脑影像与基因组数据关联的交互可视化方法研究

可视化是基因组数据分析的一个重要部分,而下一代测序技术和基于阵列的分析方法产生的数据集的数量和多样性对现有的可视化工具提出了重大挑战.针对于这些问题,通过比对已有的可视化工具,总结其优势与不足,设计了一个可视化系统,从全基因组关联研究的数据中挖掘出显著的基因组数据信息,并且将此信息与脑影像结合起来.将研究者关注的信息生成热图（Heatmap Plot）,在Heatmap图中的数据信息可以显示相应表型对应的曼哈顿图,以及相应单核苷酸多态性对应的脑影像中的表型信息（不同区域使用不同p-value进行颜色绘制）,给予研究者更加直接的可视化表现.     

双歧杆菌对慢性腹泻猕猴肠道微生物组的影响

本研究旨在结合高通量测序和平板计数实验探索含活性双歧杆菌(Bifidobacterium spp)的饲料对慢性腹泻猕猴(Macaca mulatta)肠道微生物多样性及其腹泻症状的影响.通过16S rRNA高通量测序对比分析添加双歧杆菌前后饲料的菌群组成，发现添加组双歧杆菌的相对丰度显著高于未添加组(P<0.05).向慢性腹泻猕猴投喂该饲料，一个月后收集粪便进行宏基因组测序，并与前期研究获得的未添加组慢性腹泻猕猴和健康猕猴的肠道宏基因组数据对比分析，发现添加组的肠道菌群中乳杆菌(Lactobacillus spp)相对丰度较未添加组显著上调(P<0.05)，与健康组无显著差异(P>0.05).最后对饲喂双歧杆菌后好转及持续腹泻猕猴的粪便进行乳杆菌平板计数实验.发现经饲喂，猕猴肠道中乳杆菌数量增加，验证了宏基因组测序分析的结果.     

GPU架构下的并行计算

为降低粒子群优化算法(PSO: Particle Swarm Optimization)时间和空间的复杂度随问题规模的增大而越来越高的问题, 对图形处理器（GPU: Graphic Processing Unit）用于并行计算的方法进行了分析, 利用GPU的并行特性, 实现了粒子群优化算法路径搜索过程的并行化。测试函数实验结果证明, GPU平台较CPU模式下的计算, 其搜索速率有明显提高。     

海神单胞菌属的基因组测序数据分析

海神单胞菌属（Neptunomonas）于1999年被首次鉴定,目前包含8个菌种,其中6个已经完成全基因组测序。本文总结了海神单胞菌属的菌种特征和基因组信息,并利用基因组测序数据对该菌属的碳源利用途径、聚羟基脂肪酸酯代谢途径和芳香族化合物降解途径进行了分析。研究发现,海神单胞菌属具有完整的糖酵解和乙酸利用途径,普遍含有Ⅰ型和Ⅲ型的聚羟基脂肪酸酯合成酶,存在芳香族化合物的降解途径。基因组测序数据分析结果可以为海神单胞菌属在聚羟基脂肪酸酯合成与环境治理保护等领域的应用提供理论依据。     

面向CPU+GPU异构平台的模板匹配目标识别并行算法

针对大数据量导致模板匹配目标识别算法计算时间长,难以满足快速检测的实际需求问题,在采用最新NVIDIA Tesla GPU构建的CPU+GPU异构平台上,设计了一种模板匹配目标识别并行算法.通过对模板图像数据常量化、输入图像数据极致流多处理器片上化和简化定位参数计算3方面优化了并行算法,并对算法进行性能测试.实验表明,该算法在保证识别效果的同时实时性明显提高.     

基于CUDA架构并行算法的带地形AMT二维反演实现与应用

并行计算是提高音频大地电磁（audio-frequency magnetotelluric method,AMT）数据反演效率的有效途径。本文在统一计算设备架构(compute unified device architecture,CUDA) 下开展带地形的AMT数据二维反演并行算法研究,旨在利用GPU强大的计算能力及并行计算技术实现高精度、快速度的AMT数据二维反演。首先利用有限元和自适应正则化反演算法实现AMT数据二维反演的串行化计算;然后在PGI Visual Fortran+ CUDA5.5环境下编写基于CPU+GPU的CUDA并行代码,将正演中的频率循环、反演中的模型灵敏度矩阵计算和反演方程正则化求解部分进行并行化处理;通过不同复杂程度的理论模型正反演模拟验证了该并行算法的有效性和准确性。不同模型和不同模式下的数值模拟结果对比表明,基于CPU+GPU的CUDA并行算法相较于传统的CPU串行算法,在灵敏度矩阵计算和反演方程正则化方面耗时更少,加速比最高可达10倍以上。最后将该并行算法应用于某矿区实测AMT数据的二维反演中,取得了较好的应用效果。     

半月国内科技要闻

中国首次提出＂人类泛基因组＂概念 由深圳华大基因研究院领衔、华南理工大学主要参与的合作研究成果＂构建人类泛基因组序列图谱＂发布,该研究树立了新的人类基因组测序标准,为未来医学研究指明了方向,反映出中国基因组学在世界的领先地位（Nature Biotechnology,doi：10.1038/nbt.1596）。该研究使用深圳华大基因研究院自主研发的第二代测序技术大基因组组装工具,对炎黄一号基因组（即首个亚洲人个人基因组）进行深度测序和拼接,发现了人类基因组中除原先公认的单核甘酸多态性、     

基于并行计算的湍流燃烧流场数值模拟研究

首先研究了数值模拟系统的主要体系结构并分析了并行计算基本原理,然后使用计算流体力学平台OpenFOAM建立湍流燃烧流动数值模拟系统并使用该系统在特定的燃烧室网格环境下对煤气和空气湍流射流扩散燃烧进行数值模拟。模拟实验结果表明:系统能够较好地展示煤气和空气湍流燃烧流动的反应特性,验证了系统设计的合理性,而且通过使用并行计算技术后发现计算速度也明显加快。     

二维FFT在GPU上的并行实现

FFT算法是高度并行的分治算法,因此适合在GPU（Graphics Processing Unit,图形处理器）的CUDA（Compure Unified Device Architecture,计算统一设备体系结构）构架上实现．阐述了GPU用于通用计算的原理和方法,并在Geforce8800GT平台上完成了二维卷积FfTr的运算实验．实验结果表明,随着图像尺寸的增加,CPU和GPU上的运算量和运算时间大幅度增加,GPU上运算的速度提高倍数也随之增加,平均提升20倍左右．     

基于OpenCL的图像灰度化并行算法研究

随着图像数据量的增加,传统单核处理器或多处理器结构的计算方式已无法满足图像灰度化实时处理需求.该文利用图像处理器(GPU)在异构并行计算的优势,提出了基于开放式计算语言(OpenCL)的图像灰度化并行算法.通过分析加权平均图像灰度化数据处理的并行性,对任务进行了层次化分解,设计了2级并行的并行算法并映射到“CPU+GPU”异构计算平台上.实验结果显示:图像灰度化并行算法在OpenCL架构下NVIDIA GPU计算平台上相比串行算法、多核CPU并行算法和CUDA并行算法的性能分别获得了27.04倍、4.96倍和1.21倍的加速比.该文提出的并行优化方法的有效性和性能可移植性得到了验证.     

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.     

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     

An affordable accurate evaluation of the binding conformations predicted by molecular docking studies in bio-system

Franck-Condon factors bridge the gap between theoretical modeling and experimental observations for molecular electronic spectroscopy and electron transfer.Under the displaced harmonic oscillator approximation,multidimensional Franck-Condon factors are decomposed into a product of many one-dimensional(1D)Franck-Condon(FC)factors,and each 1D-FC factor is associated with one Huang-Rhys factor that determines the leading contribution of     

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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