A platform to standardize,store, and visualize proteomics experimental data

With the development of functional genomics research, large-scale proteomics studies are now widespread, presenting significant challenges for data storage, exchange, and analysis. Here we present the Integrated Proteomics Exploring Database （IPED） as a platform for managing proteomics experimental data （both process and result data）. IPED is based on the schema of the Proteome Experimental Data Repository （PEDRo）, and complies with the General Proteomics Standard （GPS） drafted by the Proteomics Standards Committee of the Human Proteome Organization. In our work, we developed three components for the IPED platform： the IPED client editor, IPED server software, and IPED web interface. The client editor collects experimental data and generates an extensible markup language （XML） data file compliant with PEDRo and GPS; the server software parses the XML data file and loads information into a core database; and the web interface displays experimental results, to provide a convenient graphic representation of data. Given software convenience and data abundance, IPED is a powerful platform for data exchange and presents an important resource for the proteomics community. In its current release, IPED is available at http：//www. biosino.org/iped2.     

基于物质流分析和数据包络分析的区域生态效率评价——以江苏省为例

区域生态效率(eco-efficiency)评价是考量区域可持发展的重要内容.基于物质流分析(material flow analysis, MFA)构建区域生态效率评价指标体系,并将污染物排放作为一种非期望输入引入到数据包络分析(data envelopment analysis, DEA)模型中,以江苏省(1990～2005年)为例进行生态效率分析评价.结果表明,江苏省的区域生态效率在1990～2005年期间呈现逐步上升的趋势.但是,同期的总物质投入(total material input, TMI)、物质需求总量(total material requirement, TMR)和污染物排放量也呈上升趋势.因此,江苏省社会经济发展和环境影响总体上呈现"弱脱钩(weak de-link)".     

Long-term recovery of macroinvertebrate biota in grossly polluted streams: Re-colonisation as a constraint to ecological quality

To meet targets imposed by the European Water Framework Directive (2000/60/EC) it is vital that measures to improve the status of rivers are both effective and economically viable. Achievement of such aims needs robust understanding of biological responses to changes in water quality vis-à-vis mechanisms of and constraints to the colonization of previously polluted sites. This study therefore examined the long-term chemical and biological changes in historically polluted rivers to elucidate the responses of macroinvertebrate biota to improvements in chemical water quality. For three historically polluted sites in the English Midlands, data from surveys over a period of ca. 50 years were analysed. Ammonia (NH₃) and 5-day biochemical oxygen demand (BOD₅) were used as chemical water quality indicators. Variations in the ecological recovery of the study sites were assessed using an average pollution sensitivity score (Average Score Per Taxon) and the number of taxa present (usually to family level) present in hand-net samples. Ecological recovery varied widely and was influenced by the intensity and spatial extent of the pollution and the proximity of available sources of potential colonisers. At the site most isolated from potential sources of colonizing taxa, no clean-water macroinvertebrate taxa were recorded 30 years after the major sources of pollution ceased. Where clean-water colonisers were more readily available, significant improvements in ecological quality followed within 2–5 years of the improvements in chemical quality. Macroinvertebrate communities and hence monitoring data may thus be indicative of long past conditions or of biological isolation rather than contemporaneous chemical conditions. Combined chemical and biological data were used to explore a generic model for predicting recovery rates and success. Neither BOD₅ nor NH₃ were found to provide a consistent and meaningful prediction of either average pollution tolerance of macroinvertebrate taxa or of the number of taxa present. Long-term relationships between macroinvertebrate variables and chemical water quality variables, however, were non-linear, suggesting that water quality thresholds may have to be exceeded before biological recovery can occur. Even when chemical water quality has been improved substantially, the apparent ecological status of macroinvertebrate communities may not reflect reduced pollution levels attained until adequate time to allow for re-colonisation (possibly decades) has elapsed.     

Confidence intervals for the mean of diagnostic test charge data containing zeros

In this paper, we consider the problem of interval estimation for the mean of diagnostic test charges. Diagnostic test charge data may contain zero values, and the nonzero values can often be modeled by a log-normal distribution. Under such a model, we propose three different interval estimation procedures: a percentile-t bootstrap interval based on sufficient statistics and two likelihood-based confidence intervals. For theoretical properties, we show that the two likelihood-based one-sided confidence intervals are only first-order accurate and that the bootstrap-based one-sided confidence interval is second-order accurate. For two-sided confidence intervals, all three proposed methods are second-order accurate. A simulation study in finite-sample sizes suggests all three proposed intervals outperform a widely used minimum variance unbiased estimator (MVUE)-based interval except for the case of one-sided lower end-point intervals when the skewness is very small. Among the proposed one-sided intervals, the bootstrap interval has the best coverage accuracy. For the two-sided intervals, when the sample size is small, the bootstrap method still yields the best coverage accuracy unless the skewness is very small, in which case the bias-corrected ML method has the best accuracy. When the sample size is large, all three proposed intervals have similar coverage accuracy. Finally, we analyze with the proposed methods one real example assessing diagnostic test charges among older adults with depression.     

Application of Preserved Human Amniotic Membrane for Corneal Surface Reconstruction

Objective: To evaluate the efficacy of preserved human amniotic membrane transplantation for reconstruction of the corneal surface diseases. Methods: Preserved human amniotic membrane transplantations were performed in 84 eyes of 78 patients for corneal surface reconstruction. The indications were limbal stem cell deficiency from Steven–Johnson syndrome, chemical burn and herpes keratitis (27 eyes), bullous keratopathy (26 eyes), persistent epithelial defect and dellen (17 eyes), band keratopathy (11 eyes), preparing for prosthesis (1 eye), corneal ulcer (1 eye) and acute chemical burn (1 eye). Results: Success was noted in 83.3% (70/84) eyes, partial success in 13.1% (11/84) eyes, and failure in 3.6% (3/84) eyes for an average follow-up of 10.5 months (3 – 29 months). No patient developed major immediate post-operative complications. Conclusion: Amniotic membrane transplantation can reduce inflammation, promote corneal epithelial healing, and decrease irritation in corneal surface problems.     

Upper bound estimators of the population size based on ordinal models for capture‐recapture experiments

Capture‐recapture studies have attracted a lot of attention over the past few decades, especially in applied disciplines where a direct estimate for the size of a population of interest is not available. Epidemiology, ecology, public health, and biodiversity are just a few examples. The estimation of the number of unseen units has been a challenge for theoretical statisticians, and considerable progress has been made in providing lower bound estimators for the population size. In fact, it is well known that consistent estimators for this cannot be provided in the very general case. Considering a case where capture‐recapture studies are summarized by a frequency of frequencies distribution, we derive a simple upper bound of the population size based on the cumulative distribution function. We introduce two estimators of this bound, without any specific parametric assumption on the distribution of the observed frequency counts. The behavior of the proposed estimators is investigated using several benchmark datasets and a large‐scale simulation experiment based on the scheme discussed by Pledger.