Methods for estimating synonymous and nonsynonymous substitution rates among protein-coding sequences adopt different mutation (substitution) models with subtle yet significant differences, which lead to different est...Methods for estimating synonymous and nonsynonymous substitution rates among protein-coding sequences adopt different mutation (substitution) models with subtle yet significant differences, which lead to different estimates of evolutionary information. Little attention has been devoted to the comparison of methods for obtaining reliable estimates since the amount of sequence variations within targeted datasets is always unpredictable. To our knowledge, there is little information available in literature about evaluation of these different methods. In this study, we compared six widely used methods and provided with evaluation results using simulated sequences. The results indicate that incorporating sequence features (such as transition/transversion bias and nucleotide/codon frequency bias) into methods could yield better performance. We recommend that conclusions related to or derived from Ka and Ks analyses should not be readily drawn only according to results from one method.展开更多
The singularities and oscillatory performance of translating-pulsating source Green＇s function in Bessho form were analyzed. Relative numerical integration methods such as Gaussian quadrature rule, variable substitut...The singularities and oscillatory performance of translating-pulsating source Green＇s function in Bessho form were analyzed. Relative numerical integration methods such as Gaussian quadrature rule, variable substitution method （VSM）, and steepest descent integration method （SDIM） were used to evaluate this type of Green＇s function. For SDIM, the complex domain was restricted only on the 0-plane. Meanwhile, the integral along the real axis was computed by use of the VSM to avoid the complication of a numerical search of the steepest descent line. Furthermore, the steepest descent line was represented by the B-spline function. Based on this representation, a new self-compatible integration method corresponding to parametric t was established. The numerical method was validated through comparison with other existing results, and was shown to be efficient and reliable in the calculation of the velocity potentials for the 3D seakeeping and hydrodynamic performance of floating struc- tures moving in waves.展开更多
The ratio of nonsynonymous substitution rate （Ka） to synonymous substitution rate （Ks） is widely used as an indicator of selective pressure at sequence level among different species, and diverse mutation models ha...The ratio of nonsynonymous substitution rate （Ka） to synonymous substitution rate （Ks） is widely used as an indicator of selective pressure at sequence level among different species, and diverse mutation models have been incorporated into several computing methods. We have previously developed a new γ-MYN method by capturing a key dynamic evolution trait of DNA nucleotide sequences, in consideration of varying mutation rates across sites. We now report a further improvement of NG, LWL, MLWL, LPB, MLPB, and YN methods based on an introduction of gamma distribution to illustrate the variation of raw mutation rate over sites. The novelty comes in two ways： （1） we incorporate an optimal gamma distribution shape parameter a into γ-NG, γ-LWL, γ-MLWL, γ-LPB, γ-MLPB, and γ-YN methods; （2） we investigate how variable substitution rates affect the methods that adopt different models as well as the interplay among four evolutional features with respect to Ka/Ks computations. Our results suggest that variable substitution rates over sites under negative selection exhibit an opposite effect on estimates compared with those under positive selection. We believe that the sensitivity of our new methods has been improved than that of their original methods under diverse conditions and it is advantageous to introduce novel parameters for Ka/Ks computation.展开更多
With the rapid development of hydrogen energy, hydrogen storage alloys have attracted wide attention owing to their key advantages, such as high volume density, proper plateau pressure, environmental friendliness and ...With the rapid development of hydrogen energy, hydrogen storage alloys have attracted wide attention owing to their key advantages, such as high volume density, proper plateau pressure, environmental friendliness and good safety. In the present review, the research progress of the improvement in hydrogen storage alloys, including rare-earth-based alloys, Mg-based alloys, Ti/Zr-based alloys, V-based alloys and high entropy alloys are systematically summarized. The influences of elemental substitution, catalyst doping, preparation methods and nanotechnology on the crystal structure, hydrogen storage properties as well as their affecting mechanisms, are discussed. Furthermore, the development trend and future research directions are proposed, which are expected to bring novel research ideas and potentially applicable methods for the development of high-performance hydrogen storage alloys.展开更多
Aiming at the comprehensive utilization of the rare-earth resources and the preparation of the high-performance low-cost Nd-Fe-B magnets,sintered magnets with different Ce substitution amounts of 17.2 wt%,24.8 wt%and ...Aiming at the comprehensive utilization of the rare-earth resources and the preparation of the high-performance low-cost Nd-Fe-B magnets,sintered magnets with different Ce substitution amounts of 17.2 wt%,24.8 wt%and 31.8 wt%were prepared by intergranularalloy method.The influence of substitution of Ce for Nd on their microstructure and magnetic properties in this work was detailedly investigated.The results indicated that the remanence(Br)and the maximum energy product((BH)max)of the sintered magnets decreased monotonic ally with the increase in Ce substitution.However,the obvious enhancement of coercivity(Hcj)was also observed,which was mainly due to the improvement of microstructure and the smooth,continuous grain boundary(GB).It can be found that a reasonable Ce substitution of 24.8 wt%for the sintered magnets could promote the refinement of microstructure,leading to the realization of superior magnetic properties.It is expected that the investigations could be beneficial to offer a feasible method for preparing the high-performance low-cost Ce-doped magnets.展开更多
The intramolecular hydrogen-bonding energies for eighteen molecules were calculated based on the substitution method, and compared with those predicted by the cis-trans method. The energy values obtained from two meth...The intramolecular hydrogen-bonding energies for eighteen molecules were calculated based on the substitution method, and compared with those predicted by the cis-trans method. The energy values obtained from two methods are close to each other with a correlation coefficient of 0.96. Furthermore, the hydrogen-bonding energies based on the substitution method are consistent with the geometrical features of intramolecular hydrogen bonds. Both of them demonstrate that the substitution method is capable of providing a good estimation of intramolecular hydrogen-bonding energy.展开更多
基金This work was supported by the Ministry of Science and Technology of China(Grant No.2001AA231061)the National Natural Science Foundation of China(Grant No.30270748)awarded to JY.We thank Mr.Jun Li for valuable discussion.
文摘Methods for estimating synonymous and nonsynonymous substitution rates among protein-coding sequences adopt different mutation (substitution) models with subtle yet significant differences, which lead to different estimates of evolutionary information. Little attention has been devoted to the comparison of methods for obtaining reliable estimates since the amount of sequence variations within targeted datasets is always unpredictable. To our knowledge, there is little information available in literature about evaluation of these different methods. In this study, we compared six widely used methods and provided with evaluation results using simulated sequences. The results indicate that incorporating sequence features (such as transition/transversion bias and nucleotide/codon frequency bias) into methods could yield better performance. We recommend that conclusions related to or derived from Ka and Ks analyses should not be readily drawn only according to results from one method.
基金Project supported by the National Natural Science Foundation of China （No. 50879090）, and the Key Research Program of Hydrody- namics of China （No. 9140A 14030712JB 11044）
文摘The singularities and oscillatory performance of translating-pulsating source Green＇s function in Bessho form were analyzed. Relative numerical integration methods such as Gaussian quadrature rule, variable substitution method （VSM）, and steepest descent integration method （SDIM） were used to evaluate this type of Green＇s function. For SDIM, the complex domain was restricted only on the 0-plane. Meanwhile, the integral along the real axis was computed by use of the VSM to avoid the complication of a numerical search of the steepest descent line. Furthermore, the steepest descent line was represented by the B-spline function. Based on this representation, a new self-compatible integration method corresponding to parametric t was established. The numerical method was validated through comparison with other existing results, and was shown to be efficient and reliable in the calculation of the velocity potentials for the 3D seakeeping and hydrodynamic performance of floating struc- tures moving in waves.
基金supported by the National Basic Research Program of China (Grant No. 2006CB910404) awarded to JY
文摘The ratio of nonsynonymous substitution rate （Ka） to synonymous substitution rate （Ks） is widely used as an indicator of selective pressure at sequence level among different species, and diverse mutation models have been incorporated into several computing methods. We have previously developed a new γ-MYN method by capturing a key dynamic evolution trait of DNA nucleotide sequences, in consideration of varying mutation rates across sites. We now report a further improvement of NG, LWL, MLWL, LPB, MLPB, and YN methods based on an introduction of gamma distribution to illustrate the variation of raw mutation rate over sites. The novelty comes in two ways： （1） we incorporate an optimal gamma distribution shape parameter a into γ-NG, γ-LWL, γ-MLWL, γ-LPB, γ-MLPB, and γ-YN methods; （2） we investigate how variable substitution rates affect the methods that adopt different models as well as the interplay among four evolutional features with respect to Ka/Ks computations. Our results suggest that variable substitution rates over sites under negative selection exhibit an opposite effect on estimates compared with those under positive selection. We believe that the sensitivity of our new methods has been improved than that of their original methods under diverse conditions and it is advantageous to introduce novel parameters for Ka/Ks computation.
文摘With the rapid development of hydrogen energy, hydrogen storage alloys have attracted wide attention owing to their key advantages, such as high volume density, proper plateau pressure, environmental friendliness and good safety. In the present review, the research progress of the improvement in hydrogen storage alloys, including rare-earth-based alloys, Mg-based alloys, Ti/Zr-based alloys, V-based alloys and high entropy alloys are systematically summarized. The influences of elemental substitution, catalyst doping, preparation methods and nanotechnology on the crystal structure, hydrogen storage properties as well as their affecting mechanisms, are discussed. Furthermore, the development trend and future research directions are proposed, which are expected to bring novel research ideas and potentially applicable methods for the development of high-performance hydrogen storage alloys.
基金financially supported by the Sichuan Province Science and Technology Support Program(No.2014GZ0090)the Key Technology and Development Program of PanXi Experimental Area(No.2016KJT0018).
文摘Aiming at the comprehensive utilization of the rare-earth resources and the preparation of the high-performance low-cost Nd-Fe-B magnets,sintered magnets with different Ce substitution amounts of 17.2 wt%,24.8 wt%and 31.8 wt%were prepared by intergranularalloy method.The influence of substitution of Ce for Nd on their microstructure and magnetic properties in this work was detailedly investigated.The results indicated that the remanence(Br)and the maximum energy product((BH)max)of the sintered magnets decreased monotonic ally with the increase in Ce substitution.However,the obvious enhancement of coercivity(Hcj)was also observed,which was mainly due to the improvement of microstructure and the smooth,continuous grain boundary(GB).It can be found that a reasonable Ce substitution of 24.8 wt%for the sintered magnets could promote the refinement of microstructure,leading to the realization of superior magnetic properties.It is expected that the investigations could be beneficial to offer a feasible method for preparing the high-performance low-cost Ce-doped magnets.
基金the National Natural Science Foundation of China (No. 20573049)
文摘The intramolecular hydrogen-bonding energies for eighteen molecules were calculated based on the substitution method, and compared with those predicted by the cis-trans method. The energy values obtained from two methods are close to each other with a correlation coefficient of 0.96. Furthermore, the hydrogen-bonding energies based on the substitution method are consistent with the geometrical features of intramolecular hydrogen bonds. Both of them demonstrate that the substitution method is capable of providing a good estimation of intramolecular hydrogen-bonding energy.
