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Integrative genomic and transcriptomic profiling of pulmonary sarcomatoid carcinoma identifies molecular subtypes associated with distinct immune features and clinical outcomes

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Cancer Innovation 2024年第3期3卷 81-94页

作者： Sahil Seth Runzhe chen Yang Liu Junya Fujimoto Lingzhi Hong Alexandre Reuben Susan Varghese Carmen Behrens Tina McDowell Luisa Solis Soto Cara Haymaker Annikka Weissferdt Neda Kalhor Jia Wu Xiuning Le Natalie I Vokes Chao cheng john V.Heymach Don L.Gibbons P.Andrew Futreal Ignacio IWistuba Humam Kadara Jianhua Zhang Cesar Moran Jianjun Zhang Department of Genomic Medicine The University of Texas MD Anderson Cancer CenterHoustonTexasUSA TRACTION The University of Texas MD Anderson Cancer CenterHoustonTexasUSA Graduate School of Biomedical Sciences The University of Texas MD Anderson and the University of Texas Health Science CenterHoustonTexasUSA Department of Thoracic/Head and Neck Medical Oncology The University of Texas MD Anderson Cancer CenterHoustonTexasUSA Department of Translational Molecular Pathology The University of Texas MD Anderson Cancer CenterHoustonTexasUSA Department of Epidemiology The University of Texas MD Anderson Cancer CenterHoustonTexasUSA Department of Pathology The University of Texas MD Anderson Cancer CenterHoustonTexasUSA Department of Imaging Physics The University of Texas MD Anderson Cancer CenterHoustonTexasUSA Department of Medicine Baylor College of MedicineHoustonTexasUSA

Background:Pulmonary sarcomatoid carcinoma(PSC)is a rare and aggressive subtype of non-small cell lung cancer(NSCLC),characterized by the presence of epithelial and sarcoma-like *** molecular and immune landscape of PSC has not been well ***:Multiomics profiling of 21 pairs of PSCs with matched normal lung tissues was performed through targeted high-depth DNA panel,whole-exome,and RNA *** describe molecular and immune features that define subgroups of PSC with disparate genomic and immunogenic features as well as distinct clinical ***:In total,27 canonical cancer gene mutations were identified,with TP53 the most frequently mutated gene,followed by ***,most TP53 and KRAS mutations were earlier genomic events mapped to the trunks of the tumors,suggesting branching evolution in most PSC *** identified two distinct molecular subtypes of PSC,driven primarily by immune infiltration and *** Immune High(IM-H)subtype was associated with superior survival,highlighting the impact of immune infiltration on the biological and clinical features of localized ***:We provided detailed insight into the mutational landscape of PSC and identified two molecular subtypes associated with ***-H tumors were associated with favorable recurrence-free survival and overall survival,highlighting the importance of tumor immune infiltration in the biological and clinical features of PSCs.

关键词： genomic immune pulmonary sarcomatoid carcinoma survival

Predicting and Visualizing Citrus Color Transformation Using a Deep Mask-Guided Generative Network

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Plant Phenomics 2023年第3期5卷 435-446页

作者： Zehan Bao Weifu Li Jun chen Hong chen Vijay john Chi Xiao Yaohui chen College of Informatics Huazhong Agricultural UniversityWuhan 430070China Engineering Research Center of Intelligent Technology for Agriculture Ministry of EducationWuhanChina RIKEN Guardian robot project2-2-2 Hikaridai Seika-choSorakugun619-0288 KyotoJapan Key Laboratory of Biomedical Engineering of Hainan Province School of Biomedical EngineeringHainan UniversityHaikou 570100China College of Engineering Huazhong Agricultural University430070 WuhanChina

Citrus rind color is a good indicator of fruit development,and methods to monitor and predict color transformation therefore help the decisions of crop management practices and harvest *** work presents the complete workflow to predict and visualize citrus color transformation in the orchard featuring high accuracy and fidelity.A total of 107 sample Navel oranges were observed during the color transformation period,resulting in a dataset containing 7,535 citrus images.A framework is proposed that integrates visual saliency into deep learning,and it consists of a segmentation network,a deep mask-guided generative network,and a loss network with manually designed loss ***,the fusion of image features and temporal information enables one single model to predict the rind color at different time intervals,thus effectively shrinking the number of model *** semantic segmentation network of the framework achieves the mean intersection over a union score of 0.9694,and the generative network obtains a peak signal-to-noise ratio of 30.01 and a mean local style loss score of 2.710,which indicate both high quality and similarity of the generated images and are also consistent with human *** ease the applications in the real world,the model is ported to an Android-based application for mobile *** methods can be readily expanded to other fruit crops with a color transformation *** dataset and the source code are publicly available at GitHub.

关键词： Visual Deep network

Surface plasma treatment effects on the molecular structure at polyimide/air and buried polyimide/epoxy interfaces

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Chinese Chemical Letters 2015年第4期26卷 449-454页

作者： john N.Myers Zhan chen Department of Chemistry University of Michigan

Polyimides are widely used as chip passivation layers and organic substrates in microelectronic packaging. Plasma treatment has been used to enhance the interfacial properties of polyimides, but its molecular mechanism is not clear. In this research, the effects of polyimide surface plasma treatment on the molecular structures at corresponding polyimide/air and buried polyimideJepoxy interfaces were investigated in situ using sum frequency generation （SFG） vibrational spectroscopy. SFG results show that the polyimide backbone molecular structure was different at polyimide/air and polyimideJepoxy interfaces before and after plasma treatment. The different molecular structures at each interface indicate that structural reordering of the polyimide backbone occurred as a result of plasma treatment and contact with the epoxy adhesive. Furthermore, quantitative orientation analysis indicated that plasma treatment of polyimide surfaces altered the twist angle of the polyimide backbone at corresponding buried polyimide/epoxy interfaces. These SFG results indicate that plasma treatment of polymer surfaces can alter the molecular structure at corresponding polymer/air and buried polymer interfaces.

关键词： Molecular structureVibrational spectroscopySum frequency generation spectroscopy

Influence of inter-grain cementation stiffness on the effective elastic properties of porous Bentheim sandstone

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Journal of Rock Mechanics and Geotechnical Engineering 2023年第3期15卷 573-583页

作者： Bin chen Jiansheng Xiang john-Paul Latham Department of Earth Science and Engineering Faculty of EngineeringImperial College LondonLondonSW72BXUK

Effective elastic properties of porous media are known to be significantly influenced by *** this paper,we investigated the influence of another critical factor,the inter-grain cementation stiffness,on the effective elastic properties of a granular porous rock(Bentheim sandstone)using an advanced numerical workflow with realistic rock microstructure and a theoretical ***,the disparity between the experimentally tested elastic properties of Bentheim sandstone and the effective elastic properties predicted by empirical equations was ***,a micro-computed tomography(CT)-scan based approach was implemented with digital imaging software AVIZO to construct the 3D(three-dimensional)realistic microstructure of Bentheim *** microstructural model was imported to a mechanics solver based on the 3D finite element model with inter-grain boundaries modelled by cohesive *** simulations were run to test the effective elastic properties for different shear and normal intergrain cementation ***,a relation between the macroscale Young’s modulus and inter-grain cementation stiffness was derived with a theoretical model which can also account for porosity *** the numerical and theoretical results indicate the influence of the inter-grain cementation stiffness,on the effective elastic properties is significant for porous *** calibrated normal and shear stiffnesses at the inter-grain boundaries are 1.2×10^(5) and 4×10^(4) GPa/m,respectively.

关键词： Porous sandstone Cohesive finite element model Grain-based model Rock microstructure Micro-computed tomography(CT)

PVDF ultrafiltration membranes of controlled performance via blending PVDF-g-PEGMA copolymer synthesized under different reaction times

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Frontiers of Environmental Science & Engineering 2018年第2期12卷 29-40页

作者： Shuai Wang Tong Li chen chen Baicang Liu john C. Crittenden College of Architecture and Environment Sichuan University Chengdu 610207 China Institute of New Energy and Low Carbon Technology Sichuan University Chengdu 610207 China Research Center for Eco-Environmental Sciences Chinese Academy of Sciences Beijing 100085 China Litree Purifying Technology Co. Ltd Haikou 571126 China Brook Byers Institute for Sustainable Systems School of Civil and Environmental Engineering Georgia Institute of Technology Atlanta GA 30332 USA

Polyvinylidene fluoride grafted with poly（ethylene glycol） methyl ether methacrylate （PVDF-g- PEGMA） was synthesized using atomic transfer radical polymerization （ATRP） at different reaction times （9 h, 19 h, and 29 h）. The corresponding conversion rates were 10%, 20% and 30%, respectively. PVDF was blended with the copolymer mixtnre containing PVDF-g-PEGMA, solvent and residual PEGMA under different reaction times. In this study, we explored the effect of the copolymer mixture additives with different synthesis times on cast membrane performance. Increasing the reaction time of PVDF-g-PEGMA causes more PVDF-g-PEGMA and less residual PEGMA to be found in the casting solution. Incremental PVDF-g-PEGMA can dramatically increase the viscosity of the casting solution. An overly high viscosity led to a delayed phase inversion, thus hindering PEGMA segments in PVDF- g-PEGMA from migrating to the membrane surface. However, more residual PEGMA contributed to helping rnore PEGMA segments migrate to the membrane surface. The pure water fluxes of the blended membrane with reaction times of 9 h, 19 h, and 29 h are 5445 L. m 2.h I 1068 L- m 2.h land 1179 L.m 2.h I respectively, at 0.07 MPa. Delayed phase inversion can form smaller surface pore size distributions, thus decreasing the water flux for the membranes with PVDF-g-PEGMA at 19 h and 29 h. Therefore, we can control the membrane pore size distribution by decreasing the reaction time of PVDF-g-PEGMA to obtain a better flux performance. The membrane with PVDF-g-PEGMA at 19 h exhibits the best foulant rejection and cleaning recovery due to its narrow pore size distribution and high surface oxygen content.

关键词： Polyvinylidene fluoride ultrafiltvation mem-braneAmphiphilic copolymerBlended modificationHigh fluxAtomic transfer radical polymerization

Thin-film composite forward osmosis membranes with substrate layer composed of polysulfone blended with PEG or polysulfone grafted PEG methyl ether methacrylate

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Frontiers of Chemical Science and Engineering 2016年第4期10卷 562-574页

作者： Baicang Liu chen chen Pingju Zhao Tong Li Caihong Liu Qingyuan Wang Yongsheng chen john Crittenden College of Architecture and Environment Sichuan University Chengdu 610065 China Institute of New Energy and Low Carbon Technology Siehnan University Chengdu 610207 China Litree Purifying Technology Co. Ltd Haikou 571126 China Research Center for Eco-Environmental Sciences Chinese Academy of Sciences Beijing 100085 China State Key Laboratory of Urban Water Resource and Environment Harbin Institute of Technology Harbin 150090 China School of Civil and Environmental Engineering Georgia Institute of Technology Atlanta GA 30332 USA

To advance commercial application of forward osmosis （FO）, we investigated the effects of two additives on the performance of polysulfone （PSf） based FO membranes： one is poly（ethylene glycol）（PEG）, and another is PSf grafted with PEG methyl ether methacrylate （PSf-g-PEGMA）. PSf blended with PEG or PSf-g- PEGMA was used to form a substrate layer, and then polyamide was formed on a support layer by interfacial polymerization. In this study, NaC1 （1 mol·L^-1） and deionized water were used as the draw solution and the feed solution, respectively. With the increase of PEG content from 0 to 15 wt-%, FO water flux declined by 23.4% to 59.3% compared to a PSf TFC FO membrane. With the increase of PSf-g-PEGMA from 0 to 15 wt-%, the membrane flux showed almost no change at first and then declined by about 52.0% and 50.4%. The PSfwith 5 wt-% PSf-g-PEGMA FO membrane showed a higher pure water flux of 8.74 L·m^-2·h^-1 than the commercial HTI membranes （6-8 L·m^-2·h^-1） under the FO mode. Our study suggests that hydrophobic interface is very important for the formation ofpolyamide, and a small amount of PSf- g-PEGMA can maintain a good condition for the formation of polyamide and reduce internal concentration polarization.

关键词： thin-film composite forward osmosis amphi-philic copolymer interfacial polymerization poly(ethyleneglycol)

识别液态和固态水的四波段水指数及其在咸海流域的应用

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中国科学：地球科学 2024年第3期54卷 788-807页

作者：岳兵陈曦李赛博杜正平 john WILSON 杨筠慧焦毅蒙黄双燕周成虎中国科学院新疆生态与地理研究所乌鲁木齐830011 中国科学院大学资源与环境学院北京100049 中国科学院地理科学与资源研究所北京100101 Spatial Sciences Institute University of Southern CaliforniaLos AngelesCA 90089-0374USA

虽然已有许多水指数被运用于咸海和咸海流域的水域面积分析,然而已有研究尚存在很大的不确定性.由于所使用水指数存在水体误识别的问题,导致不同研究得出的结论差异很大.此外,各种研究采用的咸海流域面积也差异很大,流域面积从约1百万km... 详细信息

虽然已有许多水指数被运用于咸海和咸海流域的水域面积分析,然而已有研究尚存在很大的不确定性.由于所使用水指数存在水体误识别的问题,导致不同研究得出的结论差异很大.此外,各种研究采用的咸海流域面积也差异很大,流域面积从约1百万km^(2)到2百万km^(2)不等.因此,我们首先界定咸海流域、锡尔河和阿姆河流域以及它们的上、中、下游的边界,然后提出可识别液态水和固态水的四波段指数(ILSW),以解决传统水指数的误别偏差问题.ILSW基于绿色、红色、近红外和热红外波段反射值,是归一化差异水指数(NDWI)和地表温度(LST)的合成.验证结果显示,ILSW水指数在咸海流域的准确性远远超过其他指数.研究结果表明,南咸海的水域面积平均每年缩小963km^(2),而北咸海几乎没有变化;由于气候变暖,咸海流域上游常年冰雪面积有大幅度退缩趋势,阿姆河上游和锡尔河上游常年冰雪的退缩速率分别为年均6233和384km^(2)/a.气候变化和人类活动引起了严重的水亏问题.自20世纪90年代以来,水亏呈增长趋势,平均每年增长3.778亿m^(3).2011~2020年期间,整个咸海流域平均总水亏量为76.967亿m^(3),而锡尔河流域上游(咸海流域的一个组成部分)水盈余量为25.461亿m^(3).研究结果对制定咸海流域可持续发展战略具有重要意义.

关键词：咸海流域锡尔河流域阿姆河流域水指数水面积覆盖水亏缺气候变化

Systematic identification of wheat spike developmental regulators by integrated multiomics, transcriptional network, GWAS, and genetic analyses

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Molecular Plant 2024年第3期17卷 438-459页

作者： Xuelei Lin Yongxin Xu Dongzhi Wang Yiman Yang Xiaoyu Zhang Xiaomin Bie Lixuan Gui Zhongxu chen Yiliang Ding Long Mao Xueyong Zhang Fei Lu Xiansheng Zhang Cristobal Uauyo Xiangdong Fu Jun Xiao Key Laboratory of Plant Cell and Chromosome Engineering Institute of Genetics and Developmental BiologyChinese Academy of SciencesBeijing 100101China University of Chinese Academy of Sciences Beijing 100049China Nanjing Agricultural University NanjingJiangsu 210095China Key Laboratory of Crop Biology College of Life SciencesShandong Agricultural UniversityTaianShandong 271018China Department of Life Science Tcuni Inc.ChengduSichuan 610000China john Innes Centre Norwich Research ParkNorwich NR47UHUK Institute of Crop Sciences Chinese Academy of Agricultural SciencesBeijing 100081China CAS-JIC Centre of Excellence for Plant and Microbial Science(CEPAMS) Institute of Genetics and Developmental BiologyCASBeijing 100101China

The spike architecture of wheat plays a crucial role in determining grain number,making it a key trait for optimization in wheat breeding *** this study,we used a multi-omic approach to analyze the transcriptome and epigenome profiles of the young spike at eight developmental stages,revealing co-ordinated changes in chromatin accessibility and H3K27me3 abundance during the flowering *** constructed a core transcriptional regulatory network(TRN)that drives wheat spike formation and experimentally validated a multi-layer regulatorymodule involving TaSPL15,TaAGLG1,and *** integrating the TRN with genome-wide association studies,we identified 227 transcription factors,including 42 with known functions and 185 with unknown *** investigation of 61 novel transcription factors using multiple homozygous mutant lines revealed 36 transcription factors that regulate spike architecture or flowering time,such as TaMYC2-A1,TaMYB30-A1,and *** particular interest,TaMYB30-A1,downstream of and repressed by WFzP,was found to regulate fertile spikelet ***,the excellent haplotype of TaMYB30-A1,which contains a C allele at the WFzP binding site,was enriched during wheat breeding improvement in China,leading to improved agronomic ***,we constructed a free and open access Wheat Spike Multi-Omic Database(http://39.***.48.156:8800/#/).Our study identifies novel and high-confidence regulators and offers an effective strategy for dissecting the genetic basis of wheat spike development,with practical value forwheat breeding.

关键词： wheat spike development epigenome TRN TaMYB30-A1 breeding selection

Effect of adding a smart potassium ion-responsive copolymer into polysulfone support membrane on the performance of thin-film composite nanofiltration membrane

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Frontiers of Chemical Science and Engineering 2019年第2期13卷 400-414页

作者： Meibo He Zhuang Liu Tong Li chen chen Baicang Liu john C.Crittenden Institute of New Energy and Low-Carbon Technology Sichuan UniversityChengdu 610207China College of Architecture and Environment Sichuan UniversityChengdu 610065China School of Chemical Engineering Sichuan UniversityChengdu 610065China Research Center for Eco-Environmental Sciences Chinese Academy of SciencesBeijing 100085China Litree Purifying Technology Co. LtdHaikou 571126China Brook Byers Institute for Sustainable Systems School of Civil and Environmental EngineeringGeorgia Institute of TechnologyAtlantaGA 30332USA

Thin-film composite (TFC) nanofiltration (NF) membranes were fabricated via the interfacial polymerization of piperazine (PIP) and 1,3,5-benzenetricart)oiiyl trichloride on polysulfone (PSf) support membranes blended with K^+-responsive poly(N-isopropylacryamideco- acryloylamidobenzo-15-crown-5)(P(NIPAM-co- AAB15C5)). Membranes were characterized by attenuated total reflection Fourier transform infrared spectroscopy, X-ray photoelectron spectroscopy, atomic force microscope, scanning electron microscope, contact angle, and filtration tests. The results showed that:(1) Under K^+-free conditions, the blended P(NIPAM-co-AAB15C5)/PSf supports had porous and hydrophilic surfaces, thereby producing NF membranes with smooth surfaces and low MgSO4 rejections;(2) With K^+ in the PIP solution, the surface roughness and water permeability of the resultant NF membrane were increased due to the K^+-induced transition of low-content P(NIPAM-co-AAB15C5) from hydrophilic to hydrophobic;(3) After a curing treatment at 95℃, the improved NF membrane achieved an even higher pure water permeability of 10.97 L·m^-2·h^-1 - bar1 under 200 psi. Overall, this study provides a novel method to improve the performance of NF membranes and helps understand the influence of supports on TFC membranes.

关键词： nanofiltration interfacial polymerization support membrane potassium ion-responsive thin-film composite