Structure-stratigraphy analysis" is a new method used in the study and prediction of and small-scaled structures in coal mines. The object of this method is coalbed structure that includes the folds and fracture ...Structure-stratigraphy analysis" is a new method used in the study and prediction of and small-scaled structures in coal mines. The object of this method is coalbed structure that includes the folds and fracture occurred in the vicinity of coal-seams. It emphases the analysis on the relationship between structural deformation and stratal lithologic combination.Based on the statistics of a series of related parameters in stratigraphy and structure,comprehensive analysis and drawing, this method may provide a good means for the quantitative evaluation and prediction of small scale structure in coal mines.展开更多
Secondary structures of RNAs are the basis of understanding their tertiary structures and functions and so their predictions are widely needed due to increasing discovery of noncoding RNAs.In the last decades,a lot o...Secondary structures of RNAs are the basis of understanding their tertiary structures and functions and so their predictions are widely needed due to increasing discovery of noncoding RNAs.In the last decades,a lot of methods have been proposed to predict RNA secondary structures but their accuracies encountered bottleneck.Here we present a method for RNA secondary structure prediction using direct coupling analysis and a remove-and-expand algorithm that shows better performance than four existing popular multiple-sequence methods.We further show that the results can also be used to improve the prediction accuracy of the single-sequence methods.展开更多
Background:RNA structure is the crucial basis for RNA function in various cellular processes.Over the last decade,high throughput structure profiling(SP)experiments have brought enormous insight into RNA secondary str...Background:RNA structure is the crucial basis for RNA function in various cellular processes.Over the last decade,high throughput structure profiling(SP)experiments have brought enormous insight into RNA secondary structure.Results:In this review,we first provide an overview of approaches for RNA secondary structure prediction,including free energy-based algorithms and comparative sequence analysis.Then we introduce SP technologies,databases to document SP data,and pipelines/algorithms to normalize and interpret SP data.Computational frameworks that incorporate SP data in RNA secondary structure prediction are also presented.Conclusions:We finally discuss potential directions for improvement in the prediction and differential analysis of RNA secondary structure.展开更多
The RNA tertiary structure is essential to understanding the function and biological processes. Unfortunately, it is still challenging to determine the large RNA structure from direct experimentation or computational ...The RNA tertiary structure is essential to understanding the function and biological processes. Unfortunately, it is still challenging to determine the large RNA structure from direct experimentation or computational modeling. One promising approach is first to predict the tertiary contacts and then use the contacts as constraints to model the structure. The RNA structure modeling depends on the contact prediction accuracy. Although many contact prediction methods have been developed in the protein field, there are only several contact prediction methods in the RNA field at present. Here, we first review the theoretical basis and test the performances of recent RNA contact prediction methods for tertiary structure and complex modeling problems. Then, we summarize the advantages and limitations of these RNA contact prediction methods. We suggest some future directions for this rapidly expanding field in the last.展开更多
Nonlinear solution of reinforced concrete structures, particularly complete load-deflection response, requires tracing of the equilibrium path and proper treatment of the limit and bifurcation points. In this regard, ...Nonlinear solution of reinforced concrete structures, particularly complete load-deflection response, requires tracing of the equilibrium path and proper treatment of the limit and bifurcation points. In this regard, ordinary solution techniques lead to instability near the limit points and also have problems in case of snap-through and snap-back. Thus they fail to predict the complete load-displacement response. The arc-length method serves the purpose well in principle, received wide acceptance in finite element analysis, and has been used extensively. However modifications to the basic idea are vital to meet the particular needs of the analysis. This paper reviews some of the recent developments of the method in the last two decades, with particular emphasis on nonlinear finite element analysis of reinforced concrete structures.展开更多
文摘Structure-stratigraphy analysis" is a new method used in the study and prediction of and small-scaled structures in coal mines. The object of this method is coalbed structure that includes the folds and fracture occurred in the vicinity of coal-seams. It emphases the analysis on the relationship between structural deformation and stratal lithologic combination.Based on the statistics of a series of related parameters in stratigraphy and structure,comprehensive analysis and drawing, this method may provide a good means for the quantitative evaluation and prediction of small scale structure in coal mines.
基金Project supported by the National Natural Science Foundation of China(Grant No.31570722).
文摘Secondary structures of RNAs are the basis of understanding their tertiary structures and functions and so their predictions are widely needed due to increasing discovery of noncoding RNAs.In the last decades,a lot of methods have been proposed to predict RNA secondary structures but their accuracies encountered bottleneck.Here we present a method for RNA secondary structure prediction using direct coupling analysis and a remove-and-expand algorithm that shows better performance than four existing popular multiple-sequence methods.We further show that the results can also be used to improve the prediction accuracy of the single-sequence methods.
基金the National Natural Science Foundation of China(No.11601259)Shanghai Municipal Science and Technology Major Project(No.2017SHZDZX01).
文摘Background:RNA structure is the crucial basis for RNA function in various cellular processes.Over the last decade,high throughput structure profiling(SP)experiments have brought enormous insight into RNA secondary structure.Results:In this review,we first provide an overview of approaches for RNA secondary structure prediction,including free energy-based algorithms and comparative sequence analysis.Then we introduce SP technologies,databases to document SP data,and pipelines/algorithms to normalize and interpret SP data.Computational frameworks that incorporate SP data in RNA secondary structure prediction are also presented.Conclusions:We finally discuss potential directions for improvement in the prediction and differential analysis of RNA secondary structure.
基金Project supported by the National Natural Science Foundation of China (Grant No. 11704140)Self-determined Research Funds of CCNU from the Colleges' Basic Research and Operation of MOE (Grant No. CCNU20TS004).
文摘The RNA tertiary structure is essential to understanding the function and biological processes. Unfortunately, it is still challenging to determine the large RNA structure from direct experimentation or computational modeling. One promising approach is first to predict the tertiary contacts and then use the contacts as constraints to model the structure. The RNA structure modeling depends on the contact prediction accuracy. Although many contact prediction methods have been developed in the protein field, there are only several contact prediction methods in the RNA field at present. Here, we first review the theoretical basis and test the performances of recent RNA contact prediction methods for tertiary structure and complex modeling problems. Then, we summarize the advantages and limitations of these RNA contact prediction methods. We suggest some future directions for this rapidly expanding field in the last.
文摘Nonlinear solution of reinforced concrete structures, particularly complete load-deflection response, requires tracing of the equilibrium path and proper treatment of the limit and bifurcation points. In this regard, ordinary solution techniques lead to instability near the limit points and also have problems in case of snap-through and snap-back. Thus they fail to predict the complete load-displacement response. The arc-length method serves the purpose well in principle, received wide acceptance in finite element analysis, and has been used extensively. However modifications to the basic idea are vital to meet the particular needs of the analysis. This paper reviews some of the recent developments of the method in the last two decades, with particular emphasis on nonlinear finite element analysis of reinforced concrete structures.
