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Effects of adjacent bubble on spatiotemporal evolutions of mechanical stresses surrounding bubbles oscillating in tissues

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Chinese Physics B 2023年第1期32卷 354-361页

作者：邹青钦雷双李章勇秦对 Department of Biomedical Engineering School of BioinformaticsChongqing University of Posts and TelecommunicationsChongqing 400065China

The cavitation dynamics and mechanical stress in viscoelastic tissues, as the primary mechanisms of some ultrasound therapies, are extremely complex due to the interactions of cavitation bubble with adjacent bubbles and surrounding ***, the cavitation dynamics and resultant mechanical stress of two-interacting bubbles in the viscoelastic tissues are numerically investigated, especially focusing on the effects of the adjacent bubble. The results demonstrate that the mechanical stress is highly dependent on the bubble dynamics. The compressive stress and tensile stress are generated at the stage of bubble expansion and collapse stage, respectively. Furthermore, within the initial parameters examined in this paper, the effects of the adjacent bubble will distinctly suppress the radial expansion of the small bubble and consequently lead its associated stresses to decrease. Owing to the superimposition of two stress fields, the mechanical stresses surrounding the small bubble in the direction of the neighboring bubble are smaller than those in other directions. For two interacting cavitation bubbles, the suppression effects of the nearby bubble on both the cavitation dynamics and the stresses surrounding the small bubble increase as the ultrasound amplitude and the initial radius of the large bubble increase, whereas they decrease with the inter-bubble distance increasing. Moreover, increasing the tissue viscoelasticity will reduce the suppression effects of the nearby bubble, except in instances where the compressive stress and tensile stress first increase and then decrease with the tissue elasticity and viscosity increasing respectively. This study can provide a further understanding of the mechanisms of cavitation-associated mechanical damage to the adjacent tissues or cells.

关键词： cavitation dynamics cavitation-induced mechanical stress effects of the nearby bubble viscoelastic tissues

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Typical Aspects of the Granular Cell Tumor of the Oral Cavity

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international Journal of Otolaryngology and Head & Neck Surgery 2014年第6期3卷 318-322页

作者： Paula Prieto-Oliveira Sergio Vitorino Cardoso Florence Zumbaio Mistro Sergio Kignel Suzana Cantanhede Orsini Machado de Sousa Marco Tullio Brazao-Silva inter-institutional grad program on bioinformatics University of Sao PauloSao PauloBrazil Department of Oral Pathology School of DentistryFederal University of UberlandiaUberlandiaBrazil Department of Semiology School of DentistryFundacao Herminio OmettoArarasBrazil Department of Oral Pathology School of DentistryUniversity of Sao PauloSao PauloBrazil Department of Oral Diagnosis School of DentistrySchool of Health SciencesUniversity of the State of AmazonasManausBrazil

Granular cell tumor (GCT) is a rare neoplasm that can occur in any part of the body, but mostly they are located intraorally. Its histogenetic origin remains controversial, but it probably arises from Schwann cells and is generally benign. The tumor is typically asymptomatic and appears as a nodule, with a relatively high predilection for the tongue. This article reports a case of a 72-year-old woman treated at the Center of Oral Diagnosis of the Fundação Hermínio Ometto Dental School. The patient presented with an asymptomatic nodule in the dorsal surface of the tongue for approximately 4 months. The patient was submitted to an excisional biopsy and histopatological examination revealed polyhedral cells with granular aspect. The immunohistochemical staining for S-100 presented strong reactivity, confirming the diagnosis of GCT. Finally, we made a concise discussion about the pathogenesis and fundamental clinico-pathological aspects of GCT making the differential diagnosis.

关键词： Granular Cell Tumor Mouth Diagnosis

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Integrative clustering methods of multi-omics data for molecule-based cancer classifications

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Frontiers of Electrical and Electronic Engineering in China 2016年第1期4卷 58-67页

作者： Dongfang Wang Jin Gu Ministry of Education Key Laboratory of bioinformatics and bioinformatics Division Center for Synthetic and Systems BiologyTsinghua National Laboratory for Information Science and Technology/Department of Automation Tsinghua University Beijing100084 China

One goal of precise oncology is to re-classify cancer based on molecular features rather than its tissue origin. Integrative clustering of large-scale multi-omics data is an important way for molecule-based cancer classification. The data heterogeneity and the complexity of inter-omics variations are two major challenges for the integrative clustering analysis. According to the different strategies to deal with these difficulties, we summarized the clustering methods as three major categories： direct integrative clustering, clustering of clusters and regulatory integrative clustering. A few practical considerations on data pre-processing, post-clustering analysis and pathway-based analysis arc also discussed.

关键词： clustering cancer classification omics integrative analysis

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HiC-3DViewer： a new tool to visualize Hi-C data in 3D space

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Frontiers of Electrical and Electronic Engineering in China 2017年第2期5卷 183-190页

作者： Mohamed Nadhir Djekidel Mengjie Wang Michael Q. Zhang Juntao Gao MOE Key Laboratory of bioinformatics bioinformatics Division and Center for Synthetic & Systems Biology TNLIST Department of Automation Tsinghua University Beijing 100084 China School of Pharmaceutical Sciences Tsinghua University Beijing 100084 China Department of Biological Sciences Center for Systems Biology The University of Texas at Dallas Richardson TX 75080- 3021. USA

Background： Although significant progress has been made to map chromatin structure at unprecedented resolution and scales, we are short of tools that enable the intuitive visualization and navigation along the three-dimensional （3D） structure of chromatins. The available tools people have so far are generally script-based or present basic features that do not easily enable the integration of genomic data along with 3D chromatin structure, hence, many scientists find themselves in the obligation to hack tools designed for other purposes such as tools for protein structure study. Methods： We present HiC-3DViewer, a new browser-based interactive tool designed to provide an intuitive environment for investigators to facilitate the 3D exploratory analysis of Hi-C data along with many useful annotation functionalities. Among the key features of HiC-3DViewer relevant to chromatin conformation studies, the most important one is the 1D-to-2D-to-3D mapping, to highlight genomic regions of interest interactively. This feature enables investigators to explore their data at different levels/angels. Additionally, investigators can superpose different genomic signals （such as ChIP-Seq, SNP） on the top of the 3D structure. Results： As a proof of principle we applied HiC-3DViewer to investigate the quality of Hi-C data and to show the spatial binding of GATA1 and GATA2 along the genome. Conclusions： As a user-friendly tool, HiC-3DViewer enables the visualization of inter/intra-chromatin interactions and gives users the flexibility to customize the look-and-feel of the 3D structure with a simple click. HiC-3DViewer is implemented in Javascript and Python, and is freely available at： http：//***/member/nadhir/ HiC3DViewer/. Supplementary information （User Manual, demo data） is also available at this website.

关键词： Hi-C 3D genome visualization chromatin structure prediction

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Detection of bursts in neuronal spike trains by the mean inter-spike interval method

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Progress in Natural Science:Materials international 2009年第2期19卷 229-235页

作者： Lin Chena,b,Yong Deng c,Weihua Luo a,Zhen Wang a,Shaoqun Zenga,a Hubei bioinformatics and Molecular Imaging Key Laboratory,Huazhong University of Science and Technology,Wuhan 430074,China b College of Mechanical Engineering,Guangxi University,Nanning,530004,China c College of Optoelectronic Science of Engineering,Huazhong University of Science and Technology,Wuhan 430074,China Hubei bioinformatics and Molecular Imaging Key Laboratory Huazhong University of Science and Technology Wuhan 430074 China College of Mechanical Engineering Guangxi University Nanning 530004 China College of Optoelectronic Science of Engineering Huazhong University of Science and Technology Wuhan 430074 China

Bursts are electrical spikes firing with a high frequency,which are the most important property in synaptic plasticity and information processing in the central nervous system. However,bursts are difficult to identify because bursting activities or patterns vary with phys-iological conditions or external stimuli. In this paper,a simple method automatically to detect bursts in spike trains is described. This method auto-adaptively sets a parameter (mean inter-spike interval) according to intrinsic properties of the detected burst spike trains,without any arbitrary choices or any operator judgment. When the mean value of several successive inter-spike intervals is not larger than the parameter,a burst is identified. By this method,bursts can be automatically extracted from different bursting patterns of cultured neurons on multi-electrode arrays,as accurately as by visual inspection. Furthermore,significant changes of burst variables caused by electrical stimulus have been found in spontaneous activity of neuronal network. These suggest that the mean inter-spike interval method is robust for detecting changes in burst patterns and characteristics induced by environmental alterations.

关键词： inter-spike interval Bursts Spike trains Multi-electrode arrays

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Tracking SARS-CoV-2 Omicron diverse spike gene mutations identifies multiple inter-variant recombination events

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Signal Transduction and Targeted Therapy 2022年第5期7卷 1808-1816页

作者： Junxian Ou Wendong Lan Xiaowei Wu Tie Zhao Biyan Duan Peipei Yang Yi Ren Lulu Quan Wei Zhao Donald Seto James Chodosh Zhen Luo Jianguo Wu Qiwei Zhang Guangdong Provincial Key Laboratory of Virology Institute of Medical MicrobiologyJinan University510632 GuangzhouChina BSL-3 Laboratory(Guangdong) Guangdong Provincial Key Laboratory of Tropical Disease ResearchSchool of Public HealthSouthern Medical University510515 GuangzhouChina bioinformatics and Computational Biology program School of Systems BiologyGeorge Mason UniversityManassasVA 20110USA Department of Ophthalmology Howe Laboratory Massachusetts Eye and EarHarvard Medical SchoolBostonMA 02114USA Foshan Institute of Medical Microbiology 528315 FoshanChina

The current pandemic of COVID-19 is fueled by more infectious emergent Omicron *** concerns of emergent variants include possible recombinants,as genome recombination is an important evolutionary mechanism for the emergence and re-emergence of human viral *** this study,we identified diverse recombination events between two Omicron major subvariants(BA.1 and BA.2)and other variants of concern(VOCs)and variants of interest(VOIs),suggesting that co-infection and subsequent genome recombination play important roles in the ongoing evolution of *** scanning high-quality completed Omicron spike gene sequences.

关键词： subsequent diverse recombination

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HCCDB v2.0:Decompose Expression Variations by Single-cell RNA-seq and Spatial Transcriptomics in HCC

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Genomics, Proteomics & bioinformatics 2024年第1期22卷 131-142页

作者： Ziming Jiang Yanhong Wu Yuxin Miao Kaige Deng Fan Yang Shuhuan Xu Yupeng Wang Renke You Lei Zhang Yuhan Fan Wenbo Guo Qiuyu Lian Lei Chen Xuegong Zhang Yongchang Zheng Jin Gu Eight-Year program of Clinical Medicine Peking Union Medical College HospitalChinese Academy of Medical Sciences&Peking Union Medical CollegeBeijing 100006China MOE Key Laboratory of bioinformatics BNRIST Bioinformatics DivisionInstitute for Precision Medicine&Department of AutomationTsinghua UniversityBeijing 100084China Department of Liver Surgery Peking Union Medical College HospitalChinese Academy of Medical Sciences&Peking Union Medical CollegeBeijing 100730China Fuzhou Institute for Data Technology Fuzhou 350207China University of Michigan-Shanghai Jiao Tong University Joint Institute Shanghai Jiao Tong UniversityShanghai 200240China Department of Automation Shanghai Jiao Tong UniversityShanghai 200240China international Cooperation Laboratory on Signal Transduction Eastern Hepatobiliary Surgery InstituteSecond Military Medical UniversityShanghai 200438China National Center for Liver Cancer Shanghai 201805China

Large-scale transcriptomic data are crucial for understanding the molecular features of hepatocellular carcinoma(HCC).Integrated 15 transcriptomic datasets of HCC clinical samples,the first version of HCC database(HCCDB v1.0)was released in *** the meta-analysis of differentially expressed genes and prognosis-related genes across multiple datasets,it provides a systematic view of the altered biological processes and the inter-patient heterogeneities of HCC with high reproducibility and *** four years having passed,the database now needs integration of recently published ***,the latest single-cell and spatial transcriptomics have provided a great opportunity to decipher complex gene expression variations at the cellular level with spatial ***,we present HCCDB v2.0,an updated version that combines bulk,single-cell,and spatial transcriptomic data of HCC clinical *** dramatically expands the bulk sample size by adding 1656 new samples from 11 datasets to the existing 3917 samples,thereby enhancing the reliability of transcriptomic meta-analysis.A total of 182,832 cells and 69,352 spatial spots are added to the single-cell and spatial transcriptomics sections,respectively.A novel single-cell level and 2-dimension(sc-2D)metric is proposed as well to summarize cell type-specific and dysregulated gene expression *** are all graphically visualized in our online portal,allowing users to easily retrieve data through a user-friendly interface and navigate between different *** extensive clinical phenotypes and transcriptomic data in the database,we show two applications for identifying prognosis-associated cells and tumor *** v2.0 is available at http://***/database/hccdb2.

关键词： Hepatocellular carcinoma Database Integrative analysis Single-cell RNA sequencing Spatial transcriptomics

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CR6-interacting factor-1 contributes to osteoclastogenesis by inducing receptor activator of nuclear factor κB ligand after radiation

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World Journal of Stem Cells 2020年第3期12卷 222-240页

作者： Li-Xin Xiang Qian Ran Li Chen Yang Xiang Feng-Jie Li Xiao-Mei Zhang Yan-Ni Xiao Ling-Yun Zou Jiang F Zhong Shengwen Calvin Li Zhong-Jun Li Laboratory Medicine Center Department of Blood TransfusionLab of Radiation BiologyThe Second Affiliated HospitalThird Military Medical UniversityChongqing400037China Department of Otolaryngology Keck School of MedicineUniversity of Southern CaliforniaLos AngelesCA 90033United States bioinformatics Center College of Basic Medical SciencesThird Military Medical UniversityChongqing 400038China CHOC Children’s Research Institute Children’s Hospital of Orange CountyUniversity of CaliforniaIrvineCA 92868United States

BACKGROUND Radiation induces rapid bone loss and enhances bone resorption and adipogenesis, leading to an increased risk of bone fracture. There is still a lack of effective preventive or therapeutic method for irradiation-induced bone *** activator of nuclear factor κB ligand(RANKL) provides the crucial signal to induce osteoclast differentiation and plays an important role in bone resorption. However, the mechanisms of radiation-induced osteoporosis are not fully *** To investigate the role of CR6-interacting factor-1(Crif1) in osteoclastogenesis after radiation and its possible *** C57 BL/6 mice were exposed to Co-60 gamma rays and received 5 Gy of wholebody sublethal irradiation at a rate of 0.69 Gy/min. For in vitro study, mouse bone marrow mesenchymal stem/stromal cells(BM-MSCs) were irradiated with Co-60 at a single dose of 9 Gy. For osteoclast induction, monocyte-macrophage RAW264.7 cells were cocultured with mouse BM-MSCs for 7 d. Clus Pro and inter Pro Surf were used to investigate the interaction interface in Crif1 and protein kinase cyclic adenosine monophosphate(c AMP)-activited catalytic subunit alpha complex. Virtual screening using 462608 compounds from the Life Chemicals database around His120 of Crif1 was carried out using the program Autodock_vina. A tetrazolium salt(WST-8) assay was carried out to study the toxicity of compounds to different cells, including human BM-MSCs, mouse BMMSCs, and Vero *** Crif1 expression increased in bone marrow cells after radiation in *** of Crif1 in mouse BM-MSCs and radiation exposure could increase RANKL secretion and promote osteoclastogenesis in vitro. Deletion of Crif1 in BM-MSCs could reduce both adipogenesis and RANKL expression,resulting in the inhibition of osteoclastogenesis. Deletion of Crif1 in RAW264.7 cells did not affect the receptor activator of nuclear factor κB expression or osteoclast differentiation. Following treatment with protein

关键词： Irradiation Osteoporosis Bone marrow Mesenchymal stem cells Monocyte macrophage Bone

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Nuclear peripheral chromatin-lamin B1 interaction is required for global integrity of chromatin architecture and dynamics in human cells

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Protein & Cell 2022年第4期13卷 258-280页

作者： Lei Chang Mengfan Li Shipeng Shao Chen Li Shanshan Ai Boxin Xue Yingping Hou Yiwen Zhang Ruifeng Li Xiaoying Fan Aibin He Cheng Li Yujie Sun State Key Laboratory of Membrane Biology School of Life Sciencesand Biomedical Pioneering Innovation Center(BIOPIC)Peking UniversityBeijing 100871China Peking-Tsinghua Center for Life Sciences Academy for Advanced Interdisciplinary StudiesPeking UniversityBeijing 100871China Center for bioinformatics School of Life SciencesPeking UniversityBeijing 100871China Institute of Molecular Medicine Beijing Key Laboratory of Cardiometabolic Molecular MedicinePeking UniversityBeijing 100871China Center for Statistical Science Peking UniversityBeijing 100871China Bioland Laboratory(Guangzhou Regenerative Medicine and Health Guangdong Laboratory) Guangzhou 510530China

The eukaryotic genome is folded into higher-order conformation accompanied with constrained dynamics for coordinated genome ***,the molecular machinery underlying these hierarchically organized three-dimensional(3D)chromatin architecture and dynamics remains poorly *** by combining imaging and sequencing,we studied the role of lamin B1 in chromatin architecture and *** found that lamin B1 depletion leads to detachment of lamina-associated domains(LADs)from the nuclear periphery accompanied with global chromatin redistribution and ***,the interchromosomal as well as inter-compartment interactions are increased,but the structure of topologically associating domains(TADs)is not *** live-cell genomic loci tracking,we further proved that depletion of lamin B1 leads to increased chromatin dynamics,owing to chromatin decompaction and redistribution toward *** together,our data suggest that lamin B1 and chromatin interactions at the nuclear periphery promote LAD maintenance,chromatin compaction,genomic compartmentalization into chromosome territories and A/B compartments and confine chromatin dynamics,supporting their crucial roles in chromatin higher-order structure and chromatin dynamics.

关键词： lamin B1 3D genome Hi-C chromatin dynamics chromosome territories A/B compartments livecell imaging super-resolution imaging

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Fine-scale genetic structure of Eremosparton songoricum and implication for conservation

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Journal of Arid Land 2010年第1期2卷 26-32页

作者： Liu, Yan Zhang, DaoYuan Yang, HongLan Liu, MeiYing Shi, Xiang Chinese Acad Sci Key Lab Biogeog & Bioresources Arid Land Xinjiang Inst Ecol & Geog Urumqi 830011 Peoples R China Chinese Acad Sci Turpan Eremophytes Bot Garden Turpan 838008 Peoples R China Chinese Acad Sci Grad Univ Beijing 100049 Peoples R China

Eremosparton songoricum (Litv.) Vass. is a clonal shrub that reproduces both asexually by under-ground rhizomes and sexually by seeds. It is now a rare species with a narrow distribution in fragmented habitat patches in the Gurbantunggut Desert of Xinjiang, China. The objective of this study was to determine the spatial pattern or structure of genetic variation within population. The within-populations genetic structure of E. songoricum in a plot (10 m×10 m) was analyzed using inter simple sequence repeats (ISSR) markers. Correlograms of Moran’s I showed significant positive value was about 7 m, but changed into a negative correlation with the increase of distance, indicating strong genetic structure. The natural character of clonal reproduction, restricted seed and pollen dispersal were the main factors of influencing the spatial pattern. The knowledge of clonal structures within populations was crucial for understanding evolutionary processes and ecological adaptation. This study provided basic data for the conservation and management of E. songoricum, especially for sampling strategies for ex situ conservation.

关键词： Eremosparton songoricum genetic diversity clonal structure spatial distribution patterns conservation

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