An Algorithm Framework for Drug-Induced Liver Injury Prediction Based on Genetic Algorithm and Ensemble Learning

In the process of drug discovery, drug-induced liver injury (DILI) is still an active research field and is one of the most common and important issues in toxicity evaluation research. It directly leads to the high wear attrition of the drug. At present, there are a variety of computer algorithms based on molecular representations to predict DILI. It is found that a single molecular representation method is insufficient to complete the task of toxicity prediction, and multiple molecular fingerprint fusion methods have been used as model input. In order to solve the problem of high dimensional and unbalanced DILI prediction data, this paper integrates existing datasets and designs a new algorithm framework, Rotation-Ensemble-GA (R-E-GA). The main idea is to find a feature subset with better predictive performance after rotating the fusion vector of high-dimensional molecular representation in the feature space. Then, an Adaboost-type ensemble learning method is integrated into R-E-GA to improve the prediction accuracy. The experimental results show that the performance of R-E-GA is better than other state-of-art algorithms including ensemble learning-based and graph neural network-based methods. Through five-fold cross-validation, the R-E-GA obtains an ACC of 0.77, an F1 score of 0.769, and an AUC of 0.842.     

圆柱类构件超声相控阵聚焦模型

在利用平面相控阵超声换能器对圆柱类构件检测时,受曲界面结构引起的入射波和回波时延的影响,扫描声束的波阵面产生弯曲,在利用传统迭代遍历算法计算延迟时间时效率低,无法发挥相控阵换能器检测优势。针对上述问题,建立了一种基于圆柱类构件特征和耦合介质特性的超声相控阵扫描成像的聚焦模型。该模型基于换能器、耦合介质、圆柱类构件材料特性和几何关系以及声线模型和折射定律,建立了耦合介质及被检构件的声速、曲面曲率半径、阵列与曲面间的距离等关联的延迟时间聚焦控制模型。利用该模型计算出的延时时间,对各阵元发射时间进行控制,从而实现扫描声束的聚焦。该文以液体和有机玻璃制介质楔块为例,对圆柱钢曲面的相控阵声束聚焦进行了仿真实验,结果表明该文方法计算效率显著提升,同时声束可以在预设位置实现聚焦,验证了该模型在计算效率上的优势与有效性。     

A molecular mechanics approach for analyzing tensile nonlinear deformation behavior of single-walled carbon nanotubes

In this paper, by capturing the atomic information and reflecting the behaviour governed by the nonlinear potential function, an analytical molecular mechanics approach is proposed. A constitutive relation for single-walled carbon nanotubes (SWCNT’s) is established to describe the nonlinear stress-strain curve of SWCNT’s and to predict both the elastic properties and breaking strain of SWCNT’s during tensile deformation. An analysis based on the virtual internal bond (VIB) model proposed by P. Zhang et al. is also presented for comparison. The results indicate that the proposed molecular mechanics approach is indeed an acceptable analytical method for analyzing the mechanical behavior of SWCNT’s. The project supported by the National Natural Science Foundation of China (10121202, 90305015 and 10328203), the Key Grant Project of Chinese Ministry of Education (0306) and the Research Grants Council of the Hong Kong Special Administrative Region, China (HKU 7195/04E).     

晶格畸变检测仪研究碳化硅晶片中位错缺陷分布

利用晶格畸变检测仪研究了SiC晶片位错分布情况,通过对熔融KOH腐蚀后的SiC晶片进行全片或局部扫描,从而得到完整SiC晶片或局部区域的位错分布.与LEXT OLS40003D激光共聚焦显微镜扫描腐蚀图进行比较,晶格畸变检测仪扫描腐蚀图可以将晶片上位错腐蚀坑信息完全呈现出来,且根据腐蚀坑呈现的颜色及尺寸大小,可以分辨出...     

Spider Silk-Improved Quartz-Enhanced Conductance Spectroscopy for Medical Mask Humidity Sensing

Spider silk is one of the hottest biomaterials researched currently, due to its excellent mechanical properties. This work reports a novel humidity sensing platform based on a spider silk-modified quartz tuning fork (SSM-QTF). Since spider silk is a kind of natural moisture-sensitive material, it does not demand additional sensitization. Quartz-enhanced conductance spectroscopy (QECS) was combined with the SSM-QTF to access humidity sensing sensitively. The results indicate that the resonance frequency of the SSM-QTF decreased monotonously with the ambient humidity. The detection sensitivity of the proposed SSM-QTF sensor was 12.7 ppm at 1 min. The SSM-QTF sensor showed good linearity of ~0.99. Using this sensor, we successfully measured the humidity of disposable medical masks for different periods of wearing time. The results showed that even a 20 min wearing time can lead to a >70% humidity in the mask enclosed space. It is suggested that a disposable medical mask should be changed <2 h.     

Weak Graph Map Homotopy and Its Applications∗

The authors introduce a notion of a weak graph map homotopy (they call it M-homotopy), discuss its properties and applications. They prove that the weak graph map homotopy equivalence between graphs coincides with the graph homotopy equivalence defined by Yau et al in 2001. The difference between them is that the weak graph map homotopy transformation is defined in terms of maps, while the graph homotopy transformation is defined by means of combinatorial operations. They discuss its advantages over the graph homotopy transformation. As its applications, they investigate the mapping class group of a graph and the 1-order MP-homotopy group of a pointed simple graph. Moreover, they show that the 1-order MP-homotopy group of a pointed simple graph is invariant up to the weak graph map homotopy equivalence.     

Phosphorylation of ERK-Dependent NF-κB Triggers NLRP3 Inflammasome Mediated by Vimentin in EV71-Infected Glioblastoma Cells

Enterovirus 71 (EV71) is a dominant pathogenic agent that may cause severe central nervous system (CNS) diseases among infants and young children in the Asia-pacific. The inflammasome is closely implicated in EV71-induced CNS injuries through a series of signaling pathways. However, the activation pathway of NLRP3 inflammasome involved in EV71-mediated CNS injuries remains poorly defined. In the studies, EV71 infection, ERK1/2 phosphorylation, and activation of NLRP3 are abolished in glioblastoma cells with low vimentin expression by CRISPR/Cas9-mediated knockdown. PD098059, an inhibitor of p-ERK, remarkably blocks the vimentin-mediated ERK1/2 phosphorylation in EV71-infected cells. Nuclear translocation of NF-κB p65 is dependent on p-ERK in a time-dependent manner. Moreover, NLRP3 activation and caspase-1 production are limited in EV71-infected cells upon the caffeic acid phenethyl ester (CAPE) administration, an inhibitor of NF-κB, which contributes to the inflammasome regulation. In conclusion, these results suggest that EV71-mediated NLRP3 inflammasome could be activated via the VIM-ERK-NF-κB pathway, and the treatment of the dephosphorylation of ERK and NF-κB inhibitors is beneficial to host defense in EV71-infected CNS.     

Designed Syntheses of Three {Ni6PW9}-Based Polyoxometalates,from Isolated Cluster to Cluster-Organic Helical Chain

Three new hexa-Ni-substituted Keggin-type polyoxometalates (POMs), [Ni₆(OH)₃- (DACH)₃(H₂O)₆(PW₉O₃₄)]·31H₂O (1), [Ni(DACH)₂][Ni₆(OH)₃(DACH)₃(HMIP)₂(H₂O)₂(PW₉O₃₄)]·56 H₂O (2), and [Ni(DACH)₂][Ni₆(OH)₃(DACH)₂(AP)(H₂O)₅(PW₉O₃₄)]·2H₂O (3) (DACH = 1,2-Diami- nocyclohexane, MIP = 5-Methylisophthalate, AP = Adipate) were successfully made in the presence of DACH under hydrothermal conditions. 1 is an isolated hexa-Ni-substituted Keggin unit decorated by DACH. In order to further construct POM cluster-organic frameworks (POMCOFs) on the basis of 1, by analyzing the steric hindrances and orientations of the POM units, the rigid HMIP and flexible AP ligands were successively incorporated, and another anionic monomeric POM 2 and the new 1D POM cluster organic chain (POMCOC) 3 were obtained. HMIP ligand still acts as a decorating group on the Ni₆ core of 2 but results in the different spatial arrangement of the {Ni₆PW₉} units. AP ligands in 3 successfully bridge adjacent isolated POM cluster units to 1D POMCOC with left-hand helices. The AP in 3 is the longest aliphatic carboxylic acid ligand in POMs, and the 1D POM cluster-AP helical chain represents the first 1D POMCOC with a helical feature.     

The Classification of Rice Blast Resistant Seed Based on Ranman Spectroscopy and SVM

Rice blast is a serious threat to rice yield. Breeding disease-resistant varieties is one of the most economical and effective ways to prevent damage from rice blast. The traditional identification of resistant rice seeds has some shortcoming, such as long possession time, high cost and complex operation. The purpose of this study was to develop an optimal prediction model for determining resistant rice seeds using Ranman spectroscopy. First, the support vector machine (SVM), BP neural network (BP) and probabilistic neural network (PNN) models were initially established on the original spectral data. Second, due to the recognition accuracy of the Raw-SVM model, the running time was fast. The support vector machine model was selected for optimization, and four improved support vector machine models (ABC-SVM (artificial bee colony algorithm, ABC), IABC-SVM (improving the artificial bee colony algorithm, IABC), GSA-SVM (gravity search algorithm, GSA) and GWO-SVM (gray wolf algorithm, GWO)) were used to identify resistant rice seeds. The difference in modeling accuracy and running time between the improved support vector machine model established in feature wavelengths and full wavelengths (200–3202 cm⁻¹) was compared. Finally, five spectral preproccessing algorithms, Savitzky–Golay 1-Der (SGD), Savitzky–Golay Smoothing (SGS), baseline (Base), multivariate scatter correction (MSC) and standard normal variable (SNV), were used to preprocess the original spectra. The random forest algorithm (RF) was used to extract the characteristic wavelengths. After different spectral preproccessing algorithms and the RF feature extraction, the improved support vector machine models were established. The results show that the recognition accuracy of the optimal IABC-SVM model based on the original data was 71%. Among the five spectral preproccessing algorithms, the SNV algorithm’s accuracy was the best. The accuracy of the test set in the IABC-SVM model was 100%, and the running time was 13 s. After SNV algorithms and the RF feature extraction, the classification accuracy of the IABC-SVM model did not decrease, and the running time was shortened to 9 s. This demonstrates the feasibility and effectiveness of IABC in SVM parameter optimization, with higher prediction accuracy and better stability. Therefore, the improved support vector machine model based on Ranman spectroscopy can be applied to the fast and non-destructive identification of resistant rice seeds.     

A MALDI-MS sensing chip prepared by non-covalent assembly for quantitation of acid phosphatase

A novel sensing chip was designed for MALDI-MS quantitation of acid phosphatase(ACP).The ACP sensing chip was constructed through non-covalent interaction of streptavidin and biotin for the assembly of biotinylated peptide substrate on biotinylated polyethylene-glycol(PEG)modified indium-tin oxide(ITO)slide.In the presence of ACP,the peptide substrate was dephosphorylated under acidic condition to generate a new mass signal.The quantitative assay of ACP was achieved with the mass signal ratio of product to the sum of product and left peptide substrate.Under optimal detection conditions,the ratio was linearly correlated with the concentration of ACP in the range of 0.05–12 g/L with a detection limit(LOD)of 0.04 g/L.The designed ACP sensing chip has been used to analyze ACP in complex clinical samples,which exhibited high selectivity,good repeatability,and admirably anti-interference ability.This work further demonstrates the concept of MS sensing and the application of MALDI-MS in quantitative analysis,and provides a convenient method for the quantitation of proteases in clinical diagnosis.