紫色球杆菌视紫红质光谱特性的机器学习研究

近年来，机器学习等人工智能技术被应用于蛋白质工程，其在蛋白质结构、功能预测、催化活性等研究中具有独特优势。在未知蛋白质结构的情况下，将蛋白质序列和功能特性与机器学习相结合，基于序列-活性关系（innovative sequence-activity relationship，ISAR）算法，将蛋白质氨基酸序列数字化，用快速傅里叶变换（fast four transform，FFT）进行预处理，再进行偏最小二乘回归建模，可在数据集较少情况下拟合得到最佳模型。通过机器学习对紫色球杆菌视紫红质（gloeobacter violaceus rhodopsin，GR）的突变体蛋白质氨基酸序列与光谱最大吸收波长进行建模，获得了最佳模型。用最佳索引LEVM760106建模得到的确定系数R² 为0.944，均方误差E为11.64。用小波变换进行的预处理，其R² 虽也约为0.944，但E大于11.64，不及FFT进行的预处理。方法较好地解决了蛋白质序列与功能特性之间的数学建模问题，在蛋白质工程中可为预测更优的突变体提供支持。     

一种非正交对称条带束流位置监测器设计

介绍了一种条带束流位置监测器(BPM)的设计与仿真方法。在国家同步辐射实验室"太赫兹近场高通量材料物性测试系统"工程项目中,针对波荡器出口处真空室非正交对称性的问题,设计了矩形真空室和跑道形真空室下的两种非正交对称性条带BPM,并与传统的圆形真空室下条带BPM进行对比。基于边界元法,利用MATLAB软件分别对三种真空室下的条带BPM进行建模和仿真。仿真结果表明:相对于传统的圆形真空室下条带BPM,矩形和跑道形真空室下条带BPM灵敏度提高了30%,阻抗匹配误差相对降低了20%,束流位置拟合误差降低了80%。考虑加工精度,矩形真空室下的条带BPM更适用于该工程。     

Generating Artificial Reverberation via Genetic Algorithms for Real-Time Applications

We introduce a Virtual Studio Technology (VST) 2 audio effect plugin that performs convolution reverb using synthetic Room Impulse Responses (RIRs) generated via a Genetic Algorithm (GA). The parameters of the plugin include some of those defined under the ISO 3382-1 standard (e.g., reverberation time, early decay time, and clarity), which are used to determine the fitness values of potential RIRs so that the user has some control over the shape of the resulting RIRs. In the GA, these RIRs are initially generated via a custom Gaussian noise method, and then evolve via truncation selection, random weighted average crossover, and mutation via Gaussian multiplication in order to produce RIRs that resemble real-world, recorded ones. Binaural Room Impulse Responses (BRIRs) can also be generated by assigning two different RIRs to the left and right stereo channels. With the proposed audio effect, new RIRs that represent virtual rooms, some of which may even be impossible to replicate in the physical world, can be generated and stored. Objective evaluation of the GA shows that contradictory combinations of parameter values will produce RIRs with low fitness. Additionally, through subjective evaluation, it was determined that RIRs generated by the GA were still perceptually distinguishable from similar real-world RIRs, but the perceptual differences were reduced when longer execution times were used for generating the RIRs or the unprocessed audio signals were comprised of only speech.     

Biomolecular Release Stimulated by Electrochemical Signals at a Very Small Potential Applied

DNA release electrochemically stimulated by applying ?10 mV on the modified electrode was studied. The release process was based on the local (interfacial) pH change produced upon H₂O₂ reduction electrocatalyzed by the immobilized microperoxidase‐11. SiO₂ nanoparticles attached to the electrode surface and functionalized with trigonelline and boronic acid species changed their electrical charge from positive to negative upon the interfacial pH change, thus allowing electrostatic adsorption of negatively charged DNA on the positive interface and then its repulsion/release from the negative interface. The loaded/released DNA molecules were labeled with a fluorescent dye to allow easy detection of the released DNA molecules. The important feature of the developed system is the controlled DNA release upon applying very small electrical potential on the modified electrode.     

Dual‐signal amplification strategy for ultrasensitive chemiluminescence detection of PDGF–BB in capillary electrophoresis

Many efforts have been made toward the achievement of high sensitivity in capillary electrophoresis coupled with chemiluminescence detection (CE‐CL). This work describes a novel dual‐signal amplification strategy for highly specific and ultrasensitive CL detection of human platelet‐derived growth factor–BB (PDGF–BB) using both aptamer and horseradish peroxidase (HRP) modified gold nanoparticles (HRP–AuNPs–aptamer) as nanoprobes in CE. Both AuNPs and HRP in the nanoprobes could amplify the CL signals in the luminol–H₂O₂ CL system, owing to the excellent catalytic behavior of AuNPs and HRP in the CL system. Meanwhile, the high affinity of aptamer modified on the AuNPs allows detection with high specificity. As proof‐of‐concept, the proposed method was employed to quantify the concentration of PDGF–BB from 0.50 to 250 fm with a detection limit of 0.21 fm. The applicability of the assay was further demonstrated in the analysis of PDGF–BB in human serum samples with acceptable accuracy and reliability. The result of this study exhibits distinct advantages, such as high sensitivity, good specificity, simplicity, and very small sample consumption. The good performances of the proposed strategy provide a powerful avenue for ultrasensitive detection of rare proteins in biological sample, showing great promise in biochemical analysis. Copyright © 2015 John Wiley & Sons, Ltd.     

A new class of conformable spectral observers for signal reconstruction

In this work, the design of spectral observers for signal reconstruction based on Kalman filters is performed and evaluated. The conformable derivative and the beta‐derivative were used to design the Kalman filters. Both derivatives satisfy the same formulas of the classical derivation, eg, the chain rule. The derivative order, the Ricatti equation parameters, and the observers tuning parameters were optimized using an optimization algorithm based on the bat's echolocation behavior (Bat algorithm). The simulation results showed the advantages of using the proposed observers for the signal reconstruction.     

Molecular signal suppression by in situ microextraction in nuclear magnetic resonance spectroscopy

The detailed characterization of complex mixtures by NMR is often hampered by the presence of signals from uninformative compounds, the resonances of which overlap with those of the molecules of interest. We provide here a proof of principle for an approach to NMR signal suppression in complex samples using Molecularly Imprinted Polymers (MIPS). Addition of a few milligrams of polymer to a solution traps the target molecule in typical micromolar to millimolar concentration, thus achieving in situ signal suppression, without altering any other spectral features. This method minimized any manipulation or perturbation of the spectrum and was applied to a complex mixture of known compounds and to a plant extract, in both cases spiked with a compound (bisphenol A), which was subsequently removed by selective binding to a complementary MIP. What is described in this report is comparable with microextraction and may in due course be applied to a large number of analytical challenges. Copyright © 2014 John Wiley & Sons, Ltd.     

Chitosan/Ce(IV) redox polymerization‐based amplification for detection of DNA point mutation

Polymerization‐based signal amplification, a technique developed for use in rapid diagnostic tests, hinges on the ability to localize initiators as a function of interfacial binding events. We report here a new DNA detection method in which polymer growth in redox‐polymerization is used as a means to amplify detection signals. The introduction of biotin‐labeled chitosan (biotin‐CS) with highly dense amino groups into the polymerization amplification as macromolecular reducing agent, beneficially simplifies amplification operation, as well as, provides a large amount of initiation points to improve the sensitivity of detection. DNA hybridization, SA and biotin binding reactions led to the attachment of CS on a solid surface where specific DNA sequences were located. With the addition of the mixture containing monomer AM, crosslinker PEGDA and oxidant CAN onto the CS location, the growth of polymer films was triggered to render the corresponding spots readily distinguishable to the naked eye. Direct visualization of 0.21 fmol target DNA molecules of interest was demonstrated. Non‐small cell lung cancer p53 sequence was further selected as a proof‐of‐principle to detect DNA point mutation. The proposed method exhibited an efficient amplification performance for molecule detection, and paved a new way for visual diagnosis of biomolecules. © 2016 Wiley Periodicals, Inc. J. Polym. Sci., Part A: Polym. Chem. 2016 , 54, 1929–1937     

Directly‐coupled‐column ultra‐fast liquid chromatography with diode array detection method for the rapid quantification of allergenic disperse dyes in water preconcentrated by magnetic solid‐phase extraction

A directly‐coupled‐column ultra‐fast liquid chromatography coupled with diode array detection method for the determination of 12 allergenic disperse dyes in river water at sub‐ppb levels has been developed and successfully validated. The analytical method is based on the use of two different reversed‐phased columns connected through a two‐position switching valve. A baseline separation was achieved by proper selection of stationary phases, mobile phases, and the use of a gradient elution in both dimensions. Furthermore, an easy‐to‐handle magnetic solid‐phase extraction procedure was developed for the preconcentration of 12 allergenic disperse dyes from river water. An enrichment factor of 100 times was obtained. The results showed excellent performance in terms of trueness (76.8–99.0%), precision (intraday: 2.2–8.0%, interday: 3.3–8.2%), and sensitivity (limits of determination, 0.027–1.46 μg/L). Twenty real samples collected from the outfalls in the Yaojiang, Yongjiang and Fenghuajiang estuary were analyzed, and three of the studied compounds were found in one collected sample (12.6 μg/L for disperse blue 7, 11.6 μg/L for disperse blue 106, and 0.22 μg/L for disperse blue 3).     

Comparison of ultra high performance supercritical fluid chromatography,ultra high performance liquid chromatography,and gas chromatography for the separation of synthetic cathinones

A comparison of ultra high performance supercritical fluid chromatography, ultra high performance liquid chromatography, and gas chromatography for the separation of synthetic cathinones has been conducted. Nine different mixtures of bath salts were analyzed in this study. The three different chromatographic techniques were examined using a general set of controlled synthetic cathinones as well as a variety of other synthetic cathinones that exist as positional isomers. Overall 35 different synthetic cathinones were analyzed. A variety of column types and chromatographic modes were examined for developing each separation. For the ultra high performance supercritical fluid chromatography separations, analyses were performed using a series of Torus and Trefoil columns with either ammonium formate or ammonium hydroxide as additives, and methanol, ethanol or isopropanol organic solvents as modifiers. Ultra high performance liquid chromatographic separations were performed in both reversed phase and hydrophilic interaction chromatographic modes using SPP C18 and SPP HILIC columns. Gas chromatography separations were performed using an Elite‐5MS capillary column. The orthogonality of ultra high performance supercritical fluid chromatography, ultra high performance liquid chromatography, and gas chromatography was examined using principal component analysis. For the best overall separation of synthetic cathinones, the use of ultra high performance supercritical fluid chromatography in combination with gas chromatography is recommended.