Different synthetic routes to obtain hydrophilic matrices

The aim of this study was to examine two different synthetic routes for obtaining new hydrophilic matrices either by the modification of a synthetic matrix or by the copolymerization of hydrophilic monomers. First, the acrylic acid‐ethylene glycol dimethacrylate (AAc‐EGDMA) matrix, obtained from suspension with cyclohexane as the diluent at 70 °C after 2 h of reaction, was used as a base to be modified with TRIS(hydroxymethyl)aminomethane (TRIS). Experimental variables affecting the carbodiimide‐mediated amide‐bond development (i.e., the type of carbodiimide, reaction time, pH, and concentration of the matrix in the reaction medium) on the synthetic AAc‐EGDMA matrix with TRIS were studied. Second, the N‐acryloyl‐TRIS(hydroxymethyl)aminomethane‐ethylene glycol dimethacrylate (NAT‐EGDMA) matrix was obtained under the same experimental conditions as reported for AAc‐EGDMA. © 2000 John Wiley & Sons, Inc. J Polym Sci A: Polym Chem 38: 489–497, 2000     

Very efficient search for protein alignment--VESPA

A novel approach to the problem of protein alignments is described, which in comparison with existing approaches is visibly more efficient. This approach is based on superposition of amino acid adjacency matrices of a pair of proteins, which have been modified to record the sequential order of amino acids. As a result, one obtains simultaneously all segments of the two proteins which are shifted relative to one another by one or more positions in either directions, without need of a prior exhaustive search for an alignment that included unproductive directions and unknown displacement steps.     

Method development for analysis of short- and long-chain perfluorinated acids in solid matrices

In order to help to elucidate the transport and fate of perfluorinated acids (PFAs) in the environment, a reliable and sensitive analytical method has been developed in present study for determination of short- and long-chain PFAs in various solid matrices. The method consisted of solvent extraction of PFAs from solid matrices using sonication, solid phase extraction (SPE) using weak anion exchange (WAX) cartridges, clean-up of SPE eluent with dispersive carbon sorbent and quantitation by high performance liquid chromatography-negative electrospray-tandem mass spectrometry (HPLC-negative ESI-MS/MS). The method detection limits (MDL) and quantitation limits (MQL), which were analyte- and sample-dependent, ranged from 0.02 to 0.06?ng?g^?1 and 0.10 to 0.90?ng?g^?1, respectively. The recoveries of all PFAs were generally good enough for quantitative analysis of these chemicals (57–115%), especially for short-chain (<C8, 80–115%) PFAs excluded in previous studies because methods were not available. The precisions of this method, represented by the percent relative standard deviation (RSD) of spiked measurements, were in a range of 1–19%. In addition, matrix effect did not affect analyte quantification in solid matrices in most cases, and the validated method was successfully applied to analyses of short- and long-chain PFAs in various solid matrices.     

定量AES分析中基体效应的迭代修正法

以Shimizu提出的定量AES分析关系为基础,作者提出一种可用于二元和多元合金定量AES分析的迭代方法。通过引入合金的原子序数和原子密度的概念,计算了合金中元素的基体效应修正因子。与其它方法不同的是,本法中基体效应修正因子是合金元素浓度的函数,受到整体组分的影响。通过对文献报道的五种典型单相多晶二元合金Ag-Pd,Ni-Pd,Cr-Fe,Mo-Fe和Ni-Mg的定量分析计算发现,本法的分析精密度优于F因子法、K因子法及改进K因子修正法。     

Investigation of colloidal graphite as a matrix for matrix‐assisted laser desorption/ionisation mass spectrometry of low molecular weight analytes

The analysis of low molecular weight compounds by matrix‐assisted laser desorption/ionisation mass spectrometry is problematic due to the interference and suppression of analyte ionisation by the matrices typically employed – which are themselves low molecular weight compounds. The application of colloidal graphite is demonstrated here as an easy to use matrix that can promote the ionisation of a wide range of analytes including low molecular weight organic compounds, complex natural products and inorganic complexes. Analyte ionisation with colloidal graphite is compared with traditional organic matrices along with various other sources of graphite (e.g. graphite rods and charcoal pencils). Factors such as ease of application, spectra reproducibility, spot longevity, spot‐to‐spot reproducibility and spot homogeneity (through single spot imaging) are explored. For some analytes, considerable matrix suppression effects are observed resulting in spectra completely devoid of matrix ions. We also report the observation of radical molecular ions [M^–●] in the negative ion mode, particularly with some aromatic analytes. Copyright © 2016 John Wiley & Sons, Ltd.     

Enzyme‐Induced Matrix Softening Regulates Hepatocarcinoma Cancer Cell Phenotypes

The progression of cancer is often accompanied by changes in the mechanical properties of an extracellular matrix. However, limited efforts have been made to reproduce these biological events in vitro. To this end, this study demonstrates that matrix remodeling caused by matrix metalloproteinase (MMP)‐1 regulates phenotypic activities and modulates radiosensitivity of cancer cells exclusively in a 3D matrix. In this study, hepatocarcinoma cells are cultured in a collagen‐based gel tailored to present an elastic modulus of ≈4.0 kPa. The subsequent exposure of the gel to MMP‐1 decreases the elastic modulus from 4.0 to 0.5 kPa. In response to MMP‐1, liver cancer cells undergo active proliferation, downregulation of E‐cadherin, and the loss of detoxification capacity. The resulting spheroids are more sensitive to radiation than the spheroids cultured in the stiffer gel not exposed to MMP‐1. Overall, this study serves to better understand and control the effects of MMP‐induced matrix remodeling.     

Dual Role of Silicon-based Matrices in Electron Exchange Matrices for Waste Treatment

Para chloro aniline (PCA) is a common toxic pollutant found in pharmaceutical wastewater. Our study suggests a novel PCA treatment method based on a heterogeneous advanced oxidation process (AOP) that proceeds in an electron exchange matrix (EEM) prepared by the incorporation of redox-active specie in silica matrices using the sol-gel synthesis route. The results, which are supported by DFT calculations, show that the silicon skeleton of the EEM has two important roles, both as a porous matrix that hosts the redox species and as an oxidant species involved in the AOP. The calculations indicate that the formation of a radical on the nitrogen is favored. The suggested mechanism could shed light on the AOP, which proceeds in a heterogenous system, and on its application inside the understudied EEMs that, until now, have been a virtual black box. A better understanding of the mechanism could lead to improved control over the heterogeneous processes that can play a critical role in industries with the need to treat small amounts of toxic compounds at low concentrations, such as in the pharmaceutical industry.     

液态RbCl的态密度

给出了在分子动力学模拟基础上Fumi-Tosi势离子液体的正则模式分析方法,用Fumi-Tosi势(包括长程势)代替Lennard-Jones势,并且用等效Coulomb势处理长程Coulomb作用.讨论了Hessian矩阵元的计算方法和Hessian矩阵特征值的计算方法.计算实践表明，取用余误差函数形式的等效库仑势,可以合理地得到Hessian矩阵和态密度.液态RbCl中构型平均态密度的数值结果表明，液态RbCl的态密度表现出与Lennard-Jones液体的态密度相仿的特点.     

CAMERRA: An analysis tool for the computation of conformational dynamics by evaluating residue–residue associations

A computational method which extracts the dominant motions from an ensemble of biomolecular conformations via a correlation analysis of residue–residue contacts is presented. The algorithm first renders the structural information into contact matrices, then constructs the collective modes based on the correlated dynamics of a selected set of dynamic contacts. Associated programs can bridge the results for further visualization using graphics software. The aim of this method is to provide an analysis of conformations of biopolymers from the contact viewpoint. It may assist a systematical uncovering of conformational switching mechanisms existing in proteins and biopolymer systems in general by statistical analysis of simulation snapshots. In contrast to conventional correlation analyses of Cartesian coordinates (such as distance covariance analysis and Cartesian principal component analysis), this program also provides an alternative way to locate essential collective motions in general. Herein, we detail the algorithm in a stepwise manner and comment on the importance of the method as applied to decoding allosteric mechanisms. © 2018 Wiley Periodicals, Inc.     

Triptolide inhibits ovarian cancer cell invasion by repression of matrix metalloproteinase 7 and 19 and upregulation of E-cadherin

Triptolide, a compound extracted from the traditional Chinese medicine preparation of Tripterygium wilfordii Hook F., has been reported to have anti-inflammatory and anti-cancer activities. However, its effect on ovarian cancer invasion is unknown. We observed that MMP7 and MMP19 expression increased in ovarian cancer tissue. Triptolide treatment inhibited the migration and invasion of ovarian cancer cells SKOV3 and A2780 at the concentration of 15 nM. We also observed that triptolide suppressed MMP7 and MMP19 promoter activity in a dose-dependent manner, down-regulating the expressions of these promoters on mRNA and protein level. Moreover, triptolide enhanced E-cadherin expression in ovarian cancer cells. In vivo, triptolide inhibited tumor formation and metastasis in nude mice, and suppressed MMP7 and MMP19 expression; it also enhanced E-cadherin expression in tumor in a dose-dependent manner. Over expression of MMP7 and MMP19, or suppression of E-cadherin expression partially abolished the inhibitory effect of triptolide on invasion of ovarian cancer cells. To summarize, triptolide significantly inhibited the migration and invasion of ovarian cancer cells by suppression of MMP7 and MMP19 and up-regulation of E-cadherin expression. This study shows that triptolide is a good candidate for the treatment of ovarian cancer and reduction of metastasis.     

SPK势能面上Cl和H2反应的量子动力学计算

给出了在ＳＰＫ势能面上应用广义牛顿变分法（ＧＮＶＰ）和振幅密度衡量法（ＭＭＡＤ）对于反应系统Ｃｌ＋Ｈ２→ＨＣｌ＋Ｈ态－态之间反应几率的三维量子力学计算。总反应能量从９ｋｃａｌ．ｍｏｌ＾－１至１６ｋｃａｌ．ｍｏｌ＾－１。对于两种方法的计算结果进行了比较。为了同超球谐密耦合方法结果进行比较，还对总反应能量１９ｋｃａｌ．ｍｏｌ＾－１的情况进行了计算和分析。     

Analysis of pesticides in surface water in remote areas in Vietnam: Coping with matrix effects and test of long-term storage stability

During the last years, the increased use of pesticides and growing awareness of associated environmental and health problems have led to the implementation of various monitoring programmes in South-East Asia. The introduction of numerous new active ingredients and commercial pesticide formulations in connection with reports on pesticide-related health problems strongly indicate that the analytical procedures should be tested and evaluated for currently used pesticides. Coping with matrix effects and ensuring pesticide stability when samples are taken in remote areas are paramount. In the present study, we tested an analytical method that targets nine currently used pesticides in surface water in northern Vietnam. The method consists of solid phase extraction, storage at ?18°C in the adsorbed state, and capillary gas chromatography with nitrogen-phosphorus-detection of five insecticides (dichlorvos, fenobucarb, dimethoate, fenitrothion, and chlorpyrifos), three fungicides (chlorothalonil, metalaxyl, and edifenphos) and one herbicide (atrazine). We evaluated the potential analytical bias caused by matrix effect and investigated its possible causes. We also tested the long-term stability (up to 9 months) of pesticides adsorbed to Carbopack SPE cartridges when stored at temperatures below ?18°C. Adopting a matrix-matched calibration technique considerably improved the recovery values of seven of the nine tested pesticides. At spiking levels of 0.1?µg?L^?1 and 1?µg?L^?1 and after storage of 119 days at ?18°C, recovery values of these pesticides ranged from 67% to 107% and from 67% to 155%, respectively. For the remaining two pesticides recovered at 53–55% at both spiking levels – dichlorvos and chlorothalonil – the method could still be useful for semi-quantitative analysis or as a screening tool. Even though the general recommendation is to minimise storage time to reduce pesticides degradation, our results showed that storage times up to nine months can be adopted for atrazine, metalaxyl, fenitrothion, and chlorpyrifos.     

荧光光谱解析中矩阵病态对检测结果的影响

在工程数据处理中,经常要进行矩阵变换,矩阵病态性影响计算结果的稳定性,而矩阵的条件数与矩阵病态性密切相关.针对荧光光谱原始信号,通过分析解谱矩阵的条件数,给出通过解谱矩阵进行信号解谱时,解谱矩阵病态性对解谱数据结果的影响以及在提取解谱矩阵时如何减少矩阵病态性的方法.实验结果表明,数据突变会导致矩阵病态性增加,同时带来荧光光谱结果失真,在实际解谱矩阵提取及数据处理过程中,需重视并增强荧光染料谱图的平滑性.     

Maximum eigenvalues of the reciprocal distance matrix and the reverse Wiener matrix

We report some properties of the maximum eigenvalues of the reciprocal distance matrix and the reverse Wiener matrix of a connected graph, in particular, various lower and upper bounds, and the Nordhaus–Gaddum‐type results for them. © 2007 Wiley Periodicals, Inc. Int J Quantum Chem, 2008     

Normal Coordinate Analysis for Polymer Systems: Capabilities and New Opportunities

Normal coordinate analysis is an important tool in studying the structure, dynamics, and physical properties of polymer systems. In this article the capabilities of normal coordinate analysis (NCA) are explored in some detail. The use of the eigenvalues and eigenvectors from NCA is catalogued for a wide variety of purposes: for assigning or interpreting polymer spectra, for structural determination, for constructing force fields, for computing heat capacity and other thermodynamic properties, and for computing other physical properties. Examples are given for crystals, melts, and amorphous systems. Also described are methods for characterizing the normal mode vectors that are especially useful for larger systems, in which a large amount of data must be analyzed or where visualization or animation fails. Finally, a recently developed method for eliminating negative eigenvalues in systems with tens of thousands of atoms, trajectory averaging, is presented. Also described are several advances in numerical linear algebra for speeding up the diagonalization phase and for computing physical properties without requiring full diagonalization of the Hessian matrix.     

A pitfall of using 2‐[(2E)‐3‐(4‐tert‐butylphenyl)‐2‐methylprop‐2‐enylidene]malononitrile as a matrix in MALDI TOF MS: chemical adduction of matrix to analyte amino groups

2‐[(2E)‐3‐(4‐tert‐Butylphenyl)‐2‐methylprop‐2‐enylidene]malononitrile (DCTB) has been considered as an excellent matrix for matrix‐assisted laser desorption/ionization (MALDI) of many types of synthetic compounds. However, it might provide troublesome results for compounds containing aliphatic primary or secondary amino groups. For these compounds, strong extra ion peaks with a mass difference of 184.1 Da were usually observed, which might falsely indicate the presence of some unknown impurities that were not detected by other matrices. On the basis of the possible mechanisms proposed, these extra ions are the products of nucleophilic reactions between analyte amino groups and DCTB molecules or radical cations. In these reactions, an amino group replaces the dicyanomethylene group of DCTB forming a matrix adduct via a ? C?N‐bond. An aliphatic primary amine could react easily with DCTB and the reaction could start once they are mixed in a MALDI solution. For an aliphatic secondary amine, on the other hand, the reaction most likely occurs in the gas phase. Protonation of amino groups by adding acid seems to be a useful way to stop DCTB adduction for compounds with one single amino group, but not for compounds with multiple amino groups. Unlike aliphatic primary or secondary amines, aliphatic tertiary amines and aromatic amines do not yield DCTB adducts. This is because tertiary amines do not have the required transferrable H‐(N) atom to form an extra ? C?N‐bond, while aromatic amines are not sufficiently nucleophilic to attack DCTB. In view of the possible matrix adduction, care should be taken in MALDI time‐of‐flight mass spectrometry (TOF MS) when DCTB is used as the matrix for compounds containing amino group(s). Copyright © 2010 John Wiley & Sons, Ltd.     

Rheological behavior of fumed silica filled polyethylene oxide

Influence of molecular weight of polymer matrix on nanocomposites rheology is not yet well understood. Herein dynamic rheological responses of fumed silica (FS)/polyethylene oxide (PEO) nanocomposites are investigated as a function of viscosity‐averaged molecular weight (M_η) of PEO, volume fraction (?) and surface characteristics (hydrophilic or hydrophobic) of FS. In the nanocomposites, FS does not influence the glass transition and crystallinity of PEO in the mobile PEO phase while the interfacial interactions tend to immobilize a small fraction of PEO chains that could not undergo glass transition. In spite of the common observation that the reinforcement decreases with increasing M_η of PEO and improving hydrophobicity of FS, linear rheological responses are well reproduced by the two‐phase model, revealing the crucial contribution of the non‐Newtonian matrix undergoing microscopic strain amplified by the filler. Furthermore, nonlinear rheological responses of the nanocomposites are collapsed into master curves plotted against local strain of the matrix. Analyzing the nonlinear rheology by Fourier transform and stress waveform methods reveal the dominating contribution of the matrix and the role of strain amplification played by the filler. © 2019 Wiley Periodicals, Inc. J. Polym. Sci., Part B: Polym. Phys. 2019 , 57, 397–405