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Single-cell RNA-seq data analysis on the receptor ACE2 expression reveals the potential risk of different

Xin Zou, Ke Chen, Jiawei Zou, Peiyi Han, Jie Hao, Zeguang Han

《医学前沿（英文）》   页码 185-192 doi: 10.1007/s11684-020-0754-0

摘要：

It has been known that, the novel coronavirus, 2019-nCoV, which is considered similar to SARS-CoV and originated from Wuhan (China), invades human cells via the receptor angiotensin converting enzyme II (ACE2). Moreover, lung cells that have ACE2 expression may be the main target cells during 2019-nCoV infection. However, some patients also exhibit non-respiratory symptoms, such as kidney failure, implying that 2019-nCoV could also invade other organs. To construct a risk map of different human organs, we analyzed the single-cell RNA sequencing (scRNA-seq) datasets derived from major human physiological systems, including the respiratory, cardiovascular, digestive, and urinary systems. Through scRNA-seq data analyses, we identified the organs at risk, such as lung, heart, esophagus, kidney, bladder, and ileum, and located specific cell types (i.e., type II alveolar cells (AT2), myocardial cells, proximal tubule cells of the kidney, ileum and esophagus epithelial cells, and bladder urothelial cells), which are vulnerable to 2019-nCoV infection. Based on the findings, we constructed a risk map indicating the vulnerability of different organs to 2019-nCoV infection. This study may provide potential clues for further investigation of the pathogenesis and route of 2019-nCoV infection.

关键词： 2019-nCoV     ACE2     single-cell RNA-seq    

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锌空燃料电池电站

朱梅,徐献芝,苏润

《中国工程科学》 2004年 第6卷 第12期   页码 62-64

摘要：

燃料电池发电技术已经受到人们越来越多的重视。介绍了利用锌空气燃料电池技术建设电站，利用分体式电极技术制造世界上最大的单电池，该电站采用独特的分离循环技术，可以提高电站总体效率。给出建设电站的相关参数。

关键词： 燃料电池     锌空气燃料电池     分体式电极     单电池     分离循环技术    

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Distinct immune escape and microenvironment between RG-like and pri-OPC-like glioma revealed by single-cellRNA-seq analysis

《医学前沿（英文）》 doi: 10.1007/s11684-023-1017-7

摘要： The association of neurogenesis and gliogenesis with glioma remains unclear. By conducting single-cell RNA-seq analyses on 26 gliomas, we reported their classification into primitive oligodendrocyte precursor cell (pri-OPC)-like and radial glia (RG)-like tumors and validated it in a public cohort and TCGA glioma. The RG-like tumors exhibited wild-type isocitrate dehydrogenase and tended to carry EGFR mutations, and the pri-OPC-like ones were prone to carrying TP53 mutations. Tumor subclones only in pri-OPC-like tumors showed substantially down-regulated MHC-I genes, suggesting their distinct immune evasion programs. Furthermore, the two subgroups appeared to extensively modulate glioma-infiltrating lymphocytes in distinct manners. Some specific genes not expressed in normal immune cells were found in glioma-infiltrating lymphocytes. For example, glial/glioma stem cell markers OLIG1/PTPRZ1 and B cell-specific receptors IGLC2/IGKC were expressed in pri-OPC-like and RG-like glioma-infiltrating lymphocytes, respectively. Their expression was positively correlated with those of immune checkpoint genes (e.g., LGALS3) and poor survivals as validated by the increased expression of LGALS3 upon IGKC overexpression in Jurkat cells. This finding indicated a potential inhibitory role in tumor-infiltrating lymphocytes and could provide a new way of cancer immune evasion.

关键词： single-cell RNA-seq     glioma     radial glia     primitive oligodendrocyte precursor cell     immune escape    

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Transmembrane transport of polycyclic aromatic hydrocarbons by bacteria and functional regulation of membrane proteins

Hongqi Wang, Ruhan Jiang, Dekang Kong, Zili Liu, Xiaoxiong Wu, Jie Xu, Yi Li

《环境科学与工程前沿（英文）》 2020年 第14卷 第1期 doi: 10.1007/s11783-019-1188-2

摘要： Explaintheadsorption, uptake and transmembrane transport of PAHs by bacteria. Analyze functional regulation of membrane proteins inthe transmembrane transport. Proteomics technology such as iTRAQ labeling was used to access expressed proteins. Single cell analysis technology wereused to study the morphological structure. In recent years, increasing research has been conducted on transmembrane transport processes and the mechanisms behind the microbial breakdown of polycyclic aromatic hydrocarbons (PAHs), including the role of membrane proteins in transmembrane transport and the mode of transmission. This article explains the adsorption, uptake and transmembrane transport of PAHs by bacteria, the regulation of membrane protein function during the transmembrane transport. There are three different regulation mechanisms for uptake, depending on the state and size of the oil droplets relative to the size of the microbial cells, which are (i) direct adhesion, (ii) emulsification and pseudosolubilization, and (iii) interfacial uptake. Furthermore, two main transmembrane transport modes are introduced, which are (i) active transport and (ii) passive uptake and active efflux mechanism. Meanwhile, introduce the proteomics and single cell analysis technology used to address these areas of research, such as Isobaric tags for relative and absolute quantitation (iTRAQ) technology and Nano Secondary ion mass spectrometry (Nano-SIMS). Additionally, analyze the changes in morphology and structure and the characteristics of microbial cell membranes in the process of transmembrane transport. Finally, recognize the microscopic mechanism of PAHs biodegradation in terms of cell and membrane proteins are of great theoretical and practical significance for understanding the factors that influence the efficient degradation of PAHs contaminants in soil and for remediating the PAHs contamination in this area with biotechnology.

关键词： Polycyclic aromatic hydrocarbons     Transmembrane transport     Adsorption and uptake of hydrocarbons     Proteomics     Functional regulation of membrane protein     Single cell analysis technology    

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微生物组分析技术的发展趋势：从单细胞功能成像到菌群大数据

徐健, 马波, 苏晓泉, 黄适, 徐欣, 周学东, 黄巍, Rob Knight

《工程（英文）》 2017年 第3卷 第1期   页码 66-70 doi: 10.1016/J.ENG.2017.01.020

摘要：

方法学创新一直是微生物组学研究的核心驱动力。我们认为在未来五到十年，微生物组的方法学体系在研究理念与技术平台方面将发生三大变革：①从监测菌群“结构”变化向监测菌群“功能/状态”变化的变革；②从细胞“群体”分析精度向细胞“个体”分析精度的转变；③从“数据分析”向“数据科学”的跨越。在这里我们针对实现上述三大方法学变革需要克服的关键科学或技术挑战，重点介绍了部分中国微生物组分析方法学研究团队及其国际合作伙伴的最新工作进展。我们相信中国微生物组计划应把握住当前这一重要机遇，通过在微生物组分析方法学前沿开展富有雄心、远见、创意与竞争力的交叉合作研究，为国际微生物组计划贡献一系列“中国制造”的新方法、新工具和新仪器。

关键词： 微生物组     方法学创新     单细胞分析     大数据     中国微生物组计划    

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Computer-Aided Design System for CP Single-Screw Compressor

SHEN Jing-feng, YAO Fu-sheng

《机械工程前沿（英文）》 2006年 第1卷 第1期   页码 21-25 doi: 10.1007/s11465-005-0018-3

摘要：

To design various optimum parameters and simulate the working process of CP single-screw compressor, the Computer-Aided Design (CAD) system for the CP single-screw compressor has been established. A new method based on computer graphics technology, database technology, object-oriented programming technology, and visual simulation technology has been adopted in this CAD system. The system has integrated solid modeling function with parameterization design function and animator simulation function based on analyzing the working principle of the CP single-screw compressor. The experimental results show that the CAD system for the CP single-screw compressor is practical and feasible.

关键词： CP single-screw     database technology     simulation technology     programming technology     animator simulation    

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Distinct mononuclear diploid cardiac subpopulation with minimal cell–cell communications persists in

《医学前沿（英文）》   页码 939-956 doi: 10.1007/s11684-023-0987-9

摘要： A small proportion of mononuclear diploid cardiomyocytes (MNDCMs), with regeneration potential, could persist in adult mammalian heart. However, the heterogeneity of MNDCMs and changes during development remains to be illuminated. To this end, 12 645 cardiac cells were generated from embryonic day 17.5 and postnatal days 2 and 8 mice by single-cell RNA sequencing. Three cardiac developmental paths were identified: two switching to cardiomyocytes (CM) maturation with close CM–fibroblast (FB) communications and one maintaining MNDCM status with least CM–FB communications. Proliferative MNDCMs having interactions with macrophages and non-proliferative MNDCMs (non-pMNDCMs) with minimal cell–cell communications were identified in the third path. The non-pMNDCMs possessed distinct properties: the lowest mitochondrial metabolisms, the highest glycolysis, and high expression of Myl4 and Tnni1. Single-nucleus RNA sequencing and immunohistochemical staining further proved that the Myl4+Tnni1+ MNDCMs persisted in embryonic and adult hearts. These MNDCMs were mapped to the heart by integrating the spatial and single-cell transcriptomic data. In conclusion, a novel non-pMNDCM subpopulation with minimal cell–cell communications was unveiled, highlighting the importance of microenvironment contribution to CM fate during maturation. These findings could improve the understanding of MNDCM heterogeneity and cardiac development, thus providing new clues for approaches to effective cardiac regeneration.

关键词： mononuclear diploid cardiomyocytes     cell–cell communication     cardiac fibroblast     single-cell RNA sequencing     cardiac regeneration    

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PathogenTrack and Yeskit: tools for identifying intracellular pathogens from single-cell RNA-sequencing

《医学前沿（英文）》 2022年 第16卷 第2期   页码 251-262 doi: 10.1007/s11684-021-0915-9

摘要： Pathogenic microbes can induce cellular dysfunction, immune response, and cause infectious disease and other diseases including cancers. However, the cellular distributions of pathogens and their impact on host cells remain rarely explored due to the limited methods. Taking advantage of single-cell RNA-sequencing (scRNA-seq) analysis, we can assess the transcriptomic features at the single-cell level. Still, the tools used to interpret pathogens (such as viruses, bacteria, and fungi) at the single-cell level remain to be explored. Here, we introduced PathogenTrack, a python-based computational pipeline that uses unmapped scRNA-seq data to identify intracellular pathogens at the single-cell level. In addition, we established an R package named Yeskit to import, integrate, analyze, and interpret pathogen abundance and transcriptomic features in host cells. Robustness of these tools has been tested on various real and simulated scRNA-seq datasets. PathogenTrack is competitive to the state-of-the-art tools such as Viral-Track, and the first tools for identifying bacteria at the single-cell level. Using the raw data of bronchoalveolar lavage fluid samples (BALF) from COVID-19 patients in the SRA database, we found the SARS-CoV-2 virus exists in multiple cell types including epithelial cells and macrophages. SARS-CoV-2-positive neutrophils showed increased expression of genes related to type I interferon pathway and antigen presenting module. Additionally, we observed the Haemophilus parahaemolyticus in some macrophage and epithelial cells, indicating a co-infection of the bacterium in some severe cases of COVID-19. The PathogenTrack pipeline and the Yeskit package are publicly available at GitHub.

关键词： scRNA-seq     intracellular pathogen     microbe     COVID-19     SARS-CoV-2    

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Design and analysis of partially decoupled translational parallel mechanisms with single-loop structures

《机械工程前沿（英文）》 2022年 第17卷 第3期 doi: 10.1007/s11465-022-0695-1

摘要： This study presents a family of novel translational parallel mechanisms (TPMs) with single-loop topological structures. The proposed mechanism consists of only revolute and prismatic joints. The novel TPMs are simpler in structure and have fewer joints and components than the well-known Delta Robot. Four types of 2-degree of freedom driving systems are applied to different limb structures to avoid the moving actuator that causes the problem of increased moving mass. Four sample TPMs are constructed using the synthesized limbs, and one of them is investigated in terms of kinematic performance. First, a position analysis is performed and validated through numerical simulation to reveal the characteristics of partially decoupled motion, which improves the controllability of TPM. Second, singular configurations are identified, and the resulting singularity curve is obtained. Lastly, the workspace of TPM is analyzed, and the relationship between the singular configurations and the reachable workspace is explored. The workspace of the 3-CRR (C denotes the cylindrical joint and R denotes the revolute joint) translational mechanism is also presented to prove that the proposed TPM has a fairly large workspace.

关键词： translational parallel mechanism     single loop     multiple driving system     workspace analysis     singularity    

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Clinical characteristics and prognostic factors of patients with mature T-cell lymphoid malignancies:a single-institution study of 225 cases

null

《医学前沿（英文）》 2015年 第9卷 第4期   页码 468-477 doi: 10.1007/s11684-015-0419-6

摘要：

Mature T-cell lymphoid malignancies comprise a group of heterogeneous diseases that vary in clinicopathological features, biological behavior, treatment response, and prognosis. Bone marrow (BM) infiltration is more commonly present in mature T-cell lymphoid malignancies compared with their B-cell counterparts and hence important for differential diagnosis. In this study, clinical characteristics and prognostic factors were analyzed in 225 patients with mature T-cell lymphoid malignancies treated in a single institution. These included 29 cases of T-cell lymphoproliferative disorders (T-LPD, all with BM infiltration) and 196 cases of T-/natural-killer-cell lymphoma (T/NKCL, 56 with BM infiltration and 140 without BM infiltration). The estimated 5-year overall survival (OS) rates of T-LPD and T/NKCL were 96.6% and 37.3%, respectively. T-LPD patients were less likely to exhibit poor performance status, advanced disease stage, presence of B symptoms, or abnormal level of serum β-2 microglobulin. With similar pathological characteristics, T/NKCL patients with BM infiltration showed significantly lower response rates and shorter OS than those without BM infiltration (P = 0.0264 and P<0.0001, respectively). Multivariate analysis indicated that poor performance status, advanced disease stage, elevated serum lactate dehydrogenase level, and BM involvement were independent unfavorable prognostic factors. The Glasgow Prognostic Score may be more efficient than the International Prognostic Index in predicting disease outcome in T/NKCL. In conclusion, clinical characteristics may be useful in more effectively stratifying patients with mature T-cell lymphoid malignancies.

关键词： mature T-cell lymphoid malignancies     clonal T-cell population     bone marrow infiltration     prognostic factors    

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Numerical analysis of bearing behaviors of single batter piles under horizontal loads in various directions

《结构与土木工程前沿（英文）》 2023年 第17卷 第2期   页码 224-237 doi: 10.1007/s11709-022-0914-1

摘要： The horizontal bearing behavior of a single batter pile (SBP) is vital to its application in practical engineering; however, the horizontal responses of SBPs change with the directions of horizontal loads, and this phenomenon is rarely investigated. Therefore, the directional differences in the horizontal bearing behaviors of SBPs are investigated in this study. Four model tests are conducted to preliminarily examine the effects of the skew angle of horizontal loads on the horizontal bearing capacities and distributions of the bending moments of the SBPs. Subsequently, the differences in the responses of the SBPs under horizontal loads in various directions at full scale are analyzed comprehensively via finite-element (FE) analysis. The effects of the skew angle on SBP-soil interaction are discussed. Moreover, an empirical design method is proposed based on the FE analysis results to predict the bearing ratios of SBPs in medium-dense and dense sand while considering the effects of the skew angle, batter angle, and pile diameter. The method is confirmed to be effective, as confirmed by the close agreement between the predicting results with the model test (reported in this study) and centrifuge model test results (reported in the literature).

关键词： single batter pile     skew horizontal load     model test     finite-element analysis     empirical design method    

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Effects of vitrification and cryostorage duration on single-cell RNA-Seq profiling of vitrified-thawed

Ying Huo, Peng Yuan, Qingyuan Qin, Zhiqiang Yan, Liying Yan, Ping Liu, Rong Li, Jie Yan, Jie Qiao

《医学前沿（英文）》 2021年 第15卷 第1期   页码 144-154 doi: 10.1007/s11684-020-0792-7

摘要： Oocyte cryopreservation is widely used for clinical and social reasons. Previous studies have demonstrated that conventional slow-freezing cryopreservation procedures, but not storage time, can alter the gene expression profiles of frozen oocytes. Whether vitrification procedures and the related frozen storage durations have any effects on the transcriptomes of human metaphase II oocytes remain unknown. Four women (30–32 years old) who had undergone IVF treatment were recruited for this study. RNA-Seq profiles of 3 fresh oocytes and 13 surviving vitrified-thawed oocytes (3, 3, 4, and 3 oocytes were cryostored for 1, 2, 3, and 12 months) were analyzed at a single-cell resolution. A total of 1987 genes were differentially expressed in the 13 vitrified-thawed oocytes. However, no differentially expressed genes were found between any two groups among the 1-, 2-, 3-, and 12-month storage groups. Further analysis revealed that the aberrant genes in the vitrified oocytes were closely related to oogenesis and development. Our findings indicated that the effects of vitrification on the transcriptomes of mature human oocytes are induced by the procedure itself, suggesting that long-term cryostorage of human oocytes is safe.

关键词： human metaphase II oocyte     vitrification     cryostorage duration     single-cell RNA-Seq     lncRNA    

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A cytoprotective graphene oxide-polyelectrolytes nanoshell for single-cell encapsulation

Luanying He, Yulin Chang, Junhao Zhu, Ying Bi, Wenlin An, Yiyang Dong, Jia-Hui Liu, Shihui Wang

《化学科学与工程前沿（英文）》 2021年 第15卷 第2期   页码 410-420 doi: 10.1007/s11705-020-1950-9

摘要： Graphene oxide (GO) has been increasingly utilized in the fields of food, biomedicine, environment and other fields because of its benign biocompatible. We encapsulated two kinds of GO with different sizes on yeast cells with the assistance of polyelectrolytes poly (styrene sulfonic acid) sodium salt (PSS) and polyglutamic acid (PGA) (termed as Y@GO). The result does not show a significant difference between the properties of the two types of Y@GO (namely Y@GO1 and Y@GO2). The encapsulation layers are optimized as Yeast/PGA/PSS/PGA/GO/PGA/PSS based on the morphology, dispersity, colony-forming unit, and zeta potential. The encapsulation of GO increases the roughness of the yeast. It is proved that the Y@GO increases the survival time and enhance the activity of yeast cells. The GO shell improves the resistance of yeast cells against pH and salt stresses and extends the storage time of yeast cells.

关键词： GO     yeast     polyelectrolyte     cytoprotection     nanomaterials    

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intravenous busulfan conditioning with post-transplantation cyclophosphamide for allogeneic peripheral stem celltransplantation for adult patients with lymphoid malignancies: a prospective single-arm phase II study

Ling Wang, Lining Wang, Xing Fan, Wei Tang, Jiong Hu

《医学前沿（英文）》 2021年 第15卷 第1期   页码 108-115 doi: 10.1007/s11684-019-0730-8

摘要： Post-transplantation cyclophosphamide (PT-Cy) alone or in combination with other immunosuppressive drugs has emerged as a promising strategy in the setting of allogeneic hematopoietic stem cell transplantation. Improved survival rate was reported in lymphoid malignancies following PT-Cy strategy compared with myeloid disease in non-myeloablative bone marrow transplant setting. Thus, we aimed to evaluate the safety and efficacy of PT-Cy combined with cyclosporine as graft-versus-host disease (GVHD) prophylaxis after myeloablative conditioning and T cell-replete peripheral stem cell transplantation in lymphoid malignancies. This single-arm phase II clinical trial (NCT01435447) involving 31 adult patients was conducted from January 2013 to June 2018. The donor-type neutrophil engraftment rate was 100%, and the overall incidence of grade II to IV and grade III to IV acute GVHD was 39% and 24%, respectively. The cumulative incidence rates of chronic GVHD (35%), including moderate to severe forms (10%), were reduced compared with those of the historical group ( =0.03 and =0.04, respectively). With a median follow-up of 18 months, the estimated 2-year overall and event-free survival was 64.8% (95% confidence interval: 47.8%–86.7%) and 58.4% (95% CI: 41.9%–81.7%), respectively. The 2-year cumulative incidence rate of relapse was 19.5% (95% CI: 9.0%–35.8%), whereas the non-relapse mortality rate was 21.8% (95% CI: 11.3%–38.1%). These results demonstrated the feasibility of PT-Cy as GVHD prophylaxis in this clinical setting. This strategy could significantly reduce the incidence of chronic GVHD and its moderate to severe forms but not of acute GVHD and results in similar survival outcomes compared with the historical group. A prospective study with additional patients is warranted to confirm the role of PT-Cy in lymphoid malignancy.

关键词： post-transplantation cyclophosphamide     allogeneic hematopoietic stem cell transplantation     lymphoid malignancies    

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标题 作者 时间 类型 操作

Single-cell RNA-seq data analysis on the receptor ACE2 expression reveals the potential risk of different

Xin Zou, Ke Chen, Jiawei Zou, Peiyi Han, Jie Hao, Zeguang Han

期刊论文

锌空燃料电池电站

朱梅,徐献芝,苏润

期刊论文

福田敏男：Bio Cell Analysis and Assembly by Micro and Nano Robotic Technology（2019年8月25日）

福田敏男(院士)

2021年01月20日

会议视频

Distinct immune escape and microenvironment between RG-like and pri-OPC-like glioma revealed by single-cellRNA-seq analysis

期刊论文

Transmembrane transport of polycyclic aromatic hydrocarbons by bacteria and functional regulation of membrane proteins

Hongqi Wang, Ruhan Jiang, Dekang Kong, Zili Liu, Xiaoxiong Wu, Jie Xu, Yi Li

期刊论文

微生物组分析技术的发展趋势：从单细胞功能成像到菌群大数据

徐健, 马波, 苏晓泉, 黄适, 徐欣, 周学东, 黄巍, Rob Knight

期刊论文

Computer-Aided Design System for CP Single-Screw Compressor

SHEN Jing-feng, YAO Fu-sheng

期刊论文

Distinct mononuclear diploid cardiac subpopulation with minimal cell–cell communications persists in

期刊论文

PathogenTrack and Yeskit: tools for identifying intracellular pathogens from single-cell RNA-sequencing

期刊论文

Design and analysis of partially decoupled translational parallel mechanisms with single-loop structures

期刊论文

Clinical characteristics and prognostic factors of patients with mature T-cell lymphoid malignancies:a single-institution study of 225 cases

null

期刊论文

Numerical analysis of bearing behaviors of single batter piles under horizontal loads in various directions

期刊论文

Effects of vitrification and cryostorage duration on single-cell RNA-Seq profiling of vitrified-thawed

Ying Huo, Peng Yuan, Qingyuan Qin, Zhiqiang Yan, Liying Yan, Ping Liu, Rong Li, Jie Yan, Jie Qiao

期刊论文

A cytoprotective graphene oxide-polyelectrolytes nanoshell for single-cell encapsulation

Luanying He, Yulin Chang, Junhao Zhu, Ying Bi, Wenlin An, Yiyang Dong, Jia-Hui Liu, Shihui Wang

期刊论文

intravenous busulfan conditioning with post-transplantation cyclophosphamide for allogeneic peripheral stem celltransplantation for adult patients with lymphoid malignancies: a prospective single-arm phase II study

Ling Wang, Lining Wang, Xing Fan, Wei Tang, Jiong Hu

期刊论文