A Method to Rank Multiple Trait Performance of Biological Entities

Performance of biological entities are defined, in general by k inter-dependent traits whose error variances are heterogeneous. A method of arriving at “Performance Scores” for the entities along with a multivariate test of significance of k-trait differences is described. They are used to compute, for each entity, a “Performance Index” on which a ranking of the relative performance is obtained. The improvement in the present method over an earlier one is illustrated with a numerical example.     

Label-free quantitative proteomics and SAINT analysis enable interactome mapping for the human Ser/Thr protein phosphatase 5

Affinity purification coupled to mass spectrometry (AP-MS) represents a powerful and proven approach for the analysis of protein-protein interactions. However, the detection of true interactions for proteins that are commonly considered background contaminants is currently a limitation of AP-MS. Here using spectral counts and the new statistical tool, Significance Analysis of INTeractome (SAINT), true interaction between the serine/threonine protein phosphatase 5 (PP5) and a chaperonin, heat shock protein 90 (Hsp90), is discerned. Furthermore, we report and validate a new interaction between PP5 and an Hsp90 adaptor protein, stress-induced phosphoprotein 1 (STIP1; HOP). Mutation of PP5, replacing key basic amino acids (K97A and R101A) in the tetratricopeptide repeat (TPR) region known to be necessary for the interactions with Hsp90, abolished both the known interaction of PP5 with cell division cycle 37 homolog and the novel interaction of PP5 with stress-induced phosphoprotein 1. Taken together, the results presented demonstrate the usefulness of label-free quantitative proteomics and statistical tools to discriminate between noise and true interactions, even for proteins normally considered as background contaminants.     

The significance threshold for coherence when using the Welch's periodogram method: Effect of overlapping segments

A classical tool to identify coupling mechanisms between two biological signals is transfer function (TF) analysis, commonly estimated by the Welch's periodogram method. However, the reliability of TF estimation depends on the coherence function, an index of linear coupling in the frequency domain. Thus, a threshold value has to be determined before assuming a coupling between two signals at a given frequency.Koopmans (The spectral analysis of time series) proposed a theoretical expression in the case of non-overlapping segments. Overlapping segments, however, improves the estimation of TF.In the present study, a modification of the expression by Koopmans is proposed for taking into account the effect of the overlapping procedure, including the most common case of a 50% overlapping ratio. Simulation tests were done on non-coherent signals (using the Hanning window), and a Kolmogorov–Smirnov test was used to check for the adequacy with the proposed threshold formula. The results showed that for an overlapping ratio of 50%, no statistical difference could be found (P > 0.05), except when using less than seven segments.The method has been applied to the computation of the transfer function between systolic blood pressure and heart rate.     

Identification of differentially expressed genes using multi-resolution wavelet transformation analysis combined with SAM

Although many statistical methods have been proposed for identifying differentially expressed genes, the optimal approach has still not been resolved. Therefore, it is necessary to develop more efficient methods of finding differentially expressed genes while accounting for noise and false discovery rate (FDR). We propose a method based on multi-resolution wavelet transformation analysis combined with SAM for identifying differentially expressed genes by adjusting the Δ and computing the FDR. This method was applied to a microarray expression dataset from adenoma patients and normal subjects. The number of differentially expressed genes gradually reduced with an increasing Δ value, and the FDR was reduced after wavelet transformation. At a given Δ value, the FDR was also reduced before and after wavelet transformation. In conclusion, a greater number and quality of differentially expressed genes were detected using the method when compared to non-transformed data, and the FDRs were notably more controlled and reduced.     

浙江海岛常绿阔叶林特征及其主要植物区系分析

我国东海的浙江沿海分布有星罗棋布的岛屿,其中较大的岛屿上分布有地带性的常绿阔叶林（如：樟木林、青冈林、石栎林和特殊的亮叶猴耳环林或以落叶成分占优的其他森林）,他们是标志性的植被类型或演替阶段,我们对这些植被类型中的优势植物种类进行了区系研究。结果显示,浙江海岛常绿阔叶林或类似森林中的优势和常见维管植物共有139种,只有热带亚洲成分、东亚成分中的中国-日本成分和中国特有成分贯穿于乔木层、灌木层、草本层和层外植物4大类中;进一步对15个木本中国特有种分析表明,其区系成分属亚热带性质,真正的温带性质不显著。在海岛这些植被出现的地段,还存在一些原生植被破坏后不同演替阶段的次生落叶阔叶林,其类型和面积都超过了地带性的常绿阔叶林,说明海岛除个别岛屿外曾经历了完全的破坏。目前,浙江海岛相应的演替阶段还不明确,它是研究特殊生境次生演替和恢复生态学的重要场所,这些常绿阔叶林和落叶林中富含重要的中国-日本海滨森林种类,对研究我国不同层次的常绿阔叶林具有重要的保护生物学意义。     

Expression profiles of genes involved in apoptosis and selenium metabolism in articular cartilage of patients with Kashin–Beck osteoarthritis

Kashin–Beck disease (KBD) is a special type of endemic osteoarthritis. It has been suggested that alterations in selenium metabolism and apoptosis play a role in KBD. However, the underlying molecular mechanism remains largely unclear. We performed a microarray analysis using RNA isolated from cartilages of KBD patients and healthy controls, through Significance Analysis of Microarray (SAM) software. Functional gene networks and crucial molecules associated with differentially expressed genes were investigated via Ingenuity Pathway Analysis (IPA) and hub gene analysis. Quantitative real-time PCR was used to check the validation of chip test. We identified 52 up-regulated apoptosis-related genes and 26 down-regulated selenium-related genes between KBD and controls, and these genes associated with the “MYC-mediated apoptosis signaling pathway”. We confirmed the results from array studies with quantitative real-time PCR analysis. Our results suggest that abnormal regulation of selenium metabolism and apoptosis through the MYC mediated signaling pathway contributes to the pathogenesis of KBD, but the relationship between apoptosis gene and selenium gene was not found.     

探讨现代医院药剂管理的思路及意义

随着我国医疗体制的改革,医院也面临着新形势下自身管理体系和管理方式的改革和创新。现代医院的管理模式也发生很大变化,从传统经验管理型逐步转变为现代管理型。现代医院管理采用科学的管理方法和管理技术,广泛地运用现代自然科学和社会科学的研究成果使管理手段现代化、科学化。现代医院药剂管理是医院管理工作的重要组成部分,对医疗质量及用药安全起着重要的作用。医院药剂管理的现代化可以保证用药的安全性,提高医疗质量,提高医院的核心竞争力,促进现代市场经济体制下医疗水平的提升和医院的发展。现代医院药剂管理的关键在于如何实现新模式下的管理目标及如何提高新模式下的药剂管理水平。本文结合我院在医疗改革背景下逐渐创新各个环节的管理模式,完善管理体系,突破管理瓶颈而获得的实践体会,进一步探讨现代医院药剂管理的方法及意义,为医院药剂管理工作提供理论指导。