A Systematic Review and Meta-Analysis of Pharmacogenetic Studies in Patients with Chronic Kidney Disease

Chronic kidney disease (CKD) is an important global public health problem due to its high prevalence and morbidity. Although the treatment of nephrology patients has changed considerably, ineffectiveness and side effects of medications represent a major issue. In an effort to elucidate the contribution of genetic variants located in several genes in the response to treatment of patients with CKD, we performed a systematic review and meta-analysis of all available pharmacogenetics studies. The association between genotype distribution and response to medication was examined using the dominant, recessive, and additive inheritance models. Subgroup analysis based on ethnicity was also performed. In total, 29 studies were included in the meta-analysis, which examined the association of 11 genes (16 polymorphisms) with the response to treatment regarding CKD. Among the 29 studies, 18 studies included patients with renal transplantation, 8 involved patients with nephrotic syndrome, and 3 studies included patients with lupus nephritis. The present meta-analysis provides strong evidence for the contribution of variants harbored in the ABCB1, IL-10, ITPA, MIF, and TNF genes that creates some genetic predisposition that reduces effectiveness or is associated with adverse events of medications used in CKD.     

Predicting the mechanical properties of Cu–Al2O3 nanocomposites using machine learning and finite element simulation of indentation experiments

Micromechanics model, finite element (FE) simulation of microindentation and machine learning were deployed to predict the mechanical properties of Cu–Al₂O₃ nanocomposites. The micromechanical model was developed based on the rule of mixture and grain and grain boundary sizes evolution to predict the elastic modulus of the produced nanocomposites. Then, a FE model was developed to simulate the microindentation test. The input for the FE model was the elastic modulus that was computed using the micromechanics model and wide range of yield and tangent stresses values. Finally, the output load-displacement response from the FE model, the elastic modulus, the yield and tangent strengths used for the FE simulations, and the residual indentation depth were used to train the machine learning model (Random vector functional link network) for the prediction of the yield and tangent stresses of the produced nanocomposites. Cu–Al₂O₃ nanocomposites with different Al₂O₃ concentration were manufactured using insitu chemical method to validate the proposed model. After training the model, the microindentation experimental load-displacement curve for Cu–Al₂O₃ nanocomposites was fed to the machine learning model and the mechanical properties were obtained. The obtained mechanical properties were in very good agreement with the experimental ones achieving 0.99 coefficient of determination R2 for the yield strength.     

梁结构振动支承约束反力控制

支承或连接构件对梁结构的动力学性能有至关重要影响,必须保证其在振动过程中不发生破坏或者失效。通过合理设计和布局附加弹性支承可以实现对这些重要连接构件所承受约束反力的控制。应用微分变换法推导含附加支承的梁结构支承约束反力及其对于附加支承位置和刚度的灵敏度表达式,并通过优化设计附加支承位置和刚度实现具有弹性约束端的简支梁结构各支承约束反力的平衡,可提高结构的动力学性能。     

Two Methods,One Goal: Structural Differences between Cocrystallization and Crystal Soaking to Discover Ligand Binding Poses

In lead optimization, protein crystallography is an indispensable tool to analyze drug binding. Binding modes and non-covalent interaction inventories are essential to design follow-up synthesis candidates. Two protocols are commonly applied to produce protein–ligand complexes: cocrystallization and soaking. Because of its time and cost effectiveness, soaking is the more popular method. Taking eight ligand hinge binders of protein kinase A, we demonstrate that cocrystallization is superior. Particularly for flexible proteins, such as kinases, and larger ligands cocrystallization captures more reliable the correct binding pose and induced protein adaptations. The geometrical discrepancies between soaking and cocrystallization appear smaller for fragment-sized ligands. For larger flexible ligands that trigger conformational changes of the protein, soaking can be misleading and underestimates the number of possible polar interactions due to inadequate, highly impaired positions of protein amino-acid side and main chain atoms. Thus, if applicable cocrystallization should be the gold standard to study protein–ligand complexes.     

Sofosbuvir Selects for Drug-Resistant Amino Acid Variants in the Zika Virus RNA-Dependent RNA-Polymerase Complex In Vitro

The nucleotide analog sofosbuvir, licensed for the treatment of hepatitis C, recently revealed activity against the Zika virus (ZIKV) in vitro and in animal models. However, the ZIKV genetic barrier to sofosbuvir has not yet been characterized. In this study, in vitro selection experiments were performed in infected human hepatoma cell lines. Increasing drug pressure significantly delayed viral breakthrough (p = 0.029). A double mutant in the NS5 gene (V360L/V607I) emerged in 3 independent experiments at 40–80 µM sofosbuvir resulting in a 3.9 ± 0.9-fold half- maximal inhibitory concentration (IC₅₀) shift with respect to the wild type (WT) virus. A triple mutant (C269Y/V360L/V607I), detected in one experiment at 80 µM, conferred a 6.8-fold IC₅₀ shift with respect to the WT. Molecular dynamics simulations confirmed that the double mutant V360L/V607I impacts the binding mode of sofosbuvir, supporting its role in sofosbuvir resistance. Due to the distance from the catalytic site and to the lack of reliable structural data, the contribution of C269Y was not investigated in silico. By a combination of sequence analysis, phenotypic susceptibility testing, and molecular modeling, we characterized a double ZIKV NS5 mutant with decreased sofosbuvir susceptibility. These data add important information to the profile of sofosbuvir as a possible lead for anti-ZIKV drug development.     

Cryptanalysis of nonlinear confusion component based encryption algorithm

Recently many substitution box based encryption algorithms ensuring privacy have been proposed. Many, chaotic map based S-boxes have been generated posing high nonlinearity and strong cryptographic properties. Encryption schemes depending on the substitution box (S-box) only are weak and easily breakable with the help of chosen plaintext and ciphertext attacks. In this work, we have completely cryptanalyzed S-box based encryption scheme successfully by two types of attacks. Cryptanalysis in both types of attacks is performed by only one selected image. Moreover, we have suggested some improvements in the algorithm to defeat attacks.     

基于K-means和SOM的水下传感器数据采集方法

随着海洋资源勘探和海洋污染物监控工作的开展，水文数据的监测和采集等已经成为重要的研究方向。其中，水下无线传感器网络在水文数据采集过程中起着举足轻重的作用。本文研究的是水下无线传感器二维监测网络模型中，传感器节点数据采集的问题，其设计方法是通过自组织映射（Self-organizing mapping，SOM）对传感器节点进行路径最优化处理，结合优化的路径图形和K-means算法找到路径内部聚合点，利用聚合点和传感器的节点得到传感器通信半径内的数据采集点，最后通过SOM得到水下机器人（Autonomous underwater vehicle，AUV）到各个数据采集点采集数据的最优路径。经过实验验证，在水下1 200 m×1 750 m范围内布置52个传感器节点的情景下，数据采集点相比于传感器节点路径规划采用相同的采集顺序得到的路径优化了6.7%；对数据采集点重新进行自组织路径规划得到的路径比传感器结点路径的最优解提高了12.2%。增加传感器节点的数量，其结果也大致相同，因此采用该方法可以提高水下机器人采集数据的效率。     

Acquisition and Spread of Antimicrobial Resistance: A tet(X) Case Study

Understanding the mechanisms leading to the rise and dissemination of antimicrobial resistance (AMR) is crucially important for the preservation of power of antimicrobials and controlling infectious diseases. Measures to monitor and detect AMR, however, have been significantly delayed and introduced much later after the beginning of industrial production and consumption of antimicrobials. However, monitoring and detection of AMR is largely focused on bacterial pathogens, thus missing multiple key events which take place before the emergence and spread of AMR among the pathogens. In this regard, careful analysis of AMR development towards recently introduced antimicrobials may serve as a valuable example for the better understanding of mechanisms driving AMR evolution. Here, the example of evolution of tet(X), which confers resistance to the next-generation tetracyclines, is summarised and discussed. Initial mechanisms of resistance to these antimicrobials among pathogens were mostly via chromosomal mutations leading to the overexpression of efflux pumps. High-level resistance was achieved only after the acquisition of flavin-dependent monooxygenase-encoding genes from the environmental microbiota. These genes confer resistance to all tetracyclines, including the next-generation tetracyclines, and thus were termed tet(X). ISCR2 and IS26, as well as a variety of conjugative and mobilizable plasmids of different incompatibility groups, played an essential role in the acquisition of tet(X) genes from natural reservoirs and in further dissemination among bacterial commensals and pathogens. This process, which took place within the last decade, demonstrates how rapidly AMR evolution may progress, taking away some drugs of last resort from our arsenal.     

A customized low-rank prior model for structured cartoon–texture image decomposition

The mathematical characterization of the texture component plays an instrumental role in image decomposition. In this paper, we are concerned with a low-rank texture prior based cartoon–texture image decomposition model, which utilizes a total variation norm and a global nuclear norm to characterize the cartoon and texture components, respectively. It is promising that our decomposition model is not only extremely simple, but also works perfectly for globally well-patterned images in the sense that the model can recover cleaner texture (or details) than the other novel models. Moreover, such a model can be easily reformulated as a separable convex optimization problem, thereby enjoying a splitting nature so that we can employ a partially parallel splitting method (PPSM) to solve it efficiently. A series of numerical experiments on image restoration demonstrate that PPSM can recover slightly higher quality images than some existing algorithms in terms of taking less iterations or computing time in many cases.     

浅渍法发酵豇豆的工艺优化

以具有降解亚硝酸盐功能的植物乳杆菌（Lactobacillus plantarum）SD-7和具有优良抗氧化能力的植物乳杆菌（Lactobacillus plantarum）FM-LP-9为复合发酵剂（1∶1），采用浅渍法发酵豇豆。以硬度和感官评分为考察指标，通过单因素试验及响应面试验研究复合发酵剂接种量、发酵温度和发酵时间对浅渍法发酵豇豆品质的影响。结果表明，最佳发酵工艺条件为发酵温度25 ℃，接种量5%，发酵时间125 h，在此优化条件下，得到的浅渍法发酵豇豆硬度为47.31 N，感官评分为90.98分，香气浓郁、口感脆嫩。