Influence of protein structure databases on the predictive power of statistical pair potentials

A long standing goal in protein structure studies is the development of reliable energy functions that can be used both to verify protein models derived from experimental constraints as well as for theoretical protein folding and inverse folding computer experiments. In that respect, knowledge-based statistical pair potentials have attracted considerable interests recently mainly because they include the essential features of protein structures as well as solvent effects at a low computing cost. However, the basis on which statistical potentials are derived have been questioned. In this paper, we investigate statistical pair potentials derived from protein three-dimensional structures, addressing in particular questions related to the form of these potentials, as well as to the content of the database from which they are derived. We have shown that statistical pair potentials depend on the size of the proteins included in the database, and that this dependence can be reduced by considering only pairs of residue close in space (i.e., with a cutoff of 8 Å). We have shown also that statistical potentials carry a memory of the quality of the database in terms of the amount and diversity of secondary structure it contains. We find, for example, that potentials derived from a database containing α-proteins will only perform best on α-proteins in fold recognition computer experiments. We believe that this is an overall weakness of these potentials, which must be kept in mind when constructing a database. Proteins 31:139–149, 1998. © 1998 Wiley-Liss, Inc.     

城市社区尺度的生态交通评价指标

交通出行的便捷和绿色程度是城市生态社区评价的关键内容。基于生态社区评价研究中交通出行相关指标的筛选及分析,选择了评价社区交通出行生态水平的5项关键指标,即居民工作出行时长,社区停车状况,绿色出行比例,公共交通满意度,社区停车环境满意度,建立了基于交通出行数据采集的客观评价和基于居民满意度问卷调查的主观评价相结合的评价方式。选择北京市城区和近郊的4个不同社区案例进行调查、评价和比较,验证评价指标的有效性及北京典型社区的交通出行生态水平。北京居民工作出行时长在60 min以内的占样本总量的75%左右,7%的居民出行时长在90 min以上;居民平均绿色出行比例为69.5%;北京居民对公共交通的满意度约为46%,对社区停车环境满意度则不足19%。居民工作出行时长指标可以更直接的反应交通便捷程度,而公共交通的便利程度会影响到居民选择绿色出行方式的比例。     

Clinical utility of ICD‐11 diagnostic guidelines for high‐burden mental disorders: results from mental health settings in 13 countries

In this paper we report the clinical utility of the diagnostic guidelines for ICD‐11 mental, behavioural and neurodevelopmental disorders as assessed by 339 clinicians in 1,806 patients in 28 mental health settings in 13 countries. Clinician raters applied the guidelines for schizophrenia and other primary psychotic disorders, mood disorders (depressive and bipolar disorders), anxiety and fear‐related disorders, and disorders specifically associated with stress. Clinician ratings of the clinical utility of the proposed ICD‐11 diagnostic guidelines were very positive overall. The guidelines were perceived as easy to use, corresponding accurately to patients’ presentations (i.e., goodness of fit), clear and understandable, providing an appropriate level of detail, taking about the same or less time than clinicians’ usual practice, and providing useful guidance about distinguishing disorder from normality and from other disorders. Clinicians evaluated the guidelines as less useful for treatment selection and assessing prognosis than for communicating with other health professionals, though the former ratings were still positive overall. Field studies that assess perceived clinical utility of the proposed ICD‐11 diagnostic guidelines among their intended users have very important implications. Classification is the interface between health encounters and health information; if clinicians do not find that a new diagnostic system provides clinically useful information, they are unlikely to apply it consistently and faithfully. This would have a major impact on the validity of aggregated health encounter data used for health policy and decision making. Overall, the results of this study provide considerable reason to be optimistic about the perceived clinical utility of the ICD‐11 among global clinicians.     

Assessing anostracan (Crustacea: Branchiopoda) cyst bank size: An attempt at a standardized method

Egg (cyst) banks play a fundamental role in the survival strategy of the hydrobionts of temporary pools. Therefore a quantitative estimate, as accurate as possible, of their size is the starting point for all the possible considerations concerning the life history of the inhabiting populations. We describe here, in some details, a sampling procedure to evaluate the number of cysts laid by the anostracan Chirocephalus ruffoi Cottarelli & Mura, 1984, in an experimental pool and we show that this procedure results in a good estimate of the cyst bank consistency. A pool 150 cm in diameter was divided into five concentrical rings, 13 cm apart from each other, and a central core (with a 10 cm radius). The number of samples needed to obtain an accurate estimate was calculated by taking into account that, to perform uniform sampling, the total volume of the samples must be proportional to the volume of the pool bed in each ring. The number of cysts in each of the rings was then estimated by considering the mean of the experimental results of a previous study (61 core samples along six transects across the pool itself), multiplied by the number of samples ideally performed in each sector. Evaluating the cyst bank size by the above method resulted in an estimate with an error of only 4% compared to the real cyst bank size. We also show that the number of samples needed can significantly be reduced, with an error on the total number of cysts that can be controlled. This result, that follows from statistical considerations on the confidence interval for the mean, allows us to obtain a general sampling procedure that can be applied to statistically comparable pools.     

Assessing Stream Ecosystem Rehabilitation: Limitations of Community Structure Data

Inappropriate land use practices, pollutants, exploitation, and overpopulation have simplified stream habitats and degraded water quality worldwide. Management agencies are now being tasked to ameliorate impacts and restore stream “health,” yet there is a dearth of rigorous scientific methods and theory on which to base sound restoration design and monitoring. Despite this, many localized restoration projects are being constructed to stabilize erosion and enhance habitat heterogeneity in streams. Many restoration attempts adopt the paradigm that increasing habitat heterogeneity will lead to restoration of biotic diversity, yet there have been few studies that have manipulated variation of a physical parameter independent of the mean to isolate the effects of heterogeneity per se. We conducted a field experiment to mimic restoration of habitat heterogeneity in a shallow. stony stream. By using an experimental approach rather than a detailed assessment of existing restoration work, we were able to control the starting conditions of replicate riffles so that organism responses could be unambiguously attributed to the heterogeneity treatments. We successfully manipulated the variability of streambed particle sizes and consequently near‐bed flow characteristics of entire riffles. These factors define axes of habitat heterogeneity at scales relevant to the resident macroinvertebrate fauna. Despite this, we were unable to distinguish differences in community structure between high and low habitat heterogeneity treatments. Power analysis indicated that macroinvertebrate populations were more sensitive to individual site conditions at each riffle than to the heterogeneity treatments, suggesting that increasing habitat heterogeneity may be an ineffective technique if the restoration goals are to promote macroinvertebrate recovery in denuded streams. With extremely high variability between replicate riffles, monitoring programs for localized restoration projects or point source impacts are unlikely to detect gradual shifts in community structure until the differences between the reference and treatment sites are extreme. Innovative measurement of other parameters, such as ecosystem function variables (e.g., production, respiration, decomposition), may be more appropriate indicators of change at local scales.     

森林生态系统健康评估的一般性途径探讨

生态系统健康评估方法及指标体系成为21世纪生态系统健康研究的核心内容．作为陆地生态系统的重要组成部分,森林生态系统健康的评估研究引起了广泛的关注．学者们对森林生态系统健康的定义、测度、评估和管理开始做出积极的探讨和实践,提出了一些理论和应用上的评价方法、评估途径和框架,为解决陆地生态系统危机甚至全球环境问题提供了新的概念和一系列研究手段．但由于多种条件的限制,目前仍然没有通用有效的评估森林生态系统健康的一般模式．文中简要探讨了森林生态系统健康问题,提出有效评估森林健康的3个前提：1)清晰明确的概念框架;2)充分有效的数据信息;3)正确合理的研究途径和技术手段．并分别进行了探讨．在此基础上总结阐述了可用于森林生态系统健康评估研究的途径：长期研究和定位监测、时空互换、历史研究途径、经济价值评估及其途径等．     

Genetic characterization and phytochemical analysis of wild and cultivated populations of Scutellaria baicalensis

Scutellaria baicalensis was collected from four wild and four cultivated populations from different locations in China. Forty-two samples were analyzed using random amplification of polymorphic DNA (RAPD) techniques for genetic profiling, and high performance liquid chromatography (HPLC) techniques to determine the flavonoid content. The selected 23 RAPD primers yielded a total of 838 clear and reproducible bands of which 237 were found to be polymorphic. The wild population exhibited higher polymorphism than that of the cultivated population. The dendrogram generated by the UPGMA method via Nei's genetic distance revealed three distinct genotypes from the cultivated populations and several branches from the wild populations. The contents of baicalin and wogonoside in dried roots of the samples ranged from (w/w) 8.63 to 17.84%, and from 1.99 to 4.21%, respectively, whereas their aglycones, baicalein and wogonin, were within the range of only 0.04-0.23%. The total content of the four flavonoids varied from 9.45 to 26.24%. Comparatively, the cultivated populations contained much higher levels of baicalin and total flavonoids than those in the wild populations. The results from genetic characterization and phytochemical analysis demonstrated that the quality variation of this drug was mainly determined by extrinsic environmental or agricultural factors, rather than by genetic differences. Our findings can be used for the commercial production and germplasm management of this medicinal plant.     

四川省珍稀濒危植物优先保护序列的研究

以四川省已公布的78种珍稀濒危植物为对象,系统地研究和制定了该地区重点保护植物的综合评价指标体系.通过对一系列评价指标的定量化和权重分配,获得植物种的“濒危系数”和“综合评价系数”,进而获得该地区各重点保护植物的受威胁程度和它们的优先保护序列,该序列比较真实地反映了此地区受威胁植物保护的先后顺序.     

基于野外痕迹点和GIS技术定量评估步道对大熊猫活动的影响

道路建设不仅直接导致野生动物死亡,还能对栖息地形成阻碍效应,导致小种群出现或隔离,增加物种灭绝的风险。生态学家在道路对野生动物影响研究中的一个重要进展是道路影响域(road-effectzone)的提出,但影响域既不能反映道路影响的变化性,也难以满足栖息地评估对数据的要求。为此,我们以大熊猫(Ailuropoda melanoleuca)为例来探讨道路影响的定量评估方法。在佛坪和长青保护区内选择了3条步道,获取了步道周边1,042个大熊猫的痕迹点数据,通过GIS计算各痕迹点到步道的距离,统计距离步道每20m内的痕迹点数量,以此作为其活动频率。在距步道每100m处设置检测点,通过非参数检验比较检测点前后活动频率分布的变化,寻找道路对大熊猫活动影响的突变点,确定影响变化的阈值距离和评价标准。研究发现在距离步道1,000m内,随距离的增加,大熊猫活动频率逐渐增大,大熊猫有明显的回避效应;在距步道500m、1,000m处发现活动频率发生了显著变化,为影响的阈值距离。本研究基于痕迹点和阈值距离的评估方法可以反映道路影响连续、渐变的特点,使定量、准确评估其影响成为可能。