Codon usage is the selective and nonrandom use of synonymous codons to encode amino acids in genes for proteins. The analysis of codon usage may improve the understanding of cocion preferences between different specie...Codon usage is the selective and nonrandom use of synonymous codons to encode amino acids in genes for proteins. The analysis of codon usage may improve the understanding of cocion preferences between different species and allow to rebuild the codons of exogenous genes to increase the expression efficiency of exogenous genes, Here, codon DNA sequence (CDS) of four poplar species, including Populus tremuloides Michx., P. tomentosa Carr., P. deltoides Marsh., and P. trichocarpa Torr. & Gray., is used to analyze the relative frequency of synonymous codon (RFSC). High-frequency codons are selected by high-frequency (HF) codon analysis. The results indicate that the codon usage is common for all four poplar species and the codon preference is quite similar among the four poplar species. However, CCT encoding for Pro, and ACT coding for Thr are the preferred codons in P. tremuloides and P. tomentosa, whereas CCA coding for Pro, and ACA coding for Thr are preferred in P. deltoides and P. trichocarpa The codons such as TGC coding for Cys, TTC coding for Phe, and AAG coding for Lys, are preferred in the poplar species except P trichocarpa. GAG coding for Glu is preferred only in P deltoides, while the other three poplar species prefer to use GAA. The commonness of preferred codon allows exogenous gene designed by the preferred cocion of one of the different poplar species to be used in other poplar species.展开更多
Burkholderia mallei is regarded as a potential biological weapon by the Centers for Disease Control and Prevention. In this study, the main factors shaping codon usage in the genome of B. mallei ATCC 23344 were firstl...Burkholderia mallei is regarded as a potential biological weapon by the Centers for Disease Control and Prevention. In this study, the main factors shaping codon usage in the genome of B. mallei ATCC 23344 were firstly reported. The results showed that the primary trend in codon usage variation in the B. mallei is due to translational selection; while compositional mutation bias is relatively the weaker influence and the hydrophobicity of each protein and gene length are only the minor influences. At the same time, 21 codons defined firstly as 'optimal codons' might provide more useful information for the expression of target genes and development of a vaccine to prevent glanders.展开更多
Because the modified remote user authentication scheme proposed by Shen, Lin and Hwang is insecure, the Shen-Lin-Hwang' s scheme is improved and a new secure remote user authentication scheme based on the bi- linear ...Because the modified remote user authentication scheme proposed by Shen, Lin and Hwang is insecure, the Shen-Lin-Hwang' s scheme is improved and a new secure remote user authentication scheme based on the bi- linear parings is proposed. Moreover, the effectiveness of the new scheme is analyzed, and it is proved that the new scheme can prevent from all kinds of known attack. The one-way hash function is effective in the new scheme. The new scheme is proved that it has high effectiveness and fast convergence speed. Moreover, the ap- plication of the new scheme is easy and operational.展开更多
Analysis of the secondary structures of mRNAs which encode mature peptides shows that the location of each codon in mRNA secondary structure has a trend, which appears to be in agreement with the conformational proper...Analysis of the secondary structures of mRNAs which encode mature peptides shows that the location of each codon in mRNA secondary structure has a trend, which appears to be in agreement with the conformational property of the corresponding amino acid to some extent. Most of the codons that encode hydrophobic amino acids are located in stable stem regions of mRNA secondary structures, and vice versa, most of the codons that encode hydrophilic amino acids are located in flexible loop regions. This result supports the recent conclusion that there may be the information transfer between the three dimensional structures of mRNA and the encoded protein.展开更多
A safe and reliable application system frame based on Internet and Intranet for Stock Supervision and Administration Council of China is built up. An all sided, multi tier and multi technical security method has be...A safe and reliable application system frame based on Internet and Intranet for Stock Supervision and Administration Council of China is built up. An all sided, multi tier and multi technical security method has been adopted, which includes identity recognition, data encryption, digital signature, Domino and WWW servers, access control list, directory service, certificate authorization server, IC card and so on. The recognition system based on CA server is a high efficient, convenient and reliable system. The encryption technology and security method are proved to be reliable. The recognition system is of high security and is worthy of being popularized in some places where some special security requirements need meeting. Multi tier technology can improve the security of database. Double keys method is a useful data encryption method.展开更多
In this paper, the author analyzed some cryptographic properties of a class of logical functions, f(x,y)=(q(x),...,q(x))·y+h(x),over Galois rings and residue rings, presented the relationship between the characte...In this paper, the author analyzed some cryptographic properties of a class of logical functions, f(x,y)=(q(x),...,q(x))·y+h(x),over Galois rings and residue rings, presented the relationship between the character spectrum of f(x,y) and the character speetrum of q(x),h(x) and the relationship between the cryptographic properties of f(x,y) and the cryptographic properties of h(x).展开更多
[Objective] The research aimed to construct the discriminant classification model of DNA sequence by combining with the biology knowledge and the mathematical method.[Method] According to the polarity nature of side c...[Objective] The research aimed to construct the discriminant classification model of DNA sequence by combining with the biology knowledge and the mathematical method.[Method] According to the polarity nature of side chain radical in the amino acid,the classification information of amino acid which represented the sequence characteristic from the content and array situation of base was extracted from the different sequences that the amino acid content was different.The four-dimension vector was used to represent.Mahalanobis distance and Fisher discriminant methods were used to classify the given sequence.[Result] In the model,the back substitution rates of sample obtained by two kinds of classification methods were both 100%,and the consistent rate of classification was 90%.[Conclusion] In the model,the calculation method was simple,and the accuracy of classification result was higher.It was superior to the discriminant classification model which was only based on the base content.展开更多
The synonymous codon usage in the translational initiation and termination regions of genes of severe acute respiratory syndrome (SARS) coronavirus and five other viruses in Coronaviridae was systematically analyzed.T...The synonymous codon usage in the translational initiation and termination regions of genes of severe acute respiratory syndrome (SARS) coronavirus and five other viruses in Coronaviridae was systematically analyzed.The results indicate that most minor codons for these coronaviruses are preferentially used in the initial and terminal region.The minor codons preferentially used in the initial region are thought to have a negative effect on gene expression,which can be explained by the minor codon modulator hypothesis.It also indicates that the minor codons preferentially used in the terminal region may regulate the level of gene expression.The proposed results strongly imply that the minor codon modulator hypothesis can be applied to both some bacteria and some viruses.展开更多
The key exchange is a fundamental building block in the cryptography. Several provable security models for the key exchange protocol are proposed. To determine the exact properties required by the protocols, a single ...The key exchange is a fundamental building block in the cryptography. Several provable security models for the key exchange protocol are proposed. To determine the exact properties required by the protocols, a single unified security model is essential, The eCK , eCK and CK models are examined and the result is proved that the eCK' model is the strongest provable security model for the key exchange. The relative security strength among these models is analyzed. To support the implication or non-implication relations among these models, the formal proofs and the counter-examples are given.展开更多
To realize delegation between different users in a mixed cryptosystem,a proxy signature scheme for ID-based original signers and certificated-based proxy signers(PSS-ID-CER)is defined.Using the bilinear properties o...To realize delegation between different users in a mixed cryptosystem,a proxy signature scheme for ID-based original signers and certificated-based proxy signers(PSS-ID-CER)is defined.Using the bilinear properties of the pairings and the characters of key generations of certificate-based cryptosystems and ID-based cryptosystems,a construction for such a scheme is also presented.To prove the security of the proposed scheme,a general security model for this scheme under adaptive chosen-PKG,chosen-ID,chosen-delegation,chosen-ProxySigner-public-key,chosen-proxy-key and chosen-message attack is defined.The proposed scheme is provably secure under the random oracle model and the hardness assumption of computational Diffie-Hellman problem.展开更多
The features of DNA sequence fragments were extracted from the distribution density of the condons in the individual cases of DNA sequence fragments. Based on the polarity of side chain radicals of amino acids molecul...The features of DNA sequence fragments were extracted from the distribution density of the condons in the individual cases of DNA sequence fragments. Based on the polarity of side chain radicals of amino acids molecules, the amino acids were classified into five categories, and the frequencies of these five categories were calculated. This kind of feature extraction based on the biological meanings not only took the content of basic groups into consideration, but also considered the marshal ing sequence of the basic groups. The hierarchical clustering analysis and BP neural network were used to classify the DNA sequence fragments. The results showed that the classification results of these two kinds of algo-rithms not only had high accuracy, but also had high consistence, indicating that this kind of feature extraction was superior over the traditional feature extraction which only took the features of basic groups into consideration.展开更多
The differences among the extended Canetti & Krawezyk 2007 model (ECK2007) and other four models, i.e., the Bellare & Rogaway (1993, 1995)models (BR93,BR95), the Bellare, Pointcheval & Rogaway (2000) model ...The differences among the extended Canetti & Krawezyk 2007 model (ECK2007) and other four models, i.e., the Bellare & Rogaway (1993, 1995)models (BR93,BR95), the Bellare, Pointcheval & Rogaway (2000) model (BPR2000) and the Canetti & Krawczyk (2001) model (CK2001) are given. The relative strength of security among these models is analyzed. To support the implication or non-implication relation among these models, the formal proof or the counter-example is provided.展开更多
In this study, a comparative analysis of the codon usage bias was performed in Aeropyrum pernix K1 and two other phylogenetically related Crenarchaeota microorganisms (i.e., Pyrobaculum aerophilum str. IM2 and Sulfol...In this study, a comparative analysis of the codon usage bias was performed in Aeropyrum pernix K1 and two other phylogenetically related Crenarchaeota microorganisms (i.e., Pyrobaculum aerophilum str. IM2 and Sulfolobus acidocaldarius DSM 639). The results indicated that the synonymous codon usage in A. pernix K1 was less biased, which was highly correlated with the GC3s value. The codon usage patterns were phylogenetically conserved among these Crenarchaeota microorganisms. Comparatively, it is the species function rather than the gene function that determines their gene codon usage patterns. A. pernix K1, P. aerophilum str. IM2, and S. acidocaldarius DSM 639 live in differently extreme conditions. It is presumed that the hving environment played an important role in determining the codon usage pattern of these microorganisms. Besides, there was no strain-specific codon usage among these microorganisms. The extent of codon bias in A. pernix K1 and S. acidocaldarius DSM 639 were highly correlated with the gene expression level, but no such association was detected in P. aerophilum str. IM2 genomes.展开更多
A modified Benes network is proposed to be used as an optimal shuffle network in worldwide interoperability for microwave access (WiMAX) low density parity check (LDPC) decoders, When the size of the input is not ...A modified Benes network is proposed to be used as an optimal shuffle network in worldwide interoperability for microwave access (WiMAX) low density parity check (LDPC) decoders, When the size of the input is not a power of two, the modified Benes network can achieve the most optimal performance. This modified Benes network is non-blocking and can perform any sorts of permutations, so it can support 19 modes specified in the WiMAX system. Furthermore, an efficient algorithm to generate the control signals for all the 2 × 2 switches in this network is derived, which can reduce the hardware complexity and overall latency of the modified Benes network. Synthesis results show that the proposed control signal generator can save 25.4% chip area and the overall network latency can be reduced by 36. 2%.展开更多
基金This work was supported by the National Major Basic Research and Development Program(No.TG1999016004)Jiangsu Provincial Natural Science Foundation(No.BK2003213).
文摘Codon usage is the selective and nonrandom use of synonymous codons to encode amino acids in genes for proteins. The analysis of codon usage may improve the understanding of cocion preferences between different species and allow to rebuild the codons of exogenous genes to increase the expression efficiency of exogenous genes, Here, codon DNA sequence (CDS) of four poplar species, including Populus tremuloides Michx., P. tomentosa Carr., P. deltoides Marsh., and P. trichocarpa Torr. & Gray., is used to analyze the relative frequency of synonymous codon (RFSC). High-frequency codons are selected by high-frequency (HF) codon analysis. The results indicate that the codon usage is common for all four poplar species and the codon preference is quite similar among the four poplar species. However, CCT encoding for Pro, and ACT coding for Thr are the preferred codons in P. tremuloides and P. tomentosa, whereas CCA coding for Pro, and ACA coding for Thr are preferred in P. deltoides and P. trichocarpa The codons such as TGC coding for Cys, TTC coding for Phe, and AAG coding for Lys, are preferred in the poplar species except P trichocarpa. GAG coding for Glu is preferred only in P deltoides, while the other three poplar species prefer to use GAA. The commonness of preferred codon allows exogenous gene designed by the preferred cocion of one of the different poplar species to be used in other poplar species.
文摘Burkholderia mallei is regarded as a potential biological weapon by the Centers for Disease Control and Prevention. In this study, the main factors shaping codon usage in the genome of B. mallei ATCC 23344 were firstly reported. The results showed that the primary trend in codon usage variation in the B. mallei is due to translational selection; while compositional mutation bias is relatively the weaker influence and the hydrophobicity of each protein and gene length are only the minor influences. At the same time, 21 codons defined firstly as 'optimal codons' might provide more useful information for the expression of target genes and development of a vaccine to prevent glanders.
基金Supported by the National Science Foundation for Young Scholars of China(61001091)~~
文摘Because the modified remote user authentication scheme proposed by Shen, Lin and Hwang is insecure, the Shen-Lin-Hwang' s scheme is improved and a new secure remote user authentication scheme based on the bi- linear parings is proposed. Moreover, the effectiveness of the new scheme is analyzed, and it is proved that the new scheme can prevent from all kinds of known attack. The one-way hash function is effective in the new scheme. The new scheme is proved that it has high effectiveness and fast convergence speed. Moreover, the ap- plication of the new scheme is easy and operational.
文摘Analysis of the secondary structures of mRNAs which encode mature peptides shows that the location of each codon in mRNA secondary structure has a trend, which appears to be in agreement with the conformational property of the corresponding amino acid to some extent. Most of the codons that encode hydrophobic amino acids are located in stable stem regions of mRNA secondary structures, and vice versa, most of the codons that encode hydrophilic amino acids are located in flexible loop regions. This result supports the recent conclusion that there may be the information transfer between the three dimensional structures of mRNA and the encoded protein.
文摘A safe and reliable application system frame based on Internet and Intranet for Stock Supervision and Administration Council of China is built up. An all sided, multi tier and multi technical security method has been adopted, which includes identity recognition, data encryption, digital signature, Domino and WWW servers, access control list, directory service, certificate authorization server, IC card and so on. The recognition system based on CA server is a high efficient, convenient and reliable system. The encryption technology and security method are proved to be reliable. The recognition system is of high security and is worthy of being popularized in some places where some special security requirements need meeting. Multi tier technology can improve the security of database. Double keys method is a useful data encryption method.
文摘In this paper, the author analyzed some cryptographic properties of a class of logical functions, f(x,y)=(q(x),...,q(x))·y+h(x),over Galois rings and residue rings, presented the relationship between the character spectrum of f(x,y) and the character speetrum of q(x),h(x) and the relationship between the cryptographic properties of f(x,y) and the cryptographic properties of h(x).
基金Supported by Science Research Project of Ningbo Dahongying University in2011(CF102601)~~
文摘[Objective] The research aimed to construct the discriminant classification model of DNA sequence by combining with the biology knowledge and the mathematical method.[Method] According to the polarity nature of side chain radical in the amino acid,the classification information of amino acid which represented the sequence characteristic from the content and array situation of base was extracted from the different sequences that the amino acid content was different.The four-dimension vector was used to represent.Mahalanobis distance and Fisher discriminant methods were used to classify the given sequence.[Result] In the model,the back substitution rates of sample obtained by two kinds of classification methods were both 100%,and the consistent rate of classification was 90%.[Conclusion] In the model,the calculation method was simple,and the accuracy of classification result was higher.It was superior to the discriminant classification model which was only based on the base content.
文摘The synonymous codon usage in the translational initiation and termination regions of genes of severe acute respiratory syndrome (SARS) coronavirus and five other viruses in Coronaviridae was systematically analyzed.The results indicate that most minor codons for these coronaviruses are preferentially used in the initial and terminal region.The minor codons preferentially used in the initial region are thought to have a negative effect on gene expression,which can be explained by the minor codon modulator hypothesis.It also indicates that the minor codons preferentially used in the terminal region may regulate the level of gene expression.The proposed results strongly imply that the minor codon modulator hypothesis can be applied to both some bacteria and some viruses.
基金Supported by the National High Technology Research and Development Program of China("863"Program)(2006AA706103)~~
文摘The key exchange is a fundamental building block in the cryptography. Several provable security models for the key exchange protocol are proposed. To determine the exact properties required by the protocols, a single unified security model is essential, The eCK , eCK and CK models are examined and the result is proved that the eCK' model is the strongest provable security model for the key exchange. The relative security strength among these models is analyzed. To support the implication or non-implication relations among these models, the formal proofs and the counter-examples are given.
基金The National Natural Science Foundation of China(No.60473028)the Natural Science Foundation of Zhengzhou University of Light Industry(No.2006XXJ18)the Doctor Foundation of Zhengzhou University of Light Industry(No.20080014)
文摘To realize delegation between different users in a mixed cryptosystem,a proxy signature scheme for ID-based original signers and certificated-based proxy signers(PSS-ID-CER)is defined.Using the bilinear properties of the pairings and the characters of key generations of certificate-based cryptosystems and ID-based cryptosystems,a construction for such a scheme is also presented.To prove the security of the proposed scheme,a general security model for this scheme under adaptive chosen-PKG,chosen-ID,chosen-delegation,chosen-ProxySigner-public-key,chosen-proxy-key and chosen-message attack is defined.The proposed scheme is provably secure under the random oracle model and the hardness assumption of computational Diffie-Hellman problem.
基金Supported by the Natural Science Foundation of Zhejiang Province(LY13A010007)~~
文摘The features of DNA sequence fragments were extracted from the distribution density of the condons in the individual cases of DNA sequence fragments. Based on the polarity of side chain radicals of amino acids molecules, the amino acids were classified into five categories, and the frequencies of these five categories were calculated. This kind of feature extraction based on the biological meanings not only took the content of basic groups into consideration, but also considered the marshal ing sequence of the basic groups. The hierarchical clustering analysis and BP neural network were used to classify the DNA sequence fragments. The results showed that the classification results of these two kinds of algo-rithms not only had high accuracy, but also had high consistence, indicating that this kind of feature extraction was superior over the traditional feature extraction which only took the features of basic groups into consideration.
文摘The differences among the extended Canetti & Krawezyk 2007 model (ECK2007) and other four models, i.e., the Bellare & Rogaway (1993, 1995)models (BR93,BR95), the Bellare, Pointcheval & Rogaway (2000) model (BPR2000) and the Canetti & Krawczyk (2001) model (CK2001) are given. The relative strength of security among these models is analyzed. To support the implication or non-implication relation among these models, the formal proof or the counter-example is provided.
基金The work is supported by National Natural Science Foundation of China (No. 60121101).
文摘In this study, a comparative analysis of the codon usage bias was performed in Aeropyrum pernix K1 and two other phylogenetically related Crenarchaeota microorganisms (i.e., Pyrobaculum aerophilum str. IM2 and Sulfolobus acidocaldarius DSM 639). The results indicated that the synonymous codon usage in A. pernix K1 was less biased, which was highly correlated with the GC3s value. The codon usage patterns were phylogenetically conserved among these Crenarchaeota microorganisms. Comparatively, it is the species function rather than the gene function that determines their gene codon usage patterns. A. pernix K1, P. aerophilum str. IM2, and S. acidocaldarius DSM 639 live in differently extreme conditions. It is presumed that the hving environment played an important role in determining the codon usage pattern of these microorganisms. Besides, there was no strain-specific codon usage among these microorganisms. The extent of codon bias in A. pernix K1 and S. acidocaldarius DSM 639 were highly correlated with the gene expression level, but no such association was detected in P. aerophilum str. IM2 genomes.
基金The National Natural Science Foundation of China(No.60871079)
文摘A modified Benes network is proposed to be used as an optimal shuffle network in worldwide interoperability for microwave access (WiMAX) low density parity check (LDPC) decoders, When the size of the input is not a power of two, the modified Benes network can achieve the most optimal performance. This modified Benes network is non-blocking and can perform any sorts of permutations, so it can support 19 modes specified in the WiMAX system. Furthermore, an efficient algorithm to generate the control signals for all the 2 × 2 switches in this network is derived, which can reduce the hardware complexity and overall latency of the modified Benes network. Synthesis results show that the proposed control signal generator can save 25.4% chip area and the overall network latency can be reduced by 36. 2%.