MATLAB在代谢网络优化中的应用

生物代谢网络是一个具有高度非线性的复杂系统,如何对其进行适当的优化,一直是代谢工程领域的研究热点.MATLAB是一个应用广泛的工程计算软件,应用于代谢网络的优化,能方便、快捷得到系统的优化结果.作者以典型的代谢网络为模型,通过对目标代谢物浓度的优化来说明MATLAB在代谢网络优化中的应用.     

基于网络药理学对四君子汤干预肠梗阻解除后的代谢通路研究

目到:利用代谢组学及网络药理学研究四君子汤对机械性肠梗阻(MIO)手术后的某些代谢组学的变化规律。方法:制作大鼠可复性肠梗阻模型,通过是否给予四君子汤干预进行分组,采用超高效液相色谱与串联四级杆飞行时间质谱仪(UPLC-Q-TOF/MS)技术对大鼠血浆样本进行代谢组学研究,对比分析不同分组大鼠血浆样本中代谢物水平,并采用网络药理学方法找到相关代谢通路。结果:四君子汤干预组大鼠体内代谢发生显著改变,随着时间延长,较对照组更快趋于正常,并且通过多元统计分析、整合化分析以及相对含量变化分析筛选出17 个与肠梗阻相关的生物标志物的m/z 值。并最终得出四君子汤干预大鼠可复性肠梗阻模型主要与精氨酸和脯氨酸代谢、甘油磷脂代谢及鞘脂代谢等有关。结论:四君子汤对肠梗阻解除后肠功能障碍、全身免疫失衡和营养障碍具有良好的干预作用,主要通过影响精氨酸代谢通路和磷脂代谢通路发挥作用。     

昼夜节律与骨代谢研究现状的可视化文献计量分析

目的 分析昼夜节律与骨代谢领域研究现况、热点及发展趋势,以期为日后研究提供参考。方法 以Web of Science核心数据库2000年1月1日至2022年11月30日收录文献为基础,采用VOSviewer 1.6.16和CiteSpace 6.1.R4软件对文献发表年度、国家/地区、机构、作者、期刊、关键词、引用情况等进行数据可视化分析。结果 共检索295篇文献,发文量总体趋于平缓稳定,在地域上广泛分布于美国、英国、亚洲、欧洲等多个国家和地区,其中美国、英国在论文数量和深度上颇为突出,研究机构以大学及其附属医疗机构为主,2010年后各机构和作者间联系较为紧密。研究内容上聚焦于昼夜节律与骨吸收、骨转化等骨代谢间机制的探索,包含骨代谢标志物、基因表达等维度。研究前沿包括Rev-erb α、骨折风险等。结论 昼夜节律和骨代谢相关文献的刊文量仍相对较少,应进一步发挥高质量期刊的引领作用,以期为骨代谢异常防控提供新的思路和治疗方案。未来基于基因表达层面的影响机制以及如何在昼夜节律视角下精准降低骨折风险仍是研究的重点方向。     

利用代谢网络模型和线性规划法在线预测谷氨酸发酵中产物浓度

在好氧型的谷氨酸发酵实验中发现，溶解氧（DO）对发酵性能有很大的影响，谷氨酸的生成方式也因此有很大不同：较低的DO水平能够延长产酸期、提高谷氨酸的最终浓度，但是代谢副产物——乳酸也有较大程度的积蓄；而DO水平过高，虽然代谢副产物不会生成积蓄，但菌体消亡过快导致产酸期缩短、谷氨酸的最终浓度降低．同时，谷氨酸的生成方式与发酵过程中摄氧率（OUR）和CO2的释放率（CER）有着非常紧密的关联．作者利用代谢网络模型并结合使用线性规划优化法，通过在线测定OUR和CER，比较准确地在线推定出发酵过程中谷氨酸的质量浓度变化。与传统的非构造式动力学模型相比，上述预测方法具有建模简单、模型物理意义明确、通用性能好等优点，为后续过程的在线控制和优化提供一种全新和有效的途径。     

利用Biolog系统进行乳酸生产菌代谢能力的快速分析

利用Biolog系统考察目标菌株对产乳酸途径相关碳源的代谢能力,表明在厌氧条件下两自行筛选的候选菌株中S-18比菌株S-44具有更高的己糖激酶和乳酸脱氢酶等产乳酸代谢关键酶活力;通过好氧条件下产乳酸途径及旁路相关碳源利用能力的考察,显示在好氧条件下丙酮酸更易转向旁路代谢且L-乳酸脱氢酶受到强烈抑制,为乳酸发酵条件的优化与调控奠定了理论基础.利用Biolog系统对特定代谢途径代谢能力进行分析的方法具有快速、简便、重现性高的特点,并适合高通量分析的目的,可促进工业微生物代谢能力及代谢调控研究的普遍开展.     

二维轮廓刀具轨迹自动生成的算法

提出了一种新的二维轮廓刀具轨迹生成的算法，简化以往对各种复杂情况的编程处理，对改善ＣＡＤ／ＣＡＭ系统中ＮＣ模块的运行性能有一定的作用，对开环和闭环的二维轮廓刀具轨迹生成都适用。     

A Preconditioned 3-D Multi-Region Fast Multipole Solver for Seismic Wave Propagation in Complex Geometries

The analysis of seismic wave propagation and amplification in complex geological structures requires efficient numerical methods. In this article, following up on recent studies devoted to the formulation, implementation and evaluation of 3D single- and multi-region elastodynamic fast multipole boundary element methods (FM-BEMs), a simple preconditioning strategy is proposed. Its efficiency is demonstrated on both the single- and multi-region versions using benchmark examples (scattering of plane waves by canyons and basins). Finally, the preconditioned FM-BEM is applied to the scattering of plane seismic waves in an actual configuration (alpine basin of Grenoble, France), for which the high velocity contrast is seen to significantly affect the overall efficiency of the multi-region FM-BEM.     

A Symplectic Based Neural Network Algorithm for Quantum Controls under Uncertainty

Robust quantum control with uncertainty plays a crucial role in practicalquantum technologies. This paper presents a method for solving a quantum controlproblem by combining neural network and symplectic finite difference methods. Theneural network approach provides a framework that is easy to establish and train. Atthe same time, the symplectic methods possess the norm-preserving property for thequantum system to produce a realistic solution in physics. We construct a generalhigh dimensional quantum optimal control problem to evaluate the proposed methodand an approach that combines a neural network with forward Euler’s method. Ouranalysis and numerical experiments confirm that the neural network-based symplecticmethod achieves significantly better accuracy and robustness against noises.     

A New Modified Layout for Laparoscopic Cholecystectomy

Objective:

The aim of this study is to present an economic and convenient modification of the layout for laparoscopic cholecystectomy, utilizing a three-port technique.

Methods:

The surgeon stands on the left side of the patient, while the assistant stands between the patient''s legs. The scrub nurse stands on the right side of the patient facing the surgeon. The assistant also operates the camera. Only three ports are used. This technique was used in 119 consecutive patients over a 24-month period. Endoscopic retrograde chlolangiopancreotography (ERCP) was done preoperatively in patients suspected to have choledocholithiasis.

Results:

Sixteen patients had ERCP done preoperatively and in 12 of them sphincterotomy and stone removal was carried out. Laparoscopic cholecystectomy was successfully completed in 115 patients. The mean operative time was 35 minutes. Four cases were converted (3.6%), one due to bile duct injury, two others due to extensive adhesions, and a fourth due to cholecystoduodenal fistula. The total morbidity rate was 4.2%. The mean hospital stay was 1.8 days.

Conclusions:

Laparoscopic cholecystectomy can be safely and conveniently done using only three ports in the modified position described. You need only one assistant, only one monitor and one less trocar. There is no prolongation of the operative time and the results are comparable to the classic four-trocar technique.     

A High-Accurate Fast Poisson Solver Based on Harmonic Surface Mapping Algorithm

Poisson's equations in a cuboid are frequently solved in many scientific andengineering applications such as electric structure calculations, molecular dynamicssimulations and computational astrophysics. In this paper, a fast and highly accuratealgorithm is presented for the solution of the Poisson's equation in a cuboidal domainwith boundary conditions of mixed type. This so-called harmonic surface mappingalgorithm is a meshless algorithm which can achieve a desired order of accuracy byevaluating a body convolution of the source and the free-space Green's function withina sphere containing the cuboid, and another surface integration over the spherical surface. Numerical quadratures are introduced to approximate the integrals, resultingin the solution represented by a summation of point sources in free space, which canbe accelerated by means of the fast multipole algorithm. The complexity of the algorithm is linear to the number of quadrature points, and the convergence rate can bearbitrarily high even when the source term is a piecewise continuous function.     

A Numerical Scheme for Generalized Peierls-Nabarro Model of Dislocations Based on the Fast Multipole Method and Iterative Grid Redistribution

Dislocations are line defects in crystalline materials. The Peierls-Nabarro models are hybrid models that incorporate atomic structure of dislocation core into continuum framework. In this paper, we present a numerical method for a generalized Peierls-Nabarro model for curved dislocations, based on the fast multipole method and the iterative grid redistribution. The fast multipole method enables the calculation of the long-range elastic interaction within operations that scale linearly with the total number of grid points. The iterative grid redistribution places more mesh nodes in the regions around the dislocations than in the rest of the domain, thus increases the accuracy and efficiency. This numerical scheme improves the available numerical methods in the literature in which the long-range elastic interactions are calculated directly from summations in the physical domains; and is more flexible to handle problems with general boundary conditions compared with the previous FFT based method which applies only under periodic boundary conditions. Numerical examples using this method on the core structures of dislocations in Al and Cu and in epitaxial thin films are presented.     

High-Order and High Accurate CFD Methods and Their Applications for Complex Grid Problems

The purpose of this article is to summarize our recent progress in high-order and high accurate CFD methods for flow problems with complex grids as well as to discuss the engineering prospects in using these methods. Despite the rapid development of high-order algorithms in CFD, the applications of high-order and high accurate methods on complex configurations are still limited. One of the main reasons which hinder the widely applications of these methods is the complexity of grids. Many aspects which can be neglected for low-order schemes must be treated carefully for high-order ones when the configurations are complex. In order to implement high-order finite difference schemes on complex multi-block grids, the geometric conservation law and block-interface conditions are discussed. A conservative metric method is applied to calculate the grid derivatives, and a characteristic-based interface condition is employed to fulfil high-order multi-block computing. The fifth-order WCNS-E-5 proposed by Deng [9, 10] is applied to simulate flows with complex grids, including a double-delta wing, a transonic airplane configuration, and a hypersonic X-38 configuration. The results in this paper and the references show pleasant prospects in engineering-oriented applications of high-order schemes.     

Algorithm for Femoral and Periacetabular Osteotomies in Complex Hip Deformities

Background  

Residual acetabular dysplasia of the hip in most patients can be corrected by periacetabular osteotomy. However, some patients have intraarticular abnormalities causing insufficient coverage, containment or congruency after periacetabular osteotomy, or extraarticular abnormalities that limit either acetabular correction or hip motion. For these patients, we believe an additional proximal femoral osteotomy can improve coverage, containment, congruency and/or motion.     

A Local Velocity Grid Approach for BGK Equation

The solution of complex rarefied flows with the BGK equation and the Discrete Velocity Method (DVM) requires a large number of velocity grid points leading to significant computational costs. We propose an adaptive velocity grid approach exploiting the fact that locally in space, the distribution function is supported only by a sub-set of the global velocity grid. The velocity grid is adapted thanks to criteria based on local temperature, velocity and on the enforcement of mass conservation. Simulations in 1D and 2D are presented for different Knudsen numbers and compared to a global velocity grid BGK solution, showing the computational gain of the proposed approach.