High cancer heterogeneity and aggressiveness are major factors contributing to the poor prognosis of patients with advanced cancer~(1-5).Early detection of cancer can significantly improve the prognosis of patients wi...High cancer heterogeneity and aggressiveness are major factors contributing to the poor prognosis of patients with advanced cancer~(1-5).Early detection of cancer can significantly improve the prognosis of patients with early-stage cancer after standard treatment.Although traditional cancer detection technologies,such as endoscopy for gastrointestinal cancer,mammography for breast cancer。展开更多
The profiling of plasma cell-free DNA(cfDNA)is becoming a valuable tool rapidly for tumor diagnosis,monitoring and prognosis.Diverse plasma cfDNA technologies have been in routine or emerging use,including analyses of...The profiling of plasma cell-free DNA(cfDNA)is becoming a valuable tool rapidly for tumor diagnosis,monitoring and prognosis.Diverse plasma cfDNA technologies have been in routine or emerging use,including analyses of mutations,copy number alterations,gene fusions and DNA methylation.Recently,new technologies in cfDNA analysis have been developed in laboratories,and potentially reflect the status of epigenetic modification,the immune microenvironment and the microbiome in tumor tissues.In this review,the authors discuss the principles,methods and effects of the current cfDNA assays and provide an overview of studies that may inform clinical applications in the near future.展开更多
Accurate rice area extraction and yield simulations are important for understanding how national agricultural policies and environmental issues affect regional spatial changes in rice farming. In this study, an improv...Accurate rice area extraction and yield simulations are important for understanding how national agricultural policies and environmental issues affect regional spatial changes in rice farming. In this study, an improved regional parametric syntheses approach, that is, the rice zoning adaptability criteria and dynamic harvest index(RZAC-DHI), was established, which can effectively simulate the rice cultivation area and yield at the municipal level. The RZAC was used to extract the rice area using Moderate Resolution Imaging Spectroradiometer time-series data and phenological information. The DHI was calculated independently, and then yield was obtained based on the DHI and net primary productivity(NPP). Based on the above results, we analyzed the spatial–temporal patterns of the rice cultivation area and yield in Northeast China(NEC) during 2000–2015. The results revealed that the methods established in this study can effectively support the yearly mapping of the rice area and yield in NEC, the average precisions of which exceed 90 and 80%, respectively. The rice planting areas are mainly located on the Sanjiang, Songnen and Liaohe plains, China, which are distributed along the Songhua and Liaohe rivers. The rice cultivation area and yield in this region increased significantly from 2000 to 2015, with increases of nearly 58 and 90%, respectively. The rice crop area and yield increased the fastest in Heilongjiang Province, China, whereas small changes occurred in Jilin and Liaoning provinces, China. Their gravity centers exhibited evident northward and eastward shifts, with offset distances of 107 and 358 km, respectively. Moreover, Heilongjiang Province has gradually become the new main rice production region. The methodologies used in this study provide a valuable reference for other related studies, and the spatial-temporal variation characteristics of the rice activities have raised new attention as to how these shifts affect national food security and resource allocation.展开更多
A highly immunosuppressive tumor microenvironment(TME)and the presence of the blood‒brain barrier are the two major obstacles to eliciting an effective immune response in patients with high-grade glioma(HGG).Here,we t...A highly immunosuppressive tumor microenvironment(TME)and the presence of the blood‒brain barrier are the two major obstacles to eliciting an effective immune response in patients with high-grade glioma(HGG).Here,we tried to enhance the local innate immune response in relapsed HGG by intracranially injecting poly(I:C)to establish a robust antitumor immune response in this registered clinical trial(NCT03392545).During the follow-up,12/27(44.4%)patients who achieved tumor control concomitant with survival benefit were regarded as responders in our study.We found that the T-cell receptor(TCR)repertoire in the TME was reshaped after poly(I:C)treatment.Based on the RNA-seq analysis of tumor samples,the expression of annexin A1(ANXA1)was significantly upregulated in the tumor cells of nonresponders,which was further validated at the protein level.In vitro and in vivo experiments showed that ANXA1 could induce the production of M2-like macrophages and microglia via its surface receptor formyl peptide receptor 1(FPR1)to establish a Treg cell-driven immunosuppressive TME and suppress the antitumor immune response facilitated by poly(I:C).The ANXA1/FPR1 signaling axis can inhibit the innate immune response of glioma patients by promoting an anti-inflammatory and Treg-driven TME.Moreover,ANXA1 could serve as a reliable predictor of response to poly(I:C),with a notable predictive accuracy rate of 92.3%.In light of these notable findings,this study unveils a new perspective of immunotherapy for gliomas.展开更多
为了提高玉米的遥感长势监测的准确度,以河北省中部平原地区为研究区域,以MODIS遥感数据反演的条件植被温度指数(Vegetation Temperature Condition Index, VTCI)与叶面积指数(Leaf Area Index, LAI)作为玉米长势监测指标,通过灰色关联...为了提高玉米的遥感长势监测的准确度,以河北省中部平原地区为研究区域,以MODIS遥感数据反演的条件植被温度指数(Vegetation Temperature Condition Index, VTCI)与叶面积指数(Leaf Area Index, LAI)作为玉米长势监测指标,通过灰色关联度分析法确定玉米各生育时期(出苗—拔节期、拔节—抽雄期、抽雄—灌浆期与灌浆—成熟期)VTCI与LAI作为相应生育时期长势监测指标的权重值,以及4个生育时期的玉米长势在总体长势与产量形成中的权重值,并基于权重结果分别构建玉米在4个生育时期与主要生育期的长势综合监测指标,进而评估研究区域2011—2016年间的玉米长势。结果表明,各生育时期VTCI作为长势监测指标的权重值均大于LAI,且以拔节—抽雄期最大,抽雄—灌浆期次之,说明玉米各生育时期的长势与最终产量较易受到水分胁迫的影响,并以拔节—抽雄期与抽雄—灌浆期对水分胁迫最为敏感;而玉米长势综合监测指标在4个生育时期的权重值较为接近,并以灌浆—成熟期略大,说明该时期的玉米长势与最终产量之间的关系较为密切。研究区域5市的县域尺度玉米长势综合监测指标与单产之间的决定系数(R2)介于0.247~0.598之间,均达到了极显著水平(P<0.001),优于单一的VTCI或LAI指标,表明基于长势综合监测指标的玉米长势监测结果准确度较高。研究年份间该区域的玉米长势以2011年的长势最好,2014年与2015年长势最差,且西部长势优于东部。展开更多
以华北平原黄河以北地区为研究区域,以时间序列叶面积指数LAI(Leaf Area Index)傅里叶变换的谐波特征作为不同作物识别的数据源,利用稀疏表示的分类方法识别2007年—2016年冬小麦、春玉米、夏玉米等主要农作物种植区域。首先利用上包络...以华北平原黄河以北地区为研究区域,以时间序列叶面积指数LAI(Leaf Area Index)傅里叶变换的谐波特征作为不同作物识别的数据源,利用稀疏表示的分类方法识别2007年—2016年冬小麦、春玉米、夏玉米等主要农作物种植区域。首先利用上包络线Savitzky-Golay滤波分别对2007年—2016年的时间序列MODIS LAI曲线进行重构,进而对重构的年时间序列LAI进行傅里叶变换,以0—5级谐波振幅、1—5级谐波相位作为作物识别的依据,基于各类地物的训练样本,通过在线字典学习算法构建稀疏表示方法的判别字典,对每个待测样本利用正交匹配追踪算法求解稀疏系数,从而计算对应于各类地物的重构误差,根据最小重构误差判定待测样本的作物类型,并对作物识别结果的位置精度进行验证。结果表明,2007年—2016年作物识别的总体精度为77.97%,Kappa系数为0.74,表明本文提出的方法可以用于研究区域主要作物种植区域的提取。展开更多
Noncoding RNAs(ncRNAs) play important roles in many biological processes and provide materials for evolutionary adaptations beyond protein-coding genes, such as in the arms race between the host and pathogen. However,...Noncoding RNAs(ncRNAs) play important roles in many biological processes and provide materials for evolutionary adaptations beyond protein-coding genes, such as in the arms race between the host and pathogen. However, currently, a comprehensive high-resolution analysis of primate genomes that includes the latest annotated ncRNAs is not available. Here, we developed a computational pipeline to estimate the selections that act on noncoding regions based on comparisons with a large number of reference sequences in introns adjacent to the interested regions. Our method yields result comparable with those of the established codon-based method and phyloP method for coding genes;thus, it provides a holistic framework for estimating the selection on the entire genome. We further showed that fastevolving protein-coding genes and their corresponding 50 UTRs have a significantly lower frequency of the CpG dinucleotides than those evolving at an average pace, and these fast-evolving genes are enriched in the process of immunity and host defense. We also identified fast-evolving miRNAs with antiviral functions in cells. Our results provide a resource for high-resolution evolution analysis of the primate genomes.展开更多
基金partially supported by grants(Grant No.81972680 to X.L.)from the National Natural Science Foundation of Chinaa start-up fund from Tsinghua University-Peking University Joined Center for Life Science。
文摘High cancer heterogeneity and aggressiveness are major factors contributing to the poor prognosis of patients with advanced cancer~(1-5).Early detection of cancer can significantly improve the prognosis of patients with early-stage cancer after standard treatment.Although traditional cancer detection technologies,such as endoscopy for gastrointestinal cancer,mammography for breast cancer。
基金supported by the Beijing Natural Science Foundation(No.Z190022)the National Natural Science Foundation of China(No.81972680,81773292 and 82072748)。
文摘The profiling of plasma cell-free DNA(cfDNA)is becoming a valuable tool rapidly for tumor diagnosis,monitoring and prognosis.Diverse plasma cfDNA technologies have been in routine or emerging use,including analyses of mutations,copy number alterations,gene fusions and DNA methylation.Recently,new technologies in cfDNA analysis have been developed in laboratories,and potentially reflect the status of epigenetic modification,the immune microenvironment and the microbiome in tumor tissues.In this review,the authors discuss the principles,methods and effects of the current cfDNA assays and provide an overview of studies that may inform clinical applications in the near future.
基金supported by the National Key Research and Development Program of China(2016YFD0300110 and 2016YFD0300101)the Agricultural Science and Technology Innovation Program of Chinese Academy of Agricultural Sciences(CAAS-ASTIP-2016-AII)the Science and Technology Project of Xinjiang Production and Construction Corps,China(2019AB002)。
文摘Accurate rice area extraction and yield simulations are important for understanding how national agricultural policies and environmental issues affect regional spatial changes in rice farming. In this study, an improved regional parametric syntheses approach, that is, the rice zoning adaptability criteria and dynamic harvest index(RZAC-DHI), was established, which can effectively simulate the rice cultivation area and yield at the municipal level. The RZAC was used to extract the rice area using Moderate Resolution Imaging Spectroradiometer time-series data and phenological information. The DHI was calculated independently, and then yield was obtained based on the DHI and net primary productivity(NPP). Based on the above results, we analyzed the spatial–temporal patterns of the rice cultivation area and yield in Northeast China(NEC) during 2000–2015. The results revealed that the methods established in this study can effectively support the yearly mapping of the rice area and yield in NEC, the average precisions of which exceed 90 and 80%, respectively. The rice planting areas are mainly located on the Sanjiang, Songnen and Liaohe plains, China, which are distributed along the Songhua and Liaohe rivers. The rice cultivation area and yield in this region increased significantly from 2000 to 2015, with increases of nearly 58 and 90%, respectively. The rice crop area and yield increased the fastest in Heilongjiang Province, China, whereas small changes occurred in Jilin and Liaoning provinces, China. Their gravity centers exhibited evident northward and eastward shifts, with offset distances of 107 and 358 km, respectively. Moreover, Heilongjiang Province has gradually become the new main rice production region. The methodologies used in this study provide a valuable reference for other related studies, and the spatial-temporal variation characteristics of the rice activities have raised new attention as to how these shifts affect national food security and resource allocation.
基金supported by a grant from the National Natural Science Foundation of China(81771309,31930039 and 31821003 to Xin Lin and 82202983 to Haihui Jiang)supported by grants from the Capital’s Funds for Health Improvement and Research(2020-2-1075 to Yong Cui)the National Key Research and Development Program of China(2019YFA0508502 to Xin Lin).
文摘A highly immunosuppressive tumor microenvironment(TME)and the presence of the blood‒brain barrier are the two major obstacles to eliciting an effective immune response in patients with high-grade glioma(HGG).Here,we tried to enhance the local innate immune response in relapsed HGG by intracranially injecting poly(I:C)to establish a robust antitumor immune response in this registered clinical trial(NCT03392545).During the follow-up,12/27(44.4%)patients who achieved tumor control concomitant with survival benefit were regarded as responders in our study.We found that the T-cell receptor(TCR)repertoire in the TME was reshaped after poly(I:C)treatment.Based on the RNA-seq analysis of tumor samples,the expression of annexin A1(ANXA1)was significantly upregulated in the tumor cells of nonresponders,which was further validated at the protein level.In vitro and in vivo experiments showed that ANXA1 could induce the production of M2-like macrophages and microglia via its surface receptor formyl peptide receptor 1(FPR1)to establish a Treg cell-driven immunosuppressive TME and suppress the antitumor immune response facilitated by poly(I:C).The ANXA1/FPR1 signaling axis can inhibit the innate immune response of glioma patients by promoting an anti-inflammatory and Treg-driven TME.Moreover,ANXA1 could serve as a reliable predictor of response to poly(I:C),with a notable predictive accuracy rate of 92.3%.In light of these notable findings,this study unveils a new perspective of immunotherapy for gliomas.
文摘为了提高玉米的遥感长势监测的准确度,以河北省中部平原地区为研究区域,以MODIS遥感数据反演的条件植被温度指数(Vegetation Temperature Condition Index, VTCI)与叶面积指数(Leaf Area Index, LAI)作为玉米长势监测指标,通过灰色关联度分析法确定玉米各生育时期(出苗—拔节期、拔节—抽雄期、抽雄—灌浆期与灌浆—成熟期)VTCI与LAI作为相应生育时期长势监测指标的权重值,以及4个生育时期的玉米长势在总体长势与产量形成中的权重值,并基于权重结果分别构建玉米在4个生育时期与主要生育期的长势综合监测指标,进而评估研究区域2011—2016年间的玉米长势。结果表明,各生育时期VTCI作为长势监测指标的权重值均大于LAI,且以拔节—抽雄期最大,抽雄—灌浆期次之,说明玉米各生育时期的长势与最终产量较易受到水分胁迫的影响,并以拔节—抽雄期与抽雄—灌浆期对水分胁迫最为敏感;而玉米长势综合监测指标在4个生育时期的权重值较为接近,并以灌浆—成熟期略大,说明该时期的玉米长势与最终产量之间的关系较为密切。研究区域5市的县域尺度玉米长势综合监测指标与单产之间的决定系数(R2)介于0.247~0.598之间,均达到了极显著水平(P<0.001),优于单一的VTCI或LAI指标,表明基于长势综合监测指标的玉米长势监测结果准确度较高。研究年份间该区域的玉米长势以2011年的长势最好,2014年与2015年长势最差,且西部长势优于东部。
文摘以华北平原黄河以北地区为研究区域,以时间序列叶面积指数LAI(Leaf Area Index)傅里叶变换的谐波特征作为不同作物识别的数据源,利用稀疏表示的分类方法识别2007年—2016年冬小麦、春玉米、夏玉米等主要农作物种植区域。首先利用上包络线Savitzky-Golay滤波分别对2007年—2016年的时间序列MODIS LAI曲线进行重构,进而对重构的年时间序列LAI进行傅里叶变换,以0—5级谐波振幅、1—5级谐波相位作为作物识别的依据,基于各类地物的训练样本,通过在线字典学习算法构建稀疏表示方法的判别字典,对每个待测样本利用正交匹配追踪算法求解稀疏系数,从而计算对应于各类地物的重构误差,根据最小重构误差判定待测样本的作物类型,并对作物识别结果的位置精度进行验证。结果表明,2007年—2016年作物识别的总体精度为77.97%,Kappa系数为0.74,表明本文提出的方法可以用于研究区域主要作物种植区域的提取。
基金supported by the National Natural Science Foundation of China(81673460)Sichuan Youth Science and Technology Innovation Research Team of Experimental Formulology(2020JDTD0022)。
基金supported by the National Natural Science Foundation of China (Grant No. 31670777)the China National Funds for Distinguished Young Scientists (Grant No. 31722030)+2 种基金the Beijing Advanced Innovation Center for Structural Biology to X.T.the Tsinghua-Peking Joint Center for Life Sciences (Grant No. 61020100119)the National Thousand Young Talents Program of China (Grant No. 042021011) to X.L.
文摘Noncoding RNAs(ncRNAs) play important roles in many biological processes and provide materials for evolutionary adaptations beyond protein-coding genes, such as in the arms race between the host and pathogen. However, currently, a comprehensive high-resolution analysis of primate genomes that includes the latest annotated ncRNAs is not available. Here, we developed a computational pipeline to estimate the selections that act on noncoding regions based on comparisons with a large number of reference sequences in introns adjacent to the interested regions. Our method yields result comparable with those of the established codon-based method and phyloP method for coding genes;thus, it provides a holistic framework for estimating the selection on the entire genome. We further showed that fastevolving protein-coding genes and their corresponding 50 UTRs have a significantly lower frequency of the CpG dinucleotides than those evolving at an average pace, and these fast-evolving genes are enriched in the process of immunity and host defense. We also identified fast-evolving miRNAs with antiviral functions in cells. Our results provide a resource for high-resolution evolution analysis of the primate genomes.