Prediction of membrane protein types by means of wavelet analysis and cascaded neural networks

In this study, membrane proteins were classified using the information hidden in their sequences. It was achieved by applying the wavelet analysis to the sequences and consequently extracting several features, each of them revealing a proportion of the information content present in the sequence. The resultant features were made normalized and subsequently fed into a cascaded model developed in order to reduce the effect of the existing bias in the dataset, rising from the difference in size of the membrane protein classes. The results indicate an improvement in prediction accuracy of the model in comparison with similar works. The application of the presented model can be extended to other fields of structural biology due to its efficiency, simplicity and flexibility.     

Empirical Mode Decomposition and Wavelet Transform Based ECG Data Compression Scheme

ObjectiveIn health-care systems, compression is an essential tool to solve the storage and transmission problems. In this regard, this paper reports a new electrocardiogram (ECG) data compression scheme which employs sifting function based empirical mode decomposition (EMD) and discrete wavelet transform.MethodEMD based on sifting function is utilized to get the first intrinsic mode function (IMF). After EMD, the first IMF and four significant sifting functions are combined together. This combination is free from many irrelevant components of the signal. Discrete wavelet transform (DWT) with mother wavelet ‘bior4.4’ is applied to this combination. The transform coefficients obtained after DWT are passed through dead-zone quantization. It discards small transform coefficients lying around zero. Further, integer conversion of coefficients and run-length encoding are utilized to achieve a compressed form of ECG data.ResultsCompression performance of the proposed scheme is evaluated using 48 ECG records of the MIT-BIH arrhythmia database. In the comparison of compression results, it is observed that the proposed method exhibits better performance than many recent ECG compressors. A mean opinion score test is also conducted to evaluate the true quality of the reconstructed ECG signals.ConclusionThe proposed scheme offers better compression performance with preserving the key features of the signal very well.     

A Simple Method for Predicting Transmembrane Proteins Based on Wavelet Transform

The increasing protein sequences from the genome project require theoretical methods to predict transmembrane helical segments (TMHs). So far, several prediction methods have been reported, but there are some deficiencies in prediction accuracy and adaptability in these methods. In this paper, a method based on discrete wavelet transform (DWT) has been developed to predict the number and location of TMHs in membrane proteins. PDB coded as 1KQG is chosen as an example to describe the prediction process by this method. 80 proteins with known 3D structure from Mptopo database are chosen at random as data sets (including 325 TMHs) and 80 sequences are divided into 13 groups according to their function and type. TMHs prediction is carried out for each group of membrane protein sequences and obtain satisfactory result. To verify the feasibility of this method, 80 membrane protein sequences are treated as test sets, 308 TMHs can be predicted and the prediction accuracy is 96.3%. Compared with the main prediction results of seven popular prediction methods, the obtained results indicate that the proposed method in this paper has higher prediction accuracy.     

基于小波变换的ECG压缩

小波变换现已成为信号压缩的有力工具,小波压缩称法所基于的“嵌入零树小波”（ＥＥＷ）编码已发展为心电信号进行综压缩。     

Predicting homo-oligomers and hetero-oligomers by pseudo-amino acid composition: an approach from discrete wavelet transformation

Many proteins exist in vivo as oligomers with different quaternary structural attributes rather than as individual chains. These proteins are the structural components of various biological functions, including cooperative effects, allosteric mechanisms and ion-channel gating. With the dramatic increase in the number of protein sequences submitted to the public databank, it is important for both basic research and drug discovery research to acquire the knowledge about possible quaternary structural attributes of their interested proteins in a timely manner. A high-throughput method (DWT_SVM), fusing discrete wavelet transform (DWT) and support vector machine (SVM) classifier algorithm with various physicochemical features, has been developed to predict protein quaternary structure. The accuracy in distinguishing candidate proteins as homo-oligomer or hetero-oligomer using the dataset R₂₇₂₀ was 85.95% and 85.49% respectively by jackknife, showing that DWT_SVM is guide promising in predicting protein quaternary structures. The online service is available at http://bioinfo.ncu.edu.cn/Services.aspx. Protein sequences in FASTA format can be directly fed to the system OligoPred. The processed results will be presented in a diagram that includes the information of feature extraction and the classification error rate.     

Discrete wavelet transform analysis of surface electromyography for the fatigue assessment of neck and shoulder muscles

Assessment of neuromuscular fatigue is essential for early detection and prevention of risks associated with work-related musculoskeletal disorders. In recent years, discrete wavelet transform (DWT) of surface electromyography (SEMG) has been used to evaluate muscle fatigue, especially during dynamic contractions when the SEMG signal is non-stationary. However, its application to the assessment of work-related neck and shoulder muscle fatigue is not well established. Therefore, the purpose of this study was to establish DWT analysis as a suitable method to conduct quantitative assessment of neck and shoulder muscle fatigue under dynamic repetitive conditions. Ten human participants performed 40 min of fatiguing repetitive arm and neck exertions while SEMG data from the upper trapezius and sternocleidomastoid muscles were recorded. The ten of the most commonly used wavelet functions were used to conduct the DWT analysis. Spectral changes estimated using power of wavelet coefficients in the 12–23 Hz frequency band showed the highest sensitivity to fatigue induced by the dynamic repetitive exertions. Although most of the wavelet functions tested in this study reasonably demonstrated the expected power trend with fatigue development and recovery, the overall performance of the “Rbio3.1” wavelet in terms of power estimation and statistical significance was better than the remaining nine wavelets.     

基于小波的心电信号有效性检测方法

目的：检测采集到的信号是否为有效心电信号,提高后续心电诊断和分析的准确率。方法：将采集到的信号进行预处理,即去噪处理,主要抑制基线漂移,50Hz工频及其谐波干扰和肌电干扰;取滑动窗长度为4s,检测该段内信号是否有效。为了验证算法的准确率及对不同心电波形是否具有普遍适用性,对MIT-BIH Arrhythmia Database中48个记录,CU及MIT-BIH Noise Stress Test Database中部分记录进行了仿真、验证。结果：仿真实验证明该方法能正确区分有效和无效信号,错检率较低,实现简单,适合实时处理。结论：本方法准确率高,能减少后续心电诊断和分析的计算量并提高准确率,特别是对室颤检测,符合心电分析的要求。     

基于小波变换的心电信号去噪综合算法

目的：研究去除心电信号中的基线漂移、工频干扰和肌电干扰等噪声,提高心电信号的自动识别和诊断精度。方法：利用Coif4小波对心电信号进行8尺度分解,采用小波分解重构法去除基线漂移,然后利用改进的小波闽值算法去除工频干扰和肌电干扰。结果：利用Matlab仿真工具,选择MIT-BIH心率失常数据库中信号进行验证,能有效去除这三种噪声,并且很好的保持R波的信息。结论：本算法在不丢失心电信号有用信息的前提下,可以较好的去除三种常见的噪声,可以用于心电信号自动分析之前的预处理。     

基于独立元分析和联合小波熵检测多导联ECG信号的QRS

QRS波群的准确定位是ECG信号自动分析的基础。为提高QRS检测率,提出一种基于独立元分析（ICA）和联合小波熵（CWS）检测多导联ECG信号QRS的算法。ICA算法从滤波后的多导联ECG信号中分离出对应心室活动的独立元;然后对各独立元进行连续小波变换（CWT）,重构小波系数的相空间,结合相空间中的QRS信息对独立元排序;最后检测排序后独立元的CWS得到QRS信息。实验对St.Petersburg12导联心率失常数据库及64导联犬心外膜数据库测试,比较本文算法与单导联QRS检测算法和双导联QRS检测算法的性能。结果表明,该文算法的性能最好,检测准确率分别为99.98%和100%。     

Feature extraction and recognition of epileptiform activity in EEG by combining PCA with ApEn

This paper proposes a new method for feature extraction and recognition of epileptiform activity in EEG signals. The method improves feature extraction speed of epileptiform activity without reducing recognition rate. Firstly, Principal component analysis (PCA) is applied to the original EEG for dimension reduction and to the decorrelation of epileptic EEG and normal EEG. Then discrete wavelet transform (DWT) combined with approximate entropy (ApEn) is performed on epileptic EEG and normal EEG, respectively. At last, Neyman–Pearson criteria are applied to classify epileptic EEG and normal ones. The main procedure is that the principle component of EEG after PCA is decomposed into several sub-band signals using DWT, and ApEn algorithm is applied to the sub-band signals at different wavelet scales. Distinct difference is found between the ApEn values of epileptic and normal EEG. The method allows recognition of epileptiform activities and discriminates them from the normal EEG. The algorithm performs well at epileptiform activity recognition in the clinic EEG data and offers a flexible tool that is intended to be generalized to the simultaneous recognition of many waveforms in EEG.     

Identify submitochondria and subchloroplast locations with pseudo amino acid composition: Approach from the strategy of discrete wavelet transform feature extraction

It is very challenging and complicated to predict protein locations at the sub-subcellular level. The key to enhancing the prediction quality for protein sub-subcellular locations is to grasp the core features of a protein that can discriminate among proteins with different subcompartment locations. In this study, a different formulation of pseudoamino acid composition by the approach of discrete wavelet transform feature extraction was developed to predict submitochondria and subchloroplast locations. As a result of jackknife cross-validation, with our method, it can efficiently distinguish mitochondrial proteins from chloroplast proteins with total accuracy of 98.8% and obtained a promising total accuracy of 93.38% for predicting submitochondria locations. Especially the predictive accuracy for mitochondrial outer membrane and chloroplast thylakoid lumen were 82.93% and 82.22%, respectively, showing an improvement of 4.88% and 27.22% when other existing methods were compared. The results indicated that the proposed method might be employed as a useful assistant technique for identifying sub-subcellular locations. We have implemented our algorithm as an online service called SubIdent (http://bioinfo.ncu.edu.cn/services.aspx).     

Ultrasonic velocity assay of extracellular invertase in living yeasts

Being the largest family of cell surface receptors, G-protein-coupled receptors (GPCRs) are among the most frequent targets. The functions of many GPCRs are unknown, and it is both time-consuming and expensive to determine their ligands and signaling pathways by experimental methods. It is of great practical significance to develop an automated and reliable method for classification of GPCRs. In this study, a novel method based on the concept of Chou’s pseudo amino acid composition has been developed for predicting and recognizing GPCRs. The discrete wavelet transform was used to extract feature vectors from the hydrophobicity scales of amino acid to construct pseudo amino acid (PseAA) composition for training support vector machine. The prediction accuracies by the current method among the major families of GPCRs, subfamilies of class A, and types of amine receptors were 99.72%, 97.64%, and 99.20%, respectively, showing 9.4% to 18.0% improvement over other existing methods and indicating that the proposed method is a useful automated tool in identifying GPCRs.     

Fatigue-induced changes in muscle fiber action potentials estimated by wavelet analysis

We aimed to investigate fatigue-induced changes in the spectral parameters of slow (SMF) and fast fatigable muscle fiber (FMF) action potentials using discrete wavelet (DWT) and fast Fourier (FFT) transforms. Intracellular potentials were recorded during repetitive stimulation of isolated muscle fibers immersed in Ca²⁺-enriched medium, while extracellular potentials were obtained from muscle fibers pre-exposed to electromagnetic microwaves (MMW, 2.45 GHz, 20 mW/cm²). The changes in the frequency distribution of the action potentials during the period of uninterrupted fiber activity were used as criteria for fatigue assessment. The wavelet coefficients’ changes in the calculated frequency scales demonstrated a contribution of the increased [Ca²⁺]₀ to an earlier compression of the frequency spectrum towards lower ranges. Root mean square (RMS) analysis of the wavelet coefficients calculated from SMF potentials showed a reduction of the higher frequencies (scale 1) by 90% in elevated [Ca²⁺]₀ vs. 55% in controls and an increase of low frequencies (scale 5) by 323% vs. 187%, respectively. For FMF potentials a decrease of 71% vs. 59% for high frequencies (scale 1, elevated [Ca²⁺]₀ vs. control) and an increase of 386% vs. 295% in scale 5, respectively, were observed. MMW pre-exposure resulted in increased muscle fiber resistance to fatigue. The fatigue-induced decrease of potential high frequencies (SMF: 59% vs. 96%, MMW vs. control; FMF: 30% vs. 92%, respectively), and the increase of low frequencies (SMF: 200% vs. 207%, MMW vs. control; FMF: 93% vs. 314%, respectively) were significantly smaller and delayed in exposed muscle fibers. Data from RMS analysis indicate that DWT provides a reliable method for estimation of muscle fatigue onset and progression.     

基于小波变换的混合二维ECG数据压缩方法

提出了一种新的基于小波变换的混合二维心电(electrocardiogram,ECG)数据压缩方法。基于ECG数据的两种相关性,该方法首先将一维ECG信号转化为二维信号序列。然后对二维序列进行了小波变换,并利用改进的编码方法对变换后的系数进行了压缩编码:即先根据不同系数子带的各自特点和系数子带之间的相似性,改进了等级树集合分裂(setpartitioninghierarchicaltrees,SPIHT)算法和矢量量化(vectorquantization,VQ)算法;再利用改进后的SPIHT与VQ相混合的算法对小波变换后的系数进行了编码。利用所提算法与已有具有代表性的基于小波变换的压缩算法和其他二维ECG信号的压缩算法,对MIT/BIH数据库中的心律不齐数据进行了对比压缩实验。结果表明:所提算法适用于各种波形特征的ECG信号,并且在保证压缩质量的前提下,可以获得较大的压缩比。     

Application of wavelet analysis to ecological data

Ecological data are difficult to analyze due to complexity residing in the ecological systems with the variables varying in non-linear fashion. Efficient methods are required to properly extract information out of the complex data. Wavelets have good time–frequency (time-scale) localization, can represent data parsimoniously, and can be implemented with very fast algorithms. Brief backgrounds and computational aspects of wavelets were outlined for implementation to ecological data analysis. Wavelets are well suited for building mathematical models of ecological data and the statistical analysis of combined effects of complex factors in ecological network. Wavelet based analysis and synthesis may lead researchers in ecological studies to new insights and novel theories for understanding complex ecological and environmental phenomena.     

Application of discrete Fourier inter-coefficient difference for assessing genetic sequence similarity

Digital signal processing (DSP) techniques for biological sequence analysis continue to grow in popularity due to the inherent digital nature of these sequences. DSP methods have demonstrated early success for detection of coding regions in a gene. Recently, these methods are being used to establish DNA gene similarity. We present the inter-coefficient difference (ICD) transformation, a novel extension of the discrete Fourier transformation, which can be applied to any DNA sequence. The ICD method is a mathematical, alignment-free DNA comparison method that generates a genetic signature for any DNA sequence that is used to generate relative measures of similarity among DNA sequences. We demonstrate our method on a set of insulin genes obtained from an evolutionarily wide range of species, and on a set of avian influenza viral sequences, which represents a set of highly similar sequences. We compare phylogenetic trees generated using our technique against trees generated using traditional alignment techniques for similarity and demonstrate that the ICD method produces a highly accurate tree without requiring an alignment prior to establishing sequence similarity.     

线性时频分析在ECG信号分析中的应用

目的:心电信号(Electrocardio-signal,ECG)是人体中最重要的生物信号之一,是一种具有非平稳性和非线性特性的信号.分析ECG信号是诊断心脏疾病的有利工具,近年来国内外很多学者致力于这方面的研究.本文探讨短时Fourier变换(STFT)和离散小波变换(DWT)这两种时频分析方法在ECG信号分析中的应用.方法:本文采用麻省理工学院的MIT-BIH数据库中提供的数据,运用MATLAB软件编程,讨论短时Fourier变换和离散小波变换在ECG信号分析中的应用.结果:通过编程,做出了正常ECG信号和失常ECG信号的短时Fourier变换的时域图和频谱图以及正常ECG信号和失常ECG信号的单级离散小波变换的结果.结论:正常ECG信号和失常ECG信号的STFT变换的时域图和频谱图都能反应出信号的频率和时间的变化关系.但是,正常信号和失常信号的频率和时间有明显不同,正常信号的能量随时间和频率的变化关系有序整齐,而且周围有较少的杂波;失常信号的能量随时间和频率的变化关系杂乱,而且周围存在较多的杂波.通过离散小波变化后,正常信号和失常信号均产生了不同的离散小波系数,根据不同的离散小波系数,可以很容易判断正常信号和失常信号的区别.