Examining and Fine-tuning the Selection of Glycan Compositions with GlyConnect Compozitor

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Highlights

• •New comparative tool to assess the relevance of a glycan composition file to be used in a glycoproteomic study.
• •User-friendly and web-based interface to explore glycoproteomics data.
• •Detection of glycan compositional trends within and across protein(s) or tissues.

     

A Microcomputer Program for Evaluating Sampling Error: an Application to Stereological Methods for Electron Microscopy

In situations where there is a need to minimize sampling error or sample size, the coefficient of variation (CV) may be used to evaluate sampling error as a function of the number of observations or subjects in a sample. For example, CV is useful for estimating the minimum number of electron micrographs (N_min) required to obtain a representative field sample for stereological analysis. To facilitate the determination of N_min, we have written a program (COEFficient) for DOS microcomputers which calculates CVs. COEF assists the user in reducing error to that which solely reflects biological variability, thereby minimizing the time and cost of subsequent analyses.     

Comparison of NMR and crystal structures of membrane proteins and computational refinement to improve model quality

Membrane proteins are challenging to study and restraints for structure determination are typically sparse or of low resolution because the membrane environment that surrounds them leads to a variety of experimental challenges. When membrane protein structures are determined by different techniques in different environments, a natural question is “which structure is most biologically relevant?” Towards answering this question, we compiled a dataset of membrane proteins with known structures determined by both solution NMR and X‐ray crystallography. By investigating differences between the structures, we found that RMSDs between crystal and NMR structures are below 5 Å in the membrane region, NMR ensembles have a higher convergence in the membrane region, crystal structures typically have a straighter transmembrane region, have higher stereo‐chemical correctness, and are more tightly packed. After quantifying these differences, we used high‐resolution refinement of the NMR structures to mitigate them, which paves the way for identifying and improving the structural quality of membrane proteins.     

门诊血液透析事件监测软件的开发与应用

为加强医院门诊血液透析事件的监控,设计开发了门诊血液透析事件监测软件,对血液透析事件进行实时监测和统计分析,实现了门诊血液透析事件的信息化监测和数据的即时共享,提高了医院感染目标性监测和干预的质量和效率。     

mvmapper: Interactive spatial mapping of genetic structures

Characterizing genetic structure across geographic space is a fundamental challenge in population genetics. Multivariate statistical analyses are powerful tools for summarizing genetic variability, but geographic information and accompanying metadata are not always easily integrated into these methods in a user‐friendly fashion. Here, we present a deployable Python‐based web‐tool, mvmapper , for visualizing and exploring results of multivariate analyses in geographic space. This tool can be used to map results of virtually any multivariate analysis of georeferenced data, and routines for exporting results from a number of standard methods have been integrated in the R package adegenet , including principal components analysis (PCA), spatial PCA, discriminant analysis of principal components, principal coordinates analysis, nonmetric dimensional scaling and correspondence analysis. mvmapper 's greatest strength is facilitating dynamic and interactive exploration of the statistical and geographic frameworks side by side, a task that is difficult and time‐consuming with currently available tools. Source code and deployment instructions, as well as a link to a hosted instance of mvmapper , can be found at https://popphylotools.github.io/mvMapper/ .     

Characterizing the microenvironment surrounding protein sites.

Sites are microenvironments within a biomolecular structure, distinguished by their structural or functional role. A site can be defined by a three-dimensional location and a local neighborhood around this location in which the structure or function exists. We have developed a computer system to facilitate structural analysis (both qualitative and quantitative) of biomolecular sites. Our system automatically examines the spatial distributions of biophysical and biochemical properties, and reports those regions within a site where the distribution of these properties differs significantly from control nonsites. The properties range from simple atom-based characteristics such as charge to polypeptide-based characteristics such as type of secondary structure. Our analysis of sites uses non-sites as controls, providing a baseline for the quantitative assessment of the significance of the features that are uncovered. In this paper, we use radial distributions of properties to study three well-known sites (the binding sites for calcium, the milieu of disulfide bridges, and the serine protease active site). We demonstrate that the system automatically finds many of the previously described features of these sites and augments these features with some new details. In some cases, we cannot confirm the statistical significance of previously reported features. Our results demonstrate that analysis of protein structure is sensitive to assumptions about background distributions, and that these distributions should be considered explicitly during structural analyses.     

农业科研试验数据分析系统－LNT

分析了农业科研试验统计的基本方法,简述了统计软件包－ＬＮＴ的程序总控流程及主要功能,阐述了软件包的主要特点,提出了将农业统计分为方差分析、相关通径、回归分析、遗传分析和数据管理五大类２４小类的思想,编写了１２１种统计方法,运行于各种机型的集成软件包－ＬＮＴ。