Semi-interpenetrating polymer networks toward sulfonated poly(ether ether ketone) membranes for high concentration direct methanol fuel cell

Semi-IPNs were constructed by forming the crosslinking networks via the reaction between BPPO and diamine cross-linkers to overcome the dimensional swelling and methanol-permeation issues of SPEEK.     

A new sequence based encoding for prediction of host–pathogen protein interactions

Pathogen–host interactions are very important to figure out the infection process at the molecular level, where pathogen proteins physically bind to human proteins to manipulate critical biological processes in the host cell. Data scarcity and data unavailability are two major problems for computational approaches in the prediction of pathogen–host interactions. Developing a computational method to predict pathogen–host interactions with high accuracy, based on protein sequences alone, is of great importance because it can eliminate these problems. In this study, we propose a novel and robust sequence based feature extraction method, named Location Based Encoding, to predict pathogen–host interactions with machine learning based algorithms. In this context, we use Bacillus Anthracis and Yersinia Pestis data sets as the pathogen organisms and human proteins as the host model to compare our method with sequence based protein encoding methods, which are widely used in the literature, namely amino acid composition, amino acid pair, and conjoint triad. We use these encoding methods with decision trees (Random Forest, j48), statistical (Bayesian Networks, Naive Bayes), and instance based (kNN) classifiers to predict pathogen–host interactions. We conduct different experiments to evaluate the effectiveness of our method. We obtain the best results among all the experiments with RF classifier in terms of F1, accuracy, MCC, and AUC.     

Inference of gene regulatory networks with multi-objective cellular genetic algorithm

Reverse engineering of biochemical networks remains an important open challenge in computational systems biology. The goal of model inference is to, based on time-series gene expression data, obtain the sparse topological structure and parameters that quantitatively understand and reproduce the dynamics of biological systems. In this paper, we propose a multi-objective approach for the inference of S-System structures for Gene Regulatory Networks (GRNs) based on Pareto dominance and Pareto optimality theoretical concepts instead of the conventional single-objective evaluation of Mean Squared Error (MSE). Our motivation is that, using a multi-objective formulation for the GRN, it is possible to optimize the sparse topology of a given GRN as well as the kinetic order and rate constant parameters in a decoupled S-System, yet avoiding the use of additional penalty weights. A flexible and robust Multi-Objective Cellular Evolutionary Algorithm is adapted to perform the tasks of parameter learning and network topology inference for the proposed approach. The resulting software, called MONET, is evaluated on real-based academic and synthetic time-series of gene expression taken from the DREAM3 challenge and the IRMA in vivo datasets. The ability to reproduce biological behavior and robustness to noise is assessed and compared. The results obtained are competitive and indicate that the proposed approach offers advantages over previously used methods. In addition, MONET is able to provide experts with a set of trade-off solutions involving GRNs with different typologies and MSEs.     

A deep learning ensemble for function prediction of hypothetical proteins from pathogenic bacterial species

Protein function prediction is a crucial task in the post-genomics era due to their diverse irreplaceable roles in a biological system. Traditional methods involved cost-intensive and time-consuming molecular biology techniques but they proved to be ineffective after the outburst of sequencing data through the advent of cost-effective and advanced sequencing techniques. To manage the pace of annotation with that of data generation, there is a shift to computational approaches which are based on homology, sequence and structure-based features, protein-protein interaction networks, phylogenetic profiles, and physicochemical properties, etc. A combination of these features has proven to be promising for protein function prediction in terms of improving prediction accuracy. In the present work, we have employed a combination of features based on sequence, physicochemical property, subsequence and annotation features with a total of 9890 features extracted and/or calculated for 171,212 reviewed prokaryotic proteins of 9 bacterial phyla from UniProtKB, to train a supervised deep learning ensemble model with the aim to categorize a bacterial hypothetical/unreviewed protein’s function into 1739 GO terms as functional classes. The proposed system being fully dedicated to bacterial organisms is a novel attempt amongst various existing machine learning based protein function prediction systems based on mixed organisms. Experimental results demonstrate the success of the proposed deep learning ensemble model based on deep neural network method with F1 measure of 0.7912 on the prepared Test dataset 1 of reviewed proteins.     

Investigating How Organic Solvents Affect Tissue Culture Polystyrene Surfaces through Responses of Mesenchymal Stem Cells

Polymer coating of tissue culture polystyrene (TCPS) surfaces promotes their biofunctionality, which can aid manipulation of cellular functions. However, the effect of the solvent used for polymer coating is yet to be elucidated. In this study, solvent‐treated TCPS surfaces using water, methanol, ethanol, 2‐propanol, and dimethyl sulfoxide are fabricated. Solvent treatment of TCPS surfaces is performed by spreading solvents onto the surfaces and allowing them to dry. Solvent treatment changes the surface roughness and wettability, depending on the kind of solvents. In addition, these surface property changes affected the extension, proliferation, and differentiation of human bone marrow–derived mesenchymal stem cells. These results suggest that solvent selection for polymer coating is crucial in the regulation of cell responses. Further, treatment with an appropriate solvent can result in a more suitable culture environment for modulating cellular functions.     

Multistability and multiperiodicity of delayed Cohen-Grossberg neural networks with a general class of activation functions

In this paper, by using analysis approach and decomposition of state space, the multistability and multiperiodicity issues are discussed for Cohen-Grossberg neural networks (CGNNs) with time-varying delays and a general class of activation functions, where the general class of activation functions consist of nondecreasing functions with saturation’s including piecewise linear functions with two corner points and standard activation functions as its special case. Based on the Cauchy convergence principle, some sufficient conditions are obtained for checking the existence and uniqueness of equilibrium points of the n-neuron CGNNs. It is shown that the n-neuron CGNNs can have 2ⁿ locally exponentially stable equilibrium points located in saturation regions. Also, some conditions are derived for ascertaining equilibrium points to be locally exponentially stable or globally exponentially attractive and to be located in any designated region. As an extension of multistability, some similar results are presented for ascertaining multiple periodic orbits when external inputs of the n-neuron CGNNs are periodic. Finally, three examples are given to illustrate the effectiveness of the obtained results.     

Analog computation through high-dimensional physical chaotic neuro-dynamics

Conventional von Neumann computers have difficulty in solving complex and ill-posed real-world problems. However, living organisms often face such problems in real life, and must quickly obtain suitable solutions through physical, dynamical, and collective computations involving vast assemblies of neurons. These highly parallel computations through high-dimensional dynamics (computation through dynamics) are completely different from the numerical computations on von Neumann computers (computation through algorithms). In this paper, we explore a novel computational mechanism with high-dimensional physical chaotic neuro-dynamics. We physically constructed two hardware prototypes using analog chaotic-neuron integrated circuits. These systems combine analog computations with chaotic neuro-dynamics and digital computation through algorithms. We used quadratic assignment problems (QAPs) as benchmarks. The first prototype utilizes an analog chaotic neural network with 800-dimensional dynamics. An external algorithm constructs a solution for a QAP using the internal dynamics of the network. In the second system, 300-dimensional analog chaotic neuro-dynamics drive a tabu-search algorithm. We demonstrate experimentally that both systems efficiently solve QAPs through physical chaotic dynamics. We also qualitatively analyze the underlying mechanism of the highly parallel and collective analog computations by observing global and local dynamics. Furthermore, we introduce spatial and temporal mutual information to quantitatively evaluate the system dynamics. The experimental results confirm the validity and efficiency of the proposed computational paradigm with the physical analog chaotic neuro-dynamics.     

北京谱仪III上利用神经网络方法进行粒子鉴别的研究

本文描述了一种多层感知器的神经网络系统在BESIII粒子鉴别技术中的应用。网络按照子探测器分别进行训练, 输出结果可以作为后续网络的输入或者可以为似然函数方法构建概率密度函数。蒙特卡罗模拟样本的检验结果表明, 利用神经网络方法可以在BESIII上获得较好的粒子鉴别效果。     

Adaptive fuzzy neural network control on the acoustic field in a duct

Base on the principle of the superposition of waves, active noise control is achieved by adaptively tuning a secondary source which produces an anti-noise of equal amplitude and opposite phase with primary source. This paper presents the study on the acoustic attenuation in a duct by using the combination of fuzzy neural network with error back propagation algorithm to control secondary source. The most important advantage of fuzzy inference system is that the structured knowledge is represented in the form of fuzzy IF-THEN rules. But it lacks the ability to accommodate the change of external environments. Combining neural network with fuzzy system can help in this tuning process by adapting fuzzy sets and creating fuzzy rules. The performance of attenuation and control error can be measured by the microphone placed in the downstream of duct. The results of this study, show that the acoustic attenuation by 40 dB for pure-tone noise and nearly 30 dB for dual-tones noise are obtained.