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Journal of Beijing Institute of Technology 2023年第4期32卷 396-405页

作者： yijie guo Xiumin Shi Han Zhou School of Information and Electronics Beijing Institute of TechnologyBeijing 100081China

Drug target relationship(DTR)prediction is a rapidly evolving area of research in com-putational drug discovery.Despite recent advances in computational solutions that have overcome the challenges of in vitro and in vivo experiments,most computational methods still focus on binary classification.They ignore the importance of binding affinity,which correctly distinguishes between on-targets and off-targets.In this study,we propose a deep learning model based on the microstruc-ture of compounds and proteins to predict drug-target binding affinity(DTA),which utilizes topo-logical structure information of drug molecules and sequence semantic information of proteins.In this model,graph attention network(GAT)is used to capture the deep features of the compound molecular graph,and bidirectional long short-term memory(BiLSTM)network is used to extract the protein sequence features,and the pharmacological context of DTA is obtained by combining the two.The results show that the proposed model has achieved superior performance in both cor-rectly predicting the value of interaction strength and correctly discriminating the ranking of bind-ing strength compared to the state-of-the-art baselines.A case study experiment on COVID-19 con-firms that the proposed DTA model can be used as an effective pre-screening tool in drug discovery.

关键词： compound microstructure drug-target interaction binding affinity deep learning COVID-19

Differential Responses Between Monocytes and Monocyte-Derived Macrophages for Lipopolysaccharide Stimulation of Calves

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Cellular & Molecular Immunology 2009年第3期6卷 223-229页

作者： yijie guo guoqi Zhao Sachi Tanaka Takahiro Yamaguchi Laboratory of animal nutrition Graduate School of Animal Science and Technology Yangzhou University Wen Hui Road Jiangsu 225009 China Laboratory of Functional Morphology Graduate School of Agricultural Science Tohoku University 1-1 Tsutsumidori-Amamiyamachi Aobaku Sendai 981-8555 Japan

In this experiment Toll-like receptor expression pattern in monocytes and monocyte-derived macrophages by lipopolysaccharide （LPS） stimulation was examined. Jugular venous blood was collected from four Japanese calves, and the peripheral blood mononuclear cells （PBMCs） were isolated. The cells were directly used for collecting monocytes by magnetic cell sorting or cultured for 7 days to collect monocyte-derived macrophages in Repcell. Then we analyzed the mRNA expression pattern of TLRs and cytokines in monocytes and monocyte-derived macrophages after LPS stimulation for 24 h. LPS stimulation of both monocytes and monocyte-derived macrophages resulted in an increase in the levels of mRNA transcripts for TNF-α IL-6 and IL-8. Moreover, TNF-α and IL-6 mRNA expressions were significantly augmented by LPS stimulation in monocyte-derived macrophages. TLRs mRNA expressions were unchanged after LPS stimulation of monocytes, while TLRs mRNA expressions in monocyte-derived macrophages were complicated. TLR1, 3, 5, 8 and 10 were significantly decreased after LPS stimulation and there were no differences in the mRNA expressions of TLR2, 4, 6 and 7 between the groups of control and LPS stimulation. Besides, no expression of TLR9 was found. As antigen presenting cells, monocytes and monocyte-derived macrophages respond differently to LPS, so they may have different functions in the innate immune system.

关键词： Toll-like receptor monocyte monocyte-derived macrophage bovine

基于注意力机制的TCN-BiLSTM船舶轨迹预测

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计算机测量与控制 2024年第1期32卷 30-36页

作者：郭逸婕张君毅王鹏中国电子科技集团公司第54研究所石家庄050081 河北省电磁频谱认知与管控重点实验室石家庄050081

针对现有船舶轨迹预测模型预测准确度低的问题,提出一种基于注意力机制的时域卷积网络和双向长短时记忆网络结合的船舶轨迹预测模型;首先搭建TCN网络提取船舶轨迹的序列特征,之后将注意力机制引入网络调整不同属性特征的权值,突出对轨... 详细信息

针对现有船舶轨迹预测模型预测准确度低的问题,提出一种基于注意力机制的时域卷积网络和双向长短时记忆网络结合的船舶轨迹预测模型;首先搭建TCN网络提取船舶轨迹的序列特征,之后将注意力机制引入网络调整不同属性特征的权值,突出对轨迹预测影响更大的特征,最后搭建Bi-LSTM网络学习轨迹序列的前后状况来提取序列中更多的信息,实现对船舶未来轨迹的预测;通过实际船舶AIS数据对网络进行训练与测试实验,实验结果表明,TCN-ABiLSTM模型相比LSTM、Bi-LSTM和BiLSTM-Attention模型船舶轨迹预测精度更高,拟合程度更好,验证了所设计的TCN-ABiLSTM模型在船舶轨迹预测方面的的有效性和实用性。

关键词：轨迹预测时域卷积网络长短时记忆网络注意力机制 AIS

Survival, Proliferation and Cell Cycle of Swine Fibroblast after Infection with Salmonella enterica

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Advances in Microbiology 2016年第13期6卷 942-952页

作者： Mizuki Masuda yijie guo Kengo Kuroda Jun Xu Hiroshi Yoneyama Tomokazu Fukuda Bernard Mudenda Hang’ombe Katsuya Okuno Junko Nishimura Emiko Isogai Laboratory of Animal Microbiology Graduate School of Agricultural Science Tohoku University Sendai Japan Department of Immunobiology and Pathogenic Biology Medical School of Xi’an Jiaotong University Xi’an China Laboratory of Cell Engineering and Molecular Genetics Faculty of Science and Engineering Iwate University Morioka Japan Department of Clinical Microbiology School of Veterinary Medicine University of Zambia Lusaka Zambia Laboratory of Nutrition and Life Sciences Department of Biotechnology and Environmental Engineering Faculty of Engineering Hachinohe Institute of Technology Hachinohe Japan

Food-borne salmonellosis continues to be a major health concern worldwide. Carry-contamination of Salmonella frequently occurs in meat production. We focused on cell dynamics of swine fibroblasts after infection with Salmonella enterica serovar Enteritidis and Typhimurium, because fibroblast can be a target cell for Salmonella latent infection. It was found that both S. Enteritidis and S. Typhimurium were able to adhere and invade to swine fibroblasts. The proliferations in fibroblasts were different between each serovar. S. Enteritidis reached to the maximum at 24 hr after infection while S. Typhimurium did not. In addition, the decrease in the G0/G1 phase cells and increase in G2/M phase cells on the fibroblast were observed by both Salmonella infection. Cell death including apoptosis in the cells was inhibited by the infection of Salmonella. These results suggest that nontyphoidal Salmonella can survive for the long term by modifying bacterial cell proliferation and preventing cell death of host cells.

关键词： Salmonella enterica Fibroblast Swine Cell Death Cell Cycle

Leptospiral lipopolysaccharide induces cytokine production is toll-like receptor 2 dependent on bovine cells

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Leptospiral lipopolysaccharide induces cytokine production i...

3'-Deoxyadenosin alleviates methamphetamine-induced aberrant synaptic plasticity and seeking behavior by inhibiting the NLRP3 inflammasome

第十届全国免疫学学术大会

作者： yijie guo Jun Xu Jiru Xu Department of Pathogenic Microbiology and Immunology School of Basic Medical Sciences Xi'an Jiao Tong University Key Laboratory of Environment and Genes Related to Diseases Ministry of Education of ChinaXi'an Jiao Tong University Laboratory of Animal Microbiology Graduate School of Agricultural Science Tohoku University

Background:Bovine leptospirosis is a widespread infectious bacterial disease,causing serious economic losses and potential hazards to human health.Although it has been known that Leptospira species possess LPS,which responsible for the pathogenicity and inflammatory reactions associated with leptospirosis,little is known about the immune system of bovine respond to leptospiral LPS.Methods and materials:In this study,we evaluated leptospiral LPS-induced pro-inflammatory cytokine production in bovine fibroblasts by ELISA,and quantitatively measured gene and protein expression levels of TLR2 and TLR4,by applying real-time PCR and western blotting.In addition,the major TLRs were determined by the blocking test using antiTLRs antibodies.Escherichia coli LPS was used as the control.Results and discussions:Leptospiral LPS showed the ability to induce cytokine production in bovine fibroblasts and its induction was significantly suppressed by anti-TLR2 antibody.These results indicate that TLR2 is the main receptor of leptospiral LPS inducing cytokine production in bovine cells,while the cytokine induction by E.coli LPS was TLR2 and TLR4 dependent.This suggests that leptospiral LPS differs from E.coli LPS in its recognition receptor in bovine cells,and that the TLR2 dependent pathway might play a significant role in leptospiral LPS induced bovine chronic inflammatory disease.

关键词： Leptospiral lipopolysaccharide Toll-like receptors Bovine fibroblast

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Neural Regeneration Research 2024年第10期19卷 2270-2280页

作者： Yize Qi Yao Zhou Jiyang Li Fangyuan Zhu Gengni guo Can Wang Man Yu yijie Wang Tengfei Ma Shanwu Feng Li Zhou Institute for Stem Cell and Neural Regeneration and Key Laboratory of Cardiovascular&Cerebrovascular Medicine School of PharmacyNanjing Medical UniversityNanjingJiangsu ProvinceChina Department of Anesthesiology The Second People’s Hospital of LianyungangLianyungangJiangsu ProvinceChina Department of Anesthesiology Women’s Hospital of Nanjing Medical UniversityNanjing Maternity and Child Health Care HospitalNanjingJiangsu ProvinceChina

Methamphetamine addiction is a brain disorder characterized by persistent drug-seeking behavior, which has been linked with aberrant synaptic plasticity. An increasing body of evidence suggests that aberrant synaptic plasticity is associated with the activation of the NOD-like receptor family pyrin domain containing-3(NLRP3) inflammasome. 3′-Deoxyadenosin, an active component of the Chinese fungus Cordyceps militaris, has strong anti-inflammatory effects. However, whether 3′-deoxyadenosin attenuates methamphetamine-induced aberrant synaptic plasticity via an NLRP3-mediated inflammatory mechanism remains unclear. We first observed that 3′-deoxyadenosin attenuated conditioned place preference scores in methamphetamine-treated mice and decreased the expression of c-fos in hippocampal neurons. Furthermore, we found that 3′-deoxyadenosin reduced the aberrant potentiation of glutamatergic transmission and restored the methamphetamine-induced impairment of synaptic plasticity. We also found that 3′-deoxyadenosin decreased the expression of NLRP3 and neuronal injury. Importantly, a direct NLRP3 deficiency reduced methamphetamine-induced seeking behavior, attenuated the impaired synaptic plasticity, and prevented neuronal damage. Finally, NLRP3 activation reversed the effect of 3′-deoxyadenosin on behavior and synaptic plasticity, suggesting that the anti-neuroinflammatory mechanism of 3′-deoxyadenosin on aberrant synaptic plasticity reduces methamphetamine-induced seeking behavior. Taken together, 3′-deoxyadenosin alleviates methamphetamine-induced aberrant synaptic plasticity and seeking behavior by inhibiting the NLRP3 inflammasome.

关键词： 3′-deoxyadenosin hippocampus long-term potentiation methamphetamine NOD-like receptor family pyrin domain containing-3(NLRP3)inflammasome synaptic plasticity

Interpreting Larix principis-rupprechti radial growth in northern China based on the Vaganov-Shashkin model

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Journal of Forestry Research 2024年第3期35卷 99-110页

作者： Jiachuan Wang Shuheng Li Qiang Li Yili guo yijie Han Qi Liu Yiqi Zhao College of Urban and Environmental Sciences Northwest UniversityXi'an 710127People's Republic of China Institute of Global Environmental Change Xi'an Jiaotong UniversityXi'an 710049People's Republic of China Shaanxi Key Laboratory of Earth Surface System and Environmental Carrying Capacity Northwest UniversityXi'an 710127People's Republic of China State Key Laboratory of Loess and Quaternary Geology Institute of Earth EnvironmentChinese Academy of SciencesXi'an 710061People's Republic of China

Changes in annual radial growth is an important indication of climate change.Dendroclimatology studies in northern China have focused on linear statistical analysis,but lacking studies based on the process of ring formation to clarify the radial growth of trees.Tree-ring width standard chronology(STD)was established using samples of Larix principis-rupprechti collected at 2303 m altitude on Luya Mountain.Using the Vaganov-Shashkin(VS)model to sim-ulate growth and development,the internal physiological mechanism of radial growth is identified.It was concluded that:(1)the growing season of L.principis-rupprechti was May to September;(2)soil moisture was a significant factor in the early and late growing seasons,and temperature was the dominant factor in its main growth period;and(3)formation of narrow ring widths was closely related to drought stress,the development of wide ring widths will be restricted by increasing future temperatures.The VS model is applicable for radial growth simulation of subalpine coniferous forests and for guiding the cultivation of local tree species inthe future.

关键词： Vaganov-Shashkin model Larix principis-rupprechti Tree-ring width Annual growth

Interpreting Larix principis-rupprechtii radial growth in northern China based on the Vaganov-Shashkin model

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Journal of Forestry Research 2024年第3期 100-111页

作者： Jiachuan Wang Shuheng Li Qiang Li Yili guo yijie Han Qi Liu Yiqi Zhao College of Urban and Environmental Sciences Northwest University Institute of Global Environmental Change Xi'an Jiaotong University Shaanxi Key Laboratory of Earth Surface System and Environmental Carrying Capacity Northwest University State Key Laboratory of Loess and Quaternary Geology Institute of Earth Environment Chinese Academy of Sciences

Changes in annual radial growth is an important indication of climate change. Dendroclimatology studies in northern China have focused on linear statistical analysis,but lacking studies based on the process of ring formation to clarify the radial growth of trees. Tree-ring width standard chronology(STD) was established using samples of Larix principis-rupprechtii collected at 2303 m altitude on Luya Mountain. Using the Vaganov-Shashkin(VS) model to simulate growth and development, the internal physiological mechanism of radial growth is identified. It was concluded that:(1) the growing season of L. principis-rupprechtii was May to September;(2) soil moisture was a significant factor in the early and late growing seasons, and temperature was the dominant factor in its main growth period; and(3) formation of narrow ring widths was closely related to drought stress, the development of wide ring widths will be restricted by increasing future temperatures. The VS model is applicable for radial growth simulation of subalpine coniferous forests and for guiding the cultivation of local tree species in the future.

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Intact O-glycopeptide of haptoglobin in hepatocellular carcinoma

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Intact O-glycopeptide of haptoglobin in hepatocellular carci...

成人读者赋予动物形象的理解与寄托——以《格林童话》为例

2020年糖科学青年科技论坛

作者： Hong Shu Lei Zhang Yiwei Chen yijie guo Limin Li Xinyi Cao Zhao Cao guoquan Yan Chunlai Lu Chao Liu Shu Zhang Liver Cancer Institute Zhongshan HospitalFudan UniversityKey Laboratory of Carcinogenesis and Cancer InvasionMinistry of Education Department of Clinical Laboratory Cancer Hospital of Guangxi Medical University Institutes of Biomedical Sciences Fudan University Department of Thoracic Surgery Zhongshan HospitalFudan University Beijing Advanced Innovation Center for Precision Medicine Beihang University Department of Clinical Laboratory First Affiliated Hospital of Guangxi Medical University

Haptoglobin(Hp) is one of the acute-phase response proteins secreted by the liver [1] and its aberrant N-glycosylation was previously reported in hepatocellular carcinoma(HCC)[2].In this study,we aimed to discover and confirm its O-glycosylation in liver diseases based on lectin binding and mass spectrometry(MS) detection.First,serum Hp was purified from patients with liver cirrhosis(LC) and HCC,respectively.Then,five lectins with O-glycosylation specificity were chosen and lectin blot analysis showed that Hp in HCC bound to these lectins much stronger than that in LC.Furthermore,label-free quantification for intact O-glycopeptides of Hp was performed.Many intact O-glycopeptides were identified on Hp and most of them were elevated in HCC as compared to LC.Among them,the intensity of HYEGSTVEPKK(H1N1S1)corresponding to the glycopeptide of the Hp β chain was the highest in HCC patients.The O-glycosylation alteration was confirmed using MS quantification method based on O/O C-terminal labelling [3][4].Few studies on Hp O-glycosylation have been previously reported and our study may provide a comprehensive understanding of the glycosylation of Hp in HCC.

关键词： Haptoglobin O-glycosylation Mass spectrometry Lectin Hepatocellular carcinoma

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文化创新比较研究 2022年第23期6卷 25-28页

作者：郭一洁杨兰贵州大学贵州贵阳550000

童话是一个深受读者喜爱的文学体裁,童话中创造了各具特色的动物形象,而这些动物形象身上被赋予了成人读者的理解和多重含义。童话中的动物形象既受到儿童读者的欢迎,又引发成人读者的思考和分析。成人读者在陪伴儿童阅读童话时,会由动... 详细信息

童话是一个深受读者喜爱的文学体裁,童话中创造了各具特色的动物形象,而这些动物形象身上被赋予了成人读者的理解和多重含义。童话中的动物形象既受到儿童读者的欢迎,又引发成人读者的思考和分析。成人读者在陪伴儿童阅读童话时,会由动物形象反观自身进行思考和理解,并借用动物形象对儿童有所寄托。该文将以《格林童话》中的动物形象为例,从过去、现在、将来这三个维度探寻动物形象上所体现的成人读者的理解与寄托,以此更好地感知童话中的动物形象所蕴含的独特魅力。

关键词：动物形象理解寄托成人读者《格林童话》