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Epigenetic basis of hepatocellular carcinoma: A network-based integrative meta-analysis

World Journal of Hepatology 2018年第1期10卷 155-165页

作者： Venkat Bhat Sujitha Srinathan Elisa Pasini Marc Angeli emily chen Cristina Baciu Mamatha Bhat Department of Psychiatry University Health Network and University of Toronto Multi Organ Transplant Program University Health NetworkToronto M5G2N2 Canada Division of Gastroenterology Department of Medicine University Health Network and University of Toronto

AIM To identify the key epigenetically modulated genes and pathways in HCC by performing an integrative meta-analysis of all major, well-annotated and publicly available methylation datasets using tools of network *** Pub Med and Gene Expression Omnibus were searched for genome-wide DNA methylation datasets. Patient clinical and demographic characteristics were obtained. DNA methylation data were integrated using the Ingenuity Pathway Analysis, a software package for visualizing and analyzing biological networks. Pathway enrichment analysis was performed using IPA, which also provides literature-driven and computationallypredicted annotations for significant association of genes to curated molecular *** From an initial 928 potential abstracts, we identified and analyzed 11 eligible high-throughput methylation datasets representing 354 patients. A significant proportion of studies did not provide concomitant clinical data. In the promoter region, HIST1H2AJ and SPDYA were the most commonly methylated, whereas HRNBP3 gene was the most commonly hypomethylated. ESR1 and ERK were central genes in the principal networks. The pathways most associated with the frequently methylated genes were G-protein coupled receptor and c AMP-mediated signalling. CONCLUSION Using an integrative network-based analysis approach of genome-wide DNA methylation data of both the promoter and body of genes, we identified G-protein coupled receptor signalling as the most highly associated with HCC. This encompasses a diverse range of cancer pathways, such as the PI3 K/Akt/m TOR and Ras/Raf/MAPK pathways, and is therefore supportive of previous literature on gene expression in HCC. However, there are novel targetable genes such as HIST1H2 AJ that are epigenetically modified, suggesting their potential as biomarkers and for therapeutic targeting of the HCC epigenome.

关键词： Network analysis Hepatocellular carcinoma Methylation

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MS/MSALL Strategy for Comprehensive Lipidomics

MS/MSALL Strategy for Comprehensive Lipidomics

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2018年中国质谱学术大会（CMSC2018）

作者： Fei Gao emily chen Michael Kiebish DUBRAIN Technology LLC2. BERGLLC

The lipidome of biological samples is comprised of thousands of lipid molecular species. Its homeostatic regulation plays a pivotal role in numerous pathological disease states, such as atherosclerosis, cancer, metabolic diseases, and Alzheimer’s disease. Lipidomic analysis is largely based on electrospray ionization mass spectrometry(ESI-MS) coupled with liquid chromatography(LC) or using direct infusion, i.e., shotgun lipidomics. Traditional MS-based lipidomics has been dominated by triple quadrupole instruments and require the pre-selection of specific ions or multiple runs for the diverse capture of the lipidome. Recently, a novel data-independent acquisition(DIA) technique of mass spectrometry has been developed to overcome this shortcoming by parallelizing the fragmentation of all detectable ions within a certain m/z range. With the combination of high-resolution MS, DIA provides a powerful tool for shotgun lipidomics. MS/MSALL is a direct infusion DIA technique, using a hybrid quadrupole time-of-flight(qTOF) technology, specifically designed for lipidomics. In MS/MSALL, all precursors are selected in the Q1 quadrupole at unit-based resolution in a step-wise fashion to completely cover the entire mass range of interest. Collision induced dissociation is carried out in Q2 at high speed and the corresponding highresolution MS/MS spectra are recorded covering every precursor in each cycle. We have used this strategy to developed the shotgun lipidomics methods for profiling human blood lipidome via the dried blood spots(DBS), screening the lipid profile from human urine, as well as cardiolipin molecular species from the various mouse tissues. The combination of high resolution, sensitivity, and throughput offers significant advantages towards the identification and quantification of lipids in complex biological samples and has the potential to be to be integrated into broad scale of complex lipidomic analysis.

关键词： mass spectrometry shotgun lipidomics MS/MSALL qTOF

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Artificial cavernosa-like tissue based on multibubble Matrigel and a human corpus cavernous fibroblast scaffold

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Asian Journal of Andrology 2024年第3期26卷 260-267页

作者： Yu-Zhuo chen Yi-Hong Zhou Min-Bo Yan Ming Xiao Biao Liu Ying-Hao Yin Xiao-Li Tan Yong-Quan Huang Yu-Hong Lin Ting Xie Jia-Li Tian Qi Wang Jian-Ying Li Zi-Zhou Meng Zheng Li emily Xing Yu-Xin Tang Ya-Wei Li Zhong-Zhen Su Liang-Yu Zhao Department of Ultrasound The Fifth Affiliated HospitalSun Yat-sen UniversityZhuhai 519000China Department of Interventional Medicine Guangdong Provincial Key Laboratory of Biomedical ImagingThe Fifth Affiliated HospitalSun Yat-sen UniversityZhuhai 519000China Department of Urology The Fifth Affiliated HospitalSun Yat-sen UniversityZhuhai 519000China Department of Andrology the Center for Men’s HealthUrologic Medical CenterShanghai Key Laboratory of ReproductiveMedicineShanghai General HospitalShanghai Jiao Tong University School of MedicineShanghai 200080China Cedars-Sinai Medical Center Los AngelesCA 90024USA

Ex vivo tissue culture of the human corpus cavernosum(cc)can be used to explore the tissue structural changes and complex signaling *** present,artificial Cc-like tissues based on acellular or three-dimensional(3D)-printed scaffolds are used to solve the scarcity of primary penis tissue ***,inconvenience and high costs limit the wide application of such ***,we describe a simple,fast,and economical method of constructing artificial CC-like *** Cc fibroblasts(FBs),endothelial cells(ECs),and smooth muscle cells(SMCs)were expanded in vitro and mixed with Matrigel in specific proportions.A large number of bubbles were formed in the mixture by vortexing combined with pipette blowing,creating a porous,spongy,and spatial *** Cc FBs produced a variety of signaling factors,showed multidirectional differentiation potential,and grew in a 3D grid in Matrigel,which is necessary for CC-like tissue to maintain a porous structure as a cell *** the C-like tissue,ECs covered the surface of the lumen,and SMCs were located inside the trabeculae,similar to the structure of the primary *** cell components remained stable for 3 days in vitro,but the EC content decreased on the 7th ***/integrated(WNT)signaling activation led to lumen atrophy and increased tissue fibrosis in CC-like tissue,inducing the same changes in characteristics as in the primary *** study describes a preparation method for human artificial cC-like tissue that may provide an improved experimental platform for exploring the function and structure of the cC and conducting drug screening for erectile dysfunction therapy.

关键词： artificial tissue corpus cavernosum ex vivo fibroblasts

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Preconditioners and Electron Density Optimization in Orbital-Free Density Functional Theory

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Communications in Computational Physics 2012年第6期12卷 135-161页

作者： Linda Hung chen Huang emily A.Carter Program in Applied and ComputationalMathematics Princeton UniversityPrincetonNJ 08544USA Department of Physics Princeton UniversityPrincetonNJ 08544USA Department of Mechanical and Aerospace Engineering and Andlinger Center for Energy and the Environment Princeton UniversityPrincetonNJ 08544USA

Orbital-free density functional theory(OFDFT)is a quantum mechanical method in which the energy of a material depends only on the electron density and ionic *** examine some popular algorithms for optimizing the electron density distribution in OFDFT,explaining their suitability,benchmarking their performance,and suggesting some *** start by describing the constrained optimization problem that encompasses electron density ***,we discuss the line search(including Wolfe conditions)and the nonlinear conjugate gradient and truncated Newton algorithms,as implemented in our open source OFDFT *** finally focus on preconditioners derived from OFDFT energy *** preconditioners are successful for simulation cells of all sizes without regions of low electron-density and for small simulation cells with such regions.

关键词： Density functional theory truncated Newton method conjugate gradient method constrained optimization benchmarks

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A carbon-based 3D current collector with surface protection for Li metal anode

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Nano Research 2017年第4期10卷 1356-1365页

作者： Ying Zhang Boyang Liu emily Hitz Wei Luo Yonggang Yao Yiju Li diaqi Dai Chaoji chen Yanbin Wang Chunpeng Yang Hongbian Li Liangbing Hu Department of Materials Science and Engineering University of Maryland College Park MD 20742 USA National Center for Nanoscience and Technology Beijing 100190 China

Lithium metal is considered the ideal anode material for Li-ion-based batteries because it exhibits the highest specific capacity and lowest redox potential for this type of cells. However, growth of Li dendrites, unstable solid electrolyte interphases, low Coulombic efficiencies, and safety hazards have significantly hindered the practical application of metallic Li anodes. Herein, we propose a three-dimensional （3D） carbon nanotube sponge （CNTS） as a Li deposition host. The high specific surface area of the CNTS enables homogenous charge distribution for Li nucleation and minimizes the effective current density to overcome dendrite growth. An additional conformal A1203 layer on the CNTS coated by atomic layer deposition （ALD） robustly protects the Li metal electrode/electrolyte interface due to the good chemical stability and high mechanical strength of the layer. The Li@ALD-CNTS electrode exhibits stable voltage profiles with a small overpotential ranging from 16 to 30 mV over 100 h of cycling at 1.0 mA·cm^-2. Moreover, the electrodes display a dendrite-free morphology after cycling and a Coulombic efficiency of 92.4% over 80 cycles at 1.0 mA·cm^-2 in an organic carbonate electrolyte, thus demonstrating electrochemical stability superior to that of planar current collectors. Our results provide an important strategy for the rational design of current collectors to obtain stable Li metal anodes.

关键词： lithium metal anode Coulombic efficiency current collector carbon nanotube interfacial protection stable cycling

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Temperature-dependent deformation in silver-particle-covered copper nanowires by molecular dynamics simulation

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Journal of Materiomics 2022年第1期8卷 68-78页

作者： Pengtao Li Y.Q.Yang Vladimir Koval Xian Luo Jianxin chen Wei Zhang E.emily Lin Bowen Wang Haixue Yan State Key Laboratory of Solidification Processing Northwestern Polytechnical UniversityXi'an710072China Institute of Materials Research Slovak Academy of SciencesKosice04001Slovakia School of Chemistry and Chemical Engineering Northwestern Polytechnical UniversityXi'an71072China Northwest Institute for Nonferrous Metal Research Xi'an710016China School of Engineering&Material Science Queen Mary University of LondonMile End RoadE14NSLondonUnited Kingdom

Cu nanowires covered by Ag particles is studied for potential applications in the next-generation *** date,the deformation mechanism in the Cu-Ag core-particle is not ***,molecular dynamics simulation is used to describe the Cu-Ag core-particle *** results show that the equilibrium structure of Ag particles is reconstructed,when the particle≤1.0 *** low temperature(1 K)indicate that three different deformation processes take part in the core-particle structure,depending on the size of Ag *** the particle diameter≤2.0 nm,the prevailing deformation mechanism is the emission of dislocations from the Cu *** the particle diameters ranging from 3.0 to 6.0 nm,the emission of misfit dislocations from the Ag-Cu interface is the dominant deformation *** the Ag particle≥6.0 nm,the deformation mechanism can be characterized by the slip band,consisting of the dislocations and amorphous *** elevated temperatures(2-400 K),the mechanical properties of the Ag-Cu core-shell system are nearly independent of temperature,whereas the structure with particles larger than 2.0 nm showed a strong dependence of its mechanical properties on *** on the results,the diameter-temperature plastic deformation map is proposed.

关键词： Nanowires Deformation Cu-Ag Nano particle Dislocation

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Strong and Superhydrophobic Wood with Aligned Cellulose Nanofibers as a Waterproof Structural Material

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Chinese Journal of Chemistry 2020年第8期38卷 823-829页

作者： Yongfeng Li Chaoji chen Jianwei Song Chunpeng Yang Yudi Kuang Azhar Vellore emily Hitz Mingwei Zhu Feng Jiang Yonggang Yao Amy Gong Ashlie Martini Liangbing Hu Department of Materials Science and Engineering University of MarylandCollege ParkMaryland20742USA Mechanical Engineering University of CaliforniaMercedCalifornia95343USA

Lightweight structural materials are important for the energy efficiency of applications,particularly those in the building ***,inspired by nature,we developed a strong,superhydrophobic,yet lightweight material by simple in situ growth of nano-SiO2 and subsequent densification of the wood *** situ generation of SiO2 nanoparticles both inside the wood channels and on the wood surfaces gives the material superhydrophobicity,with static and dynamic contact angles of 159.4°and 3°,*** of the wood to remove most of the spaces among the lumen and cell walls results in a laminated,dense structure,with aligned cellulose nanofibers,which in turn contributes to a high mechanical strength up to 384.2 MPa(7-times higher than natural wood).Such treatment enables the strong and superhydrophobic wood(SH-Wood)to be stable and have excellent water,acid,and alkaline *** high mechanical strength of SH-Wood combined with its excellent structural stability in harsh environments,as well its low density,positions the strong and superhydrophobic wood as a promising candidate for strong,lightweight,and durable structural materials that could potentially replace steel.

关键词： fibers proof structural

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史密森南广场园区规划

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城市环境设计 2019年第2期118卷 160-169页

作者： Aaron Hales Alana Goldweit Alexandre Hamlyn Andriani Atmadja Annette Miller Benjamin DiNapoli Benjamin Novacinski Cadence Bayley Choonghyo Lee Chris Falla Daisy Zhong Daniele Pronesti Doug Stechschulte emily chen Gabriel Hernandez Solano Janice Rim Jennifer Shen Jeremy Alain Siegel Jihoon Hyun Julian Andres Ocampo Salazar Kalina Pilat Katarzyna Starczewska Lina Bondarenko Mahsa Malek Manon Otto Martin Voelkle Ola Hariri Otilia Pupezeanu Saecheol Oh Sara Ibrahim Stephen Kwok Stephen Steckel Suemin Jeon Tammy Teng Taylor Fulton Tianqi Zhang Vincent Fulia Wells Barber Wesley Chiang Zhifei Xu 陈子钰

通过与史密森学会、当地居民以及决策者的密切合作,我们为南广场园区制定了总体规划,作为对旧与新的重新诠释——方案利用园区内的现有元素,在严格监管与历史保护的限制中寻求自由。该提案旨在提升并扩大游客服务和教育空间,在博物馆与... 详细信息

通过与史密森学会、当地居民以及决策者的密切合作,我们为南广场园区制定了总体规划,作为对旧与新的重新诠释——方案利用园区内的现有元素,在严格监管与历史保护的限制中寻求自由。该提案旨在提升并扩大游客服务和教育空间,在博物馆与花园之间建立清晰的入口和联系,并取代已达到使用寿命的老化建筑机械系统。与此同时,团队致力于保留豪普

关键词：园区规划总体规划 Avenue 史密森史密森学会基础隔震弗里尔交通流线

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Mixed methods evaluation of a randomized control pilot trial targeting sugar-sweetened beverage behaviors

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Open Journal of Preventive Medicine 2013年第1期3卷 51-57页

作者： Jamie Zoellner emily Cook Yvonnes chen Wen You Brenda Davy Paul Estabrooks Department of Agriculture and Applied Economics Virginia Tech Blacksburg USA Department of Communications Virginia Tech Blacksburg USA Department of Human Nutrition Foods and Exercise Virginia Tech Blacksburg USA

This Excessive sugar-sweetened beverage (SSB) consumption and low health literacy skills have emerged as two public health concerns in the United States (US);however, there is limited research on how to effectively address these issues among adults. As guided by health literacy concepts and the Theory of Planned Behavior (TPB), this randomized controlled pilot trial applied the RE-AIM framework and a mixed methods approach to examine a sugar-sweetened beverage (SSB) intervention (SipSmartER), as compared to a matched-contact control intervention targeting physical activity (Move-More). Both 5-week interventions included two interactive group sessions and three support telephone calls. Executing a patient-centered developmental process, the primary aim of this paper was to evaluate patient feedback on intervention content and structure. The secondary aim was to understand the potential reach (i.e., proportion enrolled, representativeness) and effectiveness (i.e. health behaviors, theorized mediating variables, quality of life) of SipS- martER. Twenty-five participants were randomized to SipSmartER (n = 14) or MoveMore (n = 11). Participants’ intervention feedback was positive, ranging from 4.2 - 5.0 on a 5-point scale. Qualitative assessments reavealed several opportuneties to improve clarity of learning materials, enhance instructions and communication, and refine research protocols. Although SSB consumption decreased more among the SipS-martER participants (?256.9 ± 622.6 kcals), there were no significant group differences when compared to control participants (?199.7 ± 404.6 kcals). Across both groups, there were significant improvements for SSB attitudes, SSB behavioral intentions, and two media literacy constructs. The value of using a patient-centered approach in the developmental phases of this intervention was apparent, and pilot findings suggest decreased SSB may be achieved through targeted health literacy and TPB strategies. Future efforts are needed to ex

关键词： Beverages Health Literacy Health Education Public Health Health Behavior Pilot Projects

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Social-epigeneticmediators for racial disparities in pulmonary impairment among childhood cancer survivors

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Cancer Communications 2023年第2期43卷 290-293页

作者： Nan Song Qian Dong cheng chen Qian Li Heather Mulder emily Plyler John Easton emily Walker Scott Olson Geoffrey Neale Kevin RKrull Deo Kumar Srivastava Kirsten K.Ness Jinghui Zhang Melissa M.Hudson Leslie L.Robison I-Chan Huang Zhaoming Wang Department of Epidemiology and Cancer Control St.Jude Children’s Research HospitalMemphisTN 38105USA College of Pharmacy Chungbuk National UniversityCheongjuChungbuk 28160South Korea School of Public Health Shanghai Jiaotong UniversityShanghai 200025P.R.China Department of Biostatistics St.Jude Children’s Research HospitalMemphisTN 38105USA Department of Computational Biology St.Jude Children’s Research HospitalMemphisTN 38105USA Hartwell Center St.Jude Children’s Research HospitalMemphisTN 38105USA Department of Oncology St.Jude Children’s Research HospitalMemphisTN 38105USA

Dear Editor Previous research found that childhood cancer survivors of African ancestry have significantly higher morbidity and mortality than those of European ancestry[1].However,after adjusting for socio-economic factors,the magnitudes of racial health disparities are either substantially decreased or become statistically non-significant[1],suggesting that social and economic determinants may contribute to racial health ***,we conducted epigenome-wide association studies(EWAS)for three key social determinants of health(SDOHs),namely,personal educational attainment,personal income,and neighborhood deprivation among survivors of childhood cancer,where 130 epigenome-wide significant SDOH-CpG associationswere identified among European ancestry survivors,and 25 of which were also validated in African ancestry survivors[2].Notably,many SDOH-associated CpG sites are also associated with tobacco use.

关键词： vivo cancer mortality

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