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。     

Metabolomic analysis of raw Pinelliae Rhizoma and its alum‐processed products via UPLC–MS and their cytotoxicity

Alum‐processing is a traditional method to attenuate the toxicity of Pinelliae Rhizoma (tubers of Pinellia ternate, PT). The present study aimed at investigating the chemical and cytotoxic changes during alum processing. Metabolomic profiles of raw and alum‐processed PT were studied based on ultra‐performance liquid chromatography coupled with Orbitrap mass spectrometry. More than 80 chemicals in positive MS mode and 40 chemicals in negative MS mode, such as organic acids, amino acids, glucosides and nucleosides, were identified after multivariate statistical analysis, including principal component analysis and orthogonal partial least‐square discriminant analysis. Almost all of the identified chemical markers were significantly decreased ~10‐ to 100‐fold after alum processing. Meanwhile, the correlations between the chemical markers were assimilated to a positive coefficient from disorderly distribution during the processing. Raw PT extracts could inhibit the proliferation of human carcinoma cells (HCT‐116, HepG2, and A549) at the rate of 40.5, 24.8 and 31.6% more strongly than processed PT. It was concluded that the alum processing of PT could decrease the number of actively water‐soluble principles at the same time as decreasing toxicity. Given the water‐insoluble property of toxic calcium oxalate raphides in PT, we suggest that a more scientific processing method should be sought.     

Qualitative and quantitative determination of Atractylodes rhizome using ultra‐performance liquid chromatography coupled with linear ion trap–Orbitrap mass spectrometry with data‐dependent processing

A quick and effective workflow based on ultra‐performance liquid chromatography coupled with electron spray ionization and LTQ‐Orbitrap mass spectrometry (UPLC‐LTQ‐Orbitrap MS) was established for compositional analysis and screening of the characteristic compounds of three species of Atractylodes rhizome for quality evaluation. This technique was employed to determine the seven main components in Atractylodes rhizome samples. Ultimately, 78 constituents were identified; of these, seven characteristic compounds were selected for species discrimination, comprising atractylodin (63), atractylenolide I (43), atractylenolide II (49), atractylenolide III (53), atractylon (69), methyl‐atractylenolide II (54) and (4E,6E,12E)‐tetradecadecatriene‐8,10‐diyne‐1,3‐diacetate (59). The seven main compounds, including six characteristic compounds, were simultaneously determined in 29 batches of Atractylodes rhizome samples. Thus, the method validation showed acceptable results. Quantitative analysis showed significantly different contents of the seven main components among the three species of Atractylodes rhizome, which indicates possible distinctions in the pharmacological effects. This established method can simultaneously provide qualitative and quantitative results for compositional characterization of Atractylodes rhizomes and for quality control.     

Probing molecular environments with a fictitious isotopic dipole

A HD-like (HD: mono-deuterated hydrogen molecule) isotopic dipole moment is proposed as a sensible probe for molecular environments, in particular for electrostatic fields and polarizable (reactive) sites of molecules. Fictitious nuclear masses are chosen in order to yield a rigid dipole with a small appropriate magnitude. Upon subtracting the Born-Oppenheimer energy, the interaction is reduced to field-dipole-like and dipole-polarizability-like terms, the last one being particularly informative since connected to potentially reactive sites. Possible asymmetries of this term appear as signatures of charged sites in the molecule. The field strength and orientation are easily obtained by identifying the minimum field-dipole energy configuration and flipping the dipole from it. Tests with hydrogen, water, benzene, and chlorobenzene molecules confirm the good performance of the method. In an application to test the present models for hydrogen activation by a frustrated Lewis pair, the full potential of the method is assessed.     

Curvature investigation in tapered fibers and its application to sensing and mode conversion

Non-adiabatic tapered fibers are basic photonic components used in a wide range of applications. Here we investigate a way to increase their utility through the controllable bending of one of their tapered sections. The experiments carried out explain, for the first time, the mechanics of this approach showing how these tapers can be used to build more sensitive sensors. Their use as highly efficient mode converters is also discussed.     

Facile synthesis of dopa‐functional polycarbonates via thiol‐Ene‐coupling chemistry towards self‐healing gels

Since extraction of the naturally occurring mussel‐foot proteins is expensive and time‐consuming, routes towards synthetic analogues are continuously being explored. Often, these methods involve several protection and deprotection steps, making the synthesis of synthetic analogues time‐consuming and expensive as well. Herein, we show that UV‐initiated thiol‐ene coupling between a thiol‐functional dopamine derivative and an allyl‐functional aliphatic polycarbonate can be used as a fast and facile route to dopa‐functional materials. Different thiol‐to‐allyl ratios and irradiation protocols were used and it was found that nearly 50% of the allyl groups could be functionalized with dopa within short reaction times, without the need of protecting the catechol. It is also demonstrated herein that the dopa‐functional polymers can be used to form self‐healing gels through complexation with Fe³⁺ ions at increased pH. © 2016 Wiley Periodicals, Inc. J. Polym. Sci., Part A: Polym. Chem. 2016 , 54, 2370–2378     

Full physicochemical characterization of malic acid: Emphasis in the potential as food ingredient and application in pectin gels

Malic acid, a carboxylic acid most found in fruits, is a smooth taste substance used as flavoring and preservative agent in foods, although not as used as citric acid. There are no studies focusing in quantitative results or investigations on its physicochemical properties, useful to the food industry, or even the confirmation of its calcium chelating, buffer texturizer and antioxidant alleged properties. Thus, the aim of this work was the assessment of most physicochemical properties of malic acid, solid and in solution, that could be useful to the food industry understand its real potential. The following analyses were carried out: melting point; structure (NMR, XRD, FTIR and SEM/EDS); TGA/DTG; solubility, hygroscopicity; antioxidant activity, iron chelating and antibacterial activities and stability of pectin gels. The melting temperature found was 129.71 °C. TGA/DTG exhibited first loss of mass around 140 °C. In the temperature range of 10 to 55 °C, it exhibited a high solubility in water, from 48.12 to 61.49 (100w), respectively. The tested bacteria, related to food spoilage, were inhibited by DL-malic acid 10% or higher. Chelating and antioxidant activities showed expressive results even in 1% solution. Pectin gels with malic acid had stronger structure and less syneresis than citric acid gels. In addition, calcium chelating, buffer texturizer and antioxidant properties were confirmed. Thus, malic acid has potential to be applied in a wide variety of food products as fortified beverages, frozen and refrigerated items, oils, pectin gels, hard and soft candies, and biofilms, due to all the characteristics quantified.     

工业SO2及碳黑颗粒紫外成像遥感监测技术

为了准确有效监测工业烟囱排放,基于SO2及碳黑颗粒物的光学特性,设计并研制出一套双通道紫外成像遥感监测系统.该成像系统的两个光谱通道的中心波长分别定于310 nm和330 nm,利用两个通道的光学厚度之差反演SO2浓度图像,颗粒物浓度图像由330 nm通道获取,根据浓度图像结合光流法获取烟羽运动速度,进而计算得出SO2和碳黑颗粒物的排放速率.结果表明,该工业烟囱的SO2及碳黑颗粒物排放速率分别为72.48±3.16 kg/h和6.33±1.18 kg/h.实验采用紫外相机同时对工业烟囱排放的SO2及碳黑颗粒物进行监测,实验表明双通道紫外成像遥感监测兼具高时间分辨率与高空间分辨率,测量结果准确直观,在工业废气污染、船舶尾气污染以及火山喷发污染排放遥感监测中具有非常明显的技术优势及巨大的应用前景.     

NeuDATool：支持GPU硬件加速和计算机集群跨节点并行的开源中子散射数据分析软件

实验势精修是20世纪80年代英国散裂中子源无定型材料组开发的用于分析中子散射实验数据的软件. 实验势精修的目标是根据中子散射数据重建样品的三维原子结构. 在过去的几十年，实验势精修被广泛用于中子散射实验数据分析，为实验用户提供了可靠的分析结果. 但是实验势精修是基于共享内存并行计算(OpenMP)的Fortran程序，不支持计算机服务器集群跨节点并行加速和GPU加速；这限制了它的分析速度. 随着计算机服务器集群的广泛建设和GPU加速技术的普遍使用，有必要重新编写EPSR程序以提高运算速度. 本文使用面向对象的C++语言，开发了一套实现EPSR算法的开源软件包NeuDATool；软件通过MPI和CUDA C实现了计算机集群跨节点并行和GPU加速. 使用液态水和玻璃态二氧化硅的中子散射实验数据对软件进行了测试. 测试显示软件可以正确重建出样品的三维原子结构；并且模拟体系达到10万原子以上时，使用GPU加速可以比串行的CPU算法提高400倍以上的模拟速度. NeuDATool为中子实验用户尤其是对熟悉C++编程并希望定义特殊分析算法的实验科学家提供了一种新的选择.