基于集成类随机森林方法的神经胶质瘤特征基因选择的研究

神经胶质瘤(glioma)是一种严重的颅内肿瘤疾病,具有高复发率、高死亡率和低治愈率等特点。利用基因微阵列数据识别与神经胶质瘤相关的特征基因,对该疾病的临床诊断和生物医学研究将起到有益的参考和借鉴作用。作者针对神经胶质瘤数据,提出了一种集成类随机森林特征基因选择方法。首先应用有监督奇异值分解对数据进行降维并粗选出基因;其次应用类随机森林特征选择方法选出特征基因。实验结果显示,该方法对分类器的适应性强;对比其他方法,分类率优势明显;更重要的是,在选出的前50个特征基因中有39个基因与神经胶质瘤或肿瘤细胞生物过程存在着密切联系,证实该方法不仅保持了较高的分类率,而且保证了选择的特征基因具有很强的生物学关联意义,具有较高的可行性和实用性。     

Improving the objectivity of sustainability indices by a novel approach for combining contrasting effects: Happy Planet Index revisited

Measuring complex and rather intuitive qualities such as sustainability requires combining many different measures together. These measures often quantify contrasting effects. The resulting composite index then also depends not only on the component indices but also on the way that these have been combined together. An example of such a measure is the Happy Planet Index (HPI) that aggregates information on positive qualities like life-expectancy and human well-being with negative ones like ecological footprint to rank countries according to their sustainability. However, since component indices are often mutually correlated and feature quite different distributions of entities ranked, elaborate rules are used in the process of combination. As a result, the resulting composite index may look somewhat contrived and its rankings may depend heavily on subjective parameters in the combination process. We propose a geometrically motivated parameter-free method for combining indices with contrasting effects together. The method is independent of the number of contrasting indices to be combined and eliminates mutual correlation between component indices by using Singular Value Decomposition (SVD) analysis. As an example of its use, we revisit the Happy Planet Index and demonstrate the impact of adding new component indices to HPI on ranking nations by their sustainability.     

Eigenspace Time Frequency Based Features for Accurate Seizure Detection from EEG Data

Background

Epilepsy is a neurological disorder that affects over 2% of the world population. Epilepsy patients suffer from recurring seizures that can be very harmful. The unpredictability of seizures is a major concern for medical practitioners because uncontrollable seizures can lead to sudden death and morbidity. A system that could warn patients and doctors alike about the impending seizure event would dramatically enhance the quality of life for patients.

BetaVoid: Molecular voids via beta‐complexes and Voronoi diagrams

Molecular external structure is important for molecular function, with voids on the surface and interior being one of the most important features. Hence, recognition of molecular voids and accurate computation of their geometrical properties, such as volume, area and topology, are crucial, yet most popular algorithms are based on the crude use of sampling points and thus are approximations even with a significant amount of computation. In this article, we propose an analytic approach to the problem using the Voronoi diagram of atoms and the beta‐complex. The correctness and efficiency of the proposed algorithm is mathematically proved and experimentally verified. The benchmark test clearly shows the superiority of BetaVoid to two popular programs: VOIDOO and CASTp. The proposed algorithm is implemented in the BetaVoid program which is freely available at the Voronoi Diagram Research Center ( http://voronoi.hanyang.ac.kr ). Proteins 2014; 82:1829–1849. © 2014 Wiley Periodicals, Inc.     

Analytical trapping: extraction of time-independent structures from time-dependent crystallographic data

All chemical and biological reactions involve atomic motion, embodied in dynamic structural changes. Identifying these changes is the goal of time-resolved crystallography. The "raw" output of a time-resolved macromolecular crystallography experiment is the time-dependent set of difference electron density maps that span the desired time range and display the time-dependent changes in density (and underlying structure) as the reaction progresses. The goal is to interpret such data in terms of a small number of crystallographically refinable, time-independent structures, each associated with a reaction intermediate; to establish the pathways and rate coefficients by which the intermediates interconvert; and thus to establish a chemical kinetic mechanism. We review briefly the various strategies that may be used to achieve this goal and concentrate on two promising advances: singular value decomposition and cluster analysis. The strategies are illustrated by using data on the photocycle of the bacterial blue light photoreceptor, photoactive yellow protein.     

基于奇异值第一主成分的睡眠脑电分期方法研究

目的:脑电信号含多种噪声和伪迹,信噪比较低,特征提取前必须进行复杂的预处理,严重影响睡眠分期的速度。鉴于此,本文提出一种基于奇异值第一主成分的睡眠脑电分期方法,该方法抗噪性能较强,可省去预处理过程,减少计算量,提高睡眠分期的效率。方法:对未经过预处理的睡眠脑电进行奇异系统分析,研究奇异谱曲线,提取奇异值第一主成分,探索其随睡眠状态变化的规律。并通过支持向量机利用奇异值第一主成分对睡眠分期。结果:奇异值第一主成分不仅能表征脑电信号主体,而且可以抑制噪声、降低维数。随着睡眠的深入,奇异值第一主成分的值逐渐增大,但在REM期处于S1期和S2期之间。经MIT-BIH睡眠数据库中5例同导联位置的脑电数据测试(仅1导脑电数据),睡眠脑电分期的准确率达到86.4%。结论:在未对脑电信号进行预处理的情况下,提取的睡眠脑电的奇异值第一主成分能有效表征睡眠状态,是一种有效的睡眠分期依据。本文运用提出的方法仅采用1导脑电数据,就能得到较为满意的睡眠分期结果。该方法有较强的分类性能,且抗噪能力强,不需要对脑电作复杂的预处理,计算量小,方法简单,很大程度上提高了睡眠分期的效率。     

基于功能化磁珠快速提取植物病毒RNA方法的建立与优化

植物病毒病是制约作物生产的主要病害之一。及时明确其病毒病原和发展规律是有效控制其大规模传播的前提。而现有植物病毒病检测技术存在周期长、步骤繁琐、检测环境严苛等缺点。本研究以烟草花叶病毒 (Tobacco mosaic virus,TMV)为模型,基于碱基互补配对原则设计针对TMV的功能化磁珠（CMBs-ACPTMV）进行RNA提取,并对功能化磁珠的制备条件、提取反应条件以及灵敏性和稳定性等性能进行优化分析。结果表明,当添加4 μmol捕获探针（ACPTMV）、0.08 mg羧基磁珠（CMBs）时,所制备的CMBs-ACPTMV吸附RNA的能力最好;当提取时间为3 min时,CMBs-ACPTMV提取RNA的效果最好,而改变CMBs-ACPTMV的提取温度时其提取能力无明显变化;性能评价分析发现,CMBs-ACPTMV的灵敏度可达2.5 ng/μL,且检测稳定性较好。与常规RNA提取技术相比,CMBs-ACPTMV在检测时间和样品消耗量上具有突出优势。本研究所建立的功能化磁珠提取法快速、安全和简便,只需简易设备便可实现植物病毒RNA的快速提取,具有广阔的应用前景。     

Human serum albumin binding ibuprofen: A 3D description of the unfolding pathway in urea

Small angle X-ray scattering (SAXS) technique, supported by light scattering measurements and spectroscopic data (circular dichroism and fluorescence) allowed us to restore the 3D structure at low resolution of defatted human serum albumin (HSA) in interaction with ibuprofen. The data were carried out on a set of HSA solutions with urea concentrations between 0.00 and 9.00 M. The Singular Value Decomposition method, applied to the complete SAXS data set allowed us to distinguish three different states in solution. In particular a native conformation N (at 0.00 M urea), an intermediate I1 (at 6.05 M urea) and an unfolded structure U (at 9.00 M urea) were recognized. The low-resolution structures of these states were obtained by exploiting both ab initio and rigid body fitting methods. In particular, for the protein without denaturant, a conformation recently described (Leggio et al., PCCP, 2008, 10, 6741–6750), very similar to the crystallographic heart shape, with only a slight reciprocal movement of the three domains, was confirmed. The I1 structure was instead characterized by only a closed domain (domain III) and finally, the recovered structure of the U state revealed the characteristic feature of a completely open state. A direct comparison with the free HSA pointed out that the presence of the ibuprofen provokes a shift of the equilibrium towards higher urea concentrations without changing the unfolding sequence. The work represents a type of analysis which could be exploited in future investigations on proteins in solution, in the binding of drugs or endogenous compounds and in the pharmacokinetic properties as well as in the study of allosteric effects, cooperation or anticooperation mechanisms.     

医院工作量换算和奖金计算问题的方法：价值点数法

实行服务为导向的临床科室绩效考核和薪酬分配制度,需要解决两个关键问题,如何把不同性质工作量转换为统一单位的工作量,如何根据工作量计算奖金。通过引入了价值点数法来解决这两个问题。文章介绍了价值点数法的原理和计算步骤,对该方法在维持医务人员工作积极性和切断医务人员创收动力的作用进行了分析。     

基于EMD的河北省粮食产量波动的结构特征及其成因的分析

在分析河北省粮食产量变化的时间序列总体特征的基础之上,对河北粮食产量波动结构特征及其成因进行研究,旨在为指导河北省粮食安全生产提供科学的理论依据.综合运用EMD法、剩余法和方差分析法,对河北粮食产量波动结构特征及其成因进行研究.结果表明:在品种上,小麦和玉米两大主要粮食作物产量比重呈现递增趋势,两者之和达到了89.91%,其变动对粮食总产的变动起着举足轻重的作用;杂粮作物和稻谷所占比例较小,且呈逐年缩减趋势;小麦、玉米产量波动的方差贡献率分别为64.36%和31.72%,是河北省粮食总产波动的第一和第二主控作物;稻谷和杂粮作物由于其粮食产量基数较小对河北粮食总产波动的影响较小.在空间上,河北省粮食产量的波动值分布在0～0.35之间的地区比例约为90%,表明其强度主要处于中等水平;燕山太行山山前平原区和冀鲁豫低洼平原区粮食产量波动的方差贡献率分别为22.05%和17.82%,是河北省粮食总产波动的第一和第二主控区;辽吉西蒙东南冀北山地和后山坝上高原区的粮食产量波动对河北省粮食总产波动影响较小.研究表明综合运用EMD法、剩余法和方差分析法,对河北粮食产量波动结构特征及其成因进行研究是可行的.利用这种综合方法,提高了单独使用一种方法进行波动性分析的精度,为分析波动问题提供了新的科学的理论和方法.     

Intractable Unphysiologically Low Adenylate Energy Charge Values in Synaptosome Fractions: An Explanatory Hypothesis Based on the Fraction''s Heterogeneity

Synaptosomes prepared and incubated in a variety of ways from rat cerebra exhibited intractable, unphysiologically low adenylate energy charge values (approximately 0.37-0.60), low total adenine nucleotide contents (approximately 8-10 nmol/mg protein), and much higher adenylate kinase apparent Keq values (approximately 3-8) as compared to intact brain tissue (values of approximately 0.90, 25 nmol/mg, and 0.74, respectively). Synaptosomes prepared from mouse, dog, and chicken cerebra had values essentially identical to those from rat. When incubated under oxygen in a physiological salt solution containing glucose, synaptosomes metabolized more glucose to lactic acid than to CO2, and the addition of 100 microM veratridine caused a two- to threefold stimulation of O2 uptake, lactate accumulation, and CO2 output. It is known that synaptosome fractions contain a substantial number (at least 30-45% by volume) of cytoplasm-containing particles devoid of mitochondria (henceforth termed "cytosolic particles"), and that approximately 80% of brain hexokinase is bound to the outer mitochondrial membrane. For the cytosolic particles, lacking oxidative phosphorylation, to maintain their "in vivo" ATP turnover would require about a 19-fold increase in the glycolytic rate, which is not possible due to limiting amounts of hexokinase, and thus these particles are postulated to be responsible for the high level of aerobic lactate accumulation and the intractable low energy charge values found in synaptosome fractions. The mitochondria-containing particles are postulated to have a normal energy charge, a submaximal glycolytic rate, and minimal lactate production, on the basis of the capacity of veratridine to stimulate synaptosomal O2 uptake and CO2 and lactate output. Calculations based on this "two populations of particles" hypothesis indicate that for synaptosome fractions in general, (1) the cytosolic particles contain approximately 35-64% of the total adenine nucleotides and maintain an energy charge of approximately 0.12; (2) the cytosolic particles and mitochondria-containing particles have adenylate kinase apparent Keq values of approximately 0.21-1.66 and 0.74, respectively, revealing that the higher apparent Keq values of the synaptosome fractions probably are not real departures from equilibrium: and (3) approximately 31-45% of synaptosome fraction protein is contained in debris, which, when taken into account, yields total adenine nucleotide contents in the cytosolic particles and mitochondria-containing particles of approximately 15-24 and approximately 11-19 nmol/mg of particle protein, respectively.     

Composite Subsidence Vulnerability Assessment Based on an Index Model and Index Decomposition Method

The threat of damage to buildings and other infrastructures resulting from land subsidence associated with groundwater pumping in urbanized areas is an ongoing problem requiring assessment. An important goal of subsidence vulnerability assessment is to construct a composite subsidence vulnerability index (SVI) that is represented by a set of indicators that focuses on four different thematic factors: physical, social, economic, and environmental vulnerability. These indicators are evaluated on the basis of indicator selection principles and then weighted by their contribution rate to the overall index. The weights reflect different measures assigned to the township-specific conditions. A complete and composite subsidence vulnerability assessment is developed in which future vulnerability management decision-making processes can be readily made. The vulnerability assessment includes not only the construction of the SVI, which involves selecting, assigning value to, weighting, and aggregating the vulnerability indicators, but also the presentation of the SVI decomposition. Research results demonstrate that a composite subsidence vulnerability assessment method can be made by first constructing and then decomposition-presenting the overall SVI. This allows for the relative comparison of subsidence vulnerability and the identification of the main vulnerable indicators; thus providing subsidence risk, which represents an important step toward vulnerability management of water resources.     

Quinoline Based Monocarbonyl Curcumin Analogs as Potential Antifungal and Antioxidant Agents: Synthesis,Bioevaluation and Molecular Docking Study

In search for new fungicidal and free radical scavenging agents, we synthesized a focused library of 2‐chloroquinoline based monocarbonyl analogs of curcumin (MACs). The synthesized MACs were evaluated for in vitro antifungal and antioxidant activity. The antifungal activity was evaluated against five different fungal strains such as Candida albicans, Fusarium oxysporum, Aspergillus flavus, Aspergillus niger, and Cryptococcus neoformans, respectively. Most of the synthesized MACs displayed promising antifungal activity compared to the standard drug Miconazole. Furthermore, molecular docking study on a crucial fungal enzyme sterol 14α‐demethylase (CYP51) could provide insight into the plausible mechanism of antifungal activity. MACs were also screened for in vitro radical scavenging activity using butylated hydroxytoluene (BHT) as a standard. Almost all MACs exhibited better antioxidant activity compared to BHT.     

A Method for Material Parameter Determination for the Human Mandible Based on Simulation and Experiment

In cranio-maxillofacial surgery planning and implant design, it is important to know the elastic response of the mandible to load forces as they occur, e.g., in biting. The goal of the present study is to provide a method for a quantitative determination of material parameters for the human jaw bone, whose values can, e.g., be used to devise a prototype plastic model for the mandible. Non-destructive load experiments are performed on a cadaveric mandible using a specially designed test bed. The identical physiological situation is simulated in a computer program. The underlying mathematical model is based on a two component, linear elastic material law. The numerical realization of the model, difficult due to the complex geometry and morphology of the mandible, is via the finite element (FE) method. Combining the validated simulation with the results of the tests, an inverse problem for the determination of Young's modulus and the Poisson ratio of both cortical and cancellous bone can then be solved.     

Multi-Hop Routing Optimization Method Based on Improved Ant Algorithm for Vehicle to Roadside Network

This paper proposes a route optimization method to improve the performance of route selection in Vehicle Ad-hoc Network （VANET）. A novel bionic swarm intelligence algorithm, which is called ant colony algorithm, was introduced into a traditional ad-hoc route algorithm named AODV. Based on the analysis of movement characteristics of vehicles and according to the spatial relationship between the vehicles and the roadside units, the parameters in ant colony system were modified to enhance the performance of the route selection probability rules. When the vehicle moves into the range of several different roadsides, it could build the route by sending some route testing packets as ants, so that the route table can be built by the reply information of test ants, and then the node can establish the optimization path to send the application packets. The simulation results indicate that the proposed algorithm has better performance than the traditional AODV algorithm, especially when the vehicle is in higher speed or the number of nodes increases.     

microRNA的实验和生物信息学开发方法

mircroRNA是一类约22nt的内源小分子RNA,普遍存在于真核生物体内,它通过与靶基因互补结合来调控基因表达,从而对生物体的生长、发育等起到重要的调节作用。随着生物学技术的不断发展,mircroRNA研究的越发深入,越来越多的mircroRNA被开发出来。本文结合了mircroRNA的生理特点,从RNA、DNA和生物信息学预测这3个方面归纳总结有关开发microRNA的方法,以及由此衍生出来的相关的研究方法。通过对这些研究方法的分类总结,不但为mircroRNA以后的研究工作奠定良好的基础,而且有利于新技术的研发。