Autogrid-based clustering of kinases: selection of representative conformations for docking purposes

The selection of the most appropriate protein conformation is a crucial aspect in molecular docking experiments. In order to reduce the errors arising from the use of a single protein conformation, several authors suggest the use of several tridimensional structures for the target. However, the selection of the most appropriate protein conformations still remains a challenging goal. The protein 3D-structures selection is mainly performed based on pairwise root-mean-square-deviation (RMSD) values computation, followed by hierarchical clustering. Herein we report an alternative strategy, based on the computation of only two atom affinity map for each protein conformation, followed by multivariate analysis and hierarchical clustering. This methodology was applied on seven different kinases of pharmaceutical interest. The comparison with the classical RMSD-based strategy was based on cross-docking of co-crystallized ligands. In the case of epidermal growth factor receptor kinase, also the docking performance on 220 known ligands were evaluated, followed by 3D-QSAR studies. In all the cases, the herein proposed methodology outperformed the RMSD-based one.     

A method for the construction of hierarchical generalized space shift keying (GSSK) modulation for unequal error protection

In this paper, we propose a systematic method to achieve two-level unequal error protection (UEP) with generalized space shift keying (GSSK) modulation for multiple-input multiple-output (MIMO) systems. GSSK is a modulation scheme that encodes the source information in the antenna indices. To enable the nonuniform arrangement of the spatial constellation of GSSK modulation, new techniques are needed as new features of GSSK modulation are observed. The proposed method is based on first partitioning the GSSK constellation into subsets and then choosing constellation points inside a subset. The high-priority (HP) bits select the subset and the low-priority (LP) bits select constellation points inside a subset. The proposed subset partitioning procedure developed based on a theoretical study on set partitioning in the multidimensional space guarantees optimal or near-optimal HP protection, enables simple and systematic designs for LP protection, and increases the LP capacity. The proposed systematic design approach applies to systems with any numbers of transmit antennas and can create various hierarchical GSSK schemes with different HP/LP protection capabilities.     

Development of a noise sources classification system based on new method for feature selection

Feature selection of noise sources is important for noise sources detection and classification. In this paper, a new rough set based feature selection method has been given. Based on the method, a noise sources automatic classification system (NSACS) has been designed and validated. The key idea of the method is that most effective features can distinguish the most number of samples belonging to different classes of noise sources, if they are used for classification. This new approach has been applied into the system NSACS to select relevant features for artificial datasets and real-world datasets and the results have shown that this approach can correctly select all the relevant features of artificial datasets and at the same time it can drastically reduce the number of features. From the experiments, it can be found that to consider all the five datasets, the number of classification features after selection drops to 35% and the accurate classification rate increases about 14%. For the underwater noise sources dataset the number of features drops to 1/5 and the accurate classification rate increases about 6% after feature selection.     

水下噪声音色属性回归模型及其在目标识别中的应用

通过对声音的主观评价与客观分析而建立的主观感受数学模型,在许多领域都有重要的应用. 本文采用多元线性回归分析手段对水下噪声音色属性建立回归模型,提取音色特征并改善水下目标的识别效果. 首先,在前期水下噪声音色属性主观评价实验的基础上,将构成音色属性空间的5个成分的评价分值作为回归分析中的因变量,提取大量与听觉感知相关的听觉特征作为自变量;然后,通过相关分析和改进的逐步筛选法,挑选出反映音色属性的“最优”自变量子集;最后,利用向后剔除回归分析和水下目标识别实验,确定适当的音色模型,并通过假设检验证明该线性模型不仅正确有效,而且能改善水下目标识别效果. 关键词： 音色 多元线性回归 主观评价     

水下噪声音色属性回归模型及其在目标识别中的应用

通过对声音的主观评价与客观分析而建立的主观感受数学模型,在许多领域都有重要的应用. 本文采用多元线性回归分析手段对水下噪声音色属性建立回归模型,提取音色特征并改善水下目标的识别效果. 首先,在前期水下噪声音色属性主观评价实验的基础上,将构成音色属性空间的5个成分的评价分值作为回归分析中的因变量,提取大量与听觉感知相关的听觉特征作为自变量;然后,通过相关分析和改进的逐步筛选法,挑选出反映音色属性的“最优”自变量子集;最后,利用向后剔除回归分析和水下目标识别实验,确定适当的音色模型,并通过假设检验证明该线性模型不仅正确有效,而且能改善水下目标识别效果.     

Integrating sampling techniques and inverse virtual screening: toward the discovery of artificial peptide-based receptors for ligands

A novel heuristic using an iterative select-and-purge strategy is proposed. It combines statistical techniques for sampling and classification by rigid molecular docking through an inverse virtual screening scheme. This approach aims to the de novo discovery of short peptides that may act as docking receptors for small target molecules when there are no data available about known association complexes between them. The algorithm performs an unbiased stochastic exploration of the sample space, acting as a binary classifier when analyzing the entire peptides population. It uses a novel and effective criterion for weighting the likelihood of a given peptide to form an association complex with a particular ligand molecule based on amino acid sequences. The exploratory analysis relies on chemical information of peptides composition, sequence patterns, and association free energies (docking scores) in order to converge to those peptides forming the association complexes with higher affinities. Statistical estimations support these results providing an association probability by improving predictions accuracy even in cases where only a fraction of all possible combinations are sampled. False positives/false negatives ratio was also improved with this method. A simple rigid-body docking approach together with the proper information about amino acid sequences was used. The methodology was applied in a retrospective docking study to all 8000 possible tripeptide combinations using the 20 natural amino acids, screened against a training set of 77 different ligands with diverse functional groups. Afterward, all tripeptides were screened against a test set of 82 ligands, also containing different functional groups. Results show that our integrated methodology is capable of finding a representative group of the top-scoring tripeptides. The associated probability of identifying the best receptor or a group of the top-ranked receptors is more than double and about 10 times higher, respectively, when compared to classical random sampling methods.     

Reinforcement Learning for Bit-Flipping Decoding of Polar Codes

A traditional successive cancellation (SC) decoding algorithm produces error propagation in the decoding process. In order to improve the SC decoding performance, it is important to solve the error propagation. In this paper, we propose a new algorithm combining reinforcement learning and SC flip (SCF) decoding of polar codes, which is called a Q-learning-assisted SCF (QLSCF) decoding algorithm. The proposed QLSCF decoding algorithm uses reinforcement learning technology to select candidate bits for the SC flipping decoding. We establish a reinforcement learning model for selecting candidate bits, and the agent selects candidate bits to decode the information sequence. In our scheme, the decoding delay caused by the metric ordering can be removed during the decoding process. Simulation results demonstrate that the decoding delay of the proposed algorithm is reduced compared with the SCF decoding algorithm, based on critical set without loss of performance.     

Statistical Features in High-Frequency Bands of Interictal iEEG Work Efficiently in Identifying the Seizure Onset Zone in Patients with Focal Epilepsy

The design of a computer-aided system for identifying the seizure onset zone (SOZ) from interictal and ictal electroencephalograms (EEGs) is desired by epileptologists. This study aims to introduce the statistical features of high-frequency components (HFCs) in interictal intracranial electroencephalograms (iEEGs) to identify the possible seizure onset zone (SOZ) channels. It is known that the activity of HFCs in interictal iEEGs, including ripple and fast ripple bands, is associated with epileptic seizures. This paper proposes to decompose multi-channel interictal iEEG signals into a number of subbands. For every 20 s segment, twelve features are computed from each subband. A mutual information (MI)-based method with grid search was applied to select the most prominent bands and features. A gradient-boosting decision tree-based algorithm called LightGBM was used to score each segment of the channels and these were averaged together to achieve a final score for each channel. The possible SOZ channels were localized based on the higher value channels. The experimental results with eleven epilepsy patients were tested to observe the efficiency of the proposed design compared to the state-of-the-art methods.     

New insights into the extraction of uranium(VI) by an N,N-dialkylamide

This paper presents the methodology developed in order to thoroughly characterise a solvent extraction system containing high solute concentrations. The chemical system selected is N,N-(2-ethylhexyl)isobutyramide (DEHiBA) diluted in one alkane with increasing concentration of uranium(VI). Combining experiments with theoretical calculations allowed a deeper understanding of the extraction mechanism. A thermodynamic study was performed by the classical van't Hoff method and also by direct calorimetry to provide the enthalpies of extraction and specific heats. Dedicated methods like vapour pressure osmometry and electrospray ionisation mass spectrometry analysis provide information about the stoichiometry of the extracted species. Spectroscopic investigations with ultraviolet–visible and Fourier transform infrared probed the uranium coordination. Finally, a combination of molecular dynamics simulations, and small and wide-angle X-ray scattering experiments investigated the organisation in the organic phase beyond the molecular scale. It was shown that the high concentrations of uranium extracted have no influence on the stoichiometry of the complexes and the coordination of uranium in the inner sphere. The thermodynamic properties related to the extraction process and obtained with a fine consideration of the activity coefficients showed to be the same as those found with trace concentration. However, an unexpected organisation beyond the molecular scale was observed with an important role of nitrates as bridging ligands which could explain some physico-chemical properties. This approach could be applied to other chemical systems (other N,N-dialkylamides or other cations) to identify the origin of the different affinities between ligands and the difference of selectivity between cations.     

Estimating thermal transport in deep X-ray lithography with an inversion method

This study proposes a general methodology for estimating the depth profile of the heat source of the thermal transport system during deep X-ray lithography. The exposure process in a lithography system is considered as an inverse heat conduction problem with an unknown heat source. The conjugate gradient method is used to solve the inverse problem. Numerical results confirm that the method proposed herein can accurately estimate the heat source even involving the inevitable measurement errors. Furthermore, this methodology can also be applied to estimate the local distribution of temperatures when using scanning thermal microscopy (SThM) to microthermally machine materials and will contribute to increase the quality of microthermally machined products. In addition, a thermomechanical data-storage system, which utilizes a resistively heated atomic-force-microscopy (AFM) cantilever tip to read and write data bits, can also adopt this inverse methodology to control the temperature of a polymer substrate.     

Synthesis and applications of high-performance P-chiral phosphine ligands

Metal-catalyzed asymmetric synthesis is one of the most important methods for the economical and environmentally benign production of useful optically active compounds. The success of the asymmetric transformations is significantly dependent on the structure and electronic properties of the chiral ligands coordinating to the center metals, and hence the development of highly efficient ligands, especially chiral phosphine ligands, has long been an important research subject in this field. This review article describes the synthesis and applications of P-chiral phosphine ligands possessing chiral centers at the phosphorus atoms. Rationally designed P-chiral phosphine ligands are synthesized by the use of phosphine–boranes as the intermediates. Conformationally rigid and electron-rich P-chiral phosphine ligands exhibit excellent enantioselectivity and high catalytic activity in various transition-metal-catalyzed asymmetric reactions. Recent mechanistic studies of rhodium-catalyzed asymmetric hydrogenation are also described.     

A method for designing strong S-Boxes based on chaotic Lorenz system

It is important to design cryptographically strong S-Boxes in order to design secure systems. In this study, a strong, chaos-based S-Box design is proposed. Continuous-time Lorenz system is chosen as the chaotic system. Proposed methodology is analyzed and tested for the following criteria: Bijective property, nonlinearity, strict avalanche criterion, output bits independence criterion and equiprobable input/output XOR distribution. The results of the analysis show that the proposed cryptosystem is a highly reliable system suitable for secure communication.     

偏置M-Z调制器构建2-bits电光模数转换相位编码方法的分析与模拟

为了降低电光相位编码器功率消耗和解决内部M Z调制器一致性要求高的问题,利用2个偏置M Z调制器构成了用于电光模数转换的2 bits电光相位编码器。理论分析了偏置M Z调制器实现2 bits电光相位编码的方法、特点和性能。仿真结果验证了采用偏置M Z调制器构成的2 bits相位编码方法可行性,并实现了对1 GHz模拟电信号的采样速率12 GSa/s模数转换。分析和仿真结果表明,采用该方法对调制器一致性要求低,对输入信号功率要求低于0.32 W。分析结果表明,调制器直流漂移不影响最低位量化结果,引起最高位量化结果的判决模糊低于3.8%。     

重离子诱变酵母培养基的优化与研究

利用12C6+离子诱变技术对面包酵母菌种进行诱变,得到一株粗蛋白含量达到55% 以上的菌株,借助Minitab16.0,采用Plackett-Burman 实验设计法及响应面分析法,对诱变后面包酵母菌发酵培养基的成分进行了优化,得到3 个最为显著的主要影响因子:葡萄糖、酵母抽提物和硫酸镁。利用最陡爬坡实验逼近最大响应区域后,利用Box-Behnken 实验设计及响应面分析法进行回归分析。通过求解回归方程,得到优化发酵的条件为,葡萄糖:11.03 g/L、酵母抽提物:6.53 g/L、硫酸镁:5.59 g/L。面包酵母生物量为4.84 g/L,相比未进行优化时的生物量提高了15%。A mutant bread yeast strain with high protein content of 55% was gained by use of 12C6+ ions. The MINITAB 16.0 software, Plackett-Burman experimental design and response surface methodology were applied to optimize the culture medium for the irradiated yeast. The most important three factors which influenced the culture results were identified as glucose, magnesium sulphate and yeast extract. The path of the steepest ascent was undertaken to approach the optimal region of the three significant factors. Box-Behnken design and response surface methodology were used for the regression analysis. Finally, the optimal fermentation conditions were identified as glucose 11.03 g/L, yeast extract 6.53 g/L and magnesium sulphate 5.59 g/L by the regression analysis. It was found that the biomass of the bread yeasts reached 4.84 g/L and increased by 15% compared to original conditions.     

Advanced coupled PHY and MAC scheduling in IEEE 802.16e WiMAX systems

In this paper we address some issues related to the mutual influence between the PHY layer building blocks (FEC blocks) and the MAC level allocations in IEEE 802.16e /WiMAX systems, in order to increase the overall PHY and MAC combined efficiency. In these systems transmissions are carried in physical Bursts, both on the Uplink and Downlink channels. Bursts are composed of slots, which are grouped into FEC blocks. The number of slots in a Burst determines the length and number of the FEC blocks. The FEC blocks have a direct influence on the probability that bits are received successfully, and thus on the Burst Goodput, which is defined as the ratio between the average number of bits in the Burst that arrive successfully at the receiver, to the Burst length. In this paper we address a new coupled PHY and MAC scheduling methodology by investigating the relationship between the Burst length and its Goodput in different Modulation/Coding schemes, and investigate, given a Burst, the most efficient such scheme. The outcomes of the paper are twofold: first we show that the Goodput of a Burst is almost not dependent on its length. Second, we show that in most cases, the most efficient Modulation/Coding scheme is the one that enables us to transmit the largest number of bits in a Burst. However, there are a few cases where this is not the case. We show these cases in the paper.     

Computational study of the proton affinity and basicity of structurally diverse α1‐adrenoceptor ligands

The α₁‐adrenoceptor is a target for the treatment of several conditions from hypertension to benign prostatic hyperplasia. In this paper, we describe a new analysis approach to explore the conformational space of several ligands of the α₁‐adrenoceptor and we also present the calculation of their proton affinity and basicity. For each compound a conformational search followed by a semi‐empirical optimisation was performed and a selection of conformations for each ligand was subjected to further optimisation using density functional theory methods. Different positions were explored to determine the favoured site of protonation, and then, the proton affinity (in the gas phase) and basicity (using the polarisable continuum model for the aqueous solution) were calculated for each of them. In addition, an alternative method using one explicit water molecule in combination with the polarisable continuum model for aqueous solvent was explored. Moreover, the acid dissociation constant (pK_a) in water of these 26 compounds was calculated because this is an important parameter for a ligand when binding to its receptor. The experimental pK_a values of six of these ligands and those of two compounds with a very low and a very large pK_a were used to validate the theoretical methodology. Copyright © 2011 John Wiley & Sons, Ltd.     

SVM自助重加权采样的蚕茧雌雄特征波长选择

使用近红外光谱鉴别蚕茧雌雄设备成本较高,挑选有用特征可以减少成本.雌雄蚕茧的近红外光谱存在着共线性的关系,因此提出了一种包裹式的特征选择方法,基于支持向量机的自助重加权采样(BRS-SVM)的特征选择方法.使用NirQuest512近红外光谱仪采集了蚕茧的漫透射近红外光谱.用试验集的全波段建模得到特征重要度热图,并通过...     

On the Use of Space-Environmental Satellite Data for Global Magnetohydrodynamic Simulations

A global magnetohydrodynamic (MHD) model describes the solar-terrestrial system and the physical processes that live in it. Information obtained from satellites provides input to MHD model to compose a more realistic initial state for the equations and, therefore, more accurate simulations. However, the use of high resolution in time data can produce numerical instabilities that quickly interrupt the simulations. Moreover, satellite time series may have gaps which could be a problem in this context. In order to contribute to the overcoming of such challenges, we propose in this work a methodology based on a variant of the continuous wavelet transform to introduce environmental satellite data on the global resistive MHD model originally developed by Prof. Ogino at the University of Nagoya. Our methodology uses a simplified time-scale version of the original data that preserves the most important spectral features of the phenomena of interest. Then, we can do a long-term integration using this MHD model without any computational instability, while preserving the main time-scale features of the original data set and even overcome possible occurrence of gaps on the satellite data. This methodology also contributes to keeping more realistic physical results.