Multivariate analysis of extremely large ToFSIMS imaging datasets by a rapid PCA method

Principal component analysis (PCA) and other multivariate analysis methods have been used increasingly to analyse and understand depth profiles in X‐ray photoelectron spectroscopy (XPS), Auger electron spectroscopy (AES) and secondary ion mass spectrometry (SIMS). These methods have proved equally useful in fundamental studies as in applied work where speed of interpretation is very valuable. Until now these methods have been difficult to apply to very large datasets such as spectra associated with 2D images or 3D depth‐profiles. Existing algorithms for computing PCA matrices have been either too slow or demanded more memory than is available on desktop PCs. This often forces analysts to ‘bin’ spectra on much more coarse a grid than they would like, perhaps even to unity mass bins even though much higher resolution is available, or select only part of an image for PCA analysis, even though PCA of the full data would be preferred. We apply the new ‘random vectors’ method of singular value decomposition proposed by Halko and co‐authors to time‐of‐flight (ToF)SIMS data for the first time. This increases the speed of calculation by a factor of several hundred, making PCA of these datasets practical on desktop PCs for the first time. For large images or 3D depth profiles we have implemented a version of this algorithm which minimises memory needs, so that even datasets too large to store in memory can be processed into PCA results on an ordinary PC with a few gigabytes of memory in a few hours. We present results from ToFSIMS imaging of a citrate crystal and a basalt rock sample, the largest of which is 134GB in file size corresponding to 67 111 mass values at each of 512 × 512 pixels. This was processed into 100 PCA components in six hours on a conventional Windows desktop PC. © 2015 The Authors. Surface and Interface Analysis published by John Wiley & Sons Ltd.     

Nucleic acid reactivity: Challenges for next‐generation semiempirical quantum models

Semiempirical quantum models are routinely used to study mechanisms of RNA catalysis and phosphoryl transfer reactions using combined quantum mechanical (QM)/molecular mechanical methods. Herein, we provide a broad assessment of the performance of existing semiempirical quantum models to describe nucleic acid structure and reactivity to quantify their limitations and guide the development of next‐generation quantum models with improved accuracy. Neglect of diatomic differential overlap and self‐consistent density‐functional tight‐binding semiempirical models are evaluated against high‐level QM benchmark calculations for seven biologically important datasets. The datasets include: proton affinities, polarizabilities, nucleobase dimer interactions, dimethyl phosphate anion, nucleoside sugar and glycosidic torsion conformations, and RNA phosphoryl transfer model reactions. As an additional baseline, comparisons are made with several commonly used density‐functional models, including M062X and B3LYP (in some cases with dispersion corrections). The results show that, among the semiempirical models examined, the AM1/d‐PhoT model is the most robust at predicting proton affinities. AM1/d‐PhoT and DFTB3‐3ob/OPhyd reproduce the MP2 potential energy surfaces of 6 associative RNA phosphoryl transfer model reactions reasonably well. Further, a recently developed linear‐scaling “modified divide‐and‐conquer” model exhibits the most accurate results for binding energies of both hydrogen bonded and stacked nucleobase dimers. The semiempirical models considered here are shown to underestimate the isotropic polarizabilities of neutral molecules by approximately 30%. The semiempirical models also fail to adequately describe torsion profiles for the dimethyl phosphate anion, the nucleoside sugar ring puckers, and the rotations about the nucleoside glycosidic bond. The modeling of pentavalent phosphorus, particularly with thio substitutions often used experimentally as mechanistic probes, was problematic for all of the models considered. Analysis of the strengths and weakness of the models suggests that the creation of robust next‐generation models should emphasize the improvement of relative conformational energies and barriers, and nonbonded interactions. © 2015 Wiley Periodicals, Inc.     

脂质组学及其分析方法

脂质组学的研究属于生命科学的范畴,与人类的健康密切相关。目前,脂质组学已成为代谢组学最重要的分支之一,且是一个非常活跃的研究领域,尤其在研究疾病方面的重要性已经引起了科学界的广泛关注。该文简要介绍了脂质组学的研究内容,重点评述了脂质组学分析方法,包括样品处理、轮廓分析、目标分析、成像分析以及数据处理。最后提出了脂质组学分析技术和方法的展望。     

Reconstruction of the Linear Ordinary Differential System Based on Discrete Points

In this paper, we discuss an inverse problem, i.e., the reconstruction of a linear differential dynamic system from the given discrete data of the solution. We propose a model and a corresponding algorithm to recover the coefficient matrix of the differential system based on the normal vectors from the given discrete points, in order to avoid the problem of parameterization in curve fitting and approximation. We also give some theoretical analysis on our algorithm. When the data points are taken from the solution curve and the set composed of these data points is not degenerate, the coefficient matrix $A$ reconstructed by our algorithm is unique from the given discrete and noisefree data. We discuss the error bounds for the approximate coefficient matrix and the solution which are reconstructed by our algorithm. Numerical examples demonstrate the effectiveness of the algorithm.     

基于DEA-ANP的快递企业绩效评价研究

在建立快递企业绩效评价模型时,提出了利用DEA和ANP相结合对快递企业绩效进行评价的方法.不同于之前研究,文中提出的方法使用ANP替换AHP,充分考虑了物流行业的"效益背反"现象.其解决了AHP确定权重时,无法体现元素之间关联性的问题,单独使用DEA评价时,无法考虑决策者偏好的弊端.首先,方法基于.ANP方法,求出每个指标的权重,再分别对每个因素使用DEA方法求出各系统的相对效率值;然后,将各指标权重和相对效率值结合,求出各快递企业中营业部的整体效率值并进行排序;最后通过实例分析,验证了此方法的实用性、可操作性及优越性.     

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A cured model is a useful approach for analysing failure time data in which some subjects could eventually experience and others never experience the event of interest. All subjects in the test belong to one of the two groups: the susceptible group and the non-susceptible group. There has been considerable progress in the development of semi-parametric models for regression analysis of time-to-event data. However, most of the current work focuses on right-censored data, especially when the population contains a non-ignorable cured subgroup. In this paper, we propose a semi-parametric cure model for current status data. In general, treatments are developed to both increase the patients' chances of being cured and prolong the survival time among non-cured patients. A logistic regression model is proposed for whether the subject is in the susceptible group. An accelerated failure time regression model is proposed for the event time when the subject is in the non-susceptible group. An EM algorithm is used to maximize the log-likelihood of the observed data. Simulation results show that the proposed method can get efficient estimations.     

一种面板数据分位数回归模型的工具变量方法

本文将工具变量分位数回归模型(IVQR)应用到面板数据中,结合Canay对面板分位数回归的两步估计法以及Chernozhukov对IVQR模型的估计方法,提出了两步面板分位数工具变量估计法(2S-IVFEQR),并给出相应的参数估计。本文提出的方法较已有的方法计算复杂度低,蒙特卡洛模拟结果显示在数据量不大或者处理长面板数据时,2S-IVFEQR方法要优于传统的IVFEQR方法,且运算时间短。     

基于面板模型的商品房价格影响因素的实证研究

选取了我国30个省市2006~2015年的面板数据,应用面板数据计量模型回归的方法,基于R语言对影响商品房价格的因素进行实证研究.首先,经过Hausman检验与F检验确定面板数据的模型为混合估计模型;模型可以通过十折交叉验证法、残差正太性的检验、Q-Q图检验、变量间共线性的检验;最后经过逐步回归分析,结果表明土地价格、商品房销售面积、居民可支配收入、人均国内总产值财政收入占地区生产总值比重、汇率这6个指标对商品房价格都有显著性的影响.其中,土地价格和居民可支配收入对商品房价格的影响最为突出.     

应用图论分析与最优化理论来数据挖掘大规模水牛普里昂蛋白结构数据

图论、最优化理论显然在蛋白质结构的研究中大有用场. 首先, 调查/回顾了研究蛋白质结构的所有图论模型. 其后, 建立了一个图论模型: 让蛋白质的侧链来作为图的顶点, 应用图论的诸如团、 $k$-团、 社群、 枢纽、聚类等概念来建立图的边. 然后, 应用数学最优化的现代摩登数据挖掘算法/方法来分析水牛普里昂蛋白结构的大数据. 成功与令人耳目一新的数值结果将展示给朋友们.     

Efficient Data Augmentation for Fitting Stochastic Epidemic Models to Prevalence Data

Stochastic epidemic models describe the dynamics of an epidemic as a disease spreads through a population. Typically, only a fraction of cases are observed at a set of discrete times. The absence of complete information about the time evolution of an epidemic gives rise to a complicated latent variable problem in which the state space size of the epidemic grows large as the population size increases. This makes analytically integrating over the missing data infeasible for populations of even moderate size. We present a data augmentation Markov chain Monte Carlo (MCMC) framework for Bayesian estimation of stochastic epidemic model parameters, in which measurements are augmented with subject-level disease histories. In our MCMC algorithm, we propose each new subject-level path, conditional on the data, using a time-inhomogenous continuous-time Markov process with rates determined by the infection histories of other individuals. The method is general, and may be applied to a broad class of epidemic models with only minimal modifications to the model dynamics and/or emission distribution. We present our algorithm in the context of multiple stochastic epidemic models in which the data are binomially sampled prevalence counts, and apply our method to data from an outbreak of influenza in a British boarding school. Supplementary material for this article is available online.