Article
Immunology
Hao Yuan, Tiantian Jiang, Wei-Dong Zhang, Zipeng Yang, Shengjun Luo, Xiaohu Wang, Xiaojing Zhu, Shuting Qi, Yasser S. Mahmmod, Xiu-Xiang Zhang, Zi-Guo Yuan
Summary: This study investigated the molecular changes in the brain tissue of masked palm civets chronically infected with T. gondii. The differentially expressed genes were found to be associated with various cellular signaling pathways, including those that are immune- and cancer-related.
FRONTIERS IN CELLULAR AND INFECTION MICROBIOLOGY
(2023)
Article
Biochemical Research Methods
Qianru He, Fanhui Yu, Meng Cong, Yuhua Ji, Qi Zhang, Fei Ding
Summary: Peripheral nerve repair and functional recovery depend on the rate of nerve regeneration and the quality of target reinnervation. A quantitative proteomic technique was used to analyze the protein expression pattern between injured motor and sensory nerves, revealing 176 proteins with differential expressions. Functional categorization indicated that these differentially expressed proteins are linked to various molecular functions, which might play a crucial role in peripheral nerve regeneration.
JOURNAL OF PROTEOME RESEARCH
(2021)
Article
Biochemistry & Molecular Biology
Wei-Chi Ku, Badrinathan Sridharan, Jiann-Yeu Chen, Jen-Ying Li, Shu-Yu Yang, Meng-Jen Lee
Summary: The study indicated that kaempferitrin can regulate extracellular vesicle secretion, thereby affecting lipid profile expression through multiple mechanisms, demonstrating potential anti-liver cancer activity.
Review
Genetics & Heredity
Xiulan Chen, Yaping Sun, Tingting Zhang, Lian Shu, Peter Roepstorff, Fuquan Yang
Summary: Isobaric labeling technology has become a key tool for comparing protein expression in biological samples, although challenges remain in terms of quantitative accuracy and precision. The different types of isobaric mass tags and advantages and disadvantages of the labeling method are detailed, along with precautions needed at each step of the workflow for reliable quantification results. The broad applications of isobaric labeling technology in biological and clinical studies, with a focus on thermal proteome profiling and proteogenomics, are also discussed.
GENOMICS PROTEOMICS & BIOINFORMATICS
(2021)
Review
Biochemistry & Molecular Biology
Chandraprakash Yamini, Govindasamy Sharmila, Chandrasekaran Muthukumaran, Kumar Pavithran, Narasimhan Manojkumar
Summary: Thermotolerant microbes are able to survive in high temperatures and their proteins are optimally active at elevated temperatures. Proteomic analysis helps to understand the stability mechanisms of proteins in thermotolerant microbes at extreme temperatures.
MOLECULAR BIOLOGY REPORTS
(2022)
Article
Biochemical Research Methods
Rosalba Cruz-Miron, Carlos J. Ramirez-Flores, Noe Lagunas-Cortes, Monica Mondragon-Castelan, Emmanuel Rios-Castro, Sirenia Gonzalez-Pozos, M. Magdalena Aguirre-Garcia, Ricardo Mondragon-Flores
Summary: Toxoplasma gondii, a successful intracellular parasite, relies on a complex machinery located in the pellicle for its dynamic functions. The protein composition of the pellicle is not well understood, but recent research identified new SRS proteins that could potentially be targets for designing immunoprotective strategies or drugs against Toxoplasma. Further studies are needed to explore the roles of these proteins in host immune response activation and invasion mechanisms.
JOURNAL OF PROTEOMICS
(2021)
Article
Mycology
Hui Cai, Diquan Shuai, Xiaomin Xue, Yuqing Mo, Xixi Song, Ling Ye, Shuiming Li, Daiwei Wang, Yun Wang, Meiling Jin
Summary: This study identified serum differentially expressed proteins (DEPs) using iTRAQ, with serum CNDP1 found to be significantly decreased in ABPA patients, aiding in distinguishing ABPA from asthma.
Article
Parasitology
Chun-Xue Zhou, Ling-Yu Li, Cui-Qin Huang, Xu-Dong Guo, Xu-Dian An, Fang-Fang Luo, Wei Cong
Summary: This study utilized liquid chromatography-tandem mass spectrometry to analyze metabolites in urine samples of BALB/c mice infected with Toxoplasma gondii. The metabolomic patterns in infected mice differed significantly from uninfected mice, suggesting potential implications for understanding the pathogenesis and treatment of toxoplasmosis.
PARASITES & VECTORS
(2022)
Article
Plant Sciences
Renee Robinson, Vishwanath Sollapura, Philippe Couroux, Dave Sprott, Michael Ravensdale, Elizabeth Routly, Tim Xing, Laurian S. Robert
Summary: The successful pollination in Brassica involves complex molecular processes between mature pollen and stigma cells. Proteomic analysis of Brassica carinata pollen and stigma revealed common functions as well as cellular specialization differences. iTRAQ analysis highlighted proteins involved in stigma maturation and provided insight into early pollination stages. Combining proteomics and transcriptomics offers a comprehensive global perspective on pollen and stigma development and interaction.
Article
Plant Sciences
Maria Tortosa, Pablo Velasco, Victor Manuel Rodriguez, Maria Elena Cartea
Summary: Understanding plant's response mechanisms against pathogenesis is fundamental for resistant crop development. This study compared the proteomes of Brassica oleracea leaves infected with Xanthomonas campestris pv. campestris at different post-infection times. The results revealed that different cell processes, including primary metabolism, hormone signaling, and defense mechanisms, were involved in the plant's response to infection.
FRONTIERS IN PLANT SCIENCE
(2022)
Review
Oncology
Arada Vinaiphat, Jee Keem Low, Kheng Wei Yeoh, Wee Joo Chng, Siu Kwan Sze
Summary: Cancer, as a major contributor to global chronic disease burden, is closely related to low-oxygen stress. Traditional proteomic approaches have been used to study cancer mechanisms associated with oxygen deprivation, but clinical therapeutic outcomes have been limited. Therefore, the development of new strategies and technologies is crucial for multi-target drug discovery.
FRONTIERS IN ONCOLOGY
(2021)
Article
Oceanography
Xiayue Chen, Changkao Mu, Ronghua Li, Yangfang Ye, Weiwei Song, Ce Shi, Lei Liu, Huan Wang, Chunlin Wang
Summary: In this study, iTRAQ analysis was used to identify differentially expressed proteins during larval development of the swimming crab Portunus trituberculatus, leading to the discovery of 241 proteins involved in various biological processes and the formation of four protein clusters based on expression patterns.
JOURNAL OF OCEAN UNIVERSITY OF CHINA
(2021)
Article
Cell Biology
Jing Yan, Bei Xie, Ye Tian, Li Huang, Shuli Zou, Zhiheng Peng, Zhuan Liu, Linjing Li
Summary: Insulin resistance (IR) is associated with poor prognosis in hepatocellular carcinoma (HCC). This study identified differentially expressed proteins (DEPs) in insulin resistant HepG2 cells, and found that these DEPs are involved in tumorigenesis and tumor progression. High expression of SOX9 and PRKD3 is strongly associated with reduced patient survival rate.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2022)
Article
Biochemical Research Methods
Qi Cheng, Xianwen Yuan, Shibo Lin, Yinjuan Zhao, Haiquan Wang, Feng Zhu, Yuqi Wang, Tao Xu, Jing Wu, Kai Wang, Jingzi Zhang, Xitai Sun, Chaojun Li, Hui Liang, Lei Fang, Bin Xue
Summary: Nonalcoholic fatty liver disease (NAFLD) is a common chronic liver disease and is closely associated with obesity. However, there are individuals with metabolically healthy obesity (MHO) who do not develop NAFLD, suggesting the existence of factors independent of obesity that protect against NAFLD. Through a proteomic study, we identified significant differences in serum proteins between NAFLD and MHO subjects, with changes observed in immune response and triglyceride metabolism-related pathways. We also found that serum apolipoprotein H levels may be a potential blood biomarker for distinguishing NAFLD from MHO and predicting NAFLD risk.
JOURNAL OF PROTEOMICS
(2022)
Article
Parasitology
Min Chen, Lijuan Zhou, Shengmin Li, Hiaxia Wei, Jiating Chen, Pei Yang, Hongjuan Peng
Summary: Toxoplasma gondii infection causes serious diseases and can switch between acute and chronic infection under the host's immune pressure. Two functional DNA methyltransferases (DNMTs), TgDNMTa and TgDNMTb, were found to not only be involved in DNA methylation but also regulate the parasitic energy metabolism.
Article
Automation & Control Systems
Haishuai Wang, Jia Wu, Xingquan Zhu, Yixin Chen, Chengqi Zhang
IEEE TRANSACTIONS ON SYSTEMS MAN CYBERNETICS-SYSTEMS
(2020)
Article
Computer Science, Information Systems
Shuliang Wang, Qi Li, Chuanfeng Zhao, Xingquan Zhu, Hanning Yuan, Tianru Dai
Summary: Peak clustering, a density based clustering method, has shortcomings in finding cluster centers in low density clusters and detecting normal points as noises. Extreme clustering, which identifies density extreme points and introduces a noise detection module, overcomes these drawbacks and improves performance significantly.
INFORMATION SCIENCES
(2021)
Article
Parasitology
Sen Li, Yang Zou, Xue-Liang Zhang, Ping Wang, Xiao-Qing Chen, Xing-Quan Zhu
KOREAN JOURNAL OF PARASITOLOGY
(2020)
Article
Immunology
Yang Zou, Wen-Bin Yang, Feng-Cai Zou, Rui-Qing Lin, Xing-Quan Zhu, Jun-Ling Hou
Summary: This study investigated the prevalence and subtypes of Blastocystis infections in farmed pigs in southern China, with ST5 being the predominant subtype. Factors such as gender, age, and region were considered as risk factors associated with Blastocystis infection in farmed pigs. This study provided valuable data for the control of Blastocystis infections in pigs, other animals, and humans in China.
MICROBIAL PATHOGENESIS
(2021)
Article
Computer Science, Theory & Methods
Zhabiz Gharibshah, Xingquan Zhu
Summary: This survey provides a comprehensive review of user response prediction in online advertising and related recommender applications. It covers the ecosystem, stakeholders, data availability, and prediction methods in online advertising platforms. A taxonomy is proposed to categorize machine learning methods used in different online platforms, and applications and resources in the field are also reviewed.
ACM COMPUTING SURVEYS
(2022)
Article
Immunology
Xia-Xia Liang, Yang Zou, Tao-Shan Li, Hong Chen, Sha-Sha Wang, Fu-Qiong Cao, Jian-Fa Yang, Xiao-Lin Sun, Xing-Quan Zhu, Feng-Cai Zou
Summary: This study investigated the prevalence and characterization of Giardia duodenalis and Cryptosporidium spp. in Yunling cattle in Yunnan province, China. The overall prevalence of G. duodenalis was 10.49% and Cryptosporidium spp. was 0.77%. Age was identified as a risk factor for G. duodenalis infection in Yunling cattle. Two assemblages of G. duodenalis and two species of Cryptosporidium were identified using nested PCR methods. This study provides baseline data for further research on the prevalence, genetic identity, and public health implications of these parasites in Yunling cattle.
MICROBIAL PATHOGENESIS
(2021)
Article
Microbiology
Yu-Gui Wang, Yang Zou, Ze-Zhong Yu, Dan Chen, Bin-Ze Gui, Jian-Fa Yang, Xing-Quan Zhu, Guo-Hua Liu, Feng-Cai Zou
Summary: This study investigated the prevalence and genotypes of Giardia duodenalis, Enterocytozoon bieneusi, and Cryptosporidium spp. in pet dogs and cats in Yunnan province, southwestern China. The results showed a higher prevalence and genetic diversity in dogs compared to cats, with potential zoonotic threats posed by both pet dogs and cats.
Article
Mathematical & Computational Biology
Magdalyn E. Elkin, Xingquan Zhu
Summary: Clinical trials are essential for medical advancement, but there is limited analysis of the valuable data from ClinicalTrials.gov. This study uses network analysis to understand infectious disease clinical trials, focusing on summarizing research areas and recommending clinical trials to sponsors.
NETWORK MODELING AND ANALYSIS IN HEALTH INFORMATICS AND BIOINFORMATICS
(2021)
Article
Genetics & Heredity
Meilin Hao, Juncai Jiang, Yongyun Zhang, Shaoqing Wang, Guowen Fu, Fengcai Zou, Yuxiao Xie, Sumei Zhao, Weizhen Li
Summary: This study utilized RNA-seq to analyze the mammary tissue transcriptomics of water buffalo with different milk fat phenotypes, revealing differentially expressed genes (DEGs). The results indicated similar gene expression patterns between high and medium fat buffalo, with the identified DEGs involved in milk protein and fat synthesis as well as immune response.
Article
Computer Science, Artificial Intelligence
Youxi Wu, Meng Geng, Yan Li, Lei Guo, Zhao Li, Philippe Fournier-Viger, Xingquan Zhu, Xindong Wu
Summary: Nonoverlapping sequential pattern mining aims at identifying repetitive patterns in a set of discrete sequences. Compared with overlapping patterns, nonoverlapping patterns have stricter constraints on occurrences and meet the Apriori property. This paper proposes an efficient algorithm for mining high average utility nonoverlapping sequential patterns, demonstrating its efficiency and superiority through experiments.
KNOWLEDGE-BASED SYSTEMS
(2021)
Article
Agriculture, Dairy & Animal Science
Hai-Yang Song, Kai-Sheng Wang, Jian-Fa Yang, Hua-Ming Mao, Li-Hua Pu, Yang Zou, Jun Ma, Xing-Quan Zhu, Feng-Cai Zou, Jun-Jun He
Summary: This study reported the prevalence and genotype distribution of Enterocytozoon bieneusi in dairy cattle in Yunnan province, China, identifying two novel zoonotic potential genotypes. Despite the low prevalence in dairy cattle, they may still pose a risk for transmitting E. bieneusi to humans. These findings are crucial for the development of effective prevention strategies for microsporidiosis.
Proceedings Paper
Computer Science, Information Systems
Shuwen Wang, Magdalyn E. Elkin, Xingquan Zhu
11TH IEEE INTERNATIONAL CONFERENCE ON KNOWLEDGE GRAPH (ICKG 2020)
(2020)
Proceedings Paper
Computer Science, Information Systems
Zhabiz Gharibshah, Xingquan Zhu
11TH IEEE INTERNATIONAL CONFERENCE ON KNOWLEDGE GRAPH (ICKG 2020)
(2020)
Proceedings Paper
Computer Science, Information Systems
Lukasz Chmielewski, Rafina Amin, Anak Wannaphaschaiyong, Xingquan Zhu
11TH IEEE INTERNATIONAL CONFERENCE ON KNOWLEDGE GRAPH (ICKG 2020)
(2020)
Article
Computer Science, Information Systems
Zhabiz Gharibshah, Xingquan Zhu, Arthur Hainline, Michael Conway
DATA SCIENCE AND ENGINEERING
(2020)