VEGA: visual comparison of phylogenetic trees for evolutionary genome analysis (ChinaVis 2019)

In the field of evolutionary genome analysis, biologists seek to identify important genes or chromosome regions by comparing phylogenetic trees and analyzing the mutation at which locus might affect phenotypic traits. Unfortunately, the tree comparison and accompanying analysis are often performed manually. In this paper, we characterize the workflow of evolutionary genome analysis and present a task analysis for the fundamental questions asked by biologists during the analysis procedure. We propose two algorithms to enable quantitative tree comparison. One is to measure the differences between corresponding leaf nodes on two trees, and the other is to compute the classification inconsistency of each leaf node by comparing tree structure with a given biological classification. Configuring with the obtained difference and inconsistency, we present a visual analysis system, visual comparison of phylogenetic trees for evolutionary genome analysis, which not only enables biologists to intuitively explore trees but also identify locus which affects their traits by comparing SNP variants of selected leaf nodes. We conclude with case studies from two biologists who used our system to augment their previous manual analysis workflow and demonstrate that our system can reveal more insight.     

Dynamics of a Predator-Prey Model with Allee Effect and Herd Behavior

This paper deals with dynamics of a predator-prey model with Allee effect and herd behavior. We first study the stability of non-negative constant solutions for such system. We also establish the existence of Hopf bifurcation solutions for such predator-prey model. The stability and bifurcation direction of Hopf bifurcation solution in the case of spatial homogeneity are further discussed. At the same time, several examples are given by MATLAB. Finally, the numerical simulations of the system are carried out through MATLAB, which intuitively verifies and supplements the theoretical analysis results.     

Double Feature Extraction Method of Ship-Radiated Noise Signal Based on Slope Entropy and Permutation Entropy

In order to accurately identify various types of ships and develop coastal defenses, a single feature extraction method based on slope entropy (SlEn) and a double feature extraction method based on SlEn combined with permutation entropy (SlEn&PE) are proposed. Firstly, SlEn is used for the feature extraction of ship-radiated noise signal (SNS) compared with permutation entropy (PE), dispersion entropy (DE), fluctuation dispersion entropy (FDE), and reverse dispersion entropy (RDE), so that the effectiveness of SlEn is verified, and SlEn has the highest recognition rate calculated by the k-Nearest Neighbor (KNN) algorithm. Secondly, SlEn is combined with PE, DE, FDE, and RDE, respectively, to extract the feature of SNS for a higher recognition rate, and SlEn&PE has the highest recognition rate after the calculation of the KNN algorithm. Lastly, the recognition rates of SlEn and SlEn&PE are compared, and the recognition rates of SlEn&PE are higher than SlEn by 4.22%. Therefore, the double feature extraction method proposed in this paper is more effective in the application of ship type recognition.     

微乳液静电纺丝制备多孔Nb4N5纤维及其电化学性能

以五氯化锯为原料,液体石蜡为分相剂,采用微乳液静电纺丝技术制备前驱体纤维,再经氨气还原氮化得到多孔氮化锯纤维.利用XRD、SEM、BET等进行物相及微观结构表征,结果表明合成的纤维为四方Nb4N5晶相,纤维连续,直径为260 nm,由于液体石蜡分相以及助纺剂PVP的分解作用,在纤维上形成较多孔道结构,其BET比表面积为125m2/g,孔径为2～5nm范围内的孔结构比例较高,同时在5～10 nm 范围也存在较多的孔道结构,平均孔径为7.3 nm.采用CV、GCD及EIS等测试其电化学性能发现,氮化锯纤维的储能主要受电极表面电荷传递过程控制的,外表面比电容贡献高,这得益于分布在纤维中的孔结构,其可为离子传输提供通道,并为电化学反应提供空间.当电流密度为5mA/g时,比电容为151 F/g,能量密度为7.73 Wh/kg时,功率密度为3.03 W/kg,其经2000次循环后其比电容保持在95;以上.     

Fabrication of thermo-responsive polymer nanocomposites for smart window applications

Abstract

Thermo-responsive polymers have attracted much attention in recent years because they can provide a variety of applications for smart devices, but the lack of sufficient mechanical properties and late response rate of the polymers limit their applications. In the current work, we fabricated polymer nanocomposites made from poly(vinyl methyl ether) and nanofillers with photothermal conversion property such as graphene oxide, antimony tin oxide nanoparticles, and silver nanoplates. The prepared nanocomposites showed rapidly reversible and reliable transparent-opaque transitions during the repeated heating and cooling processes, suggesting that they can be applied to smart window applications.     

大锥角光纤探针的制备

用熔拉法、腐蚀法、管腐蚀法、熔拉-腐蚀法、激光消融法等制备了光纤探针,对其外形进行了分析比较.熔拉法制作的探针,锥形过渡区细长,并且获得的探针锥角不大(8°～35°).腐蚀法与管腐蚀法可以使探针的锥形过渡区短,损耗小,锥角大(15°～65°),但在制备更大的锥角光纤探针时,表面开始变得粗糙.拉伸-腐蚀的方法制作光纤探针存在一个变锥度区.激光消融腐蚀法容易获得大锥角的探针,并且表面光滑.     

A biochemometrics strategy combining quantitative determination,bioactivity evaluation and relationship analysis for identification of analgesic alkaloids of raw and vinegar‐processed Corydalis turtschaninovii

A biochemometrics strategy combining quantitative determination, bioactivity evaluation, and relationship analysis was proposed for identification of analgesic components of herbs. First, a robust liquid chromatography tandem mass spectrometry method was developed for simultaneous determination of nine major alkaloids in crude and vinegar‐processed Corydalis turtschaninovii. Nine alkaloids were separated on a BEH C₁₈ column with a mobile phase consisting of acetonitrile and water spiked with 0.1% formic acid and then detected by multiple reactions monitoring in the positive ion mode. Nitidine chloride was employed as the internal standard. The method displayed good linearity and the precisions of intra‐day and inter‐day were all within 3.0%. The recovery rates of each alkaloid ranged from 97.1 to 102.9%. The method was successfully applied for quantitative analysis of nine alkaloids in ten batches of crude and vinegar‐processed Corydalis turtschaninovii. Second, the analgesic effects of crude and vinegar‐processed Corydalis turtschaninovii were evaluated in mice. Third, principle component analysis, canonical correlation analysis, and partial least squares regression were used to analysis the relationship between the contents of nine major alkaloids and the analgesic effect of different crude and vinegar‐processed samples. Tetrahydropalmatine, coptisine, and dehydrocorydaline have a close positive correlation with the analgesic effect.     

Interaction of cellulase with sodium dodecyl sulfate at critical micelle concentration level

The interactions between Trichoderma reesei cellulase and an anionic surfactant, sodium dodecyl sulfate (SDS), at critical micelle concentration level have been investigated using isothermal titration calorimetry, fluorescence spectroscopy, and circular dichroism. SDS micelles have dual interactions with cellulase: electrostatic at first and then hydrophobic interactions. When the concentration of SDS is smaller than 45.0 mM, SDS micelles cause a partial loss in the hydrolytic activity together with a steep decrease in the -helical content of cellulase. With further increasing the concentration of SDS, however, a re-formation of the -helical structure and a partial recovery of the hydrolytic activity of cellulase induced by SDS micelles are observed. Taken together, these results indicate that SDS micelles exert dual effects on cellulase through binding as both a denaturant and a recovery reagent.     

多检测GPC/SEC技术在高分子表征中的应用Ⅳ.氘化高分子的溶液性质

采用体积排斥色谱法／ 示差折光指数／ 直角激光光散射／ 示差粘度三检测联用技术表征了氘化聚苯乙烯、聚苯乙烯和氘化聚苯乙烯－ 聚异戊二烯。结果表明,在θ条件下,虽然氘化聚苯乙烯的化学依赖性常数υＴ,ＤＰＳ比聚苯乙烯的化学依赖性常数υＴ,ＰＳ大,但２５ ℃时在四氢呋喃中,氘化聚苯乙烯的分子尺寸仍小于聚苯乙烯的分子尺寸。由于嵌段共聚物的淋洗体积随组成变化,所以用传统的ＳＥＣ／ＲＩ得不到准确的分子量。经比较膜渗透、小角激光光散射和基质辅助激光脱吸与离子化时间飞行质谱等的实验结果,证明体积排斥色谱法／ 示差折光指数／ 直角激光光散射／ 示差粘度三检测技术能准确地得到氘化二嵌段共聚物的分子量以及其它重要信息。