流感病毒分为三类:甲型(A型),乙型(B型),丙型(C型).在这三种类型中甲型(A型)流感病毒是最致命的流感病毒,对人类引起了严重疾病.本文对甲型流感病毒DNA序列建立了一种新的时间序列模型,即CGR(Chaos Game Representation)弧度序列.利用CG...流感病毒分为三类:甲型(A型),乙型(B型),丙型(C型).在这三种类型中甲型(A型)流感病毒是最致命的流感病毒,对人类引起了严重疾病.本文对甲型流感病毒DNA序列建立了一种新的时间序列模型,即CGR(Chaos Game Representation)弧度序列.利用CGR坐标将甲流病毒DNA序列转换成CGR弧度序列,且引入长记忆ARFIMA模型去拟合此类序列,发现随机找来的10条H1N1序列,10条H3N2序列都具有长相关性且拟合很好,并且还发现这两种序列可以尝试用不同的ARFIMA模型去识别,其中H1N1可用ARFIMA(0,d,5)模型去识别,H3N2可用ARFIMA(1,d,1)模型去识别.展开更多
基于DNA序列的chaos game representation(CGR)图形表示,文中给出了一种新的蛋白质序列的3D空间表示,其空间曲线的x、y轴坐标由Randic文章中的方法得到,z轴坐标由蛋白质序列中氨基酸的累积个数得到。蛋白质序列的3D空间表示得到的曲线比...基于DNA序列的chaos game representation(CGR)图形表示,文中给出了一种新的蛋白质序列的3D空间表示,其空间曲线的x、y轴坐标由Randic文章中的方法得到,z轴坐标由蛋白质序列中氨基酸的累积个数得到。蛋白质序列的3D空间表示得到的曲线比Randic的2D图形表示具有更好的可视性。利用不同的数学方法,对所得到的曲线进行了数值刻画;基于得到的数值刻画,比较了9个不同物种的线粒体NADH脱氢酶的相似性。展开更多
Over the course of human history, influenza pandemics have been seen as major disasters, so studies on the influenza virus have become an important issue for many experts and scholars. Comprehensive research has been ...Over the course of human history, influenza pandemics have been seen as major disasters, so studies on the influenza virus have become an important issue for many experts and scholars. Comprehensive research has been performed over the years on the biological properties, chemical characteristics, external environmental factors and other aspects of the virus, and some results have been achieved. Based on the chaos game representation walk model, this paper uses the time series analysis method to study the DNA sequences of the influenza virus from 1913 to 2010, and works out the early-warning signals indicator value for the outbreak of an influenza pandemic. The variances in the CCR wall〈 sequences for the pandemic years （or ＋ -1 to 2 years） are significantly higher than those for the adjacent years, while those in the non-pandemic years are usually smaller. In this way we can provide an influenza early-warning mechanism so that people can take precautions and be well prepared prior to a pandemic.展开更多
Comparison between different biological sequences is a key step in bioinformatics when analyzing similarities of sequences and phylogenetic relationships. A method of graphically representing biological sequences know...Comparison between different biological sequences is a key step in bioinformatics when analyzing similarities of sequences and phylogenetic relationships. A method of graphically representing biological sequences known as Chaos Game Representation (CGR) has achieved many applications in the studies of bioinformatics. The key issue in the application of CGR is to extract as many useful features as possible from CGR. Initially, CGR was applied to DNA sequences, but in this paper, a CGR-based approach is used to extract suitable features for comparing protein sequences of SARS-CoV-2 and other viruses. For this aim, several viral protein sequences from 12 groups are considered and CGR centroid, amino acid frequency, compounded frequency, Shannon entropy, and Kullback-Lieber Discrimination Information are applied to find the inter-relationship among the sequences. The experimental results demonstrate the potential strengths of CGR-based method for examining the evolutionary relationship of protein sequences. Our method is powerful for extracting effective features from protein sequences, and therefore important in classifying proteins and inferring the phylogeny of viruses.展开更多
Chaos game representation （CGR） is proposed as a scale-independent representation for DNA sequences and provides information about the statistical distribution of oligonucleotides in a DNA sequence. CGR images of DN...Chaos game representation （CGR） is proposed as a scale-independent representation for DNA sequences and provides information about the statistical distribution of oligonucleotides in a DNA sequence. CGR images of DNA sequences represent some kinds of fractal patterns, but the common multifractal analysis based on the box counting method cannot deal with CGR images perfectly. Here, the wavelet transform modulus maxima （WTMM） method is applied to the multifractal analysis of CGR images. The results show that the scale-invariance range of CGR edge images can be extended to three orders of magnitude, and complete singularity spectra can be calculated. Spectrum parameters such as the singularity spectrum span are extracted to describe the statistical character of DNA sequences. Compared with the singularity spectrum span, exon sequences with a minimal spectrum span have the most uniform fractal structure. Also, the singularity spectrum parameters are related to oligonueleotide length, sequence component and species, thereby providing a method of studying the length polymorphism of repeat oligonucleotides.展开更多
We developed a new approach for the reconstruction of phylogeny trees based on the chaos game representation (CGR) of biological sequences. The chaos game representation (CGR) method generates a picture from a biologi...We developed a new approach for the reconstruction of phylogeny trees based on the chaos game representation (CGR) of biological sequences. The chaos game representation (CGR) method generates a picture from a biological sequence, which displays both local and global patterns. The quantitative index of the biological sequence is extracted from the picture. The Kullback-Leibler discrimination information is used as a diversity indicator to measure the dissimilarity of each pair of biological sequences. The new method is inspected by two data sets: the Eutherian orders using concatenated H-stranded amino acid sequences and the genome sequence of the SARS and coronavirus. The phylogeny trees constructed by the new method are consistent with the commonly accepted ones. These results are very promising and suggest more efforts for further developments.展开更多
A field experiment was conducted to evaluate the agronomic and physiological responses of rice under different water management systems, types of fertilizer and seedling age. This experiment was done at the farm of Ag...A field experiment was conducted to evaluate the agronomic and physiological responses of rice under different water management systems, types of fertilizer and seedling age. This experiment was done at the farm of Agri Park, College of Agriculture, Central Experimental Station (CES), Crop Science Cluster of the University of the Philippines Los Banos, College Laguna during 2013. The strip-split plot design with three replications was used with the two types of fertilizer (vermicompost and chemical fertilizer), water management (with and without standing water) and two seedling ages (10 and 14-d old) were the treatments in the experiment. Chemical fertilizer produced the highest grain yield, total dry matter (TDM), leaf area index (LAI), net assimilation rate (NAR) and crop growth rate (CGR). Most of these characters significantly increased in 10-d old seedlings with chemical fertilizer without standing water. The shorter phyllochron and higher root pulling resistance (RPR) were observed in 10-d old seedlings without standing water. For the variety NSIC Rc 216, the use of 10-d old seedlings grown without standing water with chemical fertilizer is the optimum conditions for the better growth and high productivity.展开更多
Stress Corrosion Cracking(SCC)process through which cracks occur in a variety of susceptible materials is a result of a combination of residual or applied stresses and corrosion.In oil and gas field,buried pipeline st...Stress Corrosion Cracking(SCC)process through which cracks occur in a variety of susceptible materials is a result of a combination of residual or applied stresses and corrosion.In oil and gas field,buried pipeline steels are made of low-alloy steels with a ferritic-pearlitic structure,such as X70.In dilute solutions,these materials are prone to SCC failure.The Near-neutral simulated soil solution(NS4)solution is established to imitate SCC conditions and subsequently became the industry requirement for crack growth experiments in the majority of laboratories.The strainassisted active crack pathways are considered while modelling SCC growth as an oxide film rupture and anodic dissolution process.It’s been hypothesized that increasing the strain concentration can help with dissolution at the filmfree crack tip.This research focuses on estimating the SCC crack growth rate under various environmental conditions in oil and gas pipelines using finite element modelling.The simulation is carried out using the J-integral theory in the COMSOL Multiphysics program.Simulations are performed to model the crack growth rate(CGR)using slip anodic dissolution(film rupture)mechanism.The plastic strain gradient is required to compute the SCC CGR(da/dt).Because the plastic strain located at crack tip increases proportionally to the crack length as it propagates,the CGR increases as the stress intensity factor(SIF)increases.The crack growth rates increase when constant loads are applied and as the temperature rises,and elevating the cathodic potential has a minimal influence on the propagation rate of cracks but raises the material yield strength and imparts brittle behavior to it.展开更多
文摘流感病毒分为三类:甲型(A型),乙型(B型),丙型(C型).在这三种类型中甲型(A型)流感病毒是最致命的流感病毒,对人类引起了严重疾病.本文对甲型流感病毒DNA序列建立了一种新的时间序列模型,即CGR(Chaos Game Representation)弧度序列.利用CGR坐标将甲流病毒DNA序列转换成CGR弧度序列,且引入长记忆ARFIMA模型去拟合此类序列,发现随机找来的10条H1N1序列,10条H3N2序列都具有长相关性且拟合很好,并且还发现这两种序列可以尝试用不同的ARFIMA模型去识别,其中H1N1可用ARFIMA(0,d,5)模型去识别,H3N2可用ARFIMA(1,d,1)模型去识别.
文摘基于DNA序列的chaos game representation(CGR)图形表示,文中给出了一种新的蛋白质序列的3D空间表示,其空间曲线的x、y轴坐标由Randic文章中的方法得到,z轴坐标由蛋白质序列中氨基酸的累积个数得到。蛋白质序列的3D空间表示得到的曲线比Randic的2D图形表示具有更好的可视性。利用不同的数学方法,对所得到的曲线进行了数值刻画;基于得到的数值刻画,比较了9个不同物种的线粒体NADH脱氢酶的相似性。
基金Project supported by the Fundamental Research Funds for the Central Universities (Grant No. JUSRP21117)the Program for Innovative Research Team of Jiangnan University (Grant No. 2008CX002)
文摘Over the course of human history, influenza pandemics have been seen as major disasters, so studies on the influenza virus have become an important issue for many experts and scholars. Comprehensive research has been performed over the years on the biological properties, chemical characteristics, external environmental factors and other aspects of the virus, and some results have been achieved. Based on the chaos game representation walk model, this paper uses the time series analysis method to study the DNA sequences of the influenza virus from 1913 to 2010, and works out the early-warning signals indicator value for the outbreak of an influenza pandemic. The variances in the CCR wall〈 sequences for the pandemic years （or ＋ -1 to 2 years） are significantly higher than those for the adjacent years, while those in the non-pandemic years are usually smaller. In this way we can provide an influenza early-warning mechanism so that people can take precautions and be well prepared prior to a pandemic.
文摘Comparison between different biological sequences is a key step in bioinformatics when analyzing similarities of sequences and phylogenetic relationships. A method of graphically representing biological sequences known as Chaos Game Representation (CGR) has achieved many applications in the studies of bioinformatics. The key issue in the application of CGR is to extract as many useful features as possible from CGR. Initially, CGR was applied to DNA sequences, but in this paper, a CGR-based approach is used to extract suitable features for comparing protein sequences of SARS-CoV-2 and other viruses. For this aim, several viral protein sequences from 12 groups are considered and CGR centroid, amino acid frequency, compounded frequency, Shannon entropy, and Kullback-Lieber Discrimination Information are applied to find the inter-relationship among the sequences. The experimental results demonstrate the potential strengths of CGR-based method for examining the evolutionary relationship of protein sequences. Our method is powerful for extracting effective features from protein sequences, and therefore important in classifying proteins and inferring the phylogeny of viruses.
基金Project supported by the Science and Technology Commission of Shanghai Municipality (Grant No. 05DZ19747)the National Basic Research Program of China (Grant No. 2006CB504509)
文摘Chaos game representation （CGR） is proposed as a scale-independent representation for DNA sequences and provides information about the statistical distribution of oligonucleotides in a DNA sequence. CGR images of DNA sequences represent some kinds of fractal patterns, but the common multifractal analysis based on the box counting method cannot deal with CGR images perfectly. Here, the wavelet transform modulus maxima （WTMM） method is applied to the multifractal analysis of CGR images. The results show that the scale-invariance range of CGR edge images can be extended to three orders of magnitude, and complete singularity spectra can be calculated. Spectrum parameters such as the singularity spectrum span are extracted to describe the statistical character of DNA sequences. Compared with the singularity spectrum span, exon sequences with a minimal spectrum span have the most uniform fractal structure. Also, the singularity spectrum parameters are related to oligonueleotide length, sequence component and species, thereby providing a method of studying the length polymorphism of repeat oligonucleotides.
文摘We developed a new approach for the reconstruction of phylogeny trees based on the chaos game representation (CGR) of biological sequences. The chaos game representation (CGR) method generates a picture from a biological sequence, which displays both local and global patterns. The quantitative index of the biological sequence is extracted from the picture. The Kullback-Leibler discrimination information is used as a diversity indicator to measure the dissimilarity of each pair of biological sequences. The new method is inspected by two data sets: the Eutherian orders using concatenated H-stranded amino acid sequences and the genome sequence of the SARS and coronavirus. The phylogeny trees constructed by the new method are consistent with the commonly accepted ones. These results are very promising and suggest more efforts for further developments.
文摘A field experiment was conducted to evaluate the agronomic and physiological responses of rice under different water management systems, types of fertilizer and seedling age. This experiment was done at the farm of Agri Park, College of Agriculture, Central Experimental Station (CES), Crop Science Cluster of the University of the Philippines Los Banos, College Laguna during 2013. The strip-split plot design with three replications was used with the two types of fertilizer (vermicompost and chemical fertilizer), water management (with and without standing water) and two seedling ages (10 and 14-d old) were the treatments in the experiment. Chemical fertilizer produced the highest grain yield, total dry matter (TDM), leaf area index (LAI), net assimilation rate (NAR) and crop growth rate (CGR). Most of these characters significantly increased in 10-d old seedlings with chemical fertilizer without standing water. The shorter phyllochron and higher root pulling resistance (RPR) were observed in 10-d old seedlings without standing water. For the variety NSIC Rc 216, the use of 10-d old seedlings grown without standing water with chemical fertilizer is the optimum conditions for the better growth and high productivity.
基金This work is supported by ASPIRE Award for Research Excellence(AARE 2019)under the Advanced Technology Research Council-ASPIRE through Project Number AARE19-098.
文摘Stress Corrosion Cracking(SCC)process through which cracks occur in a variety of susceptible materials is a result of a combination of residual or applied stresses and corrosion.In oil and gas field,buried pipeline steels are made of low-alloy steels with a ferritic-pearlitic structure,such as X70.In dilute solutions,these materials are prone to SCC failure.The Near-neutral simulated soil solution(NS4)solution is established to imitate SCC conditions and subsequently became the industry requirement for crack growth experiments in the majority of laboratories.The strainassisted active crack pathways are considered while modelling SCC growth as an oxide film rupture and anodic dissolution process.It’s been hypothesized that increasing the strain concentration can help with dissolution at the filmfree crack tip.This research focuses on estimating the SCC crack growth rate under various environmental conditions in oil and gas pipelines using finite element modelling.The simulation is carried out using the J-integral theory in the COMSOL Multiphysics program.Simulations are performed to model the crack growth rate(CGR)using slip anodic dissolution(film rupture)mechanism.The plastic strain gradient is required to compute the SCC CGR(da/dt).Because the plastic strain located at crack tip increases proportionally to the crack length as it propagates,the CGR increases as the stress intensity factor(SIF)increases.The crack growth rates increase when constant loads are applied and as the temperature rises,and elevating the cathodic potential has a minimal influence on the propagation rate of cracks but raises the material yield strength and imparts brittle behavior to it.
