弯曲姿态蛾类幼虫的自动识别方法研究

【目的】为害态幼虫现场识别时, 幼虫常出现姿态弯曲情况, 使提取的特征向量失真, 影响幼虫的匹配识别结果。本文提出了一种基于扇形变换的姿态不变胡氏矩特征向量提取方法, 提取的病害幼虫特征向量具有平移、 比例、 旋转和姿态不变性, 可以实现粗短弯曲姿态幼虫的自动识别。【方法】首先在幼虫图像细化的基础上采用最优一致逼近法确定了幼虫的弯曲区域和非弯曲区域。然后, 幼虫的弯曲区域采用扇形变换实现校正变直, 非弯曲区域经旋转和平移与扇形变换后的区域拼接组成完整虫体; 采用八邻域均值法填充变换后虫体区域中的空白点, 实现幼虫像的弯曲自动校正; 在此基础上提取胡氏不变矩具有姿态不变性, 采用最小距离分类器实现了多姿态幼虫的自动识别。最后, 以多种弯曲姿态的斜纹夜蛾Prodenia litura、 棉铃虫Heliocoverpa armigera、 甜菜夜蛾Spodoptera exigua、 玉米螟Ostrinia nubilalis等病害蛾类幼虫为识别对象进行了识别验证。【结果】对于24种不同姿态的幼虫图像, 在80%的识别阈值条件下, 基于经典胡氏不变矩的幼虫识别率为25%, 基于姿态不变胡氏矩的识别率为100%。【结论】实验结果表明该方法对多种弯曲姿态的粗短幼虫具有较高的识别率。     

Binary Regression Analysis with Pooled Exposure Measurements: A Regression Calibration Approach

Summary It has become increasingly common in epidemiological studies to pool specimens across subjects to achieve accurate quantitation of biomarkers and certain environmental chemicals. In this article, we consider the problem of fitting a binary regression model when an important exposure is subject to pooling. We take a regression calibration approach and derive several methods, including plug‐in methods that use a pooled measurement and other covariate information to predict the exposure level of an individual subject, and normality‐based methods that make further adjustments by assuming normality of calibration errors. Within each class we propose two ways to perform the calibration (covariate augmentation and imputation). These methods are shown in simulation experiments to effectively reduce the bias associated with the naive method that simply substitutes a pooled measurement for all individual measurements in the pool. In particular, the normality‐based imputation method performs reasonably well in a variety of settings, even under skewed distributions of calibration errors. The methods are illustrated using data from the Collaborative Perinatal Project.     

A Graphical Weighted Power Improving Multiplicity Correction Approach for SNP Selections

Controlling for the multiplicity effect is an essential part of determining statistical significance in large-scale single-locus association genome scans on Single Nucleotide Polymorphisms (SNPs). Bonferroni adjustment is a commonly used approach due to its simplicity, but is conservative and has low power for large-scale tests. The permutation test, which is a powerful and popular tool, is computationally expensive and may mislead in the presence of family structure. We propose a computationally efficient and powerful multiple testing correction approach for Linkage Disequilibrium (LD) based Quantitative Trait Loci (QTL) mapping on the basis of graphical weighted-Bonferroni methods. The proposed multiplicity adjustment method synthesizes weighted Bonferroni-based closed testing procedures into a powerful and versatile graphical approach. By tailoring different priorities for the two hypothesis tests involved in LD based QTL mapping, we are able to increase power and maintain computational efficiency and conceptual simplicity. The proposed approach enables strong control of the familywise error rate (FWER). The performance of the proposed approach as compared to the standard Bonferroni correction is illustrated by simulation and real data. We observe a consistent and moderate increase in power under all simulated circumstances, among different sample sizes, heritabilities, and number of SNPs. We also applied the proposed method to a real outbred mouse HDL cholesterol QTL mapping project where we detected the significant QTLs that were highlighted in the literature, while still ensuring strong control of the FWER.     

Pollux: platform independent error correction of single and mixed genomes

Background

Second-generation sequencers generate millions of relatively short, but error-prone, reads. These errors make sequence assembly and other downstream projects more challenging. Correcting these errors improves the quality of assemblies and projects which benefit from error-free reads.

Results

We have developed a general-purpose error corrector that corrects errors introduced by Illumina, Ion Torrent, and Roche 454 sequencing technologies and can be applied to single- or mixed-genome data. In addition to correcting substitution errors, we locate and correct insertion, deletion, and homopolymer errors while remaining sensitive to low coverage areas of sequencing projects. Using published data sets, we correct 94% of Illumina MiSeq errors, 88% of Ion Torrent PGM errors, 85% of Roche 454 GS Junior errors. Introduced errors are 20 to 70 times more rare than successfully corrected errors. Furthermore, we show that the quality of assemblies improves when reads are corrected by our software.

Conclusions

Pollux is highly effective at correcting errors across platforms, and is consistently able to perform as well or better than currently available error correction software. Pollux provides general-purpose error correction and may be used in applications with or without assembly.     

RNA/DNA嵌合分子介导的高效基因修复

本文介绍了RNA/DNA嵌合分子介导的高效基因修复技术。这一技术是1996年开始发展起来的全新技术,它通过人工合成的双链开环RNA/DNA嵌合分子转染细胞而使特定基因靶位点产生单碱基改变,从而修复突变基因。这一技术高效（目前最高可达50％以上）、特异性强、安全、无随机插入致变的危险、无免疫反应、无明显毒性,能够用于定点突变、基因敲除、动植物功能基因组学、药物遗传学等很多方面的研究,在不久的将来能够应用于人类基因治疗,具有很高的应用价值和医学前景。 Abstract：We introduce a new technique?targeted gene correction directed by chimeric RNA/DNA oligonucleotides which began at 1996.It uses synthetic double?stranded non?circular RNA/DNA chimeric oligonucleotides to transfect cells and make a single?based change at the targeted site of the target gene.It is highly efficient (the highest efficiency is more than 50％),highly special,safe,without danger of mutation caused by random insertion,without immune response,and without obvious toxicity.It can be used to make point mutation,or gene knock?out plants and animals,and is very likely to be used in human gene therapy in the near future.It is also valuable in the study of functional genomics,pharmacogenetics,and medicine.     

时间序列修订对森林二氧化碳通量的影响

对长白山阔叶红松林2003年生长季的涡动相关实测时间序列进行了去倾修订与超声风速仪倾斜修订,并分析了不同修订方法对森林CO2通量计算值的影响．结果表明,基于未修订时间序列计算得到的森林CO2通量(Fcraw)被高估．线性与非线性去倾对Fcraw的修订量分别为1．6％、1．8％,两者差异很小．平面拟合坐标变换与流线坐标变换对Fcraw的修订量分别为3．7％、4．7％,两者差异较大．对线性去倾后的时间序列分别进行流线坐标变换与平面拟合坐标变换,二者对Fcraw的修订量分别为5．5％与4．6％．建议对时间序列进行线性去倾与平面拟合坐标变换综合修订．     

重庆市城市化与生态环境交互关系的协整分析

运用协整理论和误差修正模型考察了重庆市1978-2007年期间城市化与生态环境相互作用的关系,遴选出作用于生态环境的2项主要的城市化指标和影响城市化的4项主要的生态环境指标,它们能反映出交互作用的机制。结果发现:1978-2007年,重庆市城市化与生态环境之间存在长期均衡关系,城市化对生态环境的正向作用明显强于生态环境对城市化的反向影响,误差修正系数较长期协整方程中的系数要小。从长期来看,城市化水平对生态环境变化的解释能力正在逐步增强,这充分证明生态环境功能的弱化是城市化步伐推进的必然结果。就城市化对生态环境的响应效果而言,一方面城市化是影响重庆市生态环境的重要原因,另一方面生态环境对城市化也存在着反作用。生态环境对城市化进程产生外在压力,但这一反馈机制往往具有一定的滞后效应。城市化对解释生态环境预测方差分解起着重要作用,然而生态环境对城市化预测方差的贡献度较小。     

桂西北喀斯特区域植被变化趋势及其对气候和地形的响应

基于1999—2010年的SPOT NDVI数据,分析了河池市植被变化趋势及空间差异,并结合气象和地形数据分析了植被与气候、地形的关系。结果表明:(1)桂西北喀斯特地区植被变化总体上呈恢复趋势,年均气候因子对植被变化的作用不明显;(2)200—500m的海拔范围内植被恢复显著,但400—500m的海拔范围内有小面积植被退化现象,随着海拔增加,植被变化趋于稳定;(3)6—15°的坡度范围内植被恢复最显著,而2—6°及大于25°坡度范围存在植被退化的现象;(4)不同坡向上的植被恢复差异不明显,但随着坡向由阴坡转阳坡,植被总体恢复呈减小趋势。喀斯特地区人类生态建设取得一定成效,但由于人类活动的负面影响,在海拔400—500m、坡度大于25°的阳坡区域仍存在植被减少的现象。     

TVDI模型的农业旱情时空变化遥感应用

温度植被干旱指数(TVDI)是一种通过反演土壤湿度来反映农业干旱状况的重要方法,其中能量平衡和植被指数的变化是影响TVDI模型精度的主要因子。在研究比值植被指数(RVI)、归一化植被指数(NDVI)、增强型植被指数(EVI)和修正土壤调节植被指数(MSAVI)和下垫面温度(Ts)的基础上,引入DEM数据并对Ts做地形校正,减少了地形起伏对能量平衡的影响,建立不同植被指数的Ts-Ⅵ特征空间,选择与土壤湿度相关性最好的温度植被干旱指数(TVDI),获取研究区2005年作物生长季(5—9月)的干旱状况,并用同步的气象信息对干旱状况进行验证。结果表明:根据不同时期采用不同植被指数的TVDI模型,经过地形校正后能够更好地反映研究区的农业干旱状况。     

基于数码相片Gamma校正的水稻叶面积指数估算

随着数码相机的日益普及,利用数码相机进行作物叶面积指数(LAI)测量不断得以应用。由于数码相机成像时会对入射光辐射强度进行Gamma编码变换,输出的相片DN(Digital Number)值与入射光辐射强度呈非线性关系,会造成在确定相片中植被叶片与背景的分割阈值时出现误差,并最终导致LAI估算存在较大不确定性。以水稻为研究对象,获取不同生长期水稻冠层相片并结合同步LAI 2000测量的LAI数据,基于相片Gamma校正原理,对水稻不同生长期冠层相片进行Gamma校正,在此基础上利用冠层孔隙率方法,估算不同生长期水稻LAI。结果表明,经过Gamma校正相片估算的水稻LAI总体精度有显著提高,相片估算的IMAGE LAI与LAI-2000测量值比较的决定系数达到0.71(P0.05)。在整个观测期内,两种方法观测的LAI值在时间变化趋势上表现一致,但在不同生长期内存在差别,在水稻分蘖期和拔节期相片估算的IMAGE LAI要高于LAI-2000测量值,孕穗期到抽穗期期间IMAGE LAI低于LAI-2000测量值,乳熟期到成熟期IMAGE LAI又高于LAI-2000的观测结果。