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Intestinal organoid as an in vitro model in studying host-microbial interactions

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Frontiers in Biology 2017年第2期12卷 94-102页

作者： jun sun Division of Gastroenterology and Hepatology Department of Medicine University of Illinois at Chicago 840 S Wood Street Chicago IL 60612 USA

BACKGROUND： Organoid is an in vitro three-dimensional organ-bud that shows realistic microanatomy and physiological relevance. The progress in generating organoids that faithfully recapitulate human in vivo tissue composition has extended organoid applications from being just a basic research tool to a translational platform with a wide range of uses. Study of host- microbial interactions relies on model systems to mimic the in vivo infection. Researchers have developed various experimental models in vitro and in vivo to examine the dynamic host-microbial interactions. For some infectious pathogens, model systems are lacking whereas some of the used systems are far from optimal. OBJECTIVE： In the present work, we will review the brief history and recent findings using organoids for studying host- microbial interactions. METHODS： A systematic literature search was performed using the PubMed search engine. We also shared our data and research contribution to the field. RESULTS： we summarize the brief history of 3D organoids. We discuss the feasibility of using organoids in studying host- microbial interactions, focusing on the development of intestinal organoids and gastric organoids. We highlight the advantage and challenges of the new experimental models. Further, we discuss the future direction in using organoids in studying host- microbial interactions and its potential application in biomedical studies. CONCLUSION： In combination with genetic, transcriptome and proteomic profiling, both murine- and human-derived organoids have revealed crucial aspects of development, homeostasis and diseases. Specifically, human organoids from susceptible host will be used to test their responses to pathogens, probiotics, and drugs. Organoid system is an exciting tool for studying infectious disease, microbiome, and therapy.

关键词： bacteria colonoids enteroids gastric organoids host-microbial interactions H. pylori inflammation intestinalorganoids microbiome organoids tight junctions Salmonella stem-cell differentiation ZO-1

Nonlinear Degenerate Parabolic Equation with Nonlinear Boundary Condition

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Acta Mathematica Sinica,English Series 2005年第4期21卷 847-854页

作者： Wen jun sun Shu WANG LCP Institute of Applied Physics and Computational Mathematics P. O. Box 8009 Beijing 100080 P. R. China College of Applied Science Beijing University of Technology Ping Le Yuan Chao Yang District Beijing 100022 P. R. China

In this paper, we obtain the necessary and sufficient conditions on the global existence of all positive （weak） solutions to a nonlinear degenerate parabolic equation with nonlinear boundary condition.

关键词： Nonlinear degenerate parabolic equation Global existence Blow-up

ε_0-Regularity for Mean Curvature Flow from Surface to Flat Riemannian Manifold

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Acta Mathematica Sinica,English Series 2012年第7期28卷 1475-1490页

作者： Xiao Li HAN jun sun Department of Mathematical Sciences Tsinghua University Math.Group The Abdus Salam International Centre for Theoretical Physics

In this paper we prove an so-regularity theorem for mean curvature flow from surface to a flat Riemannian manifold. More precisely, we prove that if the initial energy ∫∑0 ｜A｜^2 ≤ ε0 and the initial area u0（∑0） is not large, then along the mean curvature flow, we have ∫∑t ｜A｜^2 ≤ ε0. As an application, we obtain the long time existence and convergence result of the mean curvature flow.

关键词： ε0-Regularity mean curvature flow

Coccolith assemblages and their response to climate and surface hydrography in the Yellow Sea, Northwest Pacific, AD 1780–2011

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Acta Oceanologica Sinica 2016年第10期35卷 56-62页

作者： YUAN Mingli HUANG Jiansheng sun jun sun Yao College of Marine and Environmental Sciences Tianjin University of Science and Technology Yellow Sea Fisheries Research Institute Chinese Fisheries Science Academy College of Ocean and Earth Science Xiamen University

A study of coccolith assemblages from a box core from the central South Yellow Sea（SYS） was performed revealing fluctuations on their relative abundance（%） that can be related to climatic and hydrographic changes over the last 230 years（1780–2011）. Total coccolith abundances ranged from 7.0 to 55.1×10^6 coccoliths·g^-1sediment. Although the abundance of different species varied widely throughout the core, seven taxa dominated the assemblage. Among these species, Gephyrocapsa oceanica was the most dominant species, and it showed an average percentage of 50.1%. The pattern of G. oceanica（eutrophic species） was opposite to that of the combined percentage of Braarudosphaera bigelowii and Umbilicosphaera sibogae（both oligotrophic species）, indicating that in the Yellow Sea（YS）, the distribution pattern of G. oceanica might be characteristic of nutrient *** patterns between G. oceanica and the Siberian High were observed on an inter-decadal time scale,indicating that the East Asian Winter Monsoon（EAWM） may be an important driver of ecological changes in the YS. When the EAWM prevails, both the Yellow Sea Coastal Current（YSCC） and Yellow Sea Warm Current（YSWC）strengthen, and the increasing nutrient availability and warmer water brought by the strengthened YSWC favor eutrophic and warm-water coccolithophore species, such as G. oceanica. This likely mechanism demonstrates that coccolith assemblages can be used as benign and reliable proxy for climate change and surface oceanography.

关键词： coccolith Yellow Sea paleooceanography East Asian Winter Monsoon current

基于放射基因组学的肾细胞癌MRI纹理特征与基因突变的相关性分析

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中华放射学杂志 2025年第1期59卷 84-90页

作者：潘靓邢兆宇孙军丁玖乐彭妍陈杰邢伟苏州大学附属第三医院医学影像科常州213003 苏州大学附属第三医院泌尿外科常州213003 苏州大学附属第三医院病理科常州213003

目的探讨肾透明细胞癌(ccRCC)和非透明细胞癌(n-ccRCC)MRI纹理特征与基因突变的相关性。方法该研究为横断面研究,回顾性分析2011年4月至2019年9月苏州大学附属第三医院经病理证实为肾细胞癌且行基因测序的31例患者资料,ccRCC组19例、n-c... 详细信息

目的探讨肾透明细胞癌(ccRCC)和非透明细胞癌(n-ccRCC)MRI纹理特征与基因突变的相关性。方法该研究为横断面研究,回顾性分析2011年4月至2019年9月苏州大学附属第三医院经病理证实为肾细胞癌且行基因测序的31例患者资料,ccRCC组19例、n-ccRCC组12例。所有患者术前2周内行MRI扫描。从T 1WI、T 2WI、Dixon-MRI,以及增强皮髓质期(CMP)、肾实质期(NGP)、延迟期(DEP)中分别提取肿瘤纹理特征,并筛选出鉴别ccRCC与n-ccRCC价值最高的MRI纹理特征。采用二代高通量测序方法分析肾脏肿瘤基因突变情况。采用Spearman相关系数分别分析ccRCC和n-ccRCC组突变基因与MRI纹理特征的相关性,并进行KEGG通路富集分析。结果共筛选出8个MRI纹理特征。在ccRCC组中,PTEN突变与DE_Phase_InverseDifferenceMoment_angle0_offset7呈负相关(r=-0.58,P=0.009)。在n-ccRCC组中,SETD2突变与CM_Phase_InverseDifferenceMoment_AllDirection_offset1和Dixon_W_InverseDifferenceMoment_AllDirection_offset7呈正相关(r=0.58、0.63,P=0.048、0.027),PBRM1突变与DE_Phase_InverseDifferenceMoment_angle0_offset7呈正相关(r=0.61,P=0.034)、与DE_Phase_HaraVariance呈负相关(r=-0.60,P=0.039),FAT1突变与DE_Phase_HaraVariance和NG_Phase_Inertia_angle135_offset4呈正相关(r=0.58、0.58,P=0.047、0.047)。KEGG通路富集分析表明,ccRCC组相关突变基因与p53信号通路、肌醇磷酸盐代谢、癌症中枢碳代谢、EGFR酪氨酸激酶抑制剂耐药性、癌症PD-L1表达和PD-1检查点通路以及磷脂酰肌醇信号通路有关。在n-ccRCC组中相关突变基因主要与赖氨酸降解有关。结论ccRCC和n-ccRCC MRI纹理特征与基因突变之间具有相关性,相关突变基因具有不同的富集通路。

关键词：癌,肾细胞磁共振成像放射基因组学

Formation of Liquid Pools Entrapped within Solid Grains of ZA27 Alloys during Partial Remelting

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Journal of Materials Science & Technology 2002年第6期18卷 481-483页

作者： Tijun CHEN Yuan HAO jun sun State Key Laboratory of Mechanical Behavior for Materials Xi'an Jiaotong UniversityXi'an 710049China School of Materials Science and Engineering Gansu University of TechnologyLanzhou 730050China

The investigations were performed into the formation processes of liquid pools entrapped within solid grains of three ZA27 alloys, produced respectively by either grain refinement, or traditional permanent casting or mechanical stirring, during partial remelting at semisolid temperature of 460℃. The results show that the rapid coalescence of primary grains due to merging of secondary arms during the initial stage of partial remelting is the main cause for the formation of the entrapped liquid pools. This coalescence resulted in that a high quality of eutectics, especially the 77 phase, was entrapped within the grains, and then remelted to form liquid pools during the subsequent heating. In addition, the growth of the η phase decomposed from the primary α' phase and β phase and the subsequent remelting is another cause for the refined and permanent mould casting alloys. Furthermore, the agglomeration of the solid grains also resulted in the entrapment of liquid in the interior of grains.

关键词： Thixoforming ZA27 alloy Partial remelting Microstructure

Cumulative prospect theory-based user equilibrium model with stochastic perception errors

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Journal of Central South University 2016年第9期23卷 2465-2474页

作者： WANG Wei sun Hui-jun Key Laboratory of Urban Transportation Complex Systems Theory and Technology of Ministry of Education Beijing Jiaotong University Beijing 100044 China

The cumulative prospect theory(CPT) is applied to study travelers' route choice behavior in a degradable transport network. A cumulative prospect theory-based user equilibrium(CPT-UE) model considering stochastic perception error(SPE) within travelers' route choice decision process is developed. The SPE is conditionally dependent on the actual travel time distribution, which is different from the deterministic perception error used in the traditional logit-based stochastic user equilibrium. The CPT-UE model is formulated as a variational inequality problem and solved by a heuristic solution algorithm. Numerical examples are provided to illustrate the application of the proposed model and efficiency of the solution algorithm. The effects of SPE on the reference point determination, cumulative prospect value estimation, route choice decision and network performance evaluation are investigated.

关键词： cumulative prospect theory user equilibrium stochastic perception error variational inequality

Hypothesis testing and statistical analysis of microbiome

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Genes & Diseases 2017年第3期4卷 138-148页

作者： Yinglin Xia jun sun Division of Academic Internal Medicine and Geriatrics Department of MedicineUniversity of Illinois at ChicagoChicagoILUSA Division of Gastroenterology and Hepatology Department of MedicineUniversity of Illinois at ChicagoChicagoILUSA

After the initiation of Human Microbiome Project in 2008,various biostatistic and bioinformatic tools for data analysis and computational methods have been developed and applied to microbiome *** this review and perspective,we discuss the research and statistical hypotheses in gut microbiome studies,focusing on mechanistic concepts that underlie the complex relationships among host,microbiome,and *** review the current available statistic tools and highlight recent progress of newly developed statistical methods and *** the current challenges and limitations in biostatistic approaches and tools,we discuss the future direction in developing statistical methods and models for the microbiome studies.

关键词： Bioinformatics Biostatistics Cancer Hypothesis testing IBD Microbiome Statistical methods and models Vitamin D receptor

Rapid design and screen high strength U-based high-entropy alloys from first-principles calculations

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Journal of Materials Science & Technology 2024年第12期179卷 174-186页

作者： Xingge Xu Hualei Zhang Xiangdong Ding jun sun State Key Laboratory for Mechanical Behavior of Materials Frontier Institute of Science and TechnologyXi'an Jiaotong UniversityXi'an 710049China

Reducing the exploration of multi-principal element alloy space is a key challenge to design high-performance U-based high-entropy alloy(UHEA).Here,the best combination of multi-principal element can be efficiently acquired because proposed alloying strategy and screening criteria can substantially reduce the space of alloy and thus accelerate alloy design,rather than enormous random combinations through a trial-and-error *** choose the best seed alloy and suitable dopants,the screening criteria include small anisotropy,high specific modulus,high dynamical stability,and high *** therefore find a shortcut to design UHEA from typical binary(UTi and UNb)to ternary(UTiNb),qua-ternary(UTiNbTa),and quinary(UTiNbTaFe).Finally,we find a best bcc senary UHEA(UTiNbTaFeMo),which has highest hardness and yield strength,while maintains good ductility among all the *** to overestimation from empirical strength-hardness relationship,improved strength prediction can be achieved using a parameter-free theory considering volume mismatch and temperature effect on yield *** finding indicates that larger volume mismatch corresponds to higher yield strength,agreeing with the available ***,the dynamical stability and mechanical properties of candidates are greatly enhanced with increasing the number of multi-principal element,indicating the feasibility and effectiveness of adopted alloying *** increasing of multi-principal element cor-responds to the increasing valence electron concentration(VEC).Alternatively,the mechanical properties significantly improve as increasing VEC,agreeing with measurements for other various bcc *** work can speed up research and development of advanced UHEA by greatly reducing the space of alloy composition.

关键词： Ab initio calculations Multi-principal element alloys Elastic properties High hardness Anisotropy Alloy design