检索结果-南通市图书馆

Single-cell omics: experimental workflow, data analyses and applications

维普期刊数据库评论

在线全文

维普期刊数据库

学校读者我要写书评

暂无评论

Science China(Life Sciences) 2025年第1期68卷 5-102页

作者： Fengying Sun Haoyan Li Dongqing Sun Shaliu Fu Lei Gu Xin Shao Qinqin Wang Xin Dong Bin Duan Feiyang Xing Jun Wu Minmin Xiao Fangqing Zhao Jing-Dong J.Han Qi Liu Xiaohui Fan Chen Li Chenfei Wang Tieliu Shi Department of Clinical laboratory the Affiliated Wuhu Hospital of East China Normal University(The Second People’s Hospital of Wuhu City)Wuhu 241000China Pharmaceutical Informatics Institute College of Pharmaceutical SciencesZhejiang UniversityHangzhou 310058China key laboratory of Spine and Spinal Cord Injury Repair and Regeneration(Tongji University) Ministry of EducationOrthopaedic DepartmentTongji HospitalBioinformatics DepartmentSchool of Life Sciences and TechnologyTongji UniversityShanghai 200082China Frontier Science Center for Stem Cells School of Life Sciences and TechnologyTongji UniversityShanghai 200092China Translational Medical Center for Stem Cell Therapy and Institute for Regenerative Medicine Shanghai East HospitalBioinformatics DepartmentSchool of Life Sciences and TechnologyTongji UniversityShanghai 200082China Research Institute of Intelligent Computing Zhejiang LabHangzhou 311121China shanghai Research Institute for Intelligent Autonomous Systems Shanghai 201210China Center for Single-cell Omics School of Public HealthShanghai Jiao Tong University School of MedicineShanghai 200025China National key laboratory of Chinese Medicine Modernization Innovation Center of Yangtze River DeltaZhejiang UniversityJiaxing 314103China Center for Bioinformatics and Computational Biology Shanghai Key Laboratory of Regulatory Biologythe Institute of Biomedical Sciences and School of Life SciencesEast China Normal UniversityShanghai 200241China Beijing Institutes of Life Science Chinese Academy of SciencesBeijing 100101China Peking-Tsinghua Center for Life Sciences Academy for Advanced Interdisciplinary StudiesCenter for Quantitative Biology(CQB)Peking UniversityBeijing 100871China Zhejiang key laboratory of Precision Diagnosis and Therapy for Major Gynecological Diseases Women’s HospitalZhejiang University School of MedicineHangzhou 310006China key laboratory of Advanced Theory and Application in Statistics and Data Science-MOE School of StatisticsEast China Normal U

Cells are the fundamental units of biological systems and exhibit unique development trajectories and molecular *** exploration of how the genomes orchestrate the formation and maintenance of each cell,and control the cellular phenotypes of various organismsis,is both captivating and *** the inception of the first single-cell RNA technology,technologies related to single-cell sequencing have experienced rapid advancements in recent *** technologies have expanded horizontally to include single-cell genome,epigenome,proteome,and metabolome,while vertically,they have progressed to integrate multiple omics data and incorporate additional information such as spatial scRNA-seq and CRISPR ***-cell omics represent a groundbreaking advancement in the biomedical field,offering profound insights into the understanding of complex diseases,including ***,we comprehensively summarize recent advances in single-cell omics technologies,with a specific focus on the methodology *** overview aims to guide researchers in selecting appropriate methods for single-cell sequencing and related data analysis.

关键词： single-cell sequencing genome epigenome proteomics metabolomics multimodal spatial transcriptomics CRISPR screening

Altered 3D genome reorganization mediates precocious myeloid differentiation of aged hematopoietic stem cells in inflammation

在线全文

学校读者我要写书评

暂无评论

Science China Life Sciences 2025年

作者： Xinyu Cui Yu Dong Qiang Zhan Yixin Huang Qianshu Zhu Zihao Zhang Guang Yang Liping Wang Shijun Shen Jia Zhao Zhiyi Lin Jiatong Sun Zhongqu Su Yihan Xiao Chuyu Zhang Yuwei Liang Lu Shen Lichen Ji Xuguang Zhang Jiqing Yin Hong Wang Zhiyang Chen Zhenyu Ju Cizhong Jiang Rongrong Le Shaorong Gao Clinical and Translational Research Center of shanghai First Maternity & Infant Hospital Frontier Science Center for Stem Cells School of Life Sciences and Technology Tongji University key laboratory of Spine and Spinal Cord Injury Repair and Regeneration of Ministry of Education Orthopaedic Department of Tongji Hospital School of Life Sciences and Technology Tongji University key laboratory of Regenerative Medicine of Ministry of Education Institute of Aging and Regenerative Medicine Department of Developmental & Regenerative Medicine College of Life Science and Technology Jinan University Shandong key laboratory of Animal Bioengineering and Disease Prevention College of Animal Science and Technology Shandong Agricultural University Department of Joint Surgery Shanghai East Hospital Tongji University School of Medicine shanghai Institute of Nutrition and Health Chinese Academy of Sciences

Inflammation is a driving force of hematopoietic stem cells(HSCs) aging, causing irreversible exhaustion of functional HSCs. However, the underlying mechanism of HSCs erosion by inflammatory insult remains poorly understood. Here, we find that transient LPS exposure primes aged HSCs to undergo accelerated differentiation at the expense of self-renewal, leading to depletion of HSCs. Meanwhile, the central regulator nuclear factor kappa B(NF-κB) mediating functional impairment by inflammation insult induces differential transcriptional response in aged HSCs compared with young HSCs, with precocious activation of myeloid lineage genes. Altered compartmentalization and chromatin loop formation are associated with aging-related differential transcriptional response in HSCs upon lipopolysaccharide(LPS)stimulation. Mechanistically, enhancer and promoter regions of myeloid lineage genes in aged HSCs are more accessible and display more rapid and prominent CTCF occupancy upon LPS stimulation. Our study provides comprehensive resources for the three-dimensional(3D)genome structure of HSCs and sheds light into the ordered genome organization and the associated transcriptome signature underlying HSCs aging.

关键词：

Accurate prediction of essential proteins using ensemble machine learning

在线全文

同方期刊数据库

学校读者我要写书评

暂无评论

Chinese Physics B 2025年第1期 112-119页

作者：鲁德志吴淏侯俞彤吴云成刘媛媛王金武 School of Medicine Shanghai University shanghai key laboratory of orthopaedic implants Department of Orthopaedic SurgeryShanghai Ninth People’s Hospital Shanghai Jiao Tong University School of Medicine University of shanghai for Science and Technology

Essential proteins are crucial for biological processes and can be identified through both experimental and computational methods. While experimental approaches are highly accurate, they often demand extensive time and *** address these challenges, we present a computational ensemble learning framework designed to identify essential proteins more efficiently. Our method begins by using node2vec to transform proteins in the protein–protein interaction(PPI)network into continuous, low-dimensional vectors. We also extract a range of features from protein sequences, including graph-theory-based, information-based, compositional, and physiochemical attributes. Additionally, we leverage deep learning techniques to analyze high-dimensional position-specific scoring matrices(PSSMs) and capture evolutionary information. We then combine these features for classification using various machine learning algorithms. To enhance performance, we integrate the outputs of these algorithms through ensemble methods such as voting, weighted averaging,and stacking. This approach effectively addresses data imbalances and improves both robustness and accuracy. Our ensemble learning framework achieves an AUC of 0.960 and an accuracy of 0.9252, outperforming other computational *** results demonstrate the effectiveness of our approach in accurately identifying essential proteins and highlight its superior feature extraction capabilities.

关键词：

Research Center of 3D Bioprinting in shanghai Ninth People’s Hospital

在线全文

同方期刊数据库

学校读者我要写书评

暂无评论

Bio-Design and Manufacturing 2019年第3期2卷 213-220页

作者： Tao Li Xiaojun Zhou Changxu Deng Xiaoxiao Yang Han Yang Zhenjiang Ma Lan Cao Zezheng Yang Lei Qiang Jinwu Wang Kerong Dai shanghai key laboratory of orthopaedic implant Department of Orthopaedic SurgeryShanghai Ninth People’s HospitalShanghai Jiao Tong University School of Medicine639 Zhizaoju RdShanghai 200011China Med-X Research Institute School of Biomedical EngineeringShanghai Jiao Tong University1804 Huashan RdShanghai 200030China

The center was first established in 2013 and affiliated to the shanghai Ninth People’s Hospital,shanghai Jiao Tong University School of *** 2015,the center was entitled as 3D Bioprinting Clinical Transformation Collaborative Innovation *** 2016,the center was renamed as Medical 3D Printing Innovation Research Center of shanghai Jiao Tong University School of *** the center was established in 2013,the clinical application of 3D printing in shanghai Ninth People’s Hospital can be traced back to the *** early as 30 years ago,*** Dai had tried to rebuild patients pelvic by manually cutting the foam boards and layering them together based on the theory of 3D printing for preoperative planning model of abnormal skeleton structures and development of personalized *** was the first application of 3D printing in the area of medicine in ***,The Research Center of 3D Bioprinting in shanghai Ninth People’s Hospital comprised of subcenters including the outpatient department of 3D printing,medical 3D printing innovation research center and shanghai key laboratory of orthopedic implant.

关键词： printing Transformation centers

Autologous fibroblasts induce fibrosis of the nucleus pulposus to maintain the stability of degenerative intervertebral discs

在线全文

学校读者我要写书评

暂无评论

Bone Research 2020年第1期8卷 63-75页

作者： Chen Chen Tangjun Zhou Xiaojiang Sun Chen Han Kai Zhang Changqing Zhao Xunlin Li Haijun Tian Xiao Yang Yifan Zhou Zhiqian Chen An Qin Jie Zhao shanghai key laboratory of orthopaedic implants Department of Orthopaedic Surgery Shanghai Ninth People’s Hospital Shanghai Jiao Tong University School of Medicine

Lumbar degenerative disc diseases cause low back pain(LBP). The maintenance of the height and stability of the intervertebral disc(IVD) space is an effective treatment for LBP. The following study evaluated the effects of fibroblast injection on intervertebral disc degeneration(IDD) in a preclinical setting. Compared with the IDD group, the fibroblast treatment group demonstrated effective maintenance of IVD height, reduced endplate degeneration, and improved nuclear magnetic resonance signals and overall histological structure. In doing so, fibrotic IVDs maintained the stability and biomechanics of the vertebra. This finding is in agreement with clinical findings that human nucleus pulposus(NP) fibrosis is essential for the maintenance of IVD height and mechanical properties in patients following percutaneous endoscopic lumbar discectomy(PELD). Mechanistically, we demonstrated that injected fibroblasts not only proliferated but also induced NP cells to adopt a fibrotic phenotype via the secretion of TGF-β.Finally, to better mimic human conditions, the efficacy of autologous fibroblast injection in the treatment of IDD was further examined in a nonhuman primate cynomolgus monkey model due to their capacity for upright posture. We showed that the injection of fibroblasts could maintain the IVD height and rescue IVD signals in cynomolgus monkeys. Taken together, the results of our study reveal that autologous fibroblast injection can enhance the natural process of fibrosis during acute and subacute stages of stress-induced IDD. Fibrotic IVDs can maintain the stability, biological activity, and mechanical properties of the intervertebral space, thus providing a new direction for the treatment of intervertebral space-derived lumbar degenerative diseases.

关键词： intervertebral degenerative degeneration

Engineering 3D approaches to model the dynamic microenvironments of cancer bone metastasis

在线全文

学校读者我要写书评

暂无评论

Bone Research 2018年第1期6卷 38-49页

作者： Han Qiao Tingting Tang shanghai key laboratory of orthopaedic implants Department of Orthopaedic Surgery Shanghai Ninth People’s Hospital Shanghai Jiao Tong University School of Medicine

Cancer metastasis to bone is a three-dimensional(3D), multistep, dynamic process that requires the sequential involvement of three microenvironments, namely, the primary tumour microenvironment, the circulation microenvironment and the bone microenvironment. Engineered 3D approaches allow for a vivid recapitulation of in vivo cancerous microenvironments in vitro, in which the biological behaviours of cancer cells can be assessed under different metastatic conditions. Therefore, modelling bone metastasis microenvironments with 3 D cultures is imperative for advancing cancer research and anti-cancer treatment strategies. In this review, multicellular tumour spheroids and bioreactors, tissue engineering constructs and scaffolds, microfluidic systems and 3D bioprinting technology are discussed to explore the progression of the 3D engineering approaches used to model the three microenvironments of bone metastasis. We aim to provide new insights into cancer biology and advance the translation of new therapies for bone metastasis.

关键词： three-dimensional anti-cancer treatment modelling bone metastasis

Kinsenoside attenuates osteoarthritis by repolarizing macrophages through inactivating NF-κB/MAPK signaling and protecting chondrocytes

在线全文

学校读者我要写书评

暂无评论

Acta Pharmaceutica Sinica B 2019年第5期9卷 973-985页

作者： Feng Zhou Jingtian Mei Xiuguo Han Hanjun Li Shengbing Yang Minqi Wang Linyang Chu Han Qiao Tingting Tang shanghai key laboratory of orthopaedic implants Department of Orthopaedic Surgery Shanghai Ninth People’s Hospital Shanghai Jiao Tong University School of Medicine

The objective was to investigate the effect of kinsenoside(Kin) treatments on macrophage polarity and evaluate the resulting protection of chondrocytes to attenuate osteoarthritis(OA) ***264.7 macrophages were polarized to M1/M2 subtypes then administered with different concentrations of Kin. The polarization transitions were evaluated with quantitative real-time polymerase chain reaction(q RT-PCR), confocal observation and flow cytometry analysis. The mechanism of Kin repolarizing M1 macrophages was evaluated by Western blot. Further, macrophage conditioned medium(CM) and IL-1β were administered to chondrocytes. Micro-CT scanning and histological observations were conducted in vivo on anterior cruciate ligament transection(ACLT) mice with or without Kin treatment. We found that Kin repolarized M1 macrophages to the M2 phenotype. Mechanistically, Kin inhibited the phosphorylation of IκBα, which further reduced the downstream phosphorylation of P65 in nuclear factor-κB(NF-κB) signaling. Moreover, Kin inhibited mitogen-activated protein kinases(MAPK) signaling molecules p-JNK, p-ERK and p-P38. Additionally, Kin attenuated macrophage CM and IL-1β-induced chondrocyte damage. In vivo, Kin reduced the infiltration of M1 macrophages,promoted M2 macrophages in the synovium, inhibited subchondral bone destruction and reduced articular cartilage damage induced by ACLT. All the results indicated that Kin is an effective therapeutic candidate for OA treatment.

关键词： Kinsenoside Osteoarthritis Macrophages Polarization Chondrocytes

Highly interconnected macroporous MBG/PLGA scaffolds with enhanced mechanical and biological properties via green foaming strategy

在线全文

学校读者我要写书评

暂无评论

Chinese Journal of Chemical Engineering 2021年第1期34卷 426-436页

作者： Chaobo Song Jiapeng Zhang Shuang Li Shengbin Yang Eryi Lu Zhenhao Xi Lian Cen Ling Zhao Weikang Yuan State key laboratory of Chemical Engineering School of Chemical EngineeringEast China University of Science and TechnologyShanghai 200237China Department of Stomatology of Renji Hospital School of MedicineShanghai Jiao Tong UniversityShanghai 200127China shanghai key laboratory of orthopaedic implant Department of Orthopaedics SurgeryShanghai Ninth People's HospitalShanghai Jiao Tong University School of MedicineNo.639Zhizaoju RoadShanghai 200011China

In this study,mesoporous bioactive glass particles(MBGs) are incorporated into poly(lactic-co-glycolic acid)(PLGA) to fabricate highly interconnected macroporous composite scaffolds with enhanced mechanical and biological properties via a developed supercritical carbon dioxide(scCO_(2)) foaming method Scaffolds show favorable highly interconnected and macroporous structure through a high foaming pressure and long venting time foaming ***,scaffolds with porosity from 73% to 85%,pore size from 120 μm to 320 μm and interconnectivity of over 95% are controllably fabricated at MBG content from 0 wt% to 20 wt%.In comparison with neat PLGA scaffolds,composite scaffolds perform improved strength(up to 1.5 folds) and Young's modulus(up to 3 folds).The interconnected macroporous structure is beneficial to the ingrowth of *** importantly,composite scaffolds also provide a more promising microenvironment for cellular proliferation and adhesion with the release of bioactive ***,MBG/PLGA scaffolds developed by the green foaming strategy in this work show promising morphological,mechanical and biological features for tissue regeneration.

关键词： Scaffold Mesoporous bioactive glass Supercritical carbon dioxide Foaming Poly(lactic-co-glycolic acid)

Progress in the Application of 3D Printing Technology in Spine Surgery

在线全文

学校读者我要写书评

暂无评论

Journal of shanghai Jiaotong university(Science) 2021年第3期26卷 352-360页

作者： SUN Xiaojiang YANG Erzhu ZHAO Changqing CHENG Xiaofei ZHANG Kai TIAN Haijun DING Baozhi LI Hua JIANG Wenbo DAI Kerong ZHAO Jie Department of orthopaedic Surgery Shanghai Key Laboratory of Orthopaedic ImplantsShanghai Ninth People’s HospitalShanghai Jiao Tong University School of MedicineShanghai200011China

We are in the midst of exciting advancements in new technologies and innovative research in precision *** these,3D printing is one of the most frequently seen in clinical orthopaedic *** new technique has been adopted in a vast range of applications in spine surgery,such as producing anatomical models,surgical templates,preoperative plans,and spinal *** studies on 3D printing technologies in spine surgery have reported the benefits of this emerging technology with more effective manufacturing,more visualisation for communication,and more precise navigation for screw insertion and *** addition,in customised implant design and fabrication processes,3D printing products with anatomical adaptions and complex porous microstructure show some attractive advantages in terms of fit and ***,there are still some concerns about the safety and feasibility of the application of 3D printing technology in spine *** review the literature on and share our experiences with the application of 3D printing from the beginning of collaborations between doctors and computer-aided design(CAD)designers to the final follow-up of clinical patients.

关键词： 3D printing spine patient-specific implants anatomical model template