu-Chian Chen
Summary: Most end-to-end discriminative trackers aim to improve performance by mining more representative target features, but it is challenging to obtain comprehensive features due to diverse challenges. To address this issue, we propose a novel feature enhancement module for richer and comprehensive feature representation, which is trainable end-to-end. Additionally, we use a metric learning method to devise a verifier for adaptive update of the sample memory and learning rate.
EXPERT SYSTEMS WITH APPLICATIONS
(2023)
Article
Chemistry, Physical
Ziduo Yang, Weihe Zhong, Qiujie Lv, Tiejun Dong, Calvin Yu -Chian Chen
Summary: This paper proposes a geometric interaction graph neural network (GIGN) that incorporates 3D structures and physical interactions for predicting protein-ligand binding affinities. GIGN achieves state-of-the-art performance on three external test sets, and the learned representations of protein-ligand complexes are biologically meaningful.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS
(2023)
Article
Business, Finance
Jianqiang Chen, Pei-Fang Hsieh, Kun Wang
Summary: This study examines the impact of infringement and counterfeiting on corporate innovation performance. A quasi-natural experiment is used to analyze the effects of the Chinese government's crackdown on intellectual property rights violations. The results show that after the implementation, companies in industries with high risk of intellectual property violations or imitation experience a significant increase in patent counts and citations, especially for financially strong and risk-taking firms. This event leads to increased R&D investment and a prioritization of invention patents over utility patents by firms.
FINANCE RESEARCH LETTERS
(2023)
Article
Chemistry, Multidisciplinary
Qiujie Lv, Guanxing Chen, Haohuai He, Ziduo Yang, Lu Zhao, Hsin-Yi Chen, Calvin Yu-Chian Chen
Summary: Traditional Chinese Medicine (TCM) is a valuable resource for modern drug discovery. However, two challenges exist in applying AI-assisted drug discovery (AIDD) to guide TCM drug discovery: lack of standardized TCM-related information and AIDD's susceptibility to failures in out-of-domain data. To address these challenges, TCMBank, the largest systematic free TCM database, was developed as an extension of TCM Database@Taiwan. TCMBank provides comprehensive information on herbs, ingredients, targets, and diseases, and enables researchers to identify potential leads and drug repurposing through an ensemble learning-based drug discovery protocol. It offers a valuable tool for accelerating drug discovery using artificial intelligence.
Letter
Biochemistry & Molecular Biology
Qiujie Lv, Guanxing Chen, Haohuai He, Ziduo Yang, Lu Zhao, Kang Zhang, Calvin Yu-Chian Chen
SIGNAL TRANSDUCTION AND TARGETED THERAPY
(2023)
Article
Computer Science, Artificial Intelligence
Qiujie Lv, Guanxing Chen, Ziduo Yang, Weihe Zhong, Calvin Yu-Chian Chen
Summary: Finding candidate molecules with favorable pharmacological activity, low toxicity, and proper pharmacokinetic properties is an important task in drug discovery. Deep neural networks have made impressive progress in accelerating and improving drug discovery, but they rely on a large amount of label data. Applying deep neural networks for low-data drug discovery is still a challenge.
IEEE TRANSACTIONS ON NEURAL NETWORKS AND LEARNING SYSTEMS
(2023)
Article
Chemistry, Physical
Ziduo Yang, Weihe Zhong, Qiujie Lv, Tiejun Dong, Calvin Yu-Chian Chen
Summary: This paper proposes a geometric interaction graph neural network (GIGN) that incorporates 3D structures and physical interactions for predicting protein-ligand binding affinities. GIGN achieves state-of-the-art performance on three external test sets and its predictions are shown to be biologically meaningful through visualization of learned representations of protein-ligand complexes.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS
(2023)
Article
Computer Science, Artificial Intelligence
Zhenchao Tang, Guanxing Chen, Hualin Yang, Weihe Zhong, Calvin Yu-Chian Chen
Summary: This article introduces a pluggable substructure interaction module called DSIL-DDI, which can learn domain-invariant representations of DDI from the source domain. It improves the generalization and interpretability of DDI prediction modeling and provides valuable insights for OOD DDI predictions.
IEEE TRANSACTIONS ON NEURAL NETWORKS AND LEARNING SYSTEMS
(2023)
Article
Computer Science, Artificial Intelligence
Yiyang Yin, Shuangling Luo, Jun Zhou, Liang Kang, Calvin Yu-Chian Chen
Summary: Medical image segmentation is crucial for modern healthcare systems, especially in reducing surgical risks and planning treatments. Transanal total mesorectal excision (TaTME) has become an important method for treating colon and rectum cancers. Real-time instance segmentation during TaTME surgeries can assist surgeons in minimizing risks. However, the dynamic variations in TaTME images pose challenges for accurate instance segmentation.
Article
Computer Science, Artificial Intelligence
Jiehui Huang, Zhenchao Tang, Xuedong He, Jun Zhou, Defeng Zhou, Calvin Yu-Chian Chen
Summary: This study proposes a progressive learning multi-scale feature blending model for image deraining tasks. The model utilizes detail dilation and texture extraction to improve the restoration of rainy images. Experimental results show that the model achieves near state-of-the-art performance in rain removal tasks and exhibits better rain removal realism.
Article
Chemistry, Physical
Tiejun Dong, Ziduo Yang, Jun Zhou, Calvin Yu-Chian Chen
Summary: This article introduces a novel geometric graph network called FlexPose, which is capable of directly modeling flexible protein-ligand complex structures. The model outperforms popular docking tools and recent deep learning methods, especially in tasks involving protein conformation changes. It also provides affinity estimation and model confidence for post-analysis.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2023)
Article
Automation & Control Systems
Guanxing Chen, Haohuai He, Calvin Yu-Chian Chen
Summary: This study constructs a drug-target affinity dataset for two novel therapeutic targets for CRC and designs a deep learning-based MFAE model. The model simulates complex drug-target interactions through hierarchical feature extraction and multilevel feature aggregation and enhancement. Evaluation demonstrates the model's superior predictive accuracy, and fine-tuning enhances its performance. Two potential repurposing candidates are identified through virtual screening.
ADVANCED INTELLIGENT SYSTEMS
(2023)
Article
Radiology, Nuclear Medicine & Medical Imaging
Jingwen Huang, Guanxing Chen, Haiqing Liu, Wei Jiang, Siyao Mai, Lingli Zhang, Hong Zeng, Shaoxu Wu, Calvin Yu-Chian Chen, Zhuo Wu
Summary: This study developed a non-invasive automated machine learning (AutoML) model to differentiate urothelial carcinoma with squamous differentiation (UC w/SD) from pure urothelial carcinoma (UC) in patients with muscle-invasive bladder carcinoma (MIBC). The model showed robust differentiation capabilities in both training and test sets, making it a potentially useful tool for pre-operative diagnosis.
EUROPEAN RADIOLOGY
(2023)
