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| 1 | The Genome Sequence Archive Family: Toward Explosive Data Growth and Diverse Data Types显示文摘The Genome Sequence Archive(GSA)is a data repository for archiving raw sequence data,which provides data storage and sharing services for worldwide scientific communities.Considering explosive data growth with diverse data types,here we present the GSA family by expanding into a set of resources for raw data archive with different purposes,namely,GSA(http://gffzz77e3413bc06540edsu55uk6cqubwc6f9u.ffgz.tsg.suse.edu.cn/gsa/),GSA for Human(GSA-Human,http://gffzz77e3413bc06540edsu55uk6cqubwc6f9u.ffgz.tsg.suse.edu.cn/gsa-human/),and Open Archive for Miscellaneous Data(OMIX,http://gffzz77e3413bc06540edsu55uk6cqubwc6f9u.ffgz.tsg.suse.edu.cn/omix/).Compared with the 2017 version,GSA has been significantly updated in data model,online functionalities,and web interfaces.GSA-Human,as a new partner of GSA,is a data repository specialized in human genetics-related data with controlled access and security.OMIX,as a critical complement to the two resources mentioned above,is an open archive for miscellaneous data.Together,all these resources form a family of resources dedicated to archiving explosive data with diverse types,accepting data submissions from all over the world,and providing free open access to all publicly available data in support of worldwide research activities. | Tingting Chen Xu Chen Sisi Zhang Junwei Zhu Bixia Tang Anke Wang Lili Dong Zhewen Zhang Caixia Yu Yanling Sun Lianjiang Chi Huanxin Chen Shuang Zhai Yubin Sun Li Lan Xin Zhang Jingfa Xiao Yiming Bao Yanqing Wang Zhang Zhang Wenming Zhao | 2021 | Genomics, Proteomics & Bioinformatics2021，19，4： | 38 |
| 2 | Whole Genome Analyses of Chinese Population and De Novo Assembly of A Northern Han Genome显示文摘To unravel the genetic mechanisms of disease and physiological traits,it requires comprehensive sequencing analysis of large sample size in Chinese populations.Here,we report the primary results of the Chinese Academy of Sciences Precision Medicine Initiative(CASPMI)project launched by the Chinese Academy of Sciences,including the de novo assembly of a northern Han reference genome(NH1.0)and whole genome analyses of 597 healthy people coming from most areas in China.Given the two existing reference genomes for Han Chinese(YH and HX1)were both from the south,we constructed NH1.0,a new reference genome from a northern individual,by combining the sequencing strategies of PacBio,10×Genomics,and Bionano mapping.Using this integrated approach,we obtained an N50 scaffold size of 46.63 Mb for the NH1.0 genome and performed a comparative genome analysis of NH1.0 with YH and HX1.In order to generate a genomic variation map of Chinese populations,we performed the whole-genome sequencing of 597 participants and identified 24.85 million(M)single nucleotide variants(SNVs),3.85 M small indels,and 106,382 structural variations.In the association analysis with collected phenotypes,we found that the T allele of rs1549293 in KAT8 significantly correlated with the waist circumference in northern Han males.Moreover,significant genetic diversity in MTHFR,TCN2,FADS1,and FADS2,which associate with circulating folate,vitamin B12,or lipid metabolism,was observed between northerners and southerners.Especially,for the homocysteine-increasing allele of rs1801133(MTHFR 677T),we hypothesize that there exists a “comfort”zone for a high frequency of 677T between latitudes of 35–45 degree North.Taken together,our results provide a high-quality northern Han reference genome and novel population-specific data sets of genetic variants for use in the personalized and precision medicine. | Zhenglin Du Liang Ma Hongzhu Qu Wei Chen Bing Zhang Xi Lu Weibo Zhai Xin Sheng Yongqiao Sun Wenjie Li Meng Lei Qiuhui Qi Na Yuan Shuo Shi Jingyao Zeng Jinyue Wang Yadong Yang Qi Liu Yaqiang Hong Lili Dong Zhewen Zhang Dong Zou Yanqing Wang Shuhui Song Fan Liu Xiangdong Fang Hua Chen Xin Liu Jingfa Xiao Changqing Zeng | 2019 | Genomics, Proteomics & Bioinformatics2019，17，3： | 4 |
| 3 | Neoadjuvant radiotherapy for resectable hepatocellular carcinoma with portal vein tumor thrombus:a systematic review显示文摘Background:The prognosis of hepatocellular carcinoma(HCC)with portal vein tumor thrombus(PVTT)is extremely poor.The clinical outcome of preoperative radiotherapy(RT)is still controversial.This study aimed to compare the clinical outcomes of combined neoadjuvant RT and hepatectomy with hepatectomy alone for HCC with PVTT.Methods:Comprehensive database searches were performed in PubMed,the Cochrane Library,EMBASE,and the Web of Science to retrieve studies published from the database creation to July 1,2020.Only comparative studies that measured survival between neoadjuvant RT followed by hepatectomy and hepatectomy alone were included.The characteristics of the included studies and patients were extracted,and the included data are presented as relative ratio(RR)estimates with 95%confidence intervals(CIs)for all outcomes.The RRs of each study were pooled using a fixed or random effects model with Review Manager(the Cochrane Collaboration,Oxford,UK)version 5.3.The response rate to RT and the overall survival(OS)rate in neoadjuvant RT followed by hepatectomy and hepatectomy alone were measured.Results:One randomized and two non-randomized controlled trials with 302 patients were included.Most patients were classified as Child-Pugh A,and Type II and III PVTT were the most common types.After RT,29(22.8%)patients were evaluated as partial response(PR)and had a positive RT response,but nine(7.1%)had progressive disease(PD).Neoadjuvant RT followed by hepatectomy was received by 127(42.1%)patients after excluding 15(5.0%)patients with severe complications or PD after RT,and 160(53.0%)patients received hepatectomy alone.In the randomized controlled trial(RCT),the 1-year OS rate in the neoadjuvant RT group and the surgery alone group was 75.2%and 43.1%,respectively(P<0.001).In the two non-randomized studies,a meta-analysis with a fixed effects model showed a longer OS in patients undergoing neoadjuvant RT followed by hepatectomy compared with hepatectomy alone at 1-year follow-up(RR=2.02;95%CI:1.45-2.80;P<0.0001).Conclusions:This systematic review showed that neoadjuvant RT followed by hepatectomy in patients with resectable HCC and PVTT was associated with a longer OS than patients who received hepatectomy alone. | Zhewen Wei Jianjun Zhao Xinyu Bi Yefan Zhang Jianguo Zhou Zhiyu Li Zhen Huang Hong Zhao Jianqiang Cai | 2022 | Hepatobiliary Surgery and Nutrition2022，11，5： | 4 |
| 4 | Recent advances in fire-retardant rigid polyurethane foam显示文摘Driven by global environmental concerns,many efforts have been made to develop halogen-free flame retardants for rigid polyurethane foam(RPUF).These environmentally benign flame retardants are mainly divided into(i)reactive,(ii)additive,and(iii)coating types.The last decade has witnessed great progress of these three strategies,which enhance the fire safety of RPUF and maintain even improve the thermal insulation properties.This comprehensive review focuses on the up-to-date design of the reactive,additive,and coating flame retardants,and their effects on flame retardancy and thermal conductivity of RPUF.Moreover,the practical applications of the as-prepared flame-retardant RPUFs are highlighted.Finally,key challenges associated with these three kinds of flame retardants are discussed and future research opportunities are also proposed. | Menghe Zhu Zhewen Ma Lei Liu Jianzhong Zhang Siqi Huo Pingan Song | 2022 | Journal of Materials Science & Technology2022，，17： | 3 |
| 5 | Aberrant cholesterol metabolic signaling impairs antitumor immunosurveillance through natural killer T cell dysfunction in obese liver显示文摘Obesity is a major risk factor for cancers including hepatocellular carcinoma(HCC)that develops from a background of non-alcoholic fatty liver disease(NAFLD).Hypercholesterolemia is a common comorbidity of obesity.Although cholesterol biosynthesis mainly occurs in the liver,its role in HCC development of obese people remains obscure.Using high-fat high-carbohydrate diet-associated orthotopic and spontaneous NAFLD-HCC mouse models,we found that hepatic cholesterol accumulation in obesity selectively suppressed natural killer T(NKT)cell-mediated antitumor immunosurveillance.Transcriptome analysis of human liver revealed aberrant cholesterol metabolism and NKT cell dysfunction in NAFLD patients.Notably,cholesterol-lowering rosuvastatin restored NKT expansion and cytotoxicity to prevent obesogenic diet-promoted HCC development.Moreover,suppression of hepatic cholesterol biosynthesis by a mammalian target of rapamycin(mTOR)inhibitor vistusertib preceded tumor regression,which was abolished by NKT inactivation but not CD8^(+)T cell depletion.Mechanistically,sterol regulatory element-binding protein 2(SREBP2)-driven excessive cholesterol production from hepatocytes induced lipid peroxide accumulation and deficient cytotoxicity in NKT cells,which were supported by findings in people with obesity,NAFLD and NAFLD-HCC.This study highlights mTORC1/SREBP2/cholesterol-mediated NKT dysfunction in the tumor-promoting NAFLD liver microenvironment,providing intervention strategies that invigorating NKT cells to control HCC in the obesity epidemic. | Wenshu Tang Jingying Zhou Weiqin Yang Yu Feng Haoran Wu Myth T.S.Mok Lingyun Zhang Zhixian Liang Xiaoyu Liu Zhewen Xiong Xuezhen Zeng Jing Wang Jiahuan Lu Jingqing Li Hanyong Sun Xiaoyu Tian Philip Chun Yeung Yong Hou Heung Man Lee Candice C.H.Lam Howard H.W.Leung Anthony W.H.Chan Ka Fai To John Wong Paul B.S.Lai Kelvin K.C.Ng Simon K.H.Wong Vincent W.S.Wong Alice P.S.Kong Joseph J.Y.Sung Alfred S.L.Cheng | 2022 | Cellular & Molecular Immunology2022，19，7： | 3 |
| 6 | Exergy Analysis of a Novel Chemical Looping Hydrogen Generation System Integrated with SOFC显示文摘In this paper,a novel system integrating chemical-looping hydrogen generation(CLH)system and solid oxide fuel cell(SOFC)has been proposed.This new methane-fuelled energy system was investigated with energy balance and exergy analysis.CLH produces the hydrogen as the fuel of the SOFC,and the Fe O and Fe3O4 are selected as the looping material.Waste heat from the SOFC is absorbed by the CLH and converted to chemical energy through the reduction reaction of CLH.Owing to the cascade utilization of the fuel between the CLH and SOFC,the net efficiency of this novel system can achieve 62.8%considering CO_(2)separation,more than 10 percentage points higher than a methane reforming fuelled SOFC system.Meanwhile,by using the CLH to produce the hydrogen,the CO_(2)can be recovered without an energy penalty.Through the analysis of the graphical exergy,the cascade utilization of waste heat and the high-efficiency hydrogen production is the main reason of high performance.This novel system also has the advantage of CO_(2)capture without energy penalty,so this combined system is an advantaged method to accomplish the efficient utilization of methane. | ZHANG Xiaosong CHEN Zhewen CHEN Zhenbin LI Jinsong | 2021 | Journal of Thermal Science2021，30，1： | 2 |
| 7 | A Brief Review of Software Tools for Pangenomics显示文摘Since the proposal for pangenomic study, there have been a dozen software tools actively in use for pangenomic analysis. By the end of 2014, Panseq and the pan-genomes analysis pipeline(PGAP) ranked as the top two most popular packages according to cumulative citations of peerreviewed scientific publications. The functions of the software packages and tools, albeit variable among them, include categorizing orthologous genes, calculating pangenomic profiles, integrating gene annotations, and constructing phylogenies. As epigenomic elements are being gradually revealed in prokaryotes, it is expected that pangenomic databases and toolkits have to be extended to handle information of detailed functional annotations for genes and non-protein-coding sequences including non-coding RNAs, insertion elements, and conserved structural elements. To develop better bioinformatic tools, user feedback and integration of novel features are both of essence. | Jingfa Xiao Zhewen Zhang Jiayan Wu Jun Yu | 2015 | Genomics, Proteomics & Bioinformatics2015，13，1： | 1 |
| 8 | AHR mediates the aflatoxin B1 toxicity associated with hepatocellular carcinoma显示文摘Aflatoxin exposure is a crucial factor in promoting the development of primary hepatocellular carcinoma(HCC)in individuals infected with the hepatitis virus.However,the molecular pathways leading to its bioactivation and subsequent toxicity in hepatocytes have not been well-defined.Here,we carried out a genome-wide CRISPR-Cas9 genetic screen to identify aflatoxin B1(AFB1)targets.Among the most significant hits was the aryl hydrocarbon receptor(AHR),a ligand-binding transcription factor regulating cell metabolism,differentiation,and immunity. | Qing Zhu Yarui Ma Junbo Liang Zhewen Wei Mo Li Ying Zhang Mei Liu Huan He Chunfeng Qu Jianqiang Cai Xiaobing Wang Yixin Zeng Yuchen Jiao | 2021 | Signal Transduction and Targeted Therapy2021，6，9： | 1 |
| 9 | Correction: AHR mediates the Aflatoxin B1 toxicity associated with hepatocellular carcinoma显示文摘Correction to:Signal Transduction and Targeted Therapy http://gffzzd3cc09b8251d45dfsu55uk6cqubwc6f9u.ffgz.tsg.suse.edu.cn/10.1038/s41392-021-00713-1 z published online 9 August 2021 After online publication of the article^(1),the authors noticed one inadvertent mistake occurred during the production process in Fig.7 that needs to be corrected.The correct data are provided as follows.The key findings of the article are not affected by these corrections.The original article has been corrected. | Qing Zhu Yarui Ma Junbo Liang Zhewen Wei Mo Li Ying Zhang Mei Liu Huan He Chunfeng Qu Jianqiang Cai Xiaobing Wang Yixin Zeng Yuchen Jiao | 2022 | Signal Transduction and Targeted Therapy2022，7，1： | 0 |
| 10 | Non-specific phospholipase C4 hydrolyzes phosphosphingolipids and phosphoglycerolipids and promotes rapeseed growth and yield显示文摘Phosphorus is a major nutrient vital for plant growth and development,with a substantial amount of cellular phosphorus being used for the biosynthesis of membrane phospholipids.Here,we report that NON-SPECIFIC PHOSPHOLIPASE C4(NPC4)in rapeseed(Brassica napus)releases phosphate from phospholipids to promote growth and seed yield,as plants with altered NPC4 levels showed significant changes in seed production under different phosphate conditions.Clustered regularly interspaced short palindromic repeat(CRISPR)/CRISPR-associated nuclease 9(Cas9)-mediated knockout of Bna NPC4 led to elevated accumulation of phospholipids and decreased growth,whereas overexpression(OE)of Bna NPC4resulted in lower phospholipid contents and increased plant growth and seed production.We demonstrate that Bna NPC4 hydrolyzes phosphosphingolipids and phosphoglycerolipids in vitro,and plants with altered Bna NPC4 function displayed changes in their sphingolipid and glycerolipid contents in roots,with a greater change in glycerolipids than sphingolipids in leaves,particularly under phosphate deficiency conditions.In addition,Bna NPC4-OE plants led to the upregulation of genes involved in lipid metabolism,phosphate release,and phosphate transport and an increase in free inorganic phosphate in leaves.These results indicate that Bna NPC4 hydrolyzes phosphosphingolipids and phosphoglycerolipids in rapeseed to enhance phosphate release from membrane phospholipids and promote growth and seed production. | Bao Yang Jianwu Li Jiayu Yan Ke Zhang Zhewen Ouyang Yefei Lu Huili Wei Qing Li Xuan Yao Shaoping Lu Yueyun Hong Xuemin Wang Liang Guo | 2023 | Journal of Integrative Plant Biology2023，65，11： | 0 |
| 11 | Fire-retardant, anti-dripping, biodegradable and biobased polyurethane elastomers enabled by hydrogen-bonding with cellulose nanocrystals显示文摘Thermoplastic polyurethane(PU)elastomers have attracted significant attention because of their many important industrial applications.However,the creation of fire-retardant and anti-dripping PU elastomers has remained a grant challenge due to the lack of crosslinking and weak interchain interactions.Herein,we report a mechanically robust,biodegradable,fire-retardant,and anti-dripping biobased PU elastomer with excellent biodegradability using an abietic acid-based compound as hard segments and polycaprolactone diol(PCL)as soft segments,followed by physically crosslinking with cellulose nanocrystals(CNC)through dynamic hydrogen-bonding.The resultant elastomer shows the balanced mechanical and fire-retardant properties,e.g.,a tensile strength and break strain of 9.1 MPa and 560%,a self-extinguishing ability(V-0 rating in UL-94 testing),and an anti-dripping behavior.Moreover,the as-developed PU can be completely degraded in 1.0 wt.%lipase solution at 37℃ in 60 days,arising from the catalytic and wicking effect of CNC on PU chains.This work provides an innovative and versatile strategy for constructing robust,fire-retardant,anti-dripping,and biodegradable PU elastomers,which hold great promise for practical applications in electronic and automobile sectors. | Yijiao Xue Tianchen Zhang Hong Peng Zhewen Ma Meng Zhang Mark Lynch Toan Dinh Zhezhe Zhou Yonghong Zhou Pingan Song | 2024 | Nano Research2024，17，3： | 0 |
| 12 | Recent Advances in Video Coding for Machines Standard and Technologies显示文摘To improve the performance of video compression for machine vision analysis tasks,a video coding for machines(VCM)standard working group was established to promote standardization procedures.In this paper,recent advances in video coding for machine standards are presented and comprehensive introductions to the use cases,requirements,evaluation frameworks and corresponding metrics of the VCM standard are given.Then the existing methods are presented,introducing the existing proposals by category and the research progress of the latest VCM conference.Finally,we give conclusions. | ZHANG Qiang MEI Junjun GUAN Tao SUN Zhewen ZHANG Zixiang YU Li | 2024 | ZTE Communications2024，22，1： | 0 |
| 13 | Conformational effect on fluorescence emission of tetraphenylethylene-based metallacycles显示文摘Herein,we designed and constructed two metallacycles,1 and 2,to illustrate the conformational effect of isomeric AIE fluoropho res on the platfo rm of supramolecular coordination complexe s(SCCs).Specifically,the dangling phenyl rings in TPE units of the metallacycle 1 align completely outside the main cyclic structure,while in the metallacycle 2,these phenyl rings align half inside and half outside.The experimental results showed that two metallacycles exhibited different behaviors in terms of AIE fluorescence and chemical sensing,which could be attributed to the subtle structural difference of the TPE units.This work repre sents the unification of topics such as self-assembly,AIE,and chemical sensing,and further promotes the understanding for the structure-property relationship of isomeric AIE fluorophores. | Zhewen Guo Jun Zhao Yuhang Liu Guangfeng Li Heng Wang Yali Hou Mingming Zhang Xiaopeng Li Xuzhou Yan | 2021 | Chinese Chemical Letters2021，32，5： | 0 |
| 14 | Chinese expert consensus on multidisciplinary diagnosis and treatment of pancreatic neuroendocrine liver metastases显示文摘Many management strategies are available for pancreatic neuroendocrine neoplasms with liver metastases.However,a lack of biological,molecular,and genomic information and an absence of data from rigorous trials limit the validity of these strategies.This review presents the viewpoints from an international conference consisting of several expert working groups.The working groups reviewed a series of questions of particular interest to clinicians taking care of patients with pancreatic neuroendocrine neoplasms with liver metastases by reviewing the existing management strategies and literature,evaluating the evidence on which management decisions were based,developing internationally acceptable recommendations for clinical practice,and making recommendations for clinical and research endeavors.The review for each question will be followed by recommendations from the panel. | Yihebali Chi Liming Jiang Susheng Shi Shun He Chunmei Bai Dan Cao Jianqiang Cai Qichen Chen Xiao Chen Yiqiao Deng Shunda Du Zhen Huang Li Huo Yuan Ji Jie Li Wenhui Lou Jie Luo Xueying Shi Lijie Song Bei Sun Huangying Tan Feng Wang Xuan Wang Zhewen Wei Wenming Wu Dianrong Xiu Jianming Xu Huadan Xue Yi Yang Fei Yin Chunhui Yuan Yefan Zhang Weixun Zhou Dongbing Zhao Hong Zhao | 2023 | Journal of Pancreatology2023，6，4： | 0 |
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