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Proteomics study of Mycoplasma pneumoniae pneumonia reveals the Fc fragment of the IgG-binding protein

《医学前沿（英文）》 2022年 第16卷 第3期   页码 378-388 doi: 10.1007/s11684-021-0840-y

摘要： Macrolide and corticosteroid resistance has been reported in patients with Mycoplasma pneumoniae (MP) pneumonia (MPP). MP clearance is difficult to achieve through antibiotic treatment in sensitive patients with severe MPP (SMPP). SMPP in children might progress to airway remodeling and even bronchiolitis/bronchitis obliterans. Therefore, identifying serum biomarkers that indicate MPP progression and exploring new targeted drugs for SMPP treatment require urgency. In this study, serum samples were collected from patients with general MPP (GMPP) and SMPP to conduct proteomics profiling. The Fc fragment of the IgG-binding protein (FCGBP) was identified as the most promising indicator of SMPP. Biological enrichment analysis indicated uncontrolled inflammation in SMPP. ELISA results proved that the FCGBP level in patients with SMPP was substantially higher than that in patients with GMPP. Furthermore, the FCGBP levels showed a decreasing trend in patients with GMPP but the opposite trend in patients with SMPP during disease progression. Connectivity map analyses identified 25 possible targeted drugs for SMPP treatment. Among them, a mechanistic target of rapamycin kinase (mTOR) inhibitor, which is a macrolide compound and a cell proliferation inhibitor, was the most promising candidate for targeting SMPP. To our knowledge, this study was the first proteomics-based characterization of patients with SMPP and GMPP.

关键词： severe Mycoplasma pneumoniae pneumonia     children     proteomics     Fc fragment of the IgG-binding protein     mechanistic target of rapamycin kinase inhibitor    

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Atomistic characterization of binding modes and affinity of peptide inhibitors to amyloid-

Fufeng LIU,Wenjie DU,Yan SUN,Jie ZHENG,Xiaoyan DONG

《化学科学与工程前沿（英文）》 2014年 第8卷 第4期   页码 433-444 doi: 10.1007/s11705-014-1454-6

摘要： The aggregation of amyloid -protein (A ) is tightly linked to the pathogenesis of Alzheimer’s disease. Previous studies have found that three peptide inhibitors (i.e., KLVFF, VVIA, and LPFFD) can inhibit A aggregation and alleviate A -induced neurotoxicity. However, atomic details of binding modes and binding affinities between these peptide inhibitors and A have not been revealed. Here, using molecular dynamics simulations and molecular mechanics Poisson Boltzmann surface area (MM/PBSA) analysis, we examined the effect of three peptide inhibitors (KLVFF, VVIA, and LPFFD) on their sequence-specific interactions with A and the molecular basis of their inhibition. All inhibitors exhibit varied binding affinity to A , in which KLVFF has the highest binding affinity, whereas LPFFD has the least. MM/PBSA analysis further revealed that different peptide inhibitors have different modes of interaction with A , consequently hotspot binding residues, and underlying driving forces. Specific residue-based interactions between inhibitors and A were determined and compared for illustrating different binding and inhibition mechanisms. This work provides structure-based binding information for further modification and optimization of these three peptide inhibitors to enhance their binding and inhibitory abilities against A aggregation.

关键词： Alzheimer’s disease     amyloid β-protein     peptide inhibitors     protein-protein interaction     molecular dynamics simulation    

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Correlativity study between expression of DNA double-strand break repair protein and radiosensitivity

Liang ZHUANG, Shiying YU, Xiaoyuan HUANG, Yang CAO, Huihua XIONG

《医学前沿（英文）》 2009年 第3卷 第1期   页码 26-29 doi: 10.1007/s11684-009-0008-7

摘要： DNA double-strand break (DSB) is generally regarded as the most lethal of all DNA lesions after radiation. Ku80, DNA-PK catalytic subunit (DNA-PKcs) and ataxia telangiectasia mutated (ATM) proteins are major DSB repair proteins. In this study, survival fraction at 2Gy (SF2) values of eight human tumor cell lines (including four human cervical carcinoma cell lines HeLa, SiHa, C33A, Caski, three human breast carcinoma cell lines MCF-7, MDA-MB-231, MDA-MB-453, and one human lung carcinoma cell line A549) were acquired by clone formation assay, and western blot was applied to detect the expressions of Ku80, DNA-PKcs and ATM protein. The correlativity of protein expression with SF2 value was analyzed by Pearson linear correlation analysis. We found that the expression of same protein in different cell lines and the expression of three proteins in the same cell line had a significant difference. The SF2 values were also different in eight tumor cell lines and there was a positive correlativity between the expression of DNA-PKcs and SF2 ( ＝0.723, = 0.043), but Ku80 and ATM expression had no correlation with SF2 ( >0.05). These findings suggest that the expression level of DNA-PKcs protein can be an indicator for predicting the radiosensitivity of tumor cells.

关键词： Ku80     DNA-PK(cs)-binding protein     human     ataxia telangiectasia mutated protein     tumor cell lines     radiosensitivity    

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Control of lupus activity during pregnancy via the engagement of IgG sialylation: novel crosstalk betweenIgG sialylation and pDC functions

《医学前沿（英文）》 2023年 第17卷 第3期   页码 549-561 doi: 10.1007/s11684-022-0965-7

摘要： Immunoglobulin (IgG) glycosylation affects the effector functions of IgG in a myriad of biological processes and has been closely associated with numerous autoimmune diseases, including systemic lupus erythematosus (SLE), thus underlining the pathogenic role of glycosylation aberration in autoimmunity. This study aims to explore the relationship between IgG sialylation patterns and lupus pregnancy. Relative to that in serum samples from the control cohort, IgG sialylation level was aberrantly downregulated in serum samples from the SLE cohort at four stages (from preconception to the third trimester of pregnancy) and was significantly associated with lupus activity and fetal loss during lupus pregnancy. The type I interferon signature of pregnant patients with SLE was negatively correlated with the level of IgG sialylation. The lack of sialylation dampened the ability of IgG to suppress the functions of plasmacytoid dendritic cells (pDCs). RNA-seq analysis further revealed that the expression of genes associated with the spleen tyrosine kinase (SYK) signaling pathway significantly differed between IgG- and deSia-IgG-treated pDCs. This finding was confirmed by the attenuation of the ability to phosphorylate SYK and BLNK in deSia-IgG. Finally, the coculture of pDCs isolated from pregnant patients with SLE with IgG/deSia-IgG demonstrated the sialylation-dependent anti-inflammatory function of IgG. Our findings suggested that IgG influences lupus activity through regulating pDCs function via the modulation of the SYK pathway in a sialic acid-dependent manner.

关键词： pregnancy     IgG glycome     type I interferon     systemic lupus erythematosus    

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Protein adsorption in two-dimensional electrochromatography packed with superporous and microporous cellulose

Dongmei WANG, Guodong JIA, Liang XU, Xiaoyan DONG, Yan SUN

《化学科学与工程前沿（英文）》 2009年 第3卷 第3期   页码 229-234 doi: 10.1007/s11705-009-0213-6

摘要： Anion-exchange superporous cellulose (DEAE-SC) and microporous cellulose (DEAE-MC) adsorbents were packed in an electrochromatographic column, and the effect of external electric field (eEF) on the dynamic adsorption was investigated. The column was designed to provide longitudinal, transverse or 2-dimensional (2D) eEF. It was found that the electro-kinetic effect caused by the introduction of an electric field played an important role in the dynamic adsorption of bovine serum albumin to the adsorbents. The dynamic binding capacity (DBC) in the presence of 2D eEF was higher than in the presence of a one-dimensional eEF. The effect of flow velocity on the DBC of the two adsorbents was also demonstrated. It was found that the effect of electric field on the DEAE-MC column was more remarkable than that on the DEAE-SC column at the same flow rate, whereas the DEAE-SC column showed higher DBC and adsorption efficiency (AE) than the DEAE-MC column. With increasing flow rate, the DEAE-SC column could still offer high DBC and AE in the presence of the 2D eEF. For example, a DBC of 21.4 mg/mL and an AE of 57.7% were obtained even at a flow rate as high as 900 cm/h. The results indicate that the 2D electrochromatography packed with the superporous cellulose adsorbent is promising for high-speed protein chromatography.

关键词： electrochromatography     two-dimensional electric field     dynamic binding capacity     superporous cellulose bead     protein    

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Regulation of NLR stability in plant immunity

Tao WANG, Jiaxin LI, Qian-Hua SHEN

《农业科学与工程前沿（英文）》 2019年 第6卷 第2期   页码 97-104 doi: 10.15302/J-FASE-2018248

摘要：

Plant nucleotide binding domain and leucine-rich repeat (NLR) receptors recognize pathogen effectors directly or indirectly and mediate innate immune responses. NLR-mediated immunity also has direct impacts on plant growth and development, as well as yield and survival. The levels of NLR proteins are therefore intricately controlled in plants to balance defense responses and other processes. In recent years, the ubiquitination-26S proteasome system and the HSP90 chaperones have emerged as having key functions in the regulation of NLR stability. The N-end rule pathway of protein degradation is also directly linked to NLR stability. Recent progress in the regulation of NLR stability and turnover is summarized here, focusing on the key components and pathways.

关键词： E3 ubiquitin ligase     degradation     nucleotide-binding leucine-rich repeat receptor     plant immunity     proteasome     protein stability     ubiquitination    

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使用数据驱动模型优化抗体纯化策略 Article

刘松崧, Lazaros G. Papageorgiou

《工程（英文）》 2019年 第5卷 第6期   页码 1077-1092 doi: 10.1016/j.eng.2019.10.011

摘要：

本工作致力于抗体片段纯化过程的多尺度优化。优化了生产过程中的色谱决策，包括色谱柱的数量及其大小，每批的循环数以及操作流速。使用基于微型实验数据的制造规模模拟数据集，建立了以负载质量、流速和柱床高度为输入的色谱通量数据驱动模型。与其他方法相比，分段线性回归建模方法具有简单、预测精度高的优点。提出了两种混合整数非线性规划（MINLP）模型，结合数据驱动模型，以最小化每克抗体纯化过程的总成本。然后，使用线性化技术和多参数分解将这些MINLP模型重新构造为混合整数线性规划（MILP）模型。研究了两个具有不同色谱柱尺寸替代品的工业相关案例，以证明所提出模型的适用性。

关键词： 抗体纯化     多尺度优化     抗原结合片段     混合整数规划     数据驱动模型     分段线性回归    

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Effects of resistin on insulin signaling in endothelial cells

Zhizhen LI, Fangping LI, Jianhong YE, Li YAN, Zuzhi FU

《医学前沿（英文）》 2009年 第3卷 第2期   页码 136-140 doi: 10.1007/s11684-009-0029-2

摘要： The objective of this study was to investigate the effects of resistin on insulin signaling in human umbilical vein endothelial cells (HUVECs). HUVECs were incubated with recombinant human resistin (0-100 ng/mL) for 24 h. Akt and endothelial nitric oxide synthase (eNOS) phosphorylation levels of endothelial cells under basal or insulin stimulated conditions were measured by Western blot. Nitric oxide (NO) production of HUVECs was also detected. The results showed that resistin could significantly inhibit Akt and eNOS phosphorylation and NO production in endothelial cells under insulin stimulated conditions ( < 0.05 control). But under basal conditions, treatment with resistin could result in a decrease in eNOS phosphorylation ( < 0.05 control) but had no effect on NO production and Akt phosphorylation levels. These findings suggested that resistin exerted an inhibitory effect on NO production by inhibiting insulin signaling and eNOS phosphorylation in endothelial cells.

关键词： resistin     endothelium     nitric oxide     endothelial nitric oxide synthase     Akt-binding protein     mouse    

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High-level expression of recombinant IgG1 by CHO K1 platform

Ningning Xu, Jianfa Ou, Al-Karim (Al) Gilani, Lufang Zhou, Margaret Liu

《化学科学与工程前沿（英文）》 2015年 第9卷 第3期   页码 376-380 doi: 10.1007/s11705-015-1531-5

摘要： The Chinese Hamster Ovary (CHO K1) cell was used to express a targeted anti-cancer monoclonal antibody by optimizing the platform of the construction of production cell line in this study. The adherent CHO K1 was first adapted to suspension culture in chemical defined medium. Then the glutamine synthetase (GS) vector was applied to construct a single plasmid to overexpress a monoclonal antibody IgG1. Post transfection, the production of cell pool was optimized by glutamine-free selection and amplification using various concentrations of methionine sulfoximine. The best cell pool of CHO K1/IgG1 was used to screen the top single clone using the limiting dilution cloning. Finally, a high IgG1 production of 780 mg/L was obtained from a batch culture. This study demonstrated that the construction of high producing cell line, from gene to clone, could be completed within six month and the gene amplification improved protein production greatly.

关键词： Chinese hamster ovary (CHO)     monoclonal antibody     IgG1     amplification     cell line development    

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CD176 single-chain variable antibody fragment inhibits the adhesion of cancer cells to endothelial cells

null

《医学前沿（英文）》 2016年 第10卷 第2期   页码 204-211 doi: 10.1007/s11684-016-0443-1

摘要：

CD176 (Thomsen-Friedenreich antigen) is a tumor-associated carbohydrate epitope (glycotope) functionally involved in blood spread and liver metastasis of cancer cells by mediating the adhesion of cancer cells to endothelial cells and hepatocytes, respectively. CD176 could be a promising target for antitumor immunotherapy. We applied B lymphocytes obtained from mice immunized with CD176 antigen and constructed a phage display library. A positive clone of CD176 single-chain variable antibody fragment (scFv) was successfully screened from this library. The CD176 scFv was expressed in Escherichia coli and purified. The purified scFv can bind to the natural CD176 expressed on the surface of cancer cells. Furthermore, the CD176 scFv inhibits the adhesion of CD176+ cancer cells to endothelial cells and hepatocytes. This CD176 scFv provides a basis for future development of recombinant CD176-specific antibodies that can be used in therapeutic application.

关键词： CD176     Thomsen-Friedenreich antigen     scFv     cancer     therapy     adhesion     metastasis    

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Chloride binding and time-dependent surface chloride content models for fly ash concrete

S. MUTHULINGAM,B. N. RAO

《结构与土木工程前沿（英文）》 2016年 第10卷 第1期   页码 112-120 doi: 10.1007/s11709-015-0322-x

摘要： Corrosion of embedded rebars is a classical deterioration mechanism of reinforced concrete structures exposed to chloride environments. Such environments can be attributed to the presence of seawater, deicing or sea-salts, which have high concentrations of chloride ion. Chloride ingress into concrete, essential for inducing rebar corrosion, is a complex interaction between many physical and chemical processes. The current study proposes two chloride ingress parameter models for fly ash concrete, namely: 1) surface chloride content under tidal exposure condition; and 2) chloride binding. First, inconsistencies in surface chloride content and chloride binding models reported in literature, due to them not being in line with past research studies, are pointed out. Secondly, to avoid such inconsistencies, surface chloride content and chloride binding models for fly ash concrete are proposed based upon the experimental work done by other researchers. It is observed that, proposed models are simple, consistent and in line with past research studies reported in literature.

关键词： binding isotherms     chloride ingress     concrete     fly ash     surface chloride content    

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Expression status of GATA3 and mismatch repair proteins in upper tract urothelial carcinoma

Yue Wang, Jinxia Zhang, Yunfan Wang, Shufang Wang, Yu Zhang, Qi Miao, Fei Gao, Huiying He

《医学前沿（英文）》 2019年 第13卷 第6期   页码 730-740 doi: 10.1007/s11684-019-0687-7

摘要： GATA binding protein 3 (GATA3) and mismatch repair (MMR) deficiency contribute to the development of urothelial carcinoma. However, the combined expression of GATA3 and microsatellite instability (MSI) in upper tract urothelial carcinoma (UTUC) and its prognostic value have not been investigated. Here, we immunohistochemically stained GATA3 and MMR proteins in 108 UTUC samples. GATA3 was positive in 74 cases, and its expression was significantly lower than in adjacent benign urothelium ( <0.001). Loss of GATA3 expression was statistically associated with adverse clinicopathologic parameters, such as advanced stage, lymphovascular invasion, neural invasion, lymph node metastasis, and extensive necrosis. Cancer-specific survival (CSS, =0.028) and disease-free survival (DFS, =0.024) were significantly shorter in patients with GATA3 negative tumors than in patients with GATA3 positive tumors. The absence of MMR proteins was observed in 8.3% of the cases, and focal staining was identified in 13.0%. When using “lax criteria” which resulted in counting cases as negative where MMR staining was in fact focally positive (<5%), we found that GATA3 was inversely associated with MSI ( =0.005). Moreover, GATA3 /microsatellite stability (MS) tumors were correlated with advanced pT stage ( <0.001) and poor outcome ( =0.019 for CSS, =0.016 for DFS) compared with GATA3 /MSI ones. The GATA3 /MSI cases had unfavorable clinical outcomes compared with GATA3 /MSI cases ( =0.008 for CSS, =0.023 for DFS). This finding raises a question as to whether GATA3 interacts with MSI through the TGF- signaling pathway and regulates UTUC progression.

关键词： upper tract urothelial carcinoma     GATA binding protein 3     mismatch repair     microsatellite instability     prognosis    

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IgG N-糖基心血管年龄独立于真实年龄精准表征心血管事件风险 Article

武志远, 郭政, 郑雨露, 王玉涛, 张海平, 潘慧颖, 李志伟, Lois Balmer, 李霞, 陶丽新, 郭秀花, 王嵬

《工程（英文）》 2023年 第26卷 第7期   页码 99-107 doi: 10.1016/j.eng.2022.12.004

摘要：

亚临床动脉粥样硬化和代谢紊乱是心血管健康的重要风险因素，应用免疫球蛋白G（IgG）N-聚糖模式作为炎症指标表征其发病风险已有研究报道然而，对于IgG N-糖基谱在心血管疾病（CVD）风险分层中的能力仍然未知。本研究旨在利用IgG N-糖基标志物开发追踪心血管疾病风险的年龄指数。使用机器学习递归特征消除和惩罚回归算法逐步筛选特征糖基，并开发IgG N-糖基化心血管年龄（GlyCage）指数，以反映归因于心血管风险的与真实年龄间的偏差。因此，本研究开发的GlyCage指数利用IgG N-糖基谱追踪心血管健康水平。GlyCage和真实年龄之间的差距能够独立地表征心血管风险，提示IgG N-糖基化在心血管疾病的发病机制中起作用。

关键词： IgG     N-糖基心血管年龄     心血管年龄     免疫球蛋白G     糖基化     炎症     特征选择     机器学习    

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reduces IgE binding ability of allergenic egg white proteins

Sen LI, Marina OFFENGENDEN, Michael G. GÄNZLE, Jianping WU

《农业科学与工程前沿（英文）》 2018年 第5卷 第3期   页码 373-381 doi: 10.15302/J-FASE-2018210

摘要：

Egg white proteins are one of the major allergens. The objective of this study was to investigate the effect of Aspergillus oryzae cultivation on IgE binding ability of egg white proteins. Effect of A. oryzae on egg white proteins was determined using ninhydrin method, SDS-PAGE, ELISA, fluorescence FITC labeling, MALDI-TOF-MS and LC-MS/MS analysis. Adding mycelium of A. oryzae ATCC 1011 and 16868 substantially reduced the IgE binding ability of acidified egg white after 24 h incubation. The binding capacity of egg white proteins to IgE in plasma from four egg allergy patients was almost completely lost after incubation with mycelium of ATCC 16868. Results from SDS-PAGE, free amino acid analysis, MALDI-TOF-MS and LC-MS/MS indicated that there was no substantial protein degradation during incubation. Therefore, the reduction of IgE binding ability of egg white proteins during A. oryzae treatment was probably due to a loss of ~1700 Da mass including a fragment of the ovomucoid N terminus.

关键词： Aspergillus oryzae     egg allergy     egg white proteins     IgE-binding ability     ovomucoid    

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Quantitative characterization of Cu binding potential of dissolved organic matter (DOM) in sediment from

Yuan ZHANG,Yan ZHANG,Tao YU

《环境科学与工程前沿（英文）》 2014年 第8卷 第5期   页码 666-674 doi: 10.1007/s11783-013-0608-y

摘要： Dissolved organic matter (DOM) plays an important role in heavy metal speciation and distribution in the aquatic environment especially for eutrophic lakes which have higher DOM concentration. Taihu Lake is the third largest freshwater and a high eutrophic lake in the downstream of the Yangtze River, China. In the lake, frequent breakout of algae blooms greatly increased the concentration of different organic matters in the lake sediment. In this study, sediment samples were collected from various part of Taihu Lake to explore the spatial difference in the binding potential of DOM with Cu. The titration experiment was adopted to quantitatively characterize the interaction between Cu(II) and DOM extracted from Taihu Lake sediments using ion selective electrode (ISE) and fluorescence quenching technology. The ISE results showed that the exogenous DOM had higher binding ability than endogenous DOM, and DOM derived from aquatic macrophytes had a higher binding ability than that derived from algae. The fluorescence quenching results indicated that humic substances played a key role in the complexation between DOM and Cu(II) in the lake. However, because of the frequent breakout of algae blooms, protein-like matters are also main component like humic matters in Taihu Lake. Therefore, the metals bound by protein-like substances should be caused concern as protein-like substances in DOM were unstable and they will release bound metal when decomposed.

关键词： binding ability     dissolved organic matters     fluorescence quenching     complex capacity     Taihu Lake    

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标题 作者 时间 类型 操作

Proteomics study of Mycoplasma pneumoniae pneumonia reveals the Fc fragment of the IgG-binding protein

期刊论文

Atomistic characterization of binding modes and affinity of peptide inhibitors to amyloid-

Fufeng LIU,Wenjie DU,Yan SUN,Jie ZHENG,Xiaoyan DONG

期刊论文

Correlativity study between expression of DNA double-strand break repair protein and radiosensitivity

Liang ZHUANG, Shiying YU, Xiaoyuan HUANG, Yang CAO, Huihua XIONG

期刊论文

Control of lupus activity during pregnancy via the engagement of IgG sialylation: novel crosstalk betweenIgG sialylation and pDC functions

期刊论文

Protein adsorption in two-dimensional electrochromatography packed with superporous and microporous cellulose

Dongmei WANG, Guodong JIA, Liang XU, Xiaoyan DONG, Yan SUN

期刊论文

Regulation of NLR stability in plant immunity

Tao WANG, Jiaxin LI, Qian-Hua SHEN

期刊论文

使用数据驱动模型优化抗体纯化策略

刘松崧, Lazaros G. Papageorgiou

期刊论文

Effects of resistin on insulin signaling in endothelial cells

Zhizhen LI, Fangping LI, Jianhong YE, Li YAN, Zuzhi FU

期刊论文

High-level expression of recombinant IgG1 by CHO K1 platform

Ningning Xu, Jianfa Ou, Al-Karim (Al) Gilani, Lufang Zhou, Margaret Liu

期刊论文

CD176 single-chain variable antibody fragment inhibits the adhesion of cancer cells to endothelial cells

null

期刊论文

Chloride binding and time-dependent surface chloride content models for fly ash concrete

S. MUTHULINGAM,B. N. RAO

期刊论文

Expression status of GATA3 and mismatch repair proteins in upper tract urothelial carcinoma

Yue Wang, Jinxia Zhang, Yunfan Wang, Shufang Wang, Yu Zhang, Qi Miao, Fei Gao, Huiying He

期刊论文

IgG N-糖基心血管年龄独立于真实年龄精准表征心血管事件风险

武志远, 郭政, 郑雨露, 王玉涛, 张海平, 潘慧颖, 李志伟, Lois Balmer, 李霞, 陶丽新, 郭秀花, 王嵬

期刊论文

reduces IgE binding ability of allergenic egg white proteins

Sen LI, Marina OFFENGENDEN, Michael G. GÄNZLE, Jianping WU

期刊论文

Quantitative characterization of Cu binding potential of dissolved organic matter (DOM) in sediment from

Yuan ZHANG,Yan ZHANG,Tao YU

期刊论文