Monitoring <i>Thosea sinensis</i> Walker in Tea Plantations Based on UAV Multi-Spectral Image

Thosea sinensis Walker (TSW) rapidly spreads and severely damages the tea plants. Therefore, finding a reliable operational method for identifying the TSW-damaged areas via remote sensing has been a focus of a research community. Such methods also enable us to calculate the precise application of pesticides and prevent the subsequent spread of the pests. In this work, based on the unmanned aerial vehicle (UAV) platform, five band images of multispectral red-edge camera were obtained and used for monitoring the TSW in tea plantations. By combining the minimum redundancy maximum relevance (mRMR) with the selected spectral features, a comprehensive spectral selection strategy was proposed. Then, based on the selected spectral features, three classic machine learning algorithms, including random forest (RF), support vector machine (SVM), and k-nearest neighbors (KNN) were used to construct the pest monitoring model and were evaluated and compared. The results showed that the strategy proposed in this work obtained ideal monitoring accuracy by only using the combination of a few optimized features (2 or 4). In order to differentiate the healthy and TSW-damaged areas (2-class model), the monitoring accuracies of all the three models were computed, which were above 96%. The RF model used the least number of features, including only SAVI and Band_red. In order to further discriminate the pest incidence levels (3-class model), the monitoring accuracies of all the three models were computed, which were above 80%, among which the RF algorithm based on SAVI, Band_red, VARI_green, and Band_{red_edge} features achieve the highest accuracy (OAA of 87%, and Kappa of 0.79). Considering the computational cost and model accuracy, this work recommends the RF model based on a few optimal feature combinations to monitor and distinguish the severity of TSW in tea plantations. According to the UAV remote sensing mapping results, the TSW infestation exhibited an aggregated distribution pattern. The spatial information of occurrence and severity can offer effective guidance for precise control of the pest. In addition, the relevant methods provide a reference for monitoring other leaf-eating pests, effectively improving the management level of plant protection in tea plantations, and guaranting the yield and quality of tea plantations.     

Label‐free diagnosis for colorectal cancer through coffee ring‐assisted surface‐enhanced Raman spectroscopy on blood serum

Surface‐enhanced Raman spectroscopy (SERS) is garnering considerable attention for the swift diagnosis of pathogens and abnormal biological status, that is, cancers. In this work, a simple, fast and inexpensive optical sensing platform is developed by the design of SERS sampling and data analysis. The pretreatment of spectral measurement employed gold nanoparticle colloid mixing with the serum from patients with colorectal cancer (CRC). The droplet of particle‐serum mixture formed coffee‐ring‐like region at the rim, providing strong and stable SERS profiles. The obtained spectra from cancer patients and healthy volunteers were analyzed by unsupervised principal component analysis (PCA) and supervised machine learning model, such as support‐vector machine (SVM), respectively. The results demonstrate that the SVM model provides the superior performance in the classification of CRC diagnosis compared with PCA. In addition, the values of carcinoembryonic antigen from the blood samples were compiled with the corresponding SERS spectra for SVM calculation, yielding improved prediction results.     

基于单细菌共焦拉曼光谱的细菌快速检测

【背景】目前利用共焦拉曼光谱技术进行成像和成分鉴别方面的研究较多,但如何快速检测与鉴别多种细菌方面的研究较少。【目的】基于共焦拉曼光谱技术,建立一种在单细菌水平上实现病原微生物快速分类鉴定的方法。【方法】以大肠杆菌为研究对象,利用共焦拉曼光谱技术在单细菌水平上进行了激发波长的优化试验,并研究了大肠杆菌存放时间对单细菌拉曼光谱信息的影响。同时,对白色葡萄球菌、大肠杆菌、金黄色葡萄球菌、沙门氏菌和铜绿假单胞菌进行了共焦拉曼光谱测试,并对5种细菌进行单细菌拉曼光谱的归属分析,设计共焦拉曼光谱技术结合支持向量机(support vector machine,SVM)模型学习算法,进行了5种细菌的快速分类鉴别。【结果】对于单细菌拉曼光谱探测,532、633和785 nm这3种常见的拉曼探测波长中,532 nm具有更好的激发效率和光谱信噪比。结合SVM模型对5种细菌的识别分类,SVM模型的灵敏度和特异性达到了96.00%以上,整体准确率为98.25%。不同存放时间下大肠杆菌拉曼光谱的重复性和稳定性都很好,且SVM模型匹配率均在90.00%以上。【结论】单细菌拉曼光谱结合SVM模型可对5种细菌进行快...     

Separation of catechin compounds from different teas

Catechin compounds from Korean and Chinese green tea, and pu-erh, Indian black, Longjing, Tieguanyin, Bamboo, Jasmine, Oolong, Flower, Red teas, as potential anticancer and antioxidant components, were target material in this work. After extracting the green tea with water at 50 degrees C for 4 h, the extract was partitioned with water/chloroform, which was best suited to remove caffeine impurity from the extract. Further, the resulting extract was partitioned with water/ethyl acetate to deeply purify the five catechin compounds epigallocatechin, (+) catechin, epicatechin, epigallocatechin gallate and epicatechin gallate. The extracted samples were analyzed by reversed-phase high performance liquid chromatography. The mobile phase applied was the binary system of A (water/acetic acid, 100/0.1 vol%) and B (acetonitrile/acetic acid 100/0.1 vol%) from 90:10 to 70:30 (A:B vol%) in a linear gradient over 30 min time. The amount of catechin compounds extracted from Chinese green tea was 114.65% higher than from the Korean green tea. Comparing various tea sorts, the green teas contained more than 1.7 times of the five catechin compounds contained in other teas.     

Incorporating evolutionary information and functional domains for identifying RNA splicing factors in humans

Regulation of pre-mRNA splicing is achieved through the interaction of RNA sequence elements and a variety of RNA-splicing related proteins (splicing factors). The splicing machinery in humans is not yet fully elucidated, partly because splicing factors in humans have not been exhaustively identified. Furthermore, experimental methods for splicing factor identification are time-consuming and lab-intensive. Although many computational methods have been proposed for the identification of RNA-binding proteins, there exists no development that focuses on the identification of RNA-splicing related proteins so far. Therefore, we are motivated to design a method that focuses on the identification of human splicing factors using experimentally verified splicing factors. The investigation of amino acid composition reveals that there are remarkable differences between splicing factors and non-splicing proteins. A support vector machine (SVM) is utilized to construct a predictive model, and the five-fold cross-validation evaluation indicates that the SVM model trained with amino acid composition could provide a promising accuracy (80.22%). Another basic feature, amino acid dipeptide composition, is also examined to yield a similar predictive performance to amino acid composition. In addition, this work presents that the incorporation of evolutionary information and domain information could improve the predictive performance. The constructed models have been demonstrated to effectively classify (73.65% accuracy) an independent data set of human splicing factors. The result of independent testing indicates that in silico identification could be a feasible means of conducting preliminary analyses of splicing factors and significantly reducing the number of potential targets that require further in vivo or in vitro confirmation.     

Mito-GSAAC: mitochondria prediction using genetic ensemble classifier and split amino acid composition

Mitochondria are all-important organelles of eukaryotic cells since they are involved in processes associated with cellular mortality and human diseases. Therefore, trustworthy techniques are highly required for the identification of new mitochondrial proteins. We propose Mito-GSAAC system for prediction of mitochondrial proteins. The aim of this work is to investigate an effective feature extraction strategy and to develop an ensemble approach that can better exploit the advantages of this feature extraction strategy for mitochondria classification. We investigate four kinds of protein representations for prediction of mitochondrial proteins: amino acid composition, dipeptide composition, pseudo amino acid composition, and split amino acid composition (SAAC). Individual classifiers such as support vector machine (SVM), k-nearest neighbor, multilayer perceptron, random forest, AdaBoost, and bagging are first trained. An ensemble classifier is then built using genetic programming (GP) for evolving a complex but effective decision space from the individual decision spaces of the trained classifiers. The highest prediction performance for Jackknife test is 92.62% using GP-based ensemble classifier on SAAC features, which is the highest accuracy, reported so far on the Mitochondria dataset being used. While on the Malaria Parasite Mitochondria dataset, the highest accuracy is obtained by SVM using SAAC and it is further enhanced to 93.21% using GP-based ensemble. It is observed that SAAC has better discrimination power for mitochondria prediction over the rest of the feature extraction strategies. Thus, the improved prediction performance is largely due to the better capability of SAAC for discriminating between mitochondria and non-mitochondria proteins at the N and C terminus and the effective combination capability of GP. Mito-GSAAC can be accessed at . It is expected that the novel approach and the accompanied predictor will have a major impact to Molecular Cell Biology, Proteomics, Bioinformatics, System Biology, and Drug Development.     

Comparative study of SVM methods combined with voxel selection for object category classification on fMRI data

Background

Support vector machine (SVM) has been widely used as accurate and reliable method to decipher brain patterns from functional MRI (fMRI) data. Previous studies have not found a clear benefit for non-linear (polynomial kernel) SVM versus linear one. Here, a more effective non-linear SVM using radial basis function (RBF) kernel is compared with linear SVM. Different from traditional studies which focused either merely on the evaluation of different types of SVM or the voxel selection methods, we aimed to investigate the overall performance of linear and RBF SVM for fMRI classification together with voxel selection schemes on classification accuracy and time-consuming.

Methodology/Principal Findings

Six different voxel selection methods were employed to decide which voxels of fMRI data would be included in SVM classifiers with linear and RBF kernels in classifying 4-category objects. Then the overall performances of voxel selection and classification methods were compared. Results showed that: (1) Voxel selection had an important impact on the classification accuracy of the classifiers: in a relative low dimensional feature space, RBF SVM outperformed linear SVM significantly; in a relative high dimensional space, linear SVM performed better than its counterpart; (2) Considering the classification accuracy and time-consuming holistically, linear SVM with relative more voxels as features and RBF SVM with small set of voxels (after PCA) could achieve the better accuracy and cost shorter time.

Conclusions/Significance

The present work provides the first empirical result of linear and RBF SVM in classification of fMRI data, combined with voxel selection methods. Based on the findings, if only classification accuracy was concerned, RBF SVM with appropriate small voxels and linear SVM with relative more voxels were two suggested solutions; if users concerned more about the computational time, RBF SVM with relative small set of voxels when part of the principal components were kept as features was a better choice.     

基于序列特征的环状RNA识别

环状RNA是新发现的一类具有重要生物学功能的RNA。现有的环状RNA识别工具依赖高通量测序数据,因数据本身和识别方式的弊端而普遍存在准确性不足、不同方法间重复性低以及假阳性率/假阴性率高等缺点。为了解决该问题,我们搭建模型来实现不依赖于测序数据而根据序列的内在特征的环状RNA从头预测。本文选取了包括剪接位点上下游内含子的长度、A-to-I密度和Alu重复序列等100个与RNA成环相关的序列特征,建立了机器学习模型,并识别了人类基因组中的环状RNA,比较了两种机器学习方法随机森林法(RF)和支持向量机(SVM)的分类效果。结果表明,所选序列特征能有效地鉴别RNA能否成环,同时,不同序列特征对模型的分类预测能力的贡献也不同。相比于SVM方法,RF分类的效果更好。     

Intravascular Optical Coherence Tomography Image Segmentation Based on Support Vector Machine Algorithm

Intravascular optical coherence tomography (IVOCT) is becoming more and more popular in clinical diagnosis of coronary atherosclerotic. However, reading IVOCT images is of large amount of work. This article describes a method based on image feature extraction and support vector machine (SVM) to achieve semi-automatic segmentation of IVOCT images. The image features utilized in this work including light attenuation coefficients and image textures based on gray level co-occurrence matrix. Different sets of hyper-parameters and image features were tested. This method achieved an accuracy of 83% on the test images. Single class accuracy of 89% for fibrous, 79.3% for calcification and 86.5% lipid tissue. The results show that this method can be a considerable way for semi-automatic segmentation of atherosclerotic plaque components in clinical IVOCT images.     

HMM-based Supervised Machine Learning Framework for the Detection of fECG R-R Peak Locations

ObjectiveFetal Electro Cardiogram (fECG) provides critical information on the wellbeing of a foetus heart in its developing stages in the mother's womb. The objective of this work is to extract fECG which is buried in a composite signal consisting of itself, maternal ECG (mECG) and noises contributed from various unavoidable sources. In the past, the challenge of extracting fECG from the composite signal was dealt with by Stochastic Weiner filter, model-based Kalman filter and other adaptive filtering techniques. Blind Source Separation (BSS) based Independent Component Analysis (ICA) has shown an edge over the adaptive filtering techniques as the former does not require a reference signal. Recently, data-driven machine learning techniques e.g., adaptive neural networks, adaptive neuro-fuzzy inference system, support vector machine (SVM) are also applied.MethodThis work pursues hidden Markov model (HMM)-based supervised machine learning frame-work for the determination of the location of fECG QRS complex from the composite abdominal signal. HMM is used to model the underlying hidden states of the observable time series of the extracted and separated fECG data with its QRS peak location as one of the hidden states. The state transition probabilities are estimated in the training phase using the annotated data sets. Afterwards, using the estimated HMM networks, fQRS locations are detected in the testing phase. To evaluate the proposed technique, the accuracy of the correct detection of QRS complex with respect to the correct annotation of QRS complex location is considered and quantified by the sensitivity, probability of false alarm, and accuracy.ResultsThe best results that have been achieved using the proposed method are: accuracy – 97.1%, correct detection rate (translated to sensitivity) – 100%, and false alarm rate – 2.89%.ConclusionTwo primary challenges in these methods are finding the right reference threshold for the normalization of the extracted fECG signal during the initial trials and limitation of discrete frame work of HMM signal (converted from continuous time) which only offers a countable number of levels in observations. By feeding the posterior probabilities, obtained from SVM, into HMM, as emission probabilities, can further improve the accuracy of fQRS location detection.     

Discriminating between ADHD adults and controls using independent ERP components and a support vector machine: a validation study

Background

There are numerous event-related potential (ERP) studies in relation to attention-deficit hyperactivity disorder (ADHD), and a substantial number of ERP correlates of the disorder have been identified. However, most of the studies are limited to group differences in children. Independent component analysis (ICA) separates a set of mixed event-related potentials into a corresponding set of statistically independent source signals, which are likely to represent different functional processes. Using a support vector machine (SVM), a classification method originating from machine learning, this study aimed at investigating the use of such independent ERP components in differentiating adult ADHD patients from non-clinical controls by selecting a most informative feature set. A second aim was to validate the predictive power of the SVM classifier by means of an independent ADHD sample recruited at a different laboratory.

Methods

Two groups of age-matched adults (75 ADHD, 75 controls) performed a visual two stimulus go/no-go task. ERP responses were decomposed into independent components, and a selected set of independent ERP component features was used for SVM classification.

Results

Using a 10-fold cross-validation approach, classification accuracy was 91%. Predictive power of the SVM classifier was verified on the basis of the independent ADHD sample (17 ADHD patients), resulting in a classification accuracy of 94%. The latency and amplitude measures which in combination differentiated best between ADHD patients and non-clinical subjects primarily originated from independent components associated with inhibitory and other executive operations.

Conclusions

This study shows that ERPs can substantially contribute to the diagnosis of ADHD when combined with up-to-date methods.     

SVM-Based Synthetic Fingerprint Discrimination Algorithm and Quantitative Optimization Strategy

Synthetic fingerprints are a potential threat to automatic fingerprint identification systems (AFISs). In this paper, we propose an algorithm to discriminate synthetic fingerprints from real ones. First, four typical characteristic factors—the ridge distance features, global gray features, frequency feature and Harris Corner feature—are extracted. Then, a support vector machine (SVM) is used to distinguish synthetic fingerprints from real fingerprints. The experiments demonstrate that this method can achieve a recognition accuracy rate of over 98% for two discrete synthetic fingerprint databases as well as a mixed database. Furthermore, a performance factor that can evaluate the SVM''s accuracy and efficiency is presented, and a quantitative optimization strategy is established for the first time. After the optimization of our synthetic fingerprint discrimination task, the polynomial kernel with a training sample proportion of 5% is the optimized value when the minimum accuracy requirement is 95%. The radial basis function (RBF) kernel with a training sample proportion of 15% is a more suitable choice when the minimum accuracy requirement is 98%.     

Green, oolong and black tea extracts modulate lipid metabolism in hyperlipidemia rats fed high-sucrose diet

The main goal of this study was to compare effects of ethanol-soluble fractions prepared from various types of teas on sucrose-induced hyperlipidemia in 5-week old male Sprague-Dawley rats. Rats (n = 6-8 per group) weighed approximately 200 g were randomly divided into control diet, sucrose-rich diet, green tea, oolong tea and black tea groups. Control-diet group was provided with modified AIN-93 diet while the others consumed sucrose-rich diet. Tea extracts (1% w/v) were supplied in the drink for green tea, oolong tea and black tea groups. Results indicated sucrose-rich diet induced hypertriglyceridemia and hypercholesterolemia. Food intake was reduced by oolong tea extract. Consuming oolong and black tea extracts also significantly decreased body weight gains and food efficiency. Hypertriglyceridemia was normalized by green and black tea drink on day 18 and by oolong tea extract on day 25, respectively. Hypercholesterolemia was normalized by green tea on day 18 and by oolong tea and black tea on day 25, respectively. Plasma HDL-cholesterol concentrations were not affected by any tea extract. The triglyeride content in the liver as well as the cholesterol content in the heart of rats fed sucrose-rich diet were elevated and were normalized by all types of tea drink tested. Although green and oolong tea extracts contained similar composition of catechin, our findings suggest green tea exerted greater antihyperlipidemic effect than oolong tea. Apparent fat absorption may be one of the mechanisms by which green tea reduced hyperlipidemia as well as fat storage in the liver and heart of rats consumed sucrose-rich diet.     

Prediction of RNA-binding proteins from primary sequence by a support vector machine approach

Elucidation of the interaction of proteins with different molecules is of significance in the understanding of cellular processes. Computational methods have been developed for the prediction of protein-protein interactions. But insufficient attention has been paid to the prediction of protein-RNA interactions, which play central roles in regulating gene expression and certain RNA-mediated enzymatic processes. This work explored the use of a machine learning method, support vector machines (SVM), for the prediction of RNA-binding proteins directly from their primary sequence. Based on the knowledge of known RNA-binding and non-RNA-binding proteins, an SVM system was trained to recognize RNA-binding proteins. A total of 4011 RNA-binding and 9781 non-RNA-binding proteins was used to train and test the SVM classification system, and an independent set of 447 RNA-binding and 4881 non-RNA-binding proteins was used to evaluate the classification accuracy. Testing results using this independent evaluation set show a prediction accuracy of 94.1%, 79.3%, and 94.1% for rRNA-, mRNA-, and tRNA-binding proteins, and 98.7%, 96.5%, and 99.9% for non-rRNA-, non-mRNA-, and non-tRNA-binding proteins, respectively. The SVM classification system was further tested on a small class of snRNA-binding proteins with only 60 available sequences. The prediction accuracy is 40.0% and 99.9% for snRNA-binding and non-snRNA-binding proteins, indicating a need for a sufficient number of proteins to train SVM. The SVM classification systems trained in this work were added to our Web-based protein functional classification software SVMProt, at http://jing.cz3.nus.edu.sg/cgi-bin/svmprot.cgi. Our study suggests the potential of SVM as a useful tool for facilitating the prediction of protein-RNA interactions.     

Study on specificity of colon carcinoma-associated serum markers and establishment of SVM prediction model

We aimed to evaluate the specificity of 12 tumor markers related to colon carcinoma and identify the most sensitive index. Logistic regression and Bhattacharyya distance were used to evaluate the index. Then, different index combinations were used to establish a support vector machine (SVM) diagnosis model of malignant colon carcinoma. The accuracy of the model was checked. High accuracy was assumed to indicate the high specificity of the index. Through Logistic regression, three indexes, CEA, HSP60 and CA199, were screened out. Using Bhattacharyya distance, four indexes with the largest Bhattacharyya distance were screened out, including CEA, NSE, AFP, and CA724. The specificity of the combination of the above six indexes was higher than that of other combinations, so did the accuracy of the established SVM identification model. Using Logistic regression and Bhattacharyya distance for detection and establishing an SVM model based on different serum marker combinations can increase diagnostic accuracy, providing a theoretical basis for application of mathematical models in cancer diagnosis.     

A novel method of protein secondary structure prediction with high segment overlap measure: support vector machine approach

We have introduced a new method of protein secondary structure prediction which is based on the theory of support vector machine (SVM). SVM represents a new approach to supervised pattern classification which has been successfully applied to a wide range of pattern recognition problems, including object recognition, speaker identification, gene function prediction with microarray expression profile, etc. In these cases, the performance of SVM either matches or is significantly better than that of traditional machine learning approaches, including neural networks.The first use of the SVM approach to predict protein secondary structure is described here. Unlike the previous studies, we first constructed several binary classifiers, then assembled a tertiary classifier for three secondary structure states (helix, sheet and coil) based on these binary classifiers. The SVM method achieved a good performance of segment overlap accuracy SOV=76.2 % through sevenfold cross validation on a database of 513 non-homologous protein chains with multiple sequence alignments, which out-performs existing methods. Meanwhile three-state overall per-residue accuracy Q(3) achieved 73.5 %, which is at least comparable to existing single prediction methods. Furthermore a useful "reliability index" for the predictions was developed. In addition, SVM has many attractive features, including effective avoidance of overfitting, the ability to handle large feature spaces, information condensing of the given data set, etc. The SVM method is conveniently applied to many other pattern classification tasks in biology.     

Multivariate adaptive embedding (MAE) for the identification of bacterial pathogens in the field

In this work, we demonstrate a new classification machine based on multivariate adaptive embedding (MAE) that is capable of a robust identification of potential bacterial biological warfare agents (BWA). By employing Raman spectroscopy, this method proves to be reliable in application, easy to use and while retaining spectral quality, it is much faster than the often used support vector machines (SVM) and other supervised multivariate statistical classification machines. The multivariate adaptive embedding multi‐species classification ability was developed in order to serve as a real‐time detection method for biological threat detection and pathogen identification. A mean classification accuracy of 99.25±0.45% could be achieved with a representative set of biological warfare agents and simulant bacteria as a first approach for a user‐friendly and fieldable classification application for first responders and researchers.     

Aroma Components Characteristic of Spring Green Tea

To investigate the aroma components characteristic of spring green tea, analysis of the aroma concentrates of green tea and fresh tea-leaves was accomplished. The research on the changes in aroma constituents of spring green tea and the aroma concentrate from fresh tea-leaves during storage, showed that cis-3-hexenylhexanoate and cis-3-hexenyl-trans-2-hexenoate contributed to the typical fresh aroma of spring green tea. Twelve isomers of hexenol esters were synthesized for comparison of the fresh green note.     

High-throughput screening of high <Emphasis Type="Italic">Monascus</Emphasis> pigment-producing strain based on digital image processing

This work proposed a new method which applied image processing and support vector machine (SVM) for screening of mold strains. Taking Monascus as example, morphological characteristics of Monascus colony were quantified by image processing. And the association between the characteristics and pigment production capability was determined by SVM. On this basis, a highly automated screening strategy was achieved. The accuracy of the proposed strategy is 80.6 %, which is compatible with the existing methods (81.1 % for microplate and 85.4 % for flask). Meanwhile, the screening of 500 colonies only takes 20–30 min, which is the highest rate among all published results. By applying this automated method, 13 strains with high-predicted production were obtained and the best one produced as 2.8-fold (226 U/mL) of pigment and 1.9-fold (51 mg/L) of lovastatin compared with the parent strain. The current study provides us with an effective and promising method for strain improvement.