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Integrated analysis of gut microbiome and host immune responses in COVID-19

《医学前沿（英文）》 2022年 第16卷 第2期   页码 263-275 doi: 10.1007/s11684-022-0921-6

摘要： Emerging evidence indicates that the gut microbiome contributes to the host immune response to infectious diseases. Here, to explore the role of the gut microbiome in the host immune responses in COVID-19, we conducted shotgun metagenomic sequencing and immune profiling of 14 severe/critical and 24 mild/moderate COVID-19 cases as well as 31 healthy control samples. We found that the diversity of the gut microbiome was reduced in severe/critical COVID-19 cases compared to mild/moderate ones. We identified the abundance of some gut microbes altered post-SARS-CoV-2 infection and related to disease severity, such as Enterococcus faecium, Coprococcus comes, Roseburia intestinalis, Akkermansia muciniphila, Bacteroides cellulosilyticus and Blautia obeum. We further analyzed the correlation between the abundance of gut microbes and host responses, and obtained a correlation map between clinical features of COVID-19 and 16 severity-related gut microbe, including Coprococcus comes that was positively correlated with CD3+/CD4+/CD8+ lymphocyte counts. In addition, an integrative analysis of gut microbiome and the transcriptome of peripheral blood mononuclear cells (PBMCs) showed that genes related to viral transcription and apoptosis were up-regulated in Coprococcus comes low samples. Moreover, a number of metabolic pathways in gut microbes were also found to be differentially enriched in severe/critical or mild/moderate COVID-19 cases, including the superpathways of polyamine biosynthesis II and sulfur oxidation that were suppressed in severe/critical COVID-19. Together, our study highlighted a potential regulatory role of severity related gut microbes in the immune response of host.

关键词： COVID-19     SARS-COV-2     gut microbiome     immune response    

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Host protection against Omicron BA.2.2 sublineages by prior vaccination in spring 2022 COVID-19 outbreak

《医学前沿（英文）》 2023年 第17卷 第3期   页码 562-575 doi: 10.1007/s11684-022-0977-3

摘要： The Omicron family of SARS-CoV-2 variants are currently driving the COVID-19 pandemic. Here we analyzed the clinical laboratory test results of 9911 Omicron BA.2.2 sublineages-infected symptomatic patients without earlier infection histories during a SARS-CoV-2 outbreak in Shanghai in spring 2022. Compared to an earlier patient cohort infected by SARS-CoV-2 prototype strains in 2020, BA.2.2 infection led to distinct fluctuations of pathophysiological markers in the peripheral blood. In particular, severe/critical cases of COVID-19 post BA.2.2 infection were associated with less pro-inflammatory macrophage activation and stronger interferon alpha response in the bronchoalveolar microenvironment. Importantly, the abnormal biomarkers were significantly subdued in individuals who had been immunized by 2 or 3 doses of SARS-CoV-2 prototype-inactivated vaccines, supporting the estimation of an overall 96.02% of protection rate against severe/critical disease in the 4854 cases in our BA.2.2 patient cohort with traceable vaccination records. Furthermore, even though age was a critical risk factor of the severity of COVID-19 post BA.2.2 infection, vaccination-elicited protection against severe/critical COVID-19 reached 90.15% in patients aged ≥ 60 years old. Together, our study delineates the pathophysiological features of Omicron BA.2.2 sublineages and demonstrates significant protection conferred by prior prototype-based inactivated vaccines.

关键词： SARS-CoV-2     COVID-19     host response     bronchoalveolar lavage fluid (BALF)    

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Gene and protein expression of proteinase-activated receptor-1, 2 in a murine model of acute graft host

Quan LI MD , Weiming LI MD , Ping ZOU MD , Jian ZHANG BM ,

《医学前沿（英文）》 2009年 第3卷 第3期   页码 309-315 doi: 10.1007/s11684-009-0043-4

摘要： Proteinase-activated receptors (PARs) are a novel subclass of seven transmembrane-spanning, G protein-coupled receptors. PAR-1 and PAR-2 are widely expressed in a variety of cells and are found to be involved in many physiological and pathological processes including inflammation and immune response. However, little is known about the function of PAR-1, 2 in acute graft host disease (GVHD). In the present study, we first detected the expression of PAR-1, 2 protein and mRNA in a murine model of acute GVHD using the methods of immunohistochemistry, Western blot and quantitative real-time polymerase chain reaction (PCR). Syngeneic hematopoietic stem cell transplantation (HSCT) mice served as controls. The relative gene expression level of PAR-1 was significantly increased in the skin, liver, small intestine of allogeneic HSCT mice (in skin: 0.039±0.013 0.008±0.002 of controls, =0.009; in liver: 0.165±0.006 0.017±0.006 of controls, =0.004; in small intestine: 0.215±0.009 0.016±0.002 of controls, =0.003), but not in the stomach, lung and kidney of allogeneic HSCT mice (>0.05). PAR-2 mRNA expression in the liver and small intestine of allogeneic HSCT mice (in liver: 0.010±0.002 0.003±0.001 of controls, =0.008; in small intestine: 0.006±0.001 0.003±0.001 of controls, =0.024) was increased significantly, but PAR-2 mRNA expression in the other organs (>0.05) was not found to be significantly elevated. PAR-1, 2 protein expression was in accordance with the mRNA expression, as shown by Western blot. Using immunohistochemistry the present study demonstrated that there was strong PAR-1, 2 immunoreactivity in the epithelial cell and vascular endothelial cell of target organs of acute GVHD. Our findings of markedly increased expression of PAR-1, 2 in target organs of acute GVHD suggest that PAR-1 and PAR-2 may play an important role in the pathogenesis of acute GVHD.

关键词： graft vs host disease     proteinase-activated receptor     murine model     hematopoietic stem cell transplantation    

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Graft versus host disease after liver transplantation: A case report

Peng-Ji GAO, Xi-Sheng LENG, Dong WANG, Guang-Ming LI, Lei HUANG, Jie GAO, JI-Ye ZHU,

《医学前沿（英文）》 2010年 第4卷 第4期   页码 469-472 doi: 10.1007/s11684-010-0120-8

摘要： In documenting clinical experience in the diagnosis and treatment of graft host disease (GVHD), we retrospectively analyzed data of one case that has developed GVHD after liver transplantation. This patient exhibited fever, skin rash, and diarrhea on day 9 after liver transplantation. His liver function was normal. Skin biopsy showed scattered keratinocytes accompanied by satellite-like lymphocyte infiltration and basal cell liquefaction degeneration. After carefully analyzing the complications, we took the strategy of decreasing the dose of tacrolimus. Thereafter, the patient’s temperature decreased to normal, his skin rashes subsided, and his diarrhea was relieved. This case suggests that reducing the dosage of immunosuppressive agents can be an effective strategy for GVHD after liver transplantation.

关键词： liver transplantation     graft versus host disease    

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INTERFERENCE BY NON-HOST PLANT ROOTS AND ROOT EXUDATES IN THE INFECTION PROCESSES OF PHYTOPHTHORA NICOTIANAE

《农业科学与工程前沿（英文）》 2021年 第8卷 第3期   页码 447-459 doi: 10.15302/J-FASE-2021399

摘要：

Crop rotations are widely used because they can significantly reduce the incidence of pests and diseases. The interactions between non-host roots and pathogens may be key in the inhibition of soilborne pathogens in crop rotations. Interactions between fennel (Foeniculum vulgare) roots/root exudates and Phytophthora nicotianae were investigated because of the known allelopathy between fennel and tobacco (Nicotiana tabacum). The effects of the key compounds in the fennel rhizosphere on the mycelial growth and zoospore behavior of P. nicotianae were assessed. The roots of fennel attracted P. nicotianae zoospores and inhibited their motility and the germination of cystospores, with some cystospores rupturing. 4-ethylacetophenone, vanillin and N-formylpiperidine were consistently identified in the fennel rhizosphere and were found to interfere with the infection of P. nicotianae, especially vanillin. Hyphae treated with these compounds produced more abnormal branches and accumulated reactive oxygen species. These interspecific interactions between non-host roots and pathogens were found to be an important factor in the inhibition by fennel of infection by P. nicotianae.

 

关键词： fennel and tobacco rotation     infection behavior     Phytophthora nicotianae     reactive oxygen species     vanillin    

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新孢子虫病——分子流行病学及发病机制综述 Review

Asis Khan, Jahangheer S. Shaik, Patricia Sikorski, Jitender P. Dubey, Michael E. Grigg

《工程（英文）》 2020年 第6卷 第1期   页码 10-19 doi: 10.1016/j.eng.2019.02.010

摘要：

犬新孢子虫（Neospora caninum）是一种囊肿形成的原生动物寄生虫，它是世界范围内牛的流产和新生儿死亡的主要原因。犬新孢子虫具有广泛的中间宿主范围，其有性繁殖只在犬科动物中发生。另一种新孢子虫——休斯新孢子虫也已经被发现，它能导致马的脑髓炎。虽然分子流行病学研究尚处于起步阶段，但核糖体小亚单位RNA（small subunit ribosomal RNA, ssuRNA）和犬新孢子虫物种特异性DNA探针（pNc5）中的18S rRNA和ITS1区域已被广泛应用于区分新孢子虫和其他密切相关的顶复门寄生虫。虽然这些重复区域比管家或抗原基因具有更高的敏感性和特异性，但它们具有较低的区分能力，无法捕捉物种内部的多样性。同样，尽管多个小卫星或微卫星标记研究显示了新孢子虫体内清晰的地理亚结构，但由于不同等位基因的大小在微卫星位点上趋同（称为同形质），虫株往往被错误分类。只有一株名为N. caninum Liverpool（Nc-Liv）的虫株被进行基因组测序，并与其近亲弓形虫（Toxoplasma gondii）进行了比较。因此，需要基于全世界多个虫株的全基因组序列进行详细的群体基因组学研究，以便更好地了解新孢子虫目前的种群遗传结构，最终
确定能够更有效对抗牛新孢子虫病的疫苗候选者。本文的目的是概述我们目前对新孢子虫的分子流行病学和基因组学的理解，并将其与密切相关的顶复门寄生虫哈蒙球虫和弓形虫结合起来。

关键词： 新孢子虫病，分子流行病学，群体遗传学，基因组学，宿主反应，疫苗    

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Permeability and thermal conductivity of host compressed natural graphite for consolidated activated

Bo TIAN, Liwei WANG, Zhequan JIN, Ruzhu WANG

《能源前沿（英文）》 2011年 第5卷 第2期   页码 159-165 doi: 10.1007/s11708-011-0145-y

摘要： Permeability and thermal conductivity test units were set up to study the heat and mass transfer performance of the host material, i.e. expanded natural graphite (ENG), for consolidated activated carbon (AC) adsorbent. The permeability was tested with nitrogen as the gas source, and the thermal conductivity was studied using steady-state heat source method. The results showed that the values of permeability and thermal conductivity were 10 to 10 m and 1.7 to 3.2 W/(m·K), respectively, while the density compressed expanded natural graphite (CENG) varied from 100 to 500 kg/m . The permeability decreased with the increasing density of CENG, whereas the thermal conductivity increased with the increasing density of CENG. Then the thermal conductivity and permeability of granular AC were researched. It was discovered that the thermal conductivity of samples with different grain size almost kept constant at 0.36 W/(m·K) while the density was approximately 600 kg/m . This means that the thermal conductivity was not related to the grain size of AC. The thermal conductivity of CENG was improved by 5 to 10 times compared with that of granular AC. Such a result showed that CENG was a promising host material for AC to improve the heat transfer performance, while the mass transfer performance should be considered in different conditions for utilization of adsorbent.

关键词： permeability     thermal conductivity     expanded nature graphite     activated carbon    

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Risk factors for chronic graft-versus-host disease after anti-thymocyte globulin-based haploidentical

Meng Lv, Xiaohui Zhang, Lanping Xu, Yu Wang, Chenhua Yan, Huan Chen, Yuhong Chen, Wei Han, Fengrong Wang, Jingzhi Wang, Kaiyan Liu, Xiaojun Huang, Xiaodong Mo

《医学前沿（英文）》 2019年 第13卷 第6期   页码 667-679 doi: 10.1007/s11684-019-0702-z

摘要： Chronic graft-versus-host disease (cGVHD) is a major complication following unmanipulated haploidentical hematopoietic stem cell transplantation (haplo-HSCT). We aimed to identify the risk factors for cGVHD in patients who underwent anti-thymocyte globulin-based haplo-HSCT for acute myeloid leukemia ( =280). The diagnosis of cGVHD was in accordance with the National Institutes of Health consensus criteria. A total of 169 patients suffered from cGVHD. The patients who had 3 loci mismatched had a higher 8-year incidence of cGVHD (total, 66.0% vs. 53.7%, =0.031; moderate to severe, 42.4% vs. 30.1%, =0.036) than the patients who had 1 to 2 loci mismatched. The patients who had maternal donors had a higher 8-year incidence of moderate to severe cGVHD (49.2% vs. 32.9%, =0.024) compared with the patients who had other donors. The patients who had grades III to IV acute GVHD (aGVHD) had higher 8-year incidence of cGVHD (total, 88.0% vs. 50.4%, <0.001; moderate to severe, 68.0% vs. 27.0%, <0.001) compared with the patients without aGVHD. In multivariate analysis, grades III to IV aGVHD was the only independent risk factor for cGVHD. Thus, further interventions should be considered in patients with severe aGVHD to prevent cGVHD.

关键词： acute graft-versus-host disease     chronic graft-versus-host disease     National Institutes of Health consensus criteria     acute myeloid leukemia     anti-thymocyte globulin    

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A pooling strategy of a PCR-based assay to detect Angiostrongylus cantonensis in snail intermediate host

Fu-Rong WEI MS, Shan LV PhD, He-Xiang LIU, Ling HU, Yi ZHANG MS,

《医学前沿（英文）》 2010年 第4卷 第2期   页码 204-207 doi: 10.1007/s11684-010-0043-4

摘要： Pooling field specimens could reduce the number of assay and thus increase the efficiency in detecting and screening pathogen infections by polymerase chain reaction (PCR)-based assay. We investigated a pooling strategy in diagnosis of in Two settings of specimens were prepared, divided into portions and detected by multiplex PCR. Specimens A was 0.4490 g positive lung tissue of 28 larval nodes from four snails mixed with 1.310€g negative lung tissue from six snails and divided into 32 portions. Specimens B was 0.5448 g positive lung tissue with 26 larval nodes from two snails mixed with 1.092 g negative lung tissue from seven snails and divided into 48 portions. Repeated sampling was performed and sample size-accumulated positive rate curves were drawn. According to the sample size-accumulated positive rate curves, the appropriate sample size of the two specimens were 18 and 15, respectively, which is 0.36–0.58 to the total sample size. These test characteristics and the relevant factors to the sample size would need to be determined in much larger studies and more appropriately in field populations. The result indicates that the number of larval node is not the most important, nor the only factor to the sample size. It also implies the feasibility to detect in by pooling strategies.

关键词： Angiostrongylus cantonensis     Pomacea canaliculata     multiplex polymerase chain reaction     diagnosis     pooling    

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基于液-液界面的主-客体分子识别 Review

王贝贝, 陈浩, 刘倓, 史少伟, Thomas P. Russell

《工程（英文）》 2021年 第7卷 第5期   页码 603-614 doi: 10.1016/j.eng.2021.02.004

摘要：

由于动态和可逆的性质，主-客体识别作为一种非共价键相互作用，赋予了液-液界面独特的性质，包括刺激响应性和自调节性等。近年来，越来越多的研究致力于通过在液-液界面上集成功能性单元（如胶体粒子、聚合物）来构筑二维薄膜和微胶囊等超分子界面体系，这为物质封装、递送、双相反应器等领域提供了重要的发展机遇。在本文中，我们总结了近年来基于主-客体相互作用构筑超分子界面体系的研究进展，并对其制备方法、功能和应用进行了概述。

关键词： 液-液界面     自组装     主-客体化学     微胶囊    

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免疫调节细胞生物学及其在急性移植物抗宿主病预防或治疗中的临床应用 Review

Bruce R. Blazar

《工程（英文）》 2019年 第5卷 第1期   页码 98-105 doi: 10.1016/j.eng.2018.11.016

摘要：

预防和治疗移植物抗宿主病（GVHD）最常见的方法是尝试耗竭或抑制能介导或支持同种异体反应的T细胞；但这会导致T细胞受体功能缺陷，并因此对感染和肿瘤复发高度敏感。通常通过广泛使用反应性抗体来实现耗竭，而功能损坏通常在使用需长期给药（一般为6个月或更长时间）且具有明显副作用的药物后发生，这种药物可能不会导致供体T细胞对耐调节方案且携带宿主同种抗原的细胞产生耐受性（即无反应性）。随着对免疫系统稳态认识的深化，我们已能鉴定和表征具有免疫调节功能的细胞群。虽然这种细胞群通常比较少见，但可通过分离和扩增此类细胞的方法在移植后晚期增补供体移植物或进行输注，来抑制GVHD。本文将探讨GVHD模型中的生物学和临床前概念验证，以及现已发展至临床测试阶段的免疫调节细胞疗法对GVHD的疗效。

关键词： 移植物抗宿主病（GVHD）     免疫调节细胞     细胞疗法    

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一种新的融合本体和主机信息的改进禁忌搜索算法的主题爬虫方法 Research Article

刘景发1,王震1,2,钟国1,杨志和1

《信息与电子工程前沿（英文）》 2023年 第24卷 第6期   页码 859-875 doi: 10.1631/FITEE.2200315

摘要： 为解决传统主题爬虫方法存在的主题描述不完整和重复爬取已访问链接的问题，本文提出一种新的融合本体和主机信息的改进禁忌搜索算法的主题爬虫方法（FCITS_OH）。该方法基于形式概念分析（FCA）构建领域本体，在语义和知识层面描述主题。为避免重复爬取已访问的链接和扩大搜索范围，提出一种改进的禁忌搜索（ITS）算法和记忆主机信息的策略。此外，为改进未访问链接的主题相关性的评估方法，提出一种基于Web文本和链接结构的综合优先度评估方法。以旅游和暴雨灾害为主题的实验结果表明，对于不同的性能指标，所提出的爬虫方法优于文献中其它主题爬虫策略。

关键词： 主题爬虫；禁忌搜索算法；本体；主机信息；优先度评估    

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Interspecies transmission and evolution of the emerging coronaviruses: perspectives from bat physiology and protein spatial structure

Baicheng HUANG, Kegong TIAN

《农业科学与工程前沿（英文）》 2020年 第7卷 第2期   页码 218-226 doi: 10.15302/J-FASE-2020324

摘要：

Emergent coronaviruses (CoVs) such as SARS-CoV and MERS-CoV have posed great threats to public health worldwide over the past two decades. Currently, the emergence of SARS-CoV-2 as a pandemic causes greater public health concern. CoV diversity is due to the large size and replication mechanisms of the genomes together with having bats as their optimum natural hosts. The ecological behavior and unique immune characteristics of bats are optimal for the homologous recombination of CoVs. The relationship of spatial structural characteristics of the spike protein, a protein that is critical for recognition by host receptors, in different CoVs may provide evidence in explaining the coevolution of CoVs and their hosts. This information may help to enhance our understanding of CoV evolution and thus provide part of the basis of preparations for any future outbreaks.

关键词： bat     coronavirus     evolution     host receptor     spike protein     transmission    

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Development of a seismic design method based on response spectra for building structures

ZHOU Xiyuan, YU Ruifang

《结构与土木工程前沿（英文）》 2007年 第1卷 第2期   页码 129-141 doi: 10.1007/s11709-007-0014-2

摘要： The assumption and problem of the mode-superposition response spectrum method in seismic design code is discussed based on a brief review of the development of the seismic design method for building structures. The scope of application for the classical damping theory is analyzed and the necessity of the research on mode-superposition method for non-classical damping is presented. The progresses on the mode superposition response spectrum theory are discussed. This includes: 1) the complex mode superposition method (in real form) for the non-classically damped linear system and the general calculation formula for the application of code; 2) the complex complete quadratic combination (CCQC) method for the non-classically damped linear system, which is based on the same assumptions as in deducing the complete quadratic combination (CQC) method which is popularly used in seismic design codes of many countries; 3) the complex complete quadratic combination with three components (CCQC3) method, which is a generalization of the CCQC method to the case of multi-components and multiple-support seismic excitations and deducing corresponding method; 4) the approach for calculation of seismic response of the non-classically damped system with overcritical damping and the calculation method of seismic response for the linear system with multiple eigenvalues; 5) the time-dependent CCQC (t) algorithm considering nonstationary earthquake ground motion; 6) an applied and effective method to solve the low order complex vector basis for the large linear non-classically damped system, which can be expediently used in practice to avoid the unknown errors coming from the forced uncoupling method; 7) bringing forward the concept of partial quadratic combination in order to reduce the calculation amount of CQC and CCQC methods, and studying the primary estimation-criterion. The reasonability and applicable scope of these methods are also briefly discussed in this paper.

关键词： generalization     classical damping     mode-superposition response     calculation formula     damping theory    

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Confining pressure effect on dynamic response of high rockfill dam

Xuexing CAO, Yunlong HE, Kun XIONG,

《结构与土木工程前沿（英文）》 2010年 第4卷 第1期   页码 116-126 doi: 10.1007/s11709-010-0014-5

摘要： Studies show that the dynamic properties of rockfill are strongly dependent on the confining pressure. Therefore, confining pressure effect has become a very important factor in the seismic analysis of high rockfill dam. The relationships of dynamic shear modulus versus dynamic shear strain and damping ratio versus dynamic shear strain had been improved to a certain degree on the basic of widely used Hardin-Drnevich constitutive model in this paper. Then a new model that could consider confining pressure effect has been established. Regression analysis was carried out of the dynamic triaxial experimental data of the damming materials in the Changheba hydropower station of Sichun Province, China. The results show that, the new model can fit the test data well under various confining pressures. A corresponding computational procedure was compiled and applied in the dynamic response analysis of the Changheba Dam. Comparing the calculation results between the new constitutive model and the ordinary Hardin-Drnevich model, it can be seen that the result is conservative to some extent without considering confining pressure effect.

关键词： confining pressure effect     high rockfill dam     dynamic response     Hardin-Drnevich constitutive model    

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标题 作者 时间 类型 操作

Integrated analysis of gut microbiome and host immune responses in COVID-19

期刊论文

Host protection against Omicron BA.2.2 sublineages by prior vaccination in spring 2022 COVID-19 outbreak

期刊论文

Gene and protein expression of proteinase-activated receptor-1, 2 in a murine model of acute graft host

Quan LI MD , Weiming LI MD , Ping ZOU MD , Jian ZHANG BM ,

期刊论文

Graft versus host disease after liver transplantation: A case report

Peng-Ji GAO, Xi-Sheng LENG, Dong WANG, Guang-Ming LI, Lei HUANG, Jie GAO, JI-Ye ZHU,

期刊论文

INTERFERENCE BY NON-HOST PLANT ROOTS AND ROOT EXUDATES IN THE INFECTION PROCESSES OF PHYTOPHTHORA NICOTIANAE

期刊论文

新孢子虫病——分子流行病学及发病机制综述

Asis Khan, Jahangheer S. Shaik, Patricia Sikorski, Jitender P. Dubey, Michael E. Grigg

期刊论文

Permeability and thermal conductivity of host compressed natural graphite for consolidated activated

Bo TIAN, Liwei WANG, Zhequan JIN, Ruzhu WANG

期刊论文

Risk factors for chronic graft-versus-host disease after anti-thymocyte globulin-based haploidentical

Meng Lv, Xiaohui Zhang, Lanping Xu, Yu Wang, Chenhua Yan, Huan Chen, Yuhong Chen, Wei Han, Fengrong Wang, Jingzhi Wang, Kaiyan Liu, Xiaojun Huang, Xiaodong Mo

期刊论文

A pooling strategy of a PCR-based assay to detect Angiostrongylus cantonensis in snail intermediate host

Fu-Rong WEI MS, Shan LV PhD, He-Xiang LIU, Ling HU, Yi ZHANG MS,

期刊论文

基于液-液界面的主-客体分子识别

王贝贝, 陈浩, 刘倓, 史少伟, Thomas P. Russell

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