SVM-PB-Pred: SVM Based Protein Block Prediction Method Using Sequence Profiles and Secondary Structures

2013 ◽  
Vol 21 (8) ◽  
pp. 736-742 ◽  
Author(s):  
V. Suresh ◽  
S. Parthasarathy
2013 ◽  
Vol 11 (03) ◽  
pp. 1341004 ◽  
Author(s):  
YUANNING LIU ◽  
YAPING CHANG ◽  
CHAO ZHANG ◽  
QINGKAI WEI ◽  
JINGBO CHEN ◽  
...  

Design of small interference RNA (siRNA) is one of the most important steps in effectively applying the RNA interference (RNAi) technology. The current siRNA design often produces inconsistent design results, which often fail to reliably select siRNA with clear silencing effects. We propose that when designing siRNA, one should consider mRNA global features and near siRNA-binding site local features. By a linear regression study, we discovered strong correlations between inhibitory efficacy and both mRNA global features and neighboring local features. This paper shows that, on average, less GC content, fewer stem secondary structures, and more loop secondary structures of mRNA at both global and local flanking regions of the siRNA binding sites lead to stronger inhibitory efficacy. Thus, the use of mRNA global features and near siRNA-binding site local features are essential to successful gene silencing and hence, a better siRNA design. We use a random forest model to predict siRNA efficacy using siRNA features, mRNA features, and near siRNA binding site features. Our prediction method achieved a correlation coefficient of 0.7 in 10-fold cross validation in contrast to 0.63 when using siRNA features only. Our study demonstrates that considering mRNA and near siRNA binding site features helps improve siRNA design accuracy. The findings may also be helpful in understanding binding efficacy between microRNA and mRNA.


2018 ◽  
pp. 214-223
Author(s):  
AM Faria ◽  
MM Pimenta ◽  
JY Saab Jr. ◽  
S Rodriguez

Wind energy expansion is worldwide followed by various limitations, i.e. land availability, the NIMBY (not in my backyard) attitude, interference on birds migration routes and so on. This undeniable expansion is pushing wind farms near populated areas throughout the years, where noise regulation is more stringent. That demands solutions for the wind turbine (WT) industry, in order to produce quieter WT units. Focusing in the subject of airfoil noise prediction, it can help the assessment and design of quieter wind turbine blades. Considering the airfoil noise as a composition of many sound sources, and in light of the fact that the main noise production mechanisms are the airfoil self-noise and the turbulent inflow (TI) noise, this work is concentrated on the latter. TI noise is classified as an interaction noise, produced by the turbulent inflow, incident on the airfoil leading edge (LE). Theoretical and semi-empirical methods for the TI noise prediction are already available, based on Amiet’s broadband noise theory. Analysis of many TI noise prediction methods is provided by this work in the literature review, as well as the turbulence energy spectrum modeling. This is then followed by comparison of the most reliable TI noise methodologies, qualitatively and quantitatively, with the error estimation, compared to the Ffowcs Williams-Hawkings solution for computational aeroacoustics. Basis for integration of airfoil inflow noise prediction into a wind turbine noise prediction code is the final goal of this work.


2018 ◽  
Vol 138 (9) ◽  
pp. 1075-1081
Author(s):  
Yasuhide Kobayashi ◽  
Mitsuyuki Saito ◽  
Yuki Amimoto ◽  
Wataru Wakita

2009 ◽  
Vol 37 (2) ◽  
pp. 62-102 ◽  
Author(s):  
C. Lecomte ◽  
W. R. Graham ◽  
D. J. O’Boy

Abstract An integrated model is under development which will be able to predict the interior noise due to the vibrations of a rolling tire structurally transmitted to the hub of a vehicle. Here, the tire belt model used as part of this prediction method is first briefly presented and discussed, and it is then compared to other models available in the literature. This component will be linked to the tread blocks through normal and tangential forces and to the sidewalls through impedance boundary conditions. The tire belt is modeled as an orthotropic cylindrical ring of negligible thickness with rotational effects, internal pressure, and prestresses included. The associated equations of motion are derived by a variational approach and are investigated for both unforced and forced motions. The model supports extensional and bending waves, which are believed to be the important features to correctly predict the hub forces in the midfrequency (50–500 Hz) range of interest. The predicted waves and forced responses of a benchmark structure are compared to the predictions of several alternative analytical models: two three dimensional models that can support multiple isotropic layers, one of these models include curvature and the other one is flat; a one-dimensional beam model which does not consider axial variations; and several shell models. Finally, the effects of internal pressure, prestress, curvature, and tire rotation on free waves are discussed.


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