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。     

NIFTy 3 – Numerical Information Field Theory: A Python Framework for Multicomponent Signal Inference on HPC Clusters

NIFTy , “Numerical Information Field Theory,” is a software framework designed to ease the development and implementation of field inference algorithms. Field equations are formulated independently of the underlying spatial geometry allowing the user to focus on the algorithmic design. Under the hood, NIFTy ensures that the discretization of the implemented equations is consistent. This enables the user to prototype an algorithm rapidly in 1D and then apply it to high‐dimensional real‐world problems. This paper introduces NIFTy  3, a major upgrade to the original NIFTy  framework. NIFTy  3 allows the user to run inference algorithms on massively parallel high performance computing clusters without changing the implementation of the field equations. It supports n‐dimensional Cartesian spaces, spherical spaces, power spaces, and product spaces as well as transforms to their harmonic counterparts. Furthermore, NIFTy  3 is able to handle non‐scalar fields, such as vector or tensor fields. The functionality and performance of the software package is demonstrated with example code, which implements a mock inference inspired by a real‐world algorithm from the realm of information field theory. NIFTy  3 is open‐source software available under the GNU General Public License v3 (GPL‐3) at https://gitlab.mpcdf.mpg.de/ift/NIFTy/tree/NIFTy_3 .     

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.     

An Introduction to Influence Theory: Kinematics and Dynamics

Influence theory is a foundational theory of physics that is not based on traditional empirically defined concepts, such as positions in space and time, mass, energy, or momentum. Instead, the aim is to derive these concepts, and their empirically determined relationships, from a more primitive model. It is postulated that there exist things, which are call particles, that influence one another in a discrete and directed fashion resulting in a partially ordered set of influence events. The problem of consistent quantification of the influence events is considered. Observers are modeled as particle chains (observer chains) as if an observer were able to track a particle and quantify the influence events that the particle experiences. From these quantified influence events, consistent quantification of the universe of events based on the observer chains is studied. Herein, the kinematics and dynamics of particles from the perspective of influence theory are both reviewed and further developed.     

基于视觉辐条图案识别方法的蓝宝石引晶机制研究

工业生产蓝宝石晶体过程中,引晶步骤有着至关重要的地位。引晶必须在温度梯度较小,温度分布趋于稳定的条件下进行。目前,工业生产蓝宝石主要依靠人工经验操控籽晶杆实现引晶操作,但是人工引晶操作的准确性不高会导致成品品质不佳、资源浪费。为此,本文提出一种基于蓝宝石视觉辐条图案识别方法来检测蓝宝石熔体状态自由液面状态,从而实现一种高效率引晶的机制。此方法利用经典骨架化算法细化辐条图案,Harris算子实现特征信息的提取,提取的特征信息放入运动轨迹模型中判断熔体稳定性,分析液面温度分布稳定性从而实现引晶。结果表明,此算法具有有效性,蓝宝石晶体引晶效率大大提高,生产出的成品良率也有提升,可有效指导蓝宝石的工业生产。     

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.     

On-chip multiphoton Greenberger–Horne–Zeilinger state based on integrated frequency combs

One of the most important multipartite entangled states, Greenberger–Horne–Zeilinger state (GHZ), serves as a fundamental resource for quantum foundation test, quantum communication and quantum computation. To increase the number of entangled particles, significant experimental efforts should been invested due to the complexity of optical setup and the difficulty in maintaining the coherence condition for high-fidelity GHZ state. Here, we propose an ultra-integrated scalable on-chip GHZ state generation scheme based on frequency combs. By designing several microrings pumped by different lasers, multiple partially overlapped quantum frequency combs are generated to supply as the basis for on-chip polarization-encoded GHZ state with each qubit occupying a certain spectral mode. Both even and odd numbers of GHZ states can be engineered with constant small number of integrated components and easily scaled up on the same chip by only adjusting one of the pump wavelengths. In addition, we give the on-chip design of projection measurement for characterizing GHZ states and show the reconfigurability of the state. Our proposal is rather simple and feasible within the existing fabrication technologies and we believe it will boost the development of multiphoton technologies.     

基于DIS数字信息化系统对透光物质透光性能的研究

采用DIS数字信息化系统,对不同浓度的蓝墨水溶液在激光光源照射下的透射平均照度及照度分布图像进行实验研究,得到了平均照度值随溶液浓度变化的规律。对不同颜色塑料膜片对白炽灯光源透过照度值及照度分布图像进行实验研究得到及其相关之规律。     

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.     

Green solvent approach for printable large deformation thermoplastic elastomer based piezoresistive sensors and their suitability for biomedical applications

Composites based on biocompatible thermoplastic elastomer styrene‐ethylene/butylene‐styrene (SEBS) as matrix and multi‐walled carbon nanotubes (MWCNT) as nanofillers show excellent mechanical and piezoresistive properties from low to large deformations. The MWCNT/SEBS composites have been prepared following a green solvent approach, to extend their range of applicability to biomedical applications. The obtained composites with 2, 4, and 5 wt % MWCNT content provide suitable piezoresistive response up to 80% deformation with a piezoresistive sensibility near 2.7, depending on the applied strain and MWCNT content. Composite sensors were also developed by spray and screen printing and integrated with an electronic data acquisition system with RF communication. The possibility to accurately control the composites properties and performance by varying MWCNT content, viscosity, and mechanical properties of the polymer matrix, shows the large potential of the system for the development of large deformation printable piezoresistive sensors. © 2016 Wiley Periodicals, Inc. J. Polym. Sci., Part B: Polym. Phys. 2016 , 54, 2092–2103