An aspect of microbiology research in New Zealand: the pursuit of water quality

World Journal of Microbiology and Biotechnology - The problems in monitoring and assessing water quality that must be overcome most urgently are associated with the development of appropriate,...     

External quality assessment in gynaecological cytology: The Trent Region experience

A Department of Health Executive Letter stated in 1998 that the principal function of external quality assessment (EQA) is educational. Subsequently, in England, it has no longer been acceptable to assess performance in gynaecological cytology by proficiency testing. This paper describes the EQA scheme in gynaecological cytology that has been run by the Trent Regional Gynaecological Pathology Quality Assurance Group for the NHS Cervical Screening Programme (NHSCSP) since 1998. It conforms as closely as possible to the recommendations published by the Department of Health Working Group on Histopathology EQA Accreditation, and replaced the national proficiency testing protocol. The educational value of the scheme is derived predominantly from a numerical score which provides confidential and quantitative feedback to all participants. Personal performance monitoring occurs as a secondary function. For primary screeners and checkers, this is based purely on the distinction between negative, inadequate and abnormal smears. For pathologists, personal performance monitoring also includes grading of abnormalities. The EQA has been designed so that all professional groups participate in a manner that closely mimics normal practice. Only slides that have achieved an 80% consensus amongst participants are used in the EQA. Substandard performance has been defined as those participants with scores falling below the 2.5%ile. The paper describes the EQA in detail and illustrates its use by means of the second round results. The EQA protocol developed within Trent and described in this paper has contributed to proposals contained in the current national EQA in gynaecological cytology for the NHSCSP. In particular this paper highlights the effectiveness of the scoring system contained within the Trent and National EQA protocols.     

An aspect of microbiology research in New Zealand: the pursuit of water quality

The problems in monitoring and assessing water quality that must be overcome most urgently are associated with the development of appropriate, simple methods for detecting living but not necessarily growing indicator and pathogenic microorganisms. These methods will allow us to assess and monitor water quality, understand the survival and distribution of microbial contaminants and truly assess the health implications of their presence in water.     

Duplicate split samples for internal quality control in routine water microbiology

In the microbiological examination of water, indicator organisms are sought by membrane filtration of 100-ml sub-samples of water. The same sample cannot be examined twice but the use of split samples, where two 100-ml sub-samples from the same batch are processed, has been explored. Binomial theory was used to determine the 95% confidence intervals for the results obtained. Two sets of 50 results were assessed by the method and the resulting control charts are illustrated.     

External quality assessment of flow cytometric HLA-B27 typing

A biannual external quality assurance (EQA) scheme for flow cytometric typing of the HLA-B27 antigen is operational in The Netherlands and Belgium since 1995. We report here on the results of the first seven send-outs to which 36 to 47 laboratories participated. With the send-out, four specimens from blood bank donors, who had been typed for HLA Class I antigens by complement-dependent cytotoxicity, were distributed. Subtyping of the HLA-B27 allele was performed by PCR-SSP. Ten samples were HLA-B27(pos) (all HLA-B*2705) and 18 were HLA-B27(neg). For flow cytometry, the most widely monoclonal antibody (MoAb) used was FD705, followed by GS145.2 and ABC-m3. The majority of laboratories used more than 1 anti-HLA-B27 MoAb for typing. The HLA-B27(pos) samples were correctly classified as positive by the large majority of participants (median 95%; range 85% to 100% per send out); some participants considered further typing necessary and misclassification as negative was only sporadically seen. The classification of HLA-B27(neg) samples as negative was less straightforward. Ten samples were correctly classified as such by 97% (82% to 100%) of the participants, whereas 64% (range 53% to 70%) of the participants classified the remaining eight samples as HLA-B27(neg). There was no significant prevalence of a particular HLA-B allele among these eight "poor concordancy" samples as compared to the ten "good concordancy" samples. Inspection of the reactivity patterns of the individual MoAb with HLA-B27(neg) samples revealed that ABC-m3 showed very little cross-reactivity apart from its well-known cross-reactivity with HLA-B7, whereas the cross-reactivity patterns of GS145.2 and FD705 were more extensive. The small sample size (n = 18) and the distribution of HLA-B alleles other than HLA-B27 did not allow assignment of specificities to these cross-reactions. Finally, we showed that standardized interpretation of the combined results of two anti-HLA-B27 MoAb reduced the frequency of false-positive conclusions on HLA-B27(neg) samples. In this series, the lowest frequency of false-positive assignments was observed with the combination of the FD705 and ABC-m3 MoAb.     

Quantifying uncertainties in biologically-based water quality assessment: A pan-European analysis of lake phytoplankton community metrics

Lake phytoplankton are adopted world-wide as a sensitive indicator of water quality. European environmental legislation, the EU Water Framework Directive (WFD), formalises this, requiring the use of phytoplankton to assess the ecological status of lakes and coastal waters. Here we provide a rigorous assessment of a number of proposed phytoplankton metrics for assessing the ecological quality of European lakes, specifically in response to nutrient enrichment, or eutrophication, the most widespread pressure affecting lakes. To be useful indicators, metrics must have a small measurement error relative to the eutrophication signal we want them to represent among lakes of different nutrient status. An understanding of variability in metric scores among different locations around a lake, or due to sampling and analytical variability can also identify how best this measurement error is minimised.To quantify metric variability, we analyse data from a multi-scale field campaign of 32 European lakes, resolving the extent to which seven phytoplankton metrics (including chlorophyll a, the most widely used metric of lake quality) vary among lakes, among sampling locations within a lake and through sample replication and processing. We also relate these metrics to environmental variables, including total phosphorus concentration as an indicator of eutrophication.For all seven metrics, 65–96% of the variance in metric scores was among lakes, much higher than variability occurring due to sampling/sample processing. Using multi-model inference, there was strong support for relationships between among-lake variation in three metrics and differences in total phosphorus concentrations. Three of the metrics were also related to mean lake depth. Variability among locations within a lake was minimal (<4%), with sub-samples and analysts accounting for much of the within-lake metric variance. This indicates that a single sampling location is representative and suggests that sub-sample replication and standardisation of analyst procedures should result in increased precision of ecological assessments based upon these metrics.For three phytoplankton metrics being used in the WFD: chlorophyll a concentration, the Phytoplankton Trophic Index (PTI) and cyanobacterial biovolume, >85% of the variance in metric scores was among-lakes and total phosphorus concentration was well supported as a predictor of this variation. Based upon this study, we can recommend that these three proposed metrics can be considered sufficiently robust for the ecological status assessment of European lakes in WFD monitoring schemes.     

Alternative statistical parameter for high-throughput screening assay quality assessment

High-throughput screening is an essential process in drug discovery. The ability to identify true active compounds depends on the high quality of assays and proper analysis of data. The Z factor, presented by Zhang et al. in 1999, provides an easy and useful summary of assay quality and has been a widely accepted standard. However, as data analysis has undergone much improvement recently, the assessment of assay quality has not evolved in parallel. In this article, the authors study the implications of Z factor values under different conditions and link the Z factor with the power of discovering true active compounds. They discuss the different interpretations of Z factor depending on error distributions and advocate direct analysis of power as assay quality assessment. They also propose that in estimating assay quality parameters, adjustments in data analysis should be taken into account. Studying the power of identifying true "hits" gives a more direct interpretation of assay quality and may provide guidance in assay optimization on some occasions.     

蒲河流域河流生境质量综合评价及其与水质响应关系

河流生境是河流生物赖以生存的环境,是维持河流生态完整性、维护河流健康的重要因素。本文结合蒲河流域环境特点,运用层次分析法建立了蒲河流域河流生境质量评价体系,对流域内25个河段的生境质量状况进行了综合评价,并进一步分析了河流生境综合评价指数与河流水质的相关关系。结果表明:(1)蒲河流域25个河段的生境质量状况差异显著,其中1个河段的生境质量等级为好,5个河段为较好等级,16个河段为一般等级,3个河段为较差等级。(2)生境综合评价指数与TP、NH4+-N、CODCr呈负相关,生境质量评价体系中其他指标也与水质指标具有相关性,表明生境质量是影响水质的重要因素。     

Assessment of surface water quality in Legedadie and Dire catchments,Central Ethiopia,using multivariate statistical analysis

The quality of surface water in an area could be determined both by anthropogenic actions and natural processes. The current study assessed surface water quality in Legedadie and Dire catchments that cover a total area of 285 km2 in Central Ethiopia northeast of the nation’s capital Addis Ababa and within close proximity (20-30 m) from this city.. Accordingly, Addis Ababa is, and will continue to be, the major beneficiary of the the catchments which are in fact the primary sources of potable water supply to the city. Despite its potential ecosystem benefits, the catchment area was seriously affected by the rapid socioeconomic development phenomena that had been taking place in and around the city over the previous six decades. As a result, the catchment water resources are characterized by decades of deterioration because of severe pollution problems directly associated with mismanagement of natural resources coupled with other several factors. Hence, the current study was sought to examine the temporal and spatial determinants of catchment water pollutants. To that end, 14 water quality monitoring stations were selected and set up both in upstream and downstream parts of six rivers and two reservoirs. The water samples collected from different sites were monitored for 30 standard water quality parameters including nutrients, inorganic variable, and trace metals. Seasonal data were then measured for the 30 parameters monitored across two seasons (summer and autumn) over a two-year period (June 2014 – November 2015). The complex two-year seasonal data matrix that comprised of 3,660 observations was treated using multivariate statistical techniques: cluster analysis (CA), factor analysis/principal components (FA/PCA), and discriminant analysis (DA). CA successfully classified both the temporal (summer, autumn, and summer predominant) and spatial (natural, agricultural, urban, and mixed) clusters of water quality monitoring sites. Dimension reduction from FA/PCA was not as substantial as expected since it enabled only30% reduction from the original data matrix. On the other hand, DA procedures demonstrated the best result regarding data reduction and pattern recognition in both temporal and spatial analysis. It extracted data significantly and provided 5 parameters (Temp, pH, DO, salinity, and TN) to afford 96.8% right allocations during temporal analysis and only 7 parameters (pH, Turbidity, TN, Total hardness, Pb, Fe, and Cu) to yield 85.2% right allocations during the spatial analysis.Thus, these water quality parameters were most significant for seasonal and spatial water quality variation in the catchment. Therefore, DA enabled a significant reduction of the dimension of the original data matrix into a few significant parameters that affect water quality. In conclusion, the study demonstrated that multivariate statistical techniques are very useful for analysis and interpretation of complex water quality data sets for efficient assessment of water quality and identification of pollution sources as well as an effective understanding of the space and time effects of water quality.     

External quality assessment of cytomegalovirus DNA detection on dried blood spots

Background  

Testing for viral DNA in neonatal blood dried on paper (DBS) has proved a valid means of diagnosing congenital CMV infection with both clinical and epidemiological relevance. To assess the quality of the detection of CMV-DNA on DBS in laboratories performing this test a proficiency panel consisting of nine samples with two blood spots on each filter paper was produced and distributed. Six samples were derived from whole blood, negative for CMV DNA and antibody, and spiked with cell-grown CMV Towne in various concentrations (7.3 × 10² - 9.6 × 10⁵ copies/ml), one was a CMV positive clinical specimen (3.9 × 10⁶ copies/ml), and two samples were CMV-negative whole blood.     

The need for biological assessment of water quality: Australian perspective

Abstract Biological assessment of water quality in Australia is entering a stage of rapid development largely because of the inclusion of biological indicators in water quality guidelines and growing concern for ecological values. Approaches to water quality assessment include toxicity testing, use of biomarkers and several methods using community structure. For assessment diverse organisms such as fish, algae and (the most commonly used) macro-invertebrates are used. Interaction of data analysis with methods of data collection requires co-ordinated research on both fronts. Recent developments in the use of multivariate statistics to produce models for predicting water quality are likely to be useful in Australia. Much innovative work is still needed in Australia on the use of algae and fish, defining tolerance categories and establishing monitoring programmes performed in time-frames equivalent to those in use for physical and chemical methods.     

Anthropogenic impact on water quality of Chilika lagoon RAMSAR site: a statistical approach

This paper investigated the spatio-temporal variability of water quality parameters (transparency, salinity, dissolved oxygen, nutrients viz. NH₃-N, NO₂-N, NO₃⁻-N, PO₄³-P, total nitrogen, total phosphorous and chlorophyll-a) in Chilika lagoon during 2001–2003 in order to better understand its ecological characteristics. Marked spatial and seasonal variations were detected with respect to almost all parameters studied. Northern sector of the lagoon is more affected by the anthropogenic stress from the catchments than the southern sector. Addition of nitrogen and phosphorous compounds to the lagoon mainly occurred through the drainage from agricultural lands and river run off during the early months of paddy cultivating seasons. Phytoplankton productivity of the lagoon was nitrogen limited, as suggested by nitrogen to phosphorous ratio. Processes affecting the water quality of the lagoon system included agricultural drainage, sewage intrusion, macrophyte litter fall and exchange of water between lagoon and the sea (Bay of Bengal). Further in depth study pertaining to quantification of exogenous material input and their disposal is recommended to ensure proper management of the lagoon and its resources.     

The issue of considering water quality in life cycle assessment of water use

The International Journal of Life Cycle Assessment - Available water-use impact assessment methods provide insight into the potential impacts of water use. As water-use impact assessment models...     

Local quality assessment in homology models using statistical potentials and support vector machines

In this study, we address the problem of local quality assessment in homology models. As a prerequisite for the evaluation of methods for predicting local model quality, we first examine the problem of measuring local structural similarities between a model and the corresponding native structure. Several local geometric similarity measures are evaluated. Two methods based on structural superposition are found to best reproduce local model quality assessments by human experts. We then examine the performance of state-of-the-art statistical potentials in predicting local model quality on three qualitatively distinct data sets. The best statistical potential, DFIRE, is shown to perform on par with the best current structure-based method in the literature, ProQres. A combination of different statistical potentials and structural features using support vector machines is shown to provide somewhat improved performance over published methods.     

参加CAP真菌检验室间质评结果分析

目的能力比对检验(Proficiency testing,PT)是室间质评的重要方案,通过参加美国病理家学会(College of American Pathologist,CAP)能力比对检验,监控实验室检验能力,确保检测结果的准确性、可重复性和可比性,促进实验室质量改进。方法中国医学科学院北京协和医学院北京协和医院检验科实验室于2009年参加CAP真菌检测能力验证活动。实验室收到标本后,按照常规真菌标本进行真菌学检查和免疫学测定,在规定的时间内将检测结果回报给CAP。CAP在同方法组内对检测结果进行评估,并提供所有参与实验室的结果统计报告。结果截至目前完成2009年3次共17份标本,回报结果正确率:F-A和F-C为100%,F-B为80%,结果评价均为满意。结论通过参加CAP能力比对检验,实现对检验结果准确性的持续性监测,提高真菌感染实验室诊断水平。     

The principles of radiological quality assessment of water resources

In the paper the main approaches to radiation safety of water objects have been analyzed. It is shown that radiation safety requirements for drinking water, fixed in the Rules and Regulations on radiation safety, do not ensure radiation safety of water objects used for the complex national economy needs. Application of the conservatism principle (choosing of the worst variant) for radiation safety ensuring is considered and proved. On the base of this principle the model is developed comparing the anthropocentric (sanitary--hygienic) with ecological (biota) principles for ensuring safety of water objects. It is proved, that the application of the Water Radiation Safety Rules currently in force, based on the norms of dose quotas, reserved for regulation of nuclear power plants and industry impact, ensures safety of the water ecological systems.     

基于组合可拓综合分析法的鄱阳湖流域水质富营养化评价

长期跟踪定位评价湖泊的水质营养化程度,对于实现地区水功能具有重要意义。针对评价方法中指标选取的可行性、单一性、权重赋值的主观随意性以及水质变化的模糊性、随机性、动态性和生物指示性等特点,采用了可拓综合评价法和浮游生物调查与室内测定法相结合,构建了组合可拓综合分析法,一方面利用可拓综合分析法对鄱阳湖流域5个代表性观测站点的10年的年均（每2年）观测数据进行评价;另一方面通过浮游生物指示法对该5个站点的水质进行富营养化评价,以生物指示评价法所得等级与可拓综合分析法评定等级吻合的最多次数所对应等级作为组合可拓综合评价法的评价等级。结果表明：（1）自2006年以来鄱阳湖流域水体富营养化水平较为平稳,总体呈好转势态。2010年有4个观测点的水体达到富营养化程度,而在2014年湖区的蛤蟆石和鄱阳水质略有所改善,达到轻富营养化程度,都昌、康山、星子站点的水体为中营养化,改善幅度较大,水质较好;（2）从湖区的地理区位看,鄱阳湖湖区的南部和西部的水质富营养化程度总体上要好于北部、东部和中部湖区,水质富营养化程度表现为区域的不均匀性。     

Bioluminescent methods of analysis in microbiology

The prospects for application of bioluminescent ATP-metry in microbiology are considered. A bioluminescent assay is proposed to analyse biomass by measuring the content of intracellular ATP by means of immobilized firefly luciferase after ATP extraction with dimethylsulfoxide. The assay can be used for plotting the growth curves of microorganisms and for determining the sensitivity of microorganisms to antibiotics. The detection limit of the assay is 700 cells per ml of the measured solution.     

Monitoring laboratory performance by statistical analysis of rescreening cervical smears

The rescreening of cervical cytology smears, although inadequate both for checking the reliability of an individual screener and for the detection of false negatives, nonetheless represents an indispensable tool for assessing morphologic diagnostic criteria and monitoring laboratory performance. Interobserver and intraobserver concordance in a given laboratory determine the reliability of diagnostic criteria and disclose the possibility of improving diagnostic consistency. The various aspects of rescreening are discussed, and a simple statistical procedure for a quantitative comparison of screening reproducibility is described. This procedure, with calculation of phi-values and mean prevalence rates, was applied to screening and rescreening data from the Cyt-U-Universitair Cytology Laboratory from 1978 to 1983, in which the morphologic findings in each smear were recorded in detail using the QISO (Quality, Infection, Squamous epithelium and Other abnormalities) coding. The reproducibility of the reported presence of endocervical cells not only steadily improved over the years assessed, but also reached a sufficiently high level that diagnostic variability should not hamper its clinical utility. The same was true of the diagnosis of Trichomonas infection and moderate atypia of squamous cells. On the other hand, the reproducibility of the diagnosis of endometrial cells in smears did not significantly improve. However, since the intraobserver concordance on this criterion was good, it seems likely that the definitions of screeners in this area can still be brought into closer agreement. Conversely, the diagnosis of "abnormal endocervical cells" had such a high level of variability even at the intraobserver level as to question its use as a diagnostic criterion. Similar variability was seen in the distinction between atypical squamous metaplasia and mild dysplasia. Use of this statistical technique for the quality control of cytologic diagnoses frees that assessment from histopathologic control, which does not address the problem of variation within the cytologic or histologic diagnoses themselves.