ENCODE experiments http://genome.ucsc.edu/ENCODE/protocols/dataStandards/ChIP_DNase_FAIRE_DNAme_v2_2010.pdf Requirements for a DNase-seq and FAIRE-seq experiments Following an analysis of deeply sequenced DNase-seq and FAIRE-seq datasets, we suggest the following requirements. Controls Deeply sequenced reference samples such as input DNA exhibit uneven coverage. For example, peaks in promoters have been observed in some input samples, perhaps as the result of endogenous nuclease activity, or sonication and solubility biases (Auerbach et al., 2009, Giresi, et al., 2007). These promoter peaks likely represent real open chromatin and therefore should not be excluded from analysis. Other reasons for uneven input signals are copy number variation, and under-representation of repetitive DNA sequence in the reference genome. However, the impact of uneven coverage in input chromatin is limited. Advances in computational methods to correct for such features are being incorporated into the analysis. For example, using reads that are not in peaks, the DNase/FAIRE-seq data itself can be used to identify regions that exhibit copy number variations in samples. In addition, the true signals from FAIRE and DNase exhibit a unique structure that differs greatly from the type of signal produced by uneven input coverage. While it is always preferable to have deeply sequenced matched input for each sample, for DNase and FAIRE experiments, input sequencing from every cell type is not required. Sequencing Depth. Since DNase and FAIRE data represent a continuum of the degree to which chromatin is “open”, achieving true saturation may not be practical, or even definable. However, a decision must be made regarding adequate level of coverage. We propose that the optimal depth of sequencing be guided by our ability to identify regions that were also identified by other methods such as tiled arrays (Giresi 2009, Giresi et al., 2007, Sabo et al., 2006, Crawford et al., 2006), qPCR (Boyle et al., Cell 2008), or Southern blots (Sabo et al., 2006). For DNase and FAIRE this is typically 20-50 million reads. In general, it is best to sequence replicates to a similar depth. We have found that similar sequence depth matters most for replicates on the lower end of the recommended read depth. Number of Replicates. By definition, at least two biological replicates are necessary to ensure that the experiment is reproducible. Experiments completed to date indicate that there will not be a significant gain in information beyond two biological replicates, when they are in reasonable agreement. For DNase, we recommend that at least 80% of the top 50,000 peaks in one replicate are detected in the top 100,000 peaks in the second replicate, and vice-versa. For FAIRE, we recommend that at least 50% of the top 50,000 peaks in one replicate are detected in the top 200,000 peaks in the second replicate, and vice-versa. Scoring. ChIP, DNase, FAIRE, DNAme standards July 2011 1 Similar to ChIP-seq, a variety of peak calling methods can be used to score peak intensity, including Fseq (Boyle et al., Bioinformatics 2008), Hotspot, and others. The following suggestions can be used to identify a statistical significant cutoff by one of the following methods. 1) Fitting the data to a gamma distribution to calculate p-values, and contiguous regions where p-values were below a 0.05 threshold can be considered significant. 2) Irreproducible discovery rate (IDR) analysis described in section IIb above. ================= ENCODE - Wikipedia, the free encyclopedia en.wikipedia.org/wiki/ENCODE The primary assays used in ENCODE are ChIP-seq, DNase I Hypersensitivity, RNA-seq, and assays of DNA methylation. ======================== Cell, tissue or DNA sample: Cell line or tissue used as the source of experimental material. cell Tier Description Lineage Tissue Karyotype Sex Documents Vendor ID Term ID Label HEEpiC 3 esophageal epithelial cells endoderm epithelium U Stam ScienCell 2700 HEEpiC http://main.genome-browser.bx.psu.edu/cgi-bin/hgEncodeVocab?ra=encode%2Fcv.raterm=%22HEEpiC%22
Materials science of chitin: Arthropods have adapted to every habitat on earth, adaptive material Building block: Organic matric, Inorganic nano-particles, Cuticle Homogenization, porous media, topological distribution X-ray wide angle diffraction, lobster Hierarchical modeling of stiffness starting from ab initio
Maximum Principle Stress Theory - According to this theory failure will occur when the maximum principal stress in a system reaches the value of the maximum stress at elastic limit in simple tension. This theory is approximately correct for cast iron and brittle materials generally. Source: http://www.roymech.co.uk/Useful_Tabl...cs/stress.html Von Mises Stress (Distortion Energy Theory) - This theory proposes that the total strain energy can be separated into two components: the volumetric (hydrostatic) strain energy and the shape (distortion or shear) strain energy. It is proposed that yield occurs when the distortion component exceeds that at the yield point for a simple tensile test. Source: http://en.wikipedia.org/wiki/Yield_(engineering ) More information on Von Mises Stress can be found here . General information on solid mechanics can be found here . The beauty of Von Mises stress is that in the real world "everything" fails by shear. That's why it has emerged as the favorite failure theory. Having said that, the world of material failure is highly stochastic - subject to statistical variation. So as good as the theory is, you still need significant factors of safety if you don't want your project to come crashing down. You find Von Mises stress from the principle stresses by using a big ol gnarly equation or three. It is always a smaller value than maximum principle stress (by definition) BUT it is aligned in the direction that has to support the maximum shear load. This can be very helpful in design.
统计学读物推荐 http://bona.ustc.edu.cn/yonglee/go.php/archiver/3/2009/1/5/ 一、统计学基础部分 1、《统计学》 David Freedman等著，魏宗舒，施锡铨等译 中国统计出版社 据说是统计思想讲得最好的一本书，读了部分章节，受益很多。整本书几乎没有公式，但是讲到了统计思想的精髓。 2、《Mind on statistics(英文版）》 机械工业出版社 只需要高中的数学水平，统计的扫盲书。有一句话影响很深： Mathematics as to statistics is something like hammer, nails, wood as to a house, it's just the material and tools but not the house itself。 3、《Mathematical Statistics and Data Analysis（英文版.第二版）》 机械工业出版社 看了就发现和国内的数理统计树有明显的不同。这本书理念很好，讲了很多新的东西，把很热门的Bootstrap方法和传统统计在一起讲了。Amazon上有书评。 4、《Business Statistics a decision making approach（影印版）》 中国统计出版社 在实务中很实用的东西，虽然往往为数理统计的老师所不屑 5、《Understanding Statistics in the behavioral science（影印版）》 中国统计出版社 和上面那本是一个系列的。老外的书都挺有意思的 6、《探索性数据分析》中国统计出版社 和第一本是一个系列的。大家好好看看陈希儒老先生做的序，可以说是对中国数理统计的一种反思。 二、回归部分 1、《应用线性回归》 中国统计出版社 还是著名的蓝皮书系列，有一定的深度，道理讲得挺透的。看看里面对于偏回归系数的说明，绝对是大开眼界啊！非常精彩的书 2、《Regression Analysis by example (3rd Ed影印版)》 这是偶第一本从头到底读完的原版统计书，太好看了。那张虚拟变量写得比小说都吸引人。没什么推导，甚至说“假定你有统计软件可以算出结果”，主要就是将分 析，怎么看图，怎么看结果。看完才觉得回归真得很好玩 3、《Logistics回归模型——方法与应用》 王济川 郭志刚 高等教育出版社 不多的国内的经典统计教材。两位都是社会学出身，不重推导重应用。每章都有详细的SAS和SPSS程序和输出的分析。两位估计洋墨水喝得比较多，中文写的书，但是明显老外写书的风格 三、多元 1、《应用多元分析（第二版）》 王学民 上海财经大学出版社 现在好像就是用的这本书，但是请注意，这本书的亮点不是推导，而是后面和SAS结合的部分，以及其中的一些想法（比如P99 n对假设检验的影响，绝对是统计的感觉，不是推推公式就能感觉到的）。这是一本国内很好的多元统计教材。 2、《Analyzing Multivariate Data（英文版）》 Lattin等著 机械工业出版社 这本书有很多直观的感觉和解释，非常有意思。对数学要求不高，证明也不够好，但的确是“统计书”，不是数学书。 3、《Applied Multivariate Statistical Analysis (5th Ed影印版)》 Johnson Wichem 著 中国统计出版社 个人认为是国内能买到的最好的多元统计书了。Amazon 上有人评论，评价很高的。不过据王学民老师说，这本书的证明还是有不太清楚，老外实务可以，证明实在不咋的，呵呵 四、时间序列 1、《商务和经济预测中的时间序列模型》 弗朗西斯著 Amazon 上五星推荐的书，讲了很多很新的东西也非常实用。我看完才知道，原来时间序列不知有AR(1) MA(1)啊，哈 2、《Forecasting and Time Series an applied approach(third edition)》 Bowerman Connell 著 本书的主讲Box-Jenkins(ARIMA)方法，附上了SAS和Minitab程序 五、抽样 1、《抽样技术》 科克伦著 张尧庭译 绝对是该领域最权威，最经典的书了。王学民老师说：这本书不是那么好懂的，数学系的人，就算看得懂每个公式，未必能懂它的意思（不是数学系的人，还是别看了吧）。 2、《Sampling: Design and Analysis（影印版)》 Lohr著 中国统计出版社 讲了很多很新的方法，无应答，非抽样误差，再抽样，都有讨论。也很不好懂，当时偶是和《Advance Microeconomic Theory》一起看的，后者被许多人认为是梦魇，但是和前者一比，好懂多了。主要还是理念上的差距。我们的统计思想和数据感觉有待加强啊 六、软件及其他 1、《SAS软件与应用统计分析》 王吉利 张尧庭 主编 好书啊！！！！ 2、《SAS V8基础教程》 汪嘉冈编 中国统计出版社 主要讲编程，没怎么讲统计。如果想加强SAS编程可以考虑。 3、《SPSS11统计分析教程（基础篇）（高级篇）》 张文彤 北京希望出版社 当初第一次看这本书，发现怎么几乎都看不懂，尤其是高级篇，现在终于搞清楚了：） 4、《金融市场的统计分析》 张尧庭著 广西师范大学出版社 张老师到底是大家，薄薄的一本书，言简意赅，把主要的金融模型都讲清楚了。看完会发现，分析金融单单数学模型还是纸上谈兵，必须加上统计模型和统计方法才能真正应用。本书用的多元统计（代数知识）比较深。
http://scienceblog.com/ New graphene-based material could revolutionize electronics industry Can Nature’s Beauty Lift Citizens From Poverty? Adding wrinkles and folds boosts solar efficiency by 47% Analytic thinking can decrease religious belief: UBC study Genes shed light on spread of agriculture in Stone Age Sea change in salinity heralds shift in rainfall New form of intellectual disability discovered Poverty Undercuts Otherwise Major Gains in HIV Treatment Built-in GPS in birds in tune with Earth’s magnetic field Polluting China for the sake of economic growth Combating global disease with a cell phone, Google Maps and a lot of ingenuity Scorpion sons suffers from dad’s antibiotics Doubling the information from the double helix ‘Warming hole’ delayed climate change over eastern United States Boron Nanotubes Show Potential in Cancer Treatment
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2010, Proceedings of the 36th International MATADOR Conference , 6 , Pages 227-230 Modeling of hard turning: effect of tool geometry on cutting force Z.Y. Shi, Z.Q. Liu, C.M. Cao Abstract. Hard machining for manufacturing dies and molds offers various advantages, but the productivity is often limited, mainly by tool life. This study investigates the influence of cutting tool geometry on the cutting forces by utilizing finite element simulations (FEM). A set of cutting conditions in numerical FEM were conducted by using four different shaped cutting tools and axial force, radial force and tangential force were found. The results of this research help to explain the conclusion that for cylindrical control, the equation of the actual geometry of the S-shaped inserts involved in cutting is a sphere; that of C-shaped, D-shaped and Tshaped inserts involved in cutting is an ellipsoid with different lengths of short-half axis. Keywords : tool geometry, material flow stress, short-half-axial, cutting force FULL TEXT
这是bioconductor 2010 会议的培训教程相关的文件。内容几乎涵盖了主流生物信息操作的所有内容： http://www.bioconductor.org/help/course-materials/2010/BioC2010/ －－－－－－－－－－－－－－－－－－－－－－－－－－－－－－－－－－－－－－－－－－－－ Introduction to R Introduction to R First Steps with R Getting Started with Lattice Install command: source(http://bioconductor.org/course-packages/install-HTSTrack.R) Efficient R Programming Efficient R Programming Efficient R Programming Exercises Install command: source(http://bioconductor.org/course-packages/install-EfficientR.R) Transcript centric annotations and high-throughput sequencing Using the GenomicFeatures package Genomic Features and Sequences in Bioconductor Install command: source(http://bioconductor.org/course-packages/install-HTSTrack.R) Bioconductor tools for input and quality assessment of high-throughput sequence data Four exercises using Bioconductor Sequence Infrastructure Exercises: Reading and Manipulating Short Reads Exercises: An Introduction to Rsamtools Exercises: A Simple ChIP-Seq Workflow Exercises: A Simple RNA-seq Use Case Install command: source(http://bioconductor.org/course-packages/install-HTSTrack.R) Analyzing and Visualizing ChIP-seq Data Some Basic Analysis of ChIP-Seq Data Analysis of genome-scale count data in Bioconductor Robinson_McCarthy_BioC2010.zip Gene centric annotations Using Annotations in Bioconductor Install command: source(http://bioconductor.org/course-packages/install-HTSTrack.R) Analyzing flow cytometry data in Bioconductor Brief Intro to R for Flow Packages Users Analyzing flow cytometry data in Bioconductor Flow cytometry analysis Lab Flow cytometry analysis Lab Solutions Automated Gating and Metaclustering for Flow Cytometry Data Automated Gating and Metaclustering for Flow Cytometry Data (white paper)
Zhang electronegativity(27): How predicts raw material for InN nanocrystals? Changzheng et al. presented an effective synthetic protocol to produce high quality InN nanocrystals using indium iodide (InI 3 ) . There has been a question: Is it possible for high-quality InN to be synthesized from indium halides? The positive answer will be found in the present work using InI 3 . Concerning the four kinds of indium halides, InF 3 , InCl 3 , InBr 3 , and InI 3 ,.InI 3 has a stronger covalent ability than the other three. As is known, when two atoms form a chemical bond, the greater the difference between the electronegativity values for the two atoms, the more ionic the chemical bond between them (Zhang, 1982) According to Zhang electronegativitymodel which is based on the quantum mechanical electron configurations, n*(I z /R) ½ /r c 2 , both the effective principle quantum number, n*,and the covalent radius, r c, for halogens are increasedin the order: FClBrI .The polarizability of the anion will be ralated to its softness, that is, to the deformability of its electron cloud. Both increasing n* and r c will cause this cloud to be lessunder the influence of the nuclear charge of the anion and more easily influenced by the charge on thecation. Soconcerning the four kinds of indium halides, InI 3 is more covalent than the other three. Soit ispossible for high-quality InN to be synthesized from indium halides (InI 3 ) . Wu. Changzheng, Li. Tanwei, Lei. Lanyu, Hu. Shuangquan, Liu. Yi and Xie. Yi, New J. Chem., 2005, 29, 1610. Y. Zhang,1982, Inorg Chem., 1982, 21, 3886;3889. Y. Zhang,, in Introduction to Modern Inorganic Chemistry ( Eds: K. M. Mackay, R. A. Mackay, W. Henderson , ) 6thed., Nelson Thornes, United Kingdom,2002, pp 53-54).
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