Data synthesis and bioindicator development for nontidal streams in the interstate Potomac River basin, USA

Water resource agencies are increasingly confronted with issues of methods and data comparability when assessing inter-jurisdictional waters. The Interstate Commission on the Potomac River Basin (ICPRB) is developing an assessment framework for the diverse nontidal monitoring data collected by Potomac basin jurisdictions. The ICPRB's goal is to augment the jurisdictions’ water quality assessments with uniform, basin-wide evaluations of habitat and biological integrity. Disparate datasets were integrated and used to select and calibrate a common suite of biological indicators of human disturbance. Aggregated physiographic regions were most effective at grouping streams into site classes with similar attributes. Common elements from states’ habitat and water quality assessments were used to define regional reference and impairment criteria. Seven macroinvertebrate metrics distinguished reference from impaired sites in most regions: EPT richness, Hilsenhoff Family Biotic Index, percent clingers, percent collectors, percent dominance, percent EPT, and taxonomic richness. Reference communities in the Piedmont region of the basin were dissimilar from those in Highland and Valley regions, suggesting a need for different reference conditions and metric thresholds in these regions. Results confirm that useful bioindicators of aquatic health can be generated from multiple datasets if the synthesis is done with care.     

An international comparability study on quantification of total methyl cytosine content

Various methods have been developed for quantitative analysis of DNA methylation. However, there is currently no reference analysis system regarding DNA methylation with which other analytical approaches can be compared and evaluated. A standard measurement system that includes reference methods and reference materials may improve comparability and credibility of data obtained from different analytical environments. In an effort to establish a standard system for measurement of DNA methylation, the Korea Research Institute of Standards and Science (KRISS) coordinated an international comparison study among different national metrology institutes. An initial stage of the study involved an intercomparison regarding quantitative measurement of total methyl cytosine contents in artificially constructed DNA samples. The measurement principle involved measurement of dNMP contents following enzymatic hydrolysis of DNA samples. Results of the study showed good comparability among four of five participants and close agreement with reference values assigned by the coordinating laboratory. Conflicting data from one participant may have resulted from incomplete hydrolysis of samples due to use of insufficient amounts of enzymes. These results indicate that comparable and accurate results can be obtained from different measurement environments if digestion conditions are controlled appropriately and valid calibration systems are employed.     

Comparison of watershed disturbance predictive models for stream benthic macroinvertebrates for three distinct ecoregions in western US

The successful use of macroinvertebrates as indicators of stream condition in bioassessments has led to heightened interest throughout the scientific community in the prediction of stream condition. For example, predictive models are increasingly being developed that use measures of watershed disturbance, including urban and agricultural land-use, as explanatory variables to predict various metrics of biological condition such as richness, tolerance, percent predators, index of biotic integrity, functional species traits, or even ordination axes scores. Our primary intent was to determine if effective models could be developed using watershed characteristics of disturbance to predict macroinvertebrate metrics among disparate and widely separated ecoregions. We aggregated macroinvertebrate data from universities and state and federal agencies in order to assemble stream data sets of high enough density appropriate for modeling in three distinct ecoregions in Oregon and California. Extensive review and quality assurance of macroinvertebrate sampling protocols, laboratory subsample counts and taxonomic resolution was completed to assure data comparability. We used widely available digital coverages of land-use and land-cover data summarized at the watershed and riparian scale as explanatory variables to predict macroinvertebrate metrics commonly used by state resource managers to assess stream condition. The “best” multiple linear regression models from each region required only two or three explanatory variables to model macroinvertebrate metrics and explained 41–74% of the variation. In each region the best model contained some measure of urban and/or agricultural land-use, yet often the model was improved by including a natural explanatory variable such as mean annual precipitation or mean watershed slope. Two macroinvertebrate metrics were common among all three regions, the metric that summarizes the richness of tolerant macroinvertebrates (RICHTOL) and some form of EPT (Ephemeroptera, Plecoptera, and Trichoptera) richness. Best models were developed for the same two invertebrate metrics even though the geographic regions reflect distinct differences in precipitation, geology, elevation, slope, population density, and land-use. With further development, models like these can be used to elicit better causal linkages to stream biological attributes or condition and can be used by researchers or managers to predict biological indicators of stream condition at unsampled sites.     

Solving parasite-related problems in cultured crustacea

Trends emphasizing intensive crustacean culture methods, expansion of culture systems into different geographic areas, culture of different crustaceans, and transfer and introduction of crustaceans all promote an increase in diseases. Whereas modern techniques for detecting, diagnosing, and controlling viral disease are considered by some institutions as the primary or only research necessary for future development, considerable additional information on other diseases must be accumulated for continued and increased success in aquaculture. Examples given above indicate that the information involves taxonomy, life histories, host specificity, host responses and their causes, environmental influences on associations, drug treatments, acceptance by regulatory agencies of chemicals for disease management, human infections, and cost-benefit analyses. Many new infectious agents are continually being encountered. Some of these, including secondary invaders, can be controlled by manipulation of water quality or crustacean stock. Other agents cannot, and biological information can be used to control or understand these infections. Much of that information can be acquired by continual moderate support of small, long-term research programs conducting detailed studies on local symbionts.     

Data quality issues impede comparability of hospital treatment delay performance indicators

Aim

To assess the comparability of five performance indicator scores for treatment delay among patients diagnosed with ST-segment elevation myocardial infarction (STEMI) undergoing primary percutaneous coronary intervention in relation to the quality of the underlying data.

Methods

Secondary analyses were performed on data from 1017 patients in seven Dutch hospitals. Data were collected using standardised forms for patients discharged in 2012. Comparability was assessed as the number of occasions the indicator threshold was reached for each hospital.

Results

Hospitals recorded different time points based on different interpretations of the definitions. This led to substantial differences in indicator scores, ranging from 57 to 100 % of the indictor threshold being reached. Some hospitals recorded all the required data elements for calculating the performance indicators but none of the data elements could be retrieved in a fully automated way. Moreover, recording accessibility and completeness of time points varied widely within and between hospitals.

Conclusion

Hospitals use different definitions for treatment delay and vary greatly in the extent to which the necessary data are available, accessible and complete, impeding comparability between hospitals. Indicator developers, users and hospitals providing data should be aware of these issues and aim to improve data quality in order to facilitate comparability of performance indicators.     

Design and implementation of rapid assessment approaches for water resource monitoring using benthic macroinvertebrates

Abstract Benthic macroinvertebrates are the group of organisms most widely used for assessment of water resources. Rapid assessment approaches are intended to be efficient and cost effective; savings are found in reduced sampling and more efficient data analysis. Rapid bioassessment programmes have been quickly accepted and now cover most of the United States (US) and equivalent programmes cover all of the United Kingdom (UK). Rapid bioassessment programmes are designed to screen large regions, pinpointing trouble spots worthy of more detailed attention. Fundamental to all rapid bioassessment methods is the classification of streams so that comparisons can be made between reference areas and areas of concern, or test sites with similar characteristics. Both the UK and US approaches assess habitat characteristics. These characteristics are used to predict the fauna expected at a test site in the UK approach; in the US they are used as an aid to classification and interpretation of aquatic faunal data. Habitat assessments in the US are also used to determine whether poor water quality or degraded habitat are stressing the invertebrate communities. This is a major development in approaches to water resource assessment. In the UK, a model developed using multivariate statistics uses a few environmental variables thought to be unaffected by human activities to predict the fauna expected at a test site. The US approaches analyse data using several indices (or metrics) presumed to represent ecological features of interest. These indices have a range of sensitivities to different kinds of stress and must be calibrated for the area of interest. The two approaches have been developed in isolation but may have much to offer each other. Developing programmes are advised to consider both. Future needs include: development of procedures that can be applied to large rivers and to lakes; further refinement of ecological principles underlying metric choice; the inclusion of chemical criteria and toxicity tests to establish thresholds that indicate impairment; and development of criteria indicating the necessity for implementation of quantitative assessment studies.     

The validation of common European class boundaries for river benthic macroinvertebrates to facilitate the intercalibration process of the Water Framework Directive

The Water Framework Directive (WFD) requires that all the water bodies in Europe be protected and enhanced to achieve Good Ecological Status by 2015. The intercalibration of the biological monitoring results of Member States has to be carried out in relation to classification tasks to guarantee a common understanding of ‘Good Ecological Status’ at a European level. An intercalibration exercise was carried out within the framework of different Geographical Intercalibration Groups (GIGs), each composed of a group of countries that share similar river types and have a discrete geographical range. By means of the intercalibration exercise, common European boundaries were proposed for river invertebrate assessment methods within each GIG. The purpose of this study was to validate the boundaries proposed for the formal intercalibration exercise. A benchmark data set was used, which comprised data, collected in different European countries that satisfied WFD requirements. The data set included a set of reference sites and provided evidence of a high degree of comparability among countries. The STAR Intercalibration Common Metric index (STAR_ICMi) was calculated for benchmark samples and was selected as the index in which national assessment boundaries were expressed. It was applied for the intercalibration exercise in two GIGs. For the STAR_ICMi, the coefficient of variation was also calculated, demonstrating a comparable variability with indices that are based on species level identification. A fixed percentile of reference samples STAR_ICMi values was selected as the boundary between High and Good status. The range from this fixed percentile to the lowest possible value was divided into four equal parts to obtain the remaining class boundaries. The resulting High/Good and Good/Moderate boundaries were compared to the boundaries proposed by GIGs and proved to be in line with those defined in the intercalibration exercise. Even if, for the intercalibration exercise, some procedures to check the Member States (MS) data sets where put into practice, it is the responsibility of each state to guarantee the WFD compliancy of their reference conditions and methods. Accordingly, the process of validation explained in this article, or similar ones, can be an important step forward and demonstrate the comparability of the actual boundaries.     

Assessing the “Short Mental Distance” in Eco‐Industrial Networks

Like many economic exchanges, industrial symbiosis (IS) is thought to be influenced by social relationships and shared norms among actors in a network. While many implicit references to social characteristics exist throughout the literature, there have been few explicit attempts to operationalize and measure the concepts. The “short mental distance,”“trust,”“openness,” and “communication” recorded among managers in Kalundborg, Denmark, set a precedent for examining and encouraging social interactions among key personnel in the dozens of eco‐industrial networks around the world. In this article we explore the relationships among various aspects of social embeddedness, social capital, and IS. We develop a conceptual framework and an approach using quantitative and qualitative methods to identify and measure these social characteristics, including social network structure, communication, and similarities in norms and conceptions of waste, and apply them in an industrial network in Nanjangud, South India. The findings suggest that there is a fairly high level of shared norms about dealing with waste—the “short mental distance”—in this network, but by‐product transactions are only weakly correlated with the structure and content of communication among managers. Replication of this approach can increase the understanding and comparability of the role of social characteristics in eco‐industrial activities around the world.     

Improving feature detection and analysis of surface-enhanced laser desorption/ionization-time of flight mass spectra

Discovering valid biological information from surface-enhanced laser desorption/ionization-time of flight mass spectrometry (SELDI-TOF MS) depends on clear experimental design, meticulous sample handling, and sophisticated data processing. Most published literature deals with the biological aspects of these experiments, or with computer-learning algorithms to locate sets of classifying biomarkers. The process of locating and measuring proteins across spectra has received less attention. This process should be tunable between sensitivity and false-discovery, and should guarantee that features are biologically meaningful in that they represent chemical species that can be identified and investigated. Existing feature detection in SELDI-TOF MS is not optimal for acquiring biologically relevant data. Most methods have so many user-defined settings that reproducibility and comparability among studies suffer considerably. To address these issues, we have developed an approach, called simultaneous spectrum analysis (SSA), which (i) locates proteins across spectra, (ii) measures their abundance, (iii) subtracts baseline, (iv) excludes irreproducible measurements, and (v) computes normalization factors for comparing spectra. SSA uses only two key parameters for feature detection and one parameter each for quality thresholds on spectra and peaks. The effectiveness of SSA is demonstrated by identifying proteins differentially expressed in SELDI-TOF spectra from plasma of wild-type and knockout mice for plasma glutathione peroxidase. Comparing analyses by SSA and CiphergenExpress Data Manager 2.1 finds similar results for large signal peaks, but SSA improves the number and quality of differences betweens groups among lower signal peaks. SSA is also less likely to introduce systematic bias when normalizing spectra.     

Correlation analysis of external RNA controls reveals its utility for assessment of microarray assay

Quality control of a microarray experiment has become an important issue for both research and regulation. External RNA controls (ERCs), which can be either added to the total RNA level (tERCs) or introduced right before hybridization (cERCs), are designed and recommended by commercial microarray platforms for assessment of performance of a microarray experiment. However, the utility of ERCs has not been fully realized mainly due to the lack of sufficient data resources. The US Food and Drug Administration (FDA)-led community-wide Microarray Quality Control (MAQC) study generates a large amount of microarray data with implementation of ERCs across several commercial microarray platforms. The utility of ERCs in quality control by assessing the ERCs’ concentration-response behavior was investigated in the MAQC study. In this work, an ERC-based correlation analysis was conducted to assess the quality of a microarray experiment. We found that the pairwise correlations of tERCs are sample independent, indicating that the array data obtained from different biological samples can be treated as technical replicates in analysis of tERCs. Consequently, the commonly used quality control method of applying correlation analysis on technical replicates can be adopted for assessing array performance based on different biological samples using tERCs. The proposed approach is sensitive to identifying outlying assays and is not dependent on the choice of normalization method.     

REBECCA databases: experiences from compilation and analyses of monitoring data from 5,000 lakes in 20 European countries

Chemical and biological data from more than 5,000 lakes in 20 European countries have been compiled into databases within the EU project REBECCA. The project’s purpose was to provide scientific support for implementation of the EU Water Framework Directive (WFD). The databases contain the biological elements phytoplankton, macrophytes, macroinvertebrates and fish, together with relevant chemistry data and station information. The common database strategy has enabled project partners to perform analyses of chemical–biological relationships and to describe reference conditions for large geographic regions in Europe. This strategy has obvious benefits compared with single-country analyses: results will be more representative for larger European regions, and the statistical power and precision will be larger. The high number of samples within some regions has also enabled analysis of type-specific relationships for several lake types. These results are essential for the intercalibration of ecological assessment systems for lakes, as required by the WFD. However, the common database approach has also involved costs and limitations. The data process has been resource-demanding, and the requirements for a flexible database structure have made it less user-friendly for project partners. Moreover, there are considerable heterogeneities among datasets from different countries regarding sampling methods and taxonomic precision; this may reduce comparability of the data and increase the uncertainty of the results. This article gives an overview of the contents and functions of the REBECCA Lakes databases, and of our experiences from constructing and using the databases. We conclude with recommendations for compilation of environmental data for future international projects.     

Presence-absence versus presence-only modelling methods for predicting bird habitat suitability

Habitat suitability models can be generated using methods requiring information on species presence or species presence and absence. Knowledge of the predictive performance of such methods becomes a critical issue to establish their optimal scope of application for mapping current species distributions under different constraints. Here, we use breeding bird atlas data in Catalonia as a working example and attempt to analyse the relative performance of two methods: the Ecological Niche factor Analysis (ENFA) using presence data only and Generalised Linear Models (GLM) using presence/absence data. Models were run on a set of forest species with similar habitat requirements, but with varying occurrence rates (prevalence) and niche positions (marginality). Our results support the idea that GLM predictions are more accurate than those obtained with ENFA. This was particularly true when species were using available habitats proportionally to their suitability, making absence data reliable and useful to enhance model calibration. Species marginality in niche space was also correlated to predictive accuracy, i.e. species with less restricted ecological requirements were modelled less accurately than species with more restricted requirements. This pattern was irrespective of the method employed. Models for wide‐ranging and tolerant species were more sensitive to absence data, suggesting that presence/absence methods may be particularly important for predicting distributions of this type of species. We conclude that modellers should consider that species ecological characteristics are critical in determining the accuracy of models and that it is difficult to predict generalist species distributions accurately and this is independent of the method used. Being based on distinct approaches regarding adjustment to data and data quality, habitat distribution modelling methods cover different application areas, making it difficult to identify one that should be universally applicable. Our results suggest however, that if absence data is available, methods using this information should be preferably used in most situations.     

Comprehensive evaluation of protein structure alignment methods: scoring by geometric measures

We report the largest and most comprehensive comparison of protein structural alignment methods. Specifically, we evaluate six publicly available structure alignment programs: SSAP, STRUCTAL, DALI, LSQMAN, CE and SSM by aligning all 8,581,970 protein structure pairs in a test set of 2930 protein domains specially selected from CATH v.2.4 to ensure sequence diversity. We consider an alignment good if it matches many residues, and the two substructures are geometrically similar. Even with this definition, evaluating structural alignment methods is not straightforward. At first, we compared the rates of true and false positives using receiver operating characteristic (ROC) curves with the CATH classification taken as a gold standard. This proved unsatisfactory in that the quality of the alignments is not taken into account: sometimes a method that finds less good alignments scores better than a method that finds better alignments. We correct this intrinsic limitation by using four different geometric match measures (SI, MI, SAS, and GSAS) to evaluate the quality of each structural alignment. With this improved analysis we show that there is a wide variation in the performance of different methods; the main reason for this is that it can be difficult to find a good structural alignment between two proteins even when such an alignment exists. We find that STRUCTAL and SSM perform best, followed by LSQMAN and CE. Our focus on the intrinsic quality of each alignment allows us to propose a new method, called "Best-of-All" that combines the best results of all methods. Many commonly used methods miss 10-50% of the good Best-of-All alignments. By putting existing structural alignments into proper perspective, our study allows better comparison of protein structures. By highlighting limitations of existing methods, it will spur the further development of better structural alignment methods. This will have significant biological implications now that structural comparison has come to play a central role in the analysis of experimental work on protein structure, protein function and protein evolution.     

A review of methods for analysing spatial and temporal patterns in coastal water quality

Coastal environments contain some of the marine world's most important ecosystems and represent significant resources for human industry and recreation. Water quality in the coastal environment is extremely important for a number of reasons from the protection of marine organisms and the well being of marine ecosystems to the health of people in the region and the safety of industries such as aquaculture. As a result it is essential that environmental health in coastal environments is monitored. Traditional monitoring methods include assessment of biological indices or direct measurements of water quality, which are based on in situ data collection and hence are often spatially or temporally limited. Remote sensing imagery is increasingly used as a rich source of spatial information, providing more detailed coverage then other methods. But the complexity of information in the imagery requires new analysis techniques that allow us to identify the components and possible causes of spatial and temporal variability.This paper presents a review of methods to analyse spatial and temporal variations in remote sensing data of coastal water quality and discusses and compares these methods and the outcomes they achieve. Selected techniques are illustrated by using a sample dataset of MODIS chlorophyll-a imagery. We consider classification methods (cluster analysis, discriminant analysis) that may be used in exploratory, confirmatory and predictive ways, methods that summarize and identify patterns within complex datasets (factor analysis, principal components analysis, self-organizing maps), and techniques that explicitly analyse spatial relationships (the semivariogram and geographically weighted regression). Each technique has a different purpose and addresses different questions. This review identifies how these methods can be utilized to address water quality variability in order to foster a wider application of such techniques for coastal water quality assessment and monitoring.     

The Joint Committee for Traceability in Laboratory Medicine (JCTLM): a global approach to promote the standardisation of clinical laboratory test results

Clinical laboratories are moving towards global standardisation to produce equivalent test results across space and time. Standardisation allows use of evidence-based medicine, eliminates the need of method-specific reference intervals, decision levels and cut-offs, and can be achieved by application of metrological principles. For example, in vitro diagnostics (IVD) manufacturers can make kit calibrators traceable to internationally recognised reference materials and reference methods.The first step towards standardisation is to identify appropriate reference materials and methods. This has been undertaken by a new international consortium, the Joint Committee for Traceability in Laboratory Medicine (JCTLM), formed in 2002. It brings together experts representing the clinical laboratory profession, government agencies, and manufacturers, to promote international comparability, reliability, and equivalence of measurement results in clinical laboratories for the purpose of improving healthcare. Through the efforts of the JCTLM, manufacturers are able to assign values to kit calibrators with consistency using appropriate higher order reference materials and methods, and traceability flowcharts, according to ISO Standards to ensure accuracy of test results and to promote assay performance harmonisation. Users of assay kits can assess suitability of calibrators on the basis of acceptable reference materials and/or methods identified by the JCTLM. The JCTLM exemplifies the dynamic nature of clinical laboratory medicine, the inherent spirit of cooperation among professionals in this scientific field, and the international desire to strive for the highest level of clinical laboratory practice for the benefit of patients.     

基于稳定氧同位素确定植物水分来源不同方法的比较

利用稳定同位素技术确定植物水分来源,对提高生态水文过程的认识和对干旱半干旱区的生态管理至关重要。目前基于稳定同位素技术确定植物水分来源的方法众多,但不同方法之间对比的研究较少。本研究基于原位样品采集,室内实验测试,利用直接对比法、多元线性混合模型(IsoSource)、贝叶斯混合模型(MixSIR、MixSIAR)和吸水深度模型分析植物水分来源,并对比各方法的优缺点。结果表明:相对于多元线性混合模型(IsoSource)而言,贝叶斯混合模型(MixSIR、MixSIAR)具有更好的水源区分性能,但对数据要求较高,且植物木质部水和潜在水源同位素组成的标准差越小,模型运行结果的可信度更高。本研究中贝叶斯混合模型(MixSIR)为最优解。在利用稳定氢氧同位素技术确定植物水分来源时,可先通过直接对比法定性判断植物可能利用的潜在水源,然后再用多元线性混合模型(IsoSource)、贝叶斯混合模型(MixSIR、MixSIAR)计算出各潜在水源对植物的贡献率和贡献范围,必要时可评估模型性能,选择出最优模型,定量分析植物的水分来源。若植物主要吸收利用不同土层深度的土壤水,可结合吸水深度模型计算出植物...     

Bayesian Network Reconstruction Using Systems Genetics Data: Comparison of MCMC Methods

Reconstructing biological networks using high-throughput technologies has the potential to produce condition-specific interactomes. But are these reconstructed networks a reliable source of biological interactions? Do some network inference methods offer dramatically improved performance on certain types of networks? To facilitate the use of network inference methods in systems biology, we report a large-scale simulation study comparing the ability of Markov chain Monte Carlo (MCMC) samplers to reverse engineer Bayesian networks. The MCMC samplers we investigated included foundational and state-of-the-art Metropolis–Hastings and Gibbs sampling approaches, as well as novel samplers we have designed. To enable a comprehensive comparison, we simulated gene expression and genetics data from known network structures under a range of biologically plausible scenarios. We examine the overall quality of network inference via different methods, as well as how their performance is affected by network characteristics. Our simulations reveal that network size, edge density, and strength of gene-to-gene signaling are major parameters that differentiate the performance of various samplers. Specifically, more recent samplers including our novel methods outperform traditional samplers for highly interconnected large networks with strong gene-to-gene signaling. Our newly developed samplers show comparable or superior performance to the top existing methods. Moreover, this performance gain is strongest in networks with biologically oriented topology, which indicates that our novel samplers are suitable for inferring biological networks. The performance of MCMC samplers in this simulation framework can guide the choice of methods for network reconstruction using systems genetics data.     

A starter kit for point-localization super-resolution imaging

Super-resolution fluorescence imaging can be achieved through the localization of single molecules. By using suitable dyes, optical configurations, and software, it is possible to study a wide variety of biological systems. Here, we summarize the different approaches to labeling proteins. We review proven imaging modalities, and the features of freely available software. Finally, we give an overview of some biological applications. We conclude by synthesizing these different technical aspects into recommendations for standards that the field might apply to ensure quality of images and comparability of algorithms and dyes.