Demonstration of two novel methods for predicting functional siRNA efficiency

BACKGROUND: siRNAs are small RNAs that serve as sequence determinants during the gene silencing process called RNA interference (RNAi). It is well know that siRNA efficiency is crucial in the RNAi pathway, and the siRNA efficiency for targeting different sites of a specific gene varies greatly. Therefore, there is high demand for reliable siRNAs prediction tools and for the design methods able to pick up high silencing potential siRNAs. RESULTS: In this paper, two systems have been established for the prediction of functional siRNAs: (1) a statistical model based on sequence information and (2) a machine learning model based on three features of siRNA sequences, namely binary description, thermodynamic profile and nucleotide composition. Both of the two methods show high performance on the two datasets we have constructed for training the model. CONCLUSION: Both of the two methods studied in this paper emphasize the importance of sequence information for the prediction of functional siRNAs. The way of denoting a bio-sequence by binary system in mathematical language might be helpful in other analysis work associated with fixed-length bio-sequence

Thermodynamic non-equilibrium effects in bubble coalescence: A discrete Boltzmann study

The Thermodynamic Non-Equilibrium (TNE) effects in the coalescing process of two initially static bubbles under thermal conditions are investigated by a Discrete Boltzmann Model (DBM). The spatial distributions of the typical none-quilibrium quantity, i.e., the Non-Organized Momentum Fluxes (NOMF) during evolutions are investigated in detail. The density-weighted statistical method is used to highlight the relationship between the TNE effects and the morphological or kinetics characteristics of bubble coalescence. It is found that the $xx$-component and $yy$-component of NOMF are anti-symmetrical; the $xy$-component changes from an anti-symmetric internal and external double quadrupole structure to an outer octupole structure during the coalescing process. More importantly, the evolution of the averaged $xx$-component of NOMF provides two characteristic instants, which divide the non-equilibrium process into three stages. The first instant corresponds to the moment when the mean coalescing speed gets the maximum and at this time the ratio of minor and major axes is about $1/2$. The second instant corresponds to the moment when the ratio of minor and major axes gets $1$ for the first time. It is interesting to find that the three quantities, TNE intensity, acceleration of coalescence and negative slope of boundary length, show a high degree of correlation and attain their maxima simultaneously. Surface tension and heat conduction accelerate the process of bubble coalescence while viscosity delays it. Both surface tension and viscosity enhance the global non-equilibrium intensity, whereas heat conduction restrains it. These TNE features and findings present some new insights into the kinetics of bubble coalescence

Robust Detection of Hierarchical Communities from Escherichia coli Gene Expression Data

Determining the functional structure of biological networks is a central goal of systems biology. One approach is to analyze gene expression data to infer a network of gene interactions on the basis of their correlated responses to environmental and genetic perturbations. The inferred network can then be analyzed to identify functional communities. However, commonly used algorithms can yield unreliable results due to experimental noise, algorithmic stochasticity, and the influence of arbitrarily chosen parameter values. Furthermore, the results obtained typically provide only a simplistic view of the network partitioned into disjoint communities and provide no information of the relationship between communities. Here, we present methods to robustly detect coregulated and functionally enriched gene communities and demonstrate their application and validity for Escherichia coli gene expression data. Applying a recently developed community detection algorithm to the network of interactions identified with the context likelihood of relatedness (CLR) method, we show that a hierarchy of network communities can be identified. These communities significantly enrich for gene ontology (GO) terms, consistent with them representing biologically meaningful groups. Further, analysis of the most significantly enriched communities identified several candidate new regulatory interactions. The robustness of our methods is demonstrated by showing that a core set of functional communities is reliably found when artificial noise, modeling experimental noise, is added to the data. We find that noise mainly acts conservatively, increasing the relatedness required for a network link to be reliably assigned and decreasing the size of the core communities, rather than causing association of genes into new communities.Comment: Due to appear in PLoS Computational Biology. Supplementary Figure S1 was not uploaded but is available by contacting the author. 27 pages, 5 figures, 15 supplementary file

TencentPretrain: A Scalable and Flexible Toolkit for Pre-training Models of Different Modalities

Recently, the success of pre-training in text domain has been fully extended to vision, audio, and cross-modal scenarios. The proposed pre-training models of different modalities are showing a rising trend of homogeneity in their model structures, which brings the opportunity to implement different pre-training models within a uniform framework. In this paper, we present TencentPretrain, a toolkit supporting pre-training models of different modalities. The core feature of TencentPretrain is the modular design. The toolkit uniformly divides pre-training models into 5 components: embedding, encoder, target embedding, decoder, and target. As almost all of common modules are provided in each component, users can choose the desired modules from different components to build a complete pre-training model. The modular design enables users to efficiently reproduce existing pre-training models or build brand-new one. We test the toolkit on text, vision, and audio benchmarks and show that it can match the performance of the original implementations

A Deep Learning Model for Three-Dimensional Nystagmus Detection and Its Preliminary Application

Symptoms of vertigo are frequently reported and are usually accompanied by eye-movements called nystagmus. In this article, we designed a three-dimensional nystagmus recognition model and a benign paroxysmal positional vertigo automatic diagnosis system based on deep neural network architectures (Chinese Clinical Trials Registry ChiCTR-IOR-17010506). An object detection model was constructed to track the movement of the pupil centre. Convolutional neural network-based models were trained to detect nystagmus patterns in three dimensions. Our nystagmus detection models obtained high areas under the curve; 0.982 in horizontal tests, 0.893 in vertical tests, and 0.957 in torsional tests. Moreover, our automatic benign paroxysmal positional vertigo diagnosis system achieved a sensitivity of 0.8848, specificity of 0.8841, accuracy of 0.8845, and an F1 score of 0.8914. Compared with previous studies, our system provides a clinical reference, facilitates nystagmus detection and diagnosis, and it can be applied in real-world medical practices