Article
Fisheries
Ruoxuan Zhao, Zhenyang Qin, Yang Feng, Yi Geng, Xiaoli Huang, Ping Ouyang, Defang Chen, Hongrui Guo, Huidan Deng, Jing Fang, Weimin Lai
Summary: This study investigated the virulence determinants of V. mimicus strain SCCF01 and its sialic acid catabolism defect strain ASaCS. The loss of sialic acid catabolism ability led to changes in bacterial morphology, decreased biofilm formation, and increased cell adherence ability. Animal experiments confirmed the contribution of SaCS to V. mimicus pathogenicity, with the ASaCS strain showing significantly higher mortality rate compared to the WT strain. Proteomics analysis revealed differences in protein expression related to pentose phosphate pathway, purine metabolism, and bacterial chemotaxis between the two strains.
Article
Microbiology
Iliana Guardiola-Avila, Leonor Sanchez-Buso, Evelia Acedo-Felix, Bruno Gomez-Gil, Manuel Zuniga-Cabrera, Fernando Gonzalez-Candelas, Lorena Noriega-Orozco
Summary: This study analyzed the genome composition of nine V. mimicus strains, revealing the core and accessory genes as well as phylogenetic relationships. The main virulence genes and categories were identified in different chromosomes, shedding light on the diversity and virulence potential of V. mimicus.
Article
Environmental Sciences
Ziyan Jiang, Shuwen Gu, Qieqi Qian, Jie Li, Peng Ji, Congcong Wu, Yingjie Zhang, Xiaojian Gao, Qun Jiang, Xiaojun Zhang
Summary: This study described the changes in survival, virulence, and gene expression of V. mimicus cells under starvation stress. It found that starved cells showed significant changes in morphology and physiological activities, and the expression of virulence-related genes was downregulated.
FRONTIERS IN MARINE SCIENCE
(2022)
Article
Biotechnology & Applied Microbiology
Shin-ichi Miyoshi, Norie Toko, Tetsuya Dodo, Ayako Nanko, Tamaki Mizuno
Summary: Vibrio mimicus is a bacterium that causes gastroenteritis in humans. This study identifies a new protease, VmtX, that is involved in the maturation of the enterotoxic hemolysin produced by this pathogen.
WORLD JOURNAL OF MICROBIOLOGY & BIOTECHNOLOGY
(2022)
Article
Genetics & Heredity
Virginia Green, Catherine Klancher, Shouji Yamamoto, Ankur Dalia
Summary: Vibrio cholerae is a facultative pathogen that primarily occupies marine environments. It commonly interacts with the chitinous shells of crustacean zooplankton, degrading chitin into soluble oligosaccharides. These oligosaccharides serve as a nutrient source and an environmental cue that induces a strong transcriptional response in V. cholerae.
Article
Microbiology
Jinli Yan, Nuoqiao Lin, Xiaoqing Wang, Xuemei Chen, Huishan Wang, Qiqi Lin, Xiaofan Zhou, Lianhui Zhang, Lisheng Liao
Summary: Functional analysis of Ralstonia solanacearum genes associated with bacterial virulence is important for understanding its pathogenicity. In this study, a markerless gene deletion method was developed using natural transformation and the FLP/FRT recombination system. The method allowed efficient gene deletion in R. solanacearum strains, providing a tool for studying putative virulence genes and elucidating the pathogenic mechanisms of R. solanacearum.
FRONTIERS IN MICROBIOLOGY
(2022)
Article
Fisheries
Yu Fu, Yong-An Zhang, Jinyu Shen, Jiagang Tu
Summary: The study demonstrates that His-OmpU elicits a potent protective immune response and is an effective vaccine candidate against V. mimicus in yellow catfish. In addition, the vaccine significantly enhances serum bactericidal activity and antibody titers.
FISH & SHELLFISH IMMUNOLOGY
(2021)
Article
Microbiology
Oluwatayo E. Abioye, Charles A. Osunla, Nolonwabo Nontongana, Anthony I. Okoh
Summary: The presence of virulence determinants in Vibrio species isolated from water resources in South Africa poses a potential public health risk. The study highlights the relevance of environmental Vibrio species to the epidemiology of vibriosis and cholera-like infections. A monitoring program for pathogenic Vibrio species, especially in surface water, is recommended.
Article
Fisheries
Ziyan Jiang, Yingjie Zhang, Xinhai Zhu, Yifan Zhou, Qieqi Qian, Xiaojian Gao, Qun Jiang, Xiaojun Zhang
Summary: In this study, the role of rpoN in V. mimicus was investigated using phenotypic and RNA-seq analysis. The results showed that rpoN positively regulated the resistance to certain stress factors and negatively regulated the resistance to others. The biofilm formation ability and siderophore production were also affected by rpoN. Additionally, rpoN was found to be involved in the regulation of various virulence-related genes and stress-protective genes in V. mimicus.
Article
Multidisciplinary Sciences
Milena Jaskolska, David W. Adams, Melanie Blokesch
Summary: Horizontal gene transfer is a key driver of bacterial evolution, facilitated by mobile genetic elements such as plasmids and bacteriophages. This study identifies two conserved plasmid defence systems in Vibrio cholerae, responsible for the ongoing cholera pandemic. These systems rapidly eliminate small plasmids and defend against bacteriophage infection. Additionally, they increase the burden of large conjugative plasmids, leading to a fitness disadvantage for plasmid-carrying cells. These findings explain the rarity of plasmids in pandemic strains and have implications for understanding antibiotic resistance plasmid dissemination and the evolution of pandemic V. cholerae.
Article
Biotechnology & Applied Microbiology
Jing Xiao, Qiaochu Wang, Kunxue Xiao, Wenlong Zhu, Junhao Huang, Xuwang Cai, Huanchun Chen, Xiaojuan Xu
Summary: In this study, a markerless and multiple-gene deletion system was established for Glaesserella parasuis, which is simple, efficient, and easy to manipulate. This system will significantly aid in understanding the etiology, pathogenesis, and genetic engineering of G. parasuis and other bacteria that can be naturally transformed in laboratory conditions.
APPLIED MICROBIOLOGY AND BIOTECHNOLOGY
(2022)
Article
Fisheries
Shou-Lin Cao, Jia-Jing Guo, Wen-ping Zhao, Wen-Fei Yang, Shu-Liu Zhang, Hui-Zhu Tao, Jin-Nian Li
Summary: The study found that the double-targeted DNA vaccine significantly altered the gut microbiota of grass carp, especially in the hindgut at 21 days post vaccination. In addition, the expression levels of immune-related genes were markedly up-regulated post vaccination, and the phagocytic ability and respiratory burst activity of intestinal macrophages were also significantly higher.
Article
Biotechnology & Applied Microbiology
Cameron J. Lloyd, Adrian Mejia-Santana, Triana N. Dalia, Ankur B. Dalia, Karl E. Klose
Summary: This study demonstrates that classical biotype V. cholerae is functionally capable of natural transformation, but its lower transformation levels and inactivation of the transformation regulator HapR compared to El Tor biotype V. cholerae suggest that the classical biotype may be less efficient at utilizing natural transformation for horizontal gene transfer.
APPLIED AND ENVIRONMENTAL MICROBIOLOGY
(2021)
Article
Microbiology
Junlin Wang, Huanying Pang, Linlin Yin, Fuyuan Zeng, Na Wang, Rowena Hoare, Sean J. Monaghan, Wanxin Li, Jichang Jian
Summary: Protein lysine acetylation is an evolutionarily conserved post-translational modification that plays a crucial role in the metabolism and virulence of V. mimicus. This study provides a comprehensive analysis of the protein lysine acetylome in V. mimicus and establishes an important foundation for further research on the biological function of lysine acetylation in V. mimicus.
FRONTIERS IN MICROBIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Claire Vit, Egill Richard, Florian Fournes, Clemence Whiteway, Xavier Eyer, Delphine Lapaillerie, Vincent Parissi, Didier Mazel, Celine Loot
Summary: In this study, it was found that cassette recruitment in the Vibrio cholerae chromosomal integron mainly occurs at the attIA site, with newly inserted cassettes being expressed and selected due to the presence of a promoter in the vicinity of this site. The RecA protein plays a critical role in this process, but the V. cholerae integron integrase is not active in other bacteria.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Neurosciences
Bin Wang, Xuewei Yang, Jincheng Lu, Michael Ntim, Min Xia, Supratik Kundu, Rong Jiang, Defang Chen, Ying Wang, Jin-Yi Yang, Shao Li
Summary: Acute stress has multiple effects on learning behaviors. The time gradient acute restraint stress (ARS) model accurately assesses the role of different restraint times in inducing acute stress. 2-hour ARS enhances escape behaviors and learning outcomes, activates synaptic plasticity and gene transcription associated with learning and memory, and activates specific phosphorylation sites on the glucocorticoid receptor.
EXPERIMENTAL NEUROLOGY
(2022)
Article
Computer Science, Artificial Intelligence
Junkun Yuan, Xu Ma, Defang Chen, Kun Kuang, Fei Wu, Lanfen Lin
Summary: This paper proposes a novel framework called Domain-Specific Bias Filtering (DSBF) to tackle the Single Labeled Domain Generalization (SLDG) task. DSBF initializes a discriminative model with the labeled source data and filters out its domain-specific bias with the unlabeled source data to improve generalization. Experimental results demonstrate that DSBF achieves superior performance in addressing both the challenging SLDG task and the CDG task.
INTERNATIONAL JOURNAL OF COMPUTER VISION
(2023)
Article
Computer Science, Artificial Intelligence
Chen Wang, Hui Ma, Gang Chen, Sven Hartmann
Summary: Web service composition combines existing web services to meet users' requests for required functionalities with the best possible quality of services (QoS). Evolutionary computation techniques have been employed to efficiently find composite services with near-optimal functional quality or nonfunctional quality for each composition request individually. Multitasking service composition approaches have been proposed to efficiently deal with multiple composition requests concurrently, but existing attempts have not effectively learned and shared knowledge among solutions for multiple requests. In this article, a new algorithm, PMFEA-EDA, is proposed to effectively and efficiently solve the problem of collectively handling multiple service composition requests.
IEEE TRANSACTIONS ON EVOLUTIONARY COMPUTATION
(2023)
Article
Immunology
Yang Feng, Jiao Wang, Wei Fan, Yi Geng, Xiaoli Huang, Ping Ouyang, Defang Chen, Hongrui Guo, Huidan Deng, Weimin Lai, Zhicai Zuo
Summary: In this study, the researchers examined the pathological changes in the skin and muscle of yellow catfish infected with Vibrio mimicus. They found significant necrosis, inflammation, and tissue remodeling, as well as changes in collagen composition. Transcriptomic and label-free analyses revealed immune pathway responses and downregulated cell signaling pathways. Key regulatory genes, such as MMP-9 and MMP-13, were identified in the cytokine and tissue remodeling pathways. These findings provide new insights into the immune response to V. mimicus infection in yellow catfish and suggest potential therapeutic targets.
FRONTIERS IN IMMUNOLOGY
(2023)
Article
Immunology
Ping Ouyang, Yongqiang Ren, Yongheng Zhou, Qiunan Li, Xiaoli Huang, Defang Chen, Yi Geng, Hongrui Guo, Jing Fang, Huidan Deng, Weiming Lai, Zhengli Chen, Gang Shu, Lizi Yin
Summary: Koi sleepy disease (KSD) is a viral disease that causes high mortality and infection in common carp and Koi. The study compared the pathology, enzyme activity, immunoglobulin activity, and gene expression differences in acutely infected and asymptomatic Koi infected with carp edema virus (CEV). The data obtained in this study provide new evidence for understanding CEV-host interactions and the infection mechanism, and will help in controlling CEV infection and spread.
FRONTIERS IN IMMUNOLOGY
(2023)
Article
Fisheries
Ruoxuan Zhao, Zhenyang Qin, Yang Feng, Yi Geng, Xiaoli Huang, Ping Ouyang, Defang Chen, Hongrui Guo, Huidan Deng, Jing Fang, Weimin Lai
Summary: This study investigated the virulence determinants of V. mimicus strain SCCF01 and its sialic acid catabolism defect strain ASaCS. The loss of sialic acid catabolism ability led to changes in bacterial morphology, decreased biofilm formation, and increased cell adherence ability. Animal experiments confirmed the contribution of SaCS to V. mimicus pathogenicity, with the ASaCS strain showing significantly higher mortality rate compared to the WT strain. Proteomics analysis revealed differences in protein expression related to pentose phosphate pathway, purine metabolism, and bacterial chemotaxis between the two strains.
Article
Computer Science, Software Engineering
Chaoli Wang, Jun Han
Summary: Since 2016, there has been a significant growth in the research of artificial intelligence and visualization (AI+VIS). However, existing survey articles mainly focus on visual analytics and information visualization, neglecting scientific visualization. This article surveys deep learning works in the field of scientific visualization, specifically in the direction of DL4SciVis: designing deep learning solutions for solving scientific visualization problems. The works are classified and discussed based on six dimensions, and the article concludes with a discussion of the remaining gaps and challenges in this field.
IEEE TRANSACTIONS ON VISUALIZATION AND COMPUTER GRAPHICS
(2023)
Article
Computer Science, Artificial Intelligence
Jiongyu Guo, Defang Chen, Can Wang
Summary: Graph neural networks (GNNs) have gained popularity due to their strong ability in handling irregular graph data, but deploying them in edge devices with limited resources and large-scale datasets poses challenges. Existing model compression techniques mainly focus on convolutional neural networks, with limited attempts for distilling knowledge from GNNs. In this paper, we propose a novel online knowledge distillation framework called Alignahead++ to address these challenges. Experimental results on four datasets demonstrate that our collaborative training framework consistently boosts the student performance without the supervision of a pre-trained teacher model, and its effectiveness can be improved by increasing the number of students.
NEURAL COMPUTING & APPLICATIONS
(2023)
Article
Computer Science, Artificial Intelligence
Can Wang, Defang Chen, Jian-Ping Mei, Yuan Zhang, Yan Feng, Chun Chen
Summary: Knowledge distillation is a technique that improves the generalization ability of a student model by using outputs from a teacher model. We propose a semantic calibration method for cross-layer knowledge distillation, which automatically assigns target layers from the teacher model to each student layer using an attention mechanism. Experimental results show that our approach achieves an average improvement of 4.27% in student model Top-1 classification accuracy on CIFAR-100.
IEEE TRANSACTIONS ON KNOWLEDGE AND DATA ENGINEERING
(2023)
Article
Computer Science, Artificial Intelligence
Jian-Ping Mei, Wenhao Qiu, Defang Chen, Rui Yan, Jing Fan
Summary: This article proposes a Cluster-based soft targets for Output Regularization (CluOReg) approach, which leverages clustering in embedding space and uses cluster-based soft targets for neural classifier training via output regularization. The results show that this approach effectively complements the ground-truth label and achieves significant reductions in classification error.
IEEE TRANSACTIONS ON NEURAL NETWORKS AND LEARNING SYSTEMS
(2023)
Article
Computer Science, Artificial Intelligence
Can Wang, Zhe Wang, Defang Chen, Sheng Zhou, Yan Feng, Chun Chen
Summary: This paper proposes an online adversarial distillation approach for graph neural networks. It tackles the issue of knowledge distillation caused by evolving graph topology and node attributes by simultaneously training a group of graph neural networks. The approach transfers both global and local knowledge to enhance the distillation performance among student models.
EXPERT SYSTEMS WITH APPLICATIONS
(2024)
Proceedings Paper
Acoustics
Hailin Zhang, Defang Chen, Can Wang
Summary: This paper proposes a confidence-aware multi-teacher knowledge distillation method, which assigns sample-wise reliability for each teacher prediction and incorporates features in intermediate layers to enhance the performance of the student model.
2022 IEEE INTERNATIONAL CONFERENCE ON ACOUSTICS, SPEECH AND SIGNAL PROCESSING (ICASSP)
(2022)
Proceedings Paper
Computer Science, Artificial Intelligence
Jiongyu Guo, Defang Chen, Can Wang
Summary: This paper introduces a novel online knowledge distillation framework that can improve student model performance without the need for a pre-trained teacher model, as opposed to traditional offline methods.
2022 INTERNATIONAL JOINT CONFERENCE ON NEURAL NETWORKS (IJCNN)
(2022)
Proceedings Paper
Computer Science, Artificial Intelligence
Defang Chen, Jian-Ping Mei, Hailin Zhang, Can Wang, Yan Feng, Chun Chen
Summary: Knowledge distillation is a method to compress a powerful but cumbersome teacher model into a lightweight student model without sacrificing performance. A simple knowledge distillation technique can significantly narrow down the performance gap between the teacher and student models.
2022 IEEE/CVF CONFERENCE ON COMPUTER VISION AND PATTERN RECOGNITION (CVPR)
(2022)
Proceedings Paper
Computer Science, Cybernetics
Can Wang, Sheng Zhou, Kang Yu, Defang Chen, Bolang Li, Yan Feng, Chun Chen
Summary: Learning low-dimensional representations for Heterogeneous Information Networks (HINs) has gained attention for its effectiveness in real-world applications. Existing methods focus on independently learning meta-path-based embeddings and integrating them, but disregard the correlations among meta-paths. To address this issue, we propose Collaborative Knowledge Distillation for Heterogeneous Information Network Embedding (CKD) to explicitly model the correlation among meta-paths. Experiments on six real-world HIN datasets demonstrate the effectiveness of the CKD method.
PROCEEDINGS OF THE ACM WEB CONFERENCE 2022 (WWW'22)
(2022)
