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。     

Nine components pharmacokinetic study of rat plasma after oral administration raw and prepared Semen Cassiae in normal and acute liver injury rats

In China, Semen Cassiae has long been used to protect liver, brighten eyes, and relieve constipation. Prepared Semen Cassiae is produced from raw Semen Cassiae by processing, the two forms of Semen Cassiae have different clinical applications. Pathological state is an important factor affecting the efficacy of drugs, the pharmacokinetic behavior of drugs could be significantly changed when people or animal were under different pathological state. To clarify the effect of processing mechanism and pathological state for pharmacokinetic behavior, the pharmacokinetics of nine components of raw and prepared Semen Cassiae under normal and acute liver injury rats were examined. The results showed that the bimodal phenomenon appeared on the plasma concentration‐time profiles of obtusin, emodin, chrysophanol, aloe emodin and rhein. The T_max of aurantio‐obtusin, obtusin, chrysoobtusin, emodin, chrysophanol, aloe emodin, physcion in normal groups administrated prepared Semen Cassiae were shorter than those administrated raw Semen Cassiae. For the AUC_0–t, aurantio‐obtusin, obtusin, chrysoobtusin, chrysophanol, aloe emodin and physcione in model groups administrated prepared Semen Cassiae were significantly higher than other groups, unlike above components, rhein had poor absorption in model groups. The study would be useful for further studies on pharmacokinetics and clinical application of raw and prepared Semen Cassiae.     

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.     

Nanoscale C‐Rich SixC1−x Bus/Ring Waveguide Based Cross‐Wavelength Data Converter

The carbon‐rich silicon carbide (C‐rich Si_xC_1?x) micro‐ring channel waveguide with asymmetric core aspect is demonstrated for all‐optical cross‐wavelength pulsed return‐to‐zero on‐off keying (PRZ‐OOK) data conversion. Enhanced nonlinear optical Kerr switching enables 12‐Gbit per second data processing with optimized modulation depth. The inverse tapered waveguide at end‐face further enlarges the edge‐coupling efficiency, and the asymmetric channel waveguide distinguishes the polarization modes. To prevent data shape distortion, the bus/ring gap spacing is adjusted to control the quality factor (Q‐factor) of the micro‐ring. Designing the waveguide cross section at 500 × 350 nm² provides the C‐rich Si_xC_1?x channel waveguide to induce strong transverse electric mode (TE‐mode) confinement with a large Kerr nonlinearity of 2.44 × 10^?12 cm² W^?1. Owing to the trade‐off between the Q‐factor and the on/off extinction ratio, the optimized bus/ring gap spacing of 1400 nm is selected to provide a coupling ratio at 5–6% for compromising the modulation depth and the switching throughput. Such a C‐rich Si_xC_1?x micro‐ring with asymmetric channel waveguide greatly enhances the cross‐wavelength data conversion efficiency to favor its on‐chip all‐optical data processing applications for future optoelectronic interconnect circuits.     

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.     

DISCRETE GRADIENT METHOD FOR IMAGE-BASED BIOMECHANICAL STRESS ANALYSIS 1)

介绍一种可用于计算生物力学的离散梯度方法,此方法可利用离散的点云模型直接进行数值模拟分析而不需要传统的几何模型。将离散梯度法应用于点云模型需要首先确定模型中点之间的相邻关系和每个点所分配的材料体积,然后通过用广义的有限差分的形式定义了梯度插值向量,并以此向量来近似函数在每个离散点上的梯度。从弱形式出发,推导建立了适用于弹性固体大变形问题的求解器,并具有和有限元法中双线性四边形单元一致的准确性和收敛性。着重描述了一种可以从医学图像中快速提取材料点并建立点云模型的方法,以及利用三角划分和重心划分确定材料点之间的相邻关系和每个材料点体积的具体过程。通过腹主动脉瘤膨胀的静力学模拟分析,展示了离散梯度法的实用性和准确性。该算法实现了基于医学图像进行生物力学分析的过程自动化,为病体特异性的研究和治疗提供便利和实用的工具。     

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.     

中应变率下材料动态拉伸关键参数测试方法

通过高速液压伺服材料试验机进行金属材料的中等应变率动态拉伸力学性能测试。为获取精确的动态拉伸载荷数据，提出了一种拉伸载荷的间接测量方法，在不改变试验机原有结构的情况下，解决了试验机自带载荷传感器测试数据在塑性段振荡导致材料真正动力学行为被掩盖的问题；通过数字图像相关的非接触测量方式进行动态拉伸应变的测量。实验验证表明，提出的载荷和应变测试方法可实现金属材料动态拉伸试验中的力学性能参数测试。     

A solids mixing rate correlation for small scale fluidized beds

A new first degree solids mixing rate is proposed to evaluate the mixing of solids in small scale fluidized beds. Particle mixing experiments were carried out in a 2D fluidized bed with a cross-section of 0.02 m × 0.2 m and a height of 1 m. White and black particles with average diameters of 850 and 450 μm were used in our experiments. Image processing was used to measure the concentration of the tracers at different times. The effects of four representative operating parameters (superficial gas velocity, ratio of tracer particles to bed particles, tracer particle position, and particle size) on mixing are discussed with reference to the mixing index. We found that the Lacey index depends on the concentration of the tracers. The position of the tracers affects the initial mixing rate but not the final degree of mixing. However, the new mixing rate equation does not depend on the initial configuration of the particles because this situation is considered to be the initial condition. Using the data obtained in this work and that found in literature, an empirical correlation is proposed to evaluate the mixing rate constant as a function of dimensionless numbers (Archimedes, Reynolds, and Froude) in small scale fluidized beds. This correlation allows for an estimation of the mixing rate under different operating conditions and for the detection of the end point and/or the time of mixing.