Perspective on new cell-free DNA technologies for early cancer detection

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。

应用粒子滤波同化条件植被温度指数的土壤水分估测

为了准确地获取2013—2015年关中平原冬小麦主要生育期土壤含水量(0~20 cm)的时空信息,基于Landsat-8遥感数据反演条件植被温度指数(CVTI),并结合CVTI和实测土壤水分间的线性相关性构建土壤水分反演模型。应用粒子滤波(PF)算法同化基于CVTI反演的和CERES-Wheat模型模拟的土壤水分,得到以天为步长的土壤水分同化值,利用土壤水分实测值分别检验土壤水分模拟值、反演值和同化值的精度。结果表明,CVTI和实测土壤水分间的线性相关性显著,尤其在小麦拔节期和抽穗~灌浆期,其相关性达到极显著水平(P<0.01);土壤水分同化值和实测值间的线性相关性(r=0.96,P<0.001)大于土壤水分模拟值和实测值间的相关性(r=0.71,P<0.01)以及土壤水分反演值和实测值间的相关性(r=0.89,P<0.001);土壤水分同化值的均方根误差(RMSE)和平均相对误差(MRE)比土壤水分模拟值的RMSE和MRE分别降低了0.025 cm^3·cm^(-3)和2.70%,比土壤水分反演值的RMSE和MRE分别降低了0.016 cm^3·cm^(-3)和4.15%,同化过程提高了时间序列土壤含水量的估测精度。因此,基于CVTI和PF算法能够较为准确估测关中平原小麦主要生育期的土壤含水量。

基于多源遥感数据融合和LSTM算法的作物分类研究

准确、及时地获取农作物的空间分布信息,对于指导农业生产、制定农业政策具有重要意义。为了检验长短时记忆网络(long short-term memory,LSTM)算法在基于时序遥感数据进行作物分类中的优势,该文以临汾盆地为研究区域,利用Savitzky-Golay滤波对MODIS NDVI进行平滑处理,并采用ESTARFM(enhanced spatial and temporal adaptive reflectance fusion model)算法对滤波后的MODIS NDVI和Landsat NDVI进行融合,生成空间分辨率为30 m、时间分辨率为8天的时序NDVI。基于Landsat NDVI利用LSTM算法进行作物分类,同时,基于融合NDVI分别利用LSTM算法和神经网络(neural network,NN)算法进行作物分类,并对比3种方法的分类精度。结果表明,Savitzky-Golay滤波后的时序MODIS NDVI能够反映不同作物的物候特征;基于融合NDVI的分类精度明显高于基于Landsat NDVI的分类精度,表明融合后的时序NDVI由于具有更高的时间分辨率,能够更加突出不同作物的物候特征,显著提高作物分类精度;基于融合NDVI和LSTM算法的分类精度高于基于融合NDVI和NN算法的分类精度,前者的冬小麦面积估测精度高于后者的估测精度,表明LSTM算法的分类精度高于NN算法。该文可为基于遥感影像进行不同作物种植区域提取的研究提供重要的方法参考。

Novel technologies in cfDNA analysis and potential utility in clinic

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.

Delineating the rice crop activities in Northeast China through regional parametric synthesis using satellite remote sensing time-series data from 2000 to 2015

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.

Glioma-derived ANXA1 suppresses the immune response to TLR3 ligands by promoting an anti-inflammatory tumor microenvironment

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.

河北省中部平原玉米长势遥感综合监测

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。

基于时间序列叶面积指数稀疏表示的作物种植区域提取

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。

大规模中药转录组研究揭示中药抑制新冠肺炎细胞因子风暴的分子机制

中药抑制新冠肺炎相关细胞因子风暴的分子机制尚不清晰.本文首先通过HTS2技术,在基因表达层面上,大规模检测了578味中药提取物对与细胞因子风暴紧密相关的信号通路的调控作用,发现53味中药对这些通路具有显著抑制作用;评估了国家及地方新冠肺炎诊疗方案中出现的338个方剂,发现理中汤、六君子汤、黄连解毒汤、清肺排毒汤在抑制细胞因子风暴方面排在前列;鉴别了相关中药的潜在活性成分,进一步揭示了中药抑制新冠肺炎相关细胞因子风暴的化学基础.本研究系统探究了中药调节新冠相关细胞因子风暴的分子机制,为中药治疗新冠肺炎药效机制的解析提供了科学依据.

Genome-wide evolution analysis reveals low CpG contents of fast-evolving genes and identifies antiviral microRNAs

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.