predForm-Site: Formylation site prediction by incorporating multiple features and resolving data imbalance

Formylation is one of the newly discovered post-translational modifications in lysine residue which is responsible for different kinds of diseases. In this work, a novel predictor, named predForm-Site, has been developed to predict formylation sites with higher accuracy. We have integrated multiple sequence features for developing a more informative representation of formylation sites. Moreover, decision function of the underlying classifier have been optimized on skewed formylation dataset during prediction model training for prediction quality improvement. On the dataset used by LFPred and Formator predictor, predForm-Site achieved 99.5% sensitivity, 99.8% specificity and 99.8% overall accuracy with AUC of 0.999 in the jackknife test. In the independent test, it has also achieved more than 97% sensitivity and 99% specificity. Similarly, in benchmarking with recent method CKSAAP_FormSite, the proposed predictor significantly outperformed in all the measures, particularly sensitivity by around 20%, specificity by nearly 30% and overall accuracy by more than 22%. These experimental results show that the proposed predForm-Site can be used as a complementary tool for the fast exploration of formylation sites. For convenience of the scientific community, predForm-Site has been deployed as an online tool, accessible at http://103.99.176.239:8080/predForm-Site.     

A combination of modified particle swarm optimization algorithm and support vector machine for gene selection and tumor classification

In the analysis of gene expression profiles, the number of tissue samples with genes expression levels available is usually small compared with the number of genes. This can lead either to possible overfitting or even to a complete failure in analysis of microarray data. The selection of genes that are really indicative of the tissue classification concerned is becoming one of the key steps in microarray studies. In the present paper, we have combined the modified discrete particle swarm optimization (PSO) and support vector machines (SVM) for tumor classification. The modified discrete PSO is applied to select genes, while SVM is used as the classifier or the evaluator. The proposed approach is used to the microarray data of 22 normal and 40 colon tumor tissues and showed good prediction performance. It has been demonstrated that the modified PSO is a useful tool for gene selection and mining high dimension data.     

6291型热变形温度和维卡软化温度测试仪的校准及故障排除

介绍6291型热变形温度和维卡软化温度测试仪的温度校准和位移校准方法，对测试仪的一些常见故障，例如电源故障，主温度传感器故障，电加热系统控制单元故障及测试站的温度偏差较大等进行了分析，并给出了排除故障的方法。     

一维〔M（tmp）〕_2ReO_4（M＝Ni、Cu、Pd）聚合物的能带结构

用紧束缚ＥＨＴ晶体轨道方法对一维〔Ｍ（ｔｍｐ）〕_２ＲｅＯ_４（Ｍ＝Ｎｉ、Ｃｕ、Ｐｄ）聚合物进行了能带计算，利用键向量近似方法对能带的结构及组成进行了讨论。结果表明，该类型聚合物具有不同的导电机理，并进一步研究了环平面间的成键性质及转角改变对聚合物导电性能的影响。     

一种基于流动注射梯度技术识别异常峰及校正的方法

基于流动注射梯度信息提出了一种利用梯度比均值进行定量的校正方法。方法具有在线自动判别和修复异常峰并自行校正的功能，和通用的标准系列定量方法相比，两者测定精度相当。但本文提出的方法抗干扰能力明显优于后者，可适用于在线过程监测。     

Complexation of well-controlled low-molecular weight polyelectrolytes with antisense oligonucleotides

The influences of polymer-related properties such as molecular weight, charge density, counter ion, and hydrophilic block on the complexation of polyelectrolytes and a fluorescein-labeled oligonucleotide (ON) were investigated. A series of well-defined and well-controlled 2-(N,N-dimethylamino)ethyl methacrylate (DMAEMA) polymers and block copolymers were prepared using living anionic and radical polymerization methods. Fluorescence measurement was used to reveal the effects of polymer molecular weight, charge density, and counter ion type on the complexation. PolyDMAEMA samples having double molecular weights of the chosen oligonucleotide gave the optimal complexation performance. Kinetic studies showed that high-molecular weight/high-charge density polymer samples produced very stable complexes. The fully charged polyDMAEMA displayed the strongest binding with the ON. These complexes were therefore less sensitive to the changes in the environment. PolyDMAEMA–DMSQ samples had slightly higher complexation ability than polyDMAEMA–MCQ (DMSQ: dimethylsulfate quat; MCQ: methylchloride quat). Both poly(DMAEMA-b-HEMA) and poly(DMAEMA–MCQ-b-PEG) block copolymers showed good complexation ability and steric stability [HEMA: 2-hydroxyethyl methacrylate; PEG: poly(ethylene glycol)]. PEG, but not HEMA block, enhanced the effectiveness of polyDMAEMA–MCQ binding with the ON.     

Mathematical studies of Kekulé structures

The perfect matching vector and forcing and the Kekulé-vector of cata-benzenoids are defined. Two theorems are given which set the sufficient and necessary conditions for HKZ-vector (Harary et al. J Math Chem 6:295, 1991) and Kekulé-vector in cata-benzenoids. Additional two theorems are obtained which give sharp bounds for the modules of HKZ- and Kekulé vectors. Dedicated to Professor Tadeusz Marek Krygowski on the happy occasion of his 70th birthday.     

Direct and simultaneous spectrofluorometric determination of naproxen and salicylate in human serum assisted by chemometric analysis

A direct method for the simultaneous determination of naproxen and salicylate in human serum is reported, based on a combination of spectrofluorometric measurements with two multivariate calibration techniques: partial least-squares (PLS-1) and the novel net analyte preprocessing (NAP). The method is rapid, selective and sensitive, and is based on the measurement of the fluorescence spectra of NH₃ alkalinized whole human sera at the excitation wavelength of 315 nm. It can be applied within the ranges of concentrations 50-200 ng ml⁻¹ for naproxen and 100-300 ng ml⁻¹ for salicylate. The employed chemometric techniques have been compared on the basis of the statistical indicators for calibration and validation. Reproducibility and interference studies in abnormal sera have also been carried out.     

Performance of quantitative analyses by liquid chromatography–electrospray ionisation tandem mass spectrometry: from external calibration to isotopomer-based exact matching

Liquid chromatography–tandem mass spectrometry (LC-MS/MS) is a versatile coupling system which combines both selectivity and sensitivity and certainty. Hence, it is generally considered as the most reliable technique to quantify chemical compounds in complex matrices. In the present paper, we evaluate the performance of LC-MS/MS methods for the quantification of 3-nitrotyrosine in human urine in order to point out its dependence on the design of the quantification method, and emphasize the role of matrix effects in the performance. We compare external and internal calibrations, isotope dilution and isotopomer-based exact matching. The role of both sample preparation and multiple transitions monitoring is particularly addressed.