基因组"k字"频数普适关系的研究

寻找物种基因组中k-m er频数分布的特征,对几个典型物种的基因组序列进行了统计分析.区分“字”域和“频数”域,运用两种求信息熵的方法Shannon信息熵和F isher信息熵,定义了五种k-m er频数的泛函.发现对于每一物种,由Shannon信息熵定义的四种泛函与k之间都具有很好的线性关系,并且这种线性关系在所研究的物种间具有普适性.     

几种模式生物密码对的使用和基因组进化

以闪烁古生球菌、枯草杆菌、大肠杆菌、酿酒酵母、拟南芥和线虫基因组为样本,分别分析了编码序列中密码对、基因间序列中三联体对的相对模式数目随频数的分布,验证这种分布是r(α,β)分布.发现分布参数与基因组进化相关;另外,比较了密码对的观测值与期望值之差的分布,发现密码对的使用普遍具有偏好性,且不同的物种所偏好的密码对是不同的.     

以信息关联和偏信息关联为工具标记基因组

在30个物种中分别随机选取长度为20万碱基的序列片断,通过方差分析和多重比较检验考察其多项信息参数作为基因组识别码的有效性.结果表明:在16种偏信息关联中,FA(k)C,FC(k)A,FG(k)T和FT(k)G的识别能力最强.这说明基因组签名偏好AC和GT语言.并且将信息关联与上述四种偏信息关联结合可大幅提高识别能力.这表明信息关联和偏信息关联是标识基因组的有效工具.     

由繁衍所奠定和揭示的"物种生命形态"

该文分析提出了生命物质除了具有个体生命的这一生命形态以外,还存在着"物种生命"的这一生命形态。通过"物种生命"的生命表现,能够了解到物种内部的互利协作,是保障物种生存延续的根本;能够了解到争取物种生命的长久性生存延续,是同类中每个生命个体共同的最高生存目标及责任;能够了解到物种内部的利益矛盾,与物种外部各物种之间的利益矛盾具有着本质上的差别。因此,对于"物种生命"的确认,和对"物种生命"形成更加深入的认识,对于生物学、哲学、和社会学的研究都具有意义。     

DNA序列信息内容的普适关系

为描述基因组中k tuple(k字)频数分布的特征,定义了4种信息量,对若干典型基因组序列进行了统计分析,研究了信息量与字长k的普适关系,解释了普适性的根源在于DNA序列的近中性进化,指出真正的挑战在于对特异字的探索,对特异字在DNA RNA 蛋白质相互作用信息系统中的含义做了初步讨论。     

基于信息熵的省域制造业价值链测度方法研究

制造业是国民经济的主体,是立国之本、兴国之器、强国之基,中国省域制造业价值链高度测量的研究对促进国民经济的发展有着重要意义。基于信息熵的客观性对中国省域制造业价值链地位的相关信息进行量化分析,针对中国8个区域的26个省级行政区的制造业展开实证研究,首先通过建立评价指标,构建评价模型并根据信息熵来计算各指标权重,然后对中国制造业的省域价值链高度进行测度与分析,最后对影响制造业价值链高度的指标进行回归实证分析。结果表明:全国制造业水平差异显著,各地区之间发展不平衡,据此提出增强创新能力、注重品牌影响力、引进高级人才、结合"引进来"与"走出去"、提高制造业国际化发展水平等建议。     

基于闪电定位系统的海南岛闪电活动特征分析

利用ADTD-2C型闪电定位探测系统监测的2014—2015年海南岛闪电信息,通过数理统计等方法,分析和研究了海南岛闪电的时空分布规律和活动特征,结果表明:ADTD-2C型闪电定位系统能够全面监测海南岛的闪电信息,闪电信息能够有效反映海南岛的闪电活动特征.海南岛闪电频数具有"单峰"特征,全年各月均有发生闪电的记录,4~11月份是海南岛发生闪电的主要月份.闪电发生时段较为集中,主要是从午后开始,至傍晚达到最高峰.海南岛负地闪频数远大于正地闪频数,且负地闪强度显著高于正地闪强度.正地闪的雷电流幅值主要集中在6 k A~30 k A,负地闪的强度主要集中在-60 k A~-7 k A.海南岛北部的闪电密度要明显高于南部地区,北部和南部闪电强度相对较大,西部和中部地区闪电强度相对较小.     

基因组比较数据可视化的快速实现

Circos软件是一款功能强大的用于基因组比较分析数据可视化的图形生成软件,但是该软件需要使用者自己编程提取所需数据,因此如何将基因组注释和比较分析结果与该软件衔接是个非常实际的问题.这里,我们开发了一个能够将基因组数据快速与Circos~([1])软件衔接的工具一Geno2Cir.这个工具可以处理对位排列好的基因组数据,进行物种间序列差异的比较,得到能够直接用于生成Circos图像的文件.本工具不仅可以进行基因组之间的两两比较,也可以进行多个基因组之间的同时比较.前者利用窗口步移法进行序列之间的直接比较,后者利用K2P(Kimura-2-parameter)方法先计算两两序列之间的距离,然后得到所有序列之间的距离矩阵之后再计算总体的差异.这一工具可以应用于裸子植物松属物种的叶绿体基因组,以及亲缘关系较远但是序列差异较小的凤蝶总科线粒体基因组的比较.     

利用物种的蛋白质系统发生图谱研究物种进化

随着后基因组时代的到来,越来越多的物种基因组序列被测定出来.基因组信息的大量增加,使得从基因组的水平研究物种进化成为可能.文中定义了物种的蛋白质系统发生图谱的概念,将之用于进化分析,并从蛋白质组的水平研究了物种间的进化关系.此方法与目前较流行的分子进化方法相比,具有适用范围广,结果稳定等特点.随着基因组测序工作的迅速发展,用蛋白质系统发生图谱构建进化树的方法将有很大的发展空间.     

人类核糖体蛋白加工假基因在进化中的熵变

用生物信息学方法计算出人类核糖体蛋白加工假基因(RP加工假基因)的进化距离.假定在统计意义上,不同进化距离的假基因可粗略代表假基因的进化历程.在此假定基础上从信息论的角度去研究假基因在进化中的熵变.结果发现,1) 假基因序列的紧邻碱基关联随进化逐步增强;2) k-mer信息熵中,小k-mer(k=1,2,…,5)信息熵随进化减少,大k-mer(k=7,8)信息熵随进化先迅速减少,随后增加;3) 关联信息熵随进化减少,其中紧邻碱基关联信息熵的减少幅度最明显.这些可能与背景突变压力作用有关.     

Markedness and its Interpretation in Language Use

Language markedness is a common phenomenon in languages, and is reflected from hearing, vision and sense, i.e. the variation in the three aspects such as phonology, morphology and semantics. This paper focuses on the interpretation of markedness in language use following the three perspectives, i.e. pragmatic interpretation, psychological interpretation and cognitive interpretation, with an aim to define the function of markedness.     

Features of Women's language

Language is a means of verbal communication. People use language to communicate with each other. In the society, no two speakers are exactly alike in the way of speaking. Some differences are due to age, gender, statue and personality. Above all, gender is one of the obvious reasons. The writer of this paper tries to describe the features of women＇s language from these perspectives： pronunciation, intonation, diction, subjects, grammar and discourse. From the discussion of the features of women＇s language, more attention should be paid to language use in social context. What＇s more, the linguistic phenomena in a speaking community can be understood more thoroughly.     

低渗透非均质砂岩油藏启动压力梯度研究

理论推导与室内实验相结合,建立了低渗透非均质砂岩油藏启动压力梯度确定方法。首先借助油藏流场与电场相似的原理,推导了非均质砂岩油藏启动压力梯度计算公式。其次基于稳定流实验方法,建立了非均质砂岩油藏启动压力梯度测试方法。结果表明:低渗透非均质砂岩油藏的启动压力梯度确定遵循两个等效原则。平面非均质油藏的启动压力梯度等于各级渗透率段的启动压力梯度关于长度的加权平均;纵向非均质油藏的启动压力梯度等于各渗透率层的启动压力梯度关于渗透率与渗流面积乘积的加权平均。研究成果可用于有效指导低渗透非均质砂岩油藏的合理井距确定,促进该类油藏的高效开发。     

On Tragic Consciousness In The Works By Ernest Hemingway

As an American modern novelist who were famous in the literary world, Hemingway was not a person who always followed the trend but a sharp observer. At the same time, he was a tragedy maestro, he paid great attention on existence, fate and end-result. The dramatis personae's tragedy of his works was an extreme limit by all means tragedy on the meaning of fearless challenge that failed. The beauty of tragedy was not produced on the destruction of life, but now this kind of value was in the impact activity. They performed for the reader about the tragedy on challenging for the limit and the death.     

Achieving Unusual States of Matter Under High Pressure

正The periodicity of the elements and the non-reactivity of the inner-shell electrons are two related principles of chemistry,rooted in the atomic shell structure.Within compounds,Group I elements,for example,invariably assume the+1 oxidation state,and their chemical properties differ completely from those of the p-block elements.These general rules govern our understanding of chemical structures and reactions.Using first principles calcula-     

Exchange-Correlation and Electronic Excitation Energies from Pairing Matrix Fluctuations

We have developed an adiabatic connection to formulate the ground-state exchange-correlation energy in terms of pairing matrix linear fluctuations.This formulation of the exchange-correlation energy opens a new channel for density functional approximations based on the many-body perturbation theory.We illustrate the potential of such approaches with an approximation based on the particle-particle Random Phase Approximation(pp-RPA).This re-     

Density Functional Theory for the Response of Periodic Systems to Electric Fields Based on the Vector Potential Approach

正The electronic and nuclear(structural/vibrational)response of 1D-3D nanoscale systems to electric fields gives rise to a host of optical,mechanical,spectral,etc.properties that are of high theoretical and applied interest.Due to the computational difficulty of treating such large systems it is convenient to model them as infinite and periodic(at least,in first approximation).The fundamental theoretical/computational problem in doing so is that     

On the Thermodynamic Limit for Responses to Static Electromagnetic Fields

For molecular systems,the quantum-mechanical treatment of their responses to static electromagnetic fields usually employs a scalar-potential treatment of the electric field and a vector-potential treatment of the magnetic field.Although the potential for each field separately is associated with the choice of an(unphysical)origin,the precise choice of the origin for the electrostatic field has little consequences for the results.This is different for the     

Call for Papers

<正>"The Journal of Shanghai Normal University:Mathematics"is published by Shanghai Normal University as regular issues of The Journal of Shanghai Normal University each year from 2014 in English.The editors-in-chief of the issues are professors Yuhao Cong and Maoan Han.The Journal of Shanghai Normal University was started in 1958 with     

Journal of Donghua University ( English Edition) Contents of Volume 31

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