Oscore: a combined score to reduce false negative rates for peptide identification in tandem mass spectrometry analysis

Tandem mass spectrometry (MS/MS) has been widely used in proteomics studies. Multiple algorithms have been developed for assessing matches between MS/MS spectra and peptide sequences in databases. However, it is still a challenge to reduce false negative rates without compromising the high confidence of peptide identification. In this study, we developed the score, Oscore, by logistic regression using SEQUEST and AMASS variables to identify fully tryptic peptides. Since these variables showed complicated association with each other, combining them together rather than applying them to a threshold model improved the classification of correct and incorrect peptide identifications. Oscore achieved both a lower false negative rate and a lower false positive rate than PeptideProphet on datasets from 18 known protein mixtures and several proteome-scale samples of different complexity, database size and separation methods. By a three-way comparison among Oscore, PeptideProphet and another logistic regression model which made use of PeptideProphet's variables, the main contributor for the improvement made by Oscore is discussed.     

Comparison of perchloroethylene extraction techniques in soil gas survey quantification

Subsurface pollution by volatile organic compounds has emerged as a widespread problem in industrialized countries. This study compares static headspace technique and methanol extraction/purge-and-trap analysis followed by thermal desorption/gas chromatography in attempts for quantification of gas survey results in the determination of these chemicals in soil. Several soils were contaminated with aqueous solution of perchloroethylene (PCE) (140 mg L⁻¹) using a vapor treatment method. Soil spiking took place up to 24 h in desiccator by exposing individual soil samples contained in open 40 mL glass vials to PCE evaporated from the solution. After exposure the samples were stored and analyzed within 2 days. The achieved results strongly suggest that gas extraction can provide quantitative results, regarding PCE concentration in soils, which are not significantly different from liquid based extraction analysis.      

Bootstrapping to choose an estimator after sampling on two occasions

Email: a.brint{at}sheffield.ac.uk Received on 22 August 2007. Accepted on 13 June 2008. When successive surveys are undertaken so as to keep a populationestimate up to date, combining the data from the most recentsurvey with data from earlier surveys is more efficient thanjust using the most recent survey. The standard approach tocombining the data forms separate estimates from the set ofitems observed on the earlier occasion and the set observedon the later occasion and then forms a combined estimate. Theapproach assumes that the population is very large and thatthe observed values of the variable of interest are continuous.In many situations, neither assumption is particularly appropriate.This paper compares an alternative approach with the standardapproach and finds that the alternative approach sometimes providesa better estimator. It then puts forward an improved estimatorbased on choosing between these approaches using a bootstrapprocedure.     

核电站温排水分布卫星遥感监测及验证

以大亚湾核电站附近海域为研究区,基于HJ-1B卫星热红外遥感数据IRS4,对核电站温排水空间分布特征进行了识别与验证。首先利用时空插值后的NCEP大气廓线数据,结合近地面气象观测信息对IRS4数据进行大气订正;其次查找表数据建立IRS4宽通道辐亮度与辐射温度转换公式,完成研究区海表温度反演。利用温盐深测量仪,与卫星同步采集了84个离散点的水温,经空间插值获得地面调查海水“体温度”（bulk temperature, BT）的分布,并与海表温度（sea surface temperature, SST）反演结果进行了对比。结果表明,调查区平均BT比平均SST高0.47 ℃。在远离热排放口区域,SST高于BT,两者差异在1.0 ℃以内;在靠近热排放口区域,SST低于BT,并且越接近排放口两者之间差距越大。遥感与地面调查两种手段获得的温升分布基本一致,总温升区域面积相近。遥感手段获得的温升等级较少（小于4级）,地面调查获得温升等级较多（大于5级）;后者高温升等级（2级以上）区域面积较大,但对于1级温升区面积而言,两种手段差异较小。上午10时左右海表BT与SST差异较小,“肤-体”温差效应可以忽略,在IRS4业务化SST应用中,这一时段的卫星遥感可以作为核电站温排水分布监测的常规手段。     

土地监察移动数据库技术及其应用

近年来,基于移动数据库的移动GIS技术发展呈加速趋势,并在越来越多领域的应用中取得成功.在土地监察工作中采用移动GIS手段,有利于实现实时、快速执行土地违法勘察、执法动态监察等工作,为建立完善的土地管理长效机制提供技术支持,保障人民群众的利益和社会的稳定.本文先介绍移动数据库的原理和架构,然后结合土地监察实际需求,重点探讨移动数据库在土地监察中需要解决的数据同步、数据复制与缓存和数据安全存储等关键技术问题.     

液相色谱-四极杆/ 飞行时间质谱快速筛查与确证苹果、番茄和甘蓝中的281种农药残留

建立了苹果、番茄和甘蓝中281种农药残留的QuEChERS结合液相色谱-四极杆/飞行时间质谱(LC-Q-TOF/MS)快速筛查方法。方法采用1%醋酸乙腈提取样品,经丙基乙二胺(PSA)净化,LC-Q-TOF/MS测定。281种农药在苹果、番茄和甘蓝中3个添加水平下的回收率在70%～120%范围的比例分别为98.6%、99.3%和98.2%;回收率的相对标准偏差(RSD)均≤20%(n=5);在0.25～10倍最大残留限量(MRL)的含量范围内,线性相关系数r²≥0.99的农药比例分别为95.7%、96.1%和98.2%;检出限分别为0.03～4.47、0.01～4.49和0.02～3.61 μg/kg。本方法采用精确质量数据库和谱图库检索的方式,实现了不用农药标准品对照而完成对果蔬中农药残留的快速筛查,提高了定性鉴别的准确性。应用所建立的方法对30个市售果蔬样品进行筛查,共检出13种农药残留。其中,甘蓝中甲胺磷的含量超过了GB 2763-2012《食品安全国家标准\5食品中农药最大残留限量》和欧盟的MRL;番茄中鱼藤酮的含量超出欧盟的MRL。     

Thirty years of density functional theory in computational chemistry: an overview and extensive assessment of 200 density functionals

In the past 30 years, Kohn–Sham density functional theory has emerged as the most popular electronic structure method in computational chemistry. To assess the ever-increasing number of approximate exchange-correlation functionals, this review benchmarks a total of 200 density functionals on a molecular database (MGCDB84) of nearly 5000 data points. The database employed, provided as Supplemental Data, is comprised of 84 data-sets and contains non-covalent interactions, isomerisation energies, thermochemistry, and barrier heights. In addition, the evolution of non-empirical and semi-empirical density functional design is reviewed, and guidelines are provided for the proper and effective use of density functionals. The most promising functional considered is ωB97M-V, a range-separated hybrid meta-GGA with VV10 nonlocal correlation, designed using a combinatorial approach. From the local GGAs, B97-D3, revPBE-D3, and BLYP-D3 are recommended, while from the local meta-GGAs, B97M-rV is the leading choice, followed by MS1-D3 and M06-L-D3. The best hybrid GGAs are ωB97X-V, ωB97X-D3, and ωB97X-D, while useful hybrid meta-GGAs (besides ωB97M-V) include ωM05-D, M06-2X-D3, and MN15. Ultimately, today's state-of-the-art functionals are close to achieving the level of accuracy desired for a broad range of chemical applications, and the principal remaining limitations are associated with systems that exhibit significant self-interaction/delocalisation errors and/or strong correlation effects.     

基于UML技术的空间基础数据库设计与实现

设计合理的空间基础数据库不仅能提高整个空间数据操作时的性能和效率,而且还可以减少后期的维护修复工作,使整个空间基础数据运行的更加快捷,需要对空间基础数据建立数据库。当前的空间基础数据库设计方法采用ArcSDE数据引擎对空间基础数据进行不断地更新调整,再利用多源空间数据格式转换的技术对空间基础数据库进行设计,存在空间基础数据运行时速度缓慢,计算精度低的问题。为此,提出了一种基于UML技术的空间基础数据库设计方法。该方法首先在空间基础数据库设计中建立空间基础数据索引结构,利用R-树族构建空间基础数据索引树,依据空间基础数据索引树,扫描索引空间基础数据,过滤掉不满足查询条件的空间基础数据对象,使空间数据查询结果可以在额定时间内获得,然后采用空间基础数据点、数据线、以及由数据线组成的区域、一组区域、空间基础数据网络的详细存储方式对空间基础数据进行存储,利用MongoDB驱动程序对矢量空间数据进行存储存储,最后通过对空间基础数据库索引、查询、存储等设计实现了空间基础数据库的建立。仿真实验结果证明,所提方法提高了空间基础数据的建库速度,减少了数据运行的时间,提升了空间基础数据的利用率。     

混合架构下ORACLE数据快速查找方法研究

为了提高对混合架构下ORACLE数据的挖掘和查找速度,提出一种基于频繁项目集关联规则挖掘的数据快速查找方法。构建ORACLE数据的内部关联属性映射关系模型,在异质网络混合构架模式下,采用Graph OLAP数据仓库模型进行数据库检索的关系维度表,提取表达ORACLE数据属性信息的特征参量,通过同态标签检索方法,实现对目标数据的快速查找定位。仿真结果表明,采用该方法进行ORACLE数据查找的查准率和查全率较高,计算速度较快,性能优于传统方法。     

基于VBA与Access的有机化学人名反应查询系统的开发与设计

人名反应是有机化学的重要组成部分,采用计算机来高效地分类、检索这些人名反应,可以大力促进有机化学的学习和科研工作。基于微软Access数据库和VBA编程语言,开发了有机化学人名反应交互查询系统,实现了有机化学人名反应的名称、反应过程、反应机理和实例的查询及编辑。软件能够实现按人名、反应类型、官能团等查询、浏览和打印等操作。软件的用户管理、数据管理等附加功能保证了软件的安全性,实现了软件生命力的延续。