Identification of hot spots within harbour sediments through a new cumulative hazard index. Case study: Port of Bari,Italy

While numerous quality guidelines unquestionably drive the management of harbour sediments, port managers increasingly require easy-to-use tools supporting them in assessing the sediment quality. In this work, a new hazard index, named cumulative Normalized and Weighted Average Concentration (c_NWAC), is proposed, considering the concentrations of main hazardous, toxic and bio-accumulative sediment contaminants. This index is an upgraded version of the previously introduced NWAC index, which considered only the metal concentrations. The c_NWAC values range from 0 to 10 scores, and their visualization on a colour base code map leads to an easy identification of hotspots. The applicability of the new index was verified using a dataset derived from the analyses of 42 samples collected at different depths of the seabed of the Port of Bari (Italy). The concentrations of 58 parameters were considered, namely 11 metals and metalloids, 17 congeners of polychlorinated biphenyls (PCBs), 16 congeners of polycyclic aromatic hydrocarbons (PAHs), further 11 organic micropollutants, total organic carbon (TOC) and nutrients (N_tot, P_tot). For the study area, the obtained c_NWAC values resulted well correlated to the corresponding values of the commonly used mean Effects Range Median quotient (mERMq), and similar hazard categories were developed for the new index, even if the latter do not necessarily explain the real sediment toxicity, because they were derived from a different sediment dataset and different test species.Moreover, the hazard predictive ability of the new index was verified (with satisfactory results) by testing the considered samples by eco-toxicological assays, using three different biological species, and comparing the obtained results to the corresponding hazard categories developed for c_NWAC.     

Novel scales based on hydrophobicity indices for secondary protein structure

This paper is concerned with a branch of computational biology related to protein prediction and analysis of secondary structure of proteins. Although traditional methods use a simple amino acid composition to predict the secondary structure content, hydrophobicity has been recently found to improve the results in this and several related prediction tasks. To this end, we propose and analyze advantages of two new hydrophobicity index-based scales that incorporate information about long-range interactions along the protein sequence and contrast them with currently used raw hydrophobic index values. We also compare three leading hydrophobicity indices, i.e., Eisenberg's, Fauchere-Pliska's, and Cid's, using the proposed scales. The analysis is performed using fuzzy cognitive maps that quantify the strength of relation between the hydrophobicity scales/indices and the protein content values. A set of empirical tests that involve generation of fuzzy cognitive map models for a set of 200 low homology proteins have been performed. The results show that the secondary structure content along the protein sequence is characterized by about 2.5 times stronger relation with the two proposed hydrophobicity scales when compared with the currently used raw index values. The new scales exhibit stronger relation irrespective of the applied hydrobhobicity indices. Analysis of different scales shows superiority of the Eisenberg's hydrophobicity index, when used with the new scales. In contrast, the Fauchere-Pliska's index is found to perform better when compared with the two other indices when using raw hydrophobic index values that disregard the long-range interactions.     

增强现实技术于洪水风险沟通中的应用

气候变迁,特别是洪水问题给地处三角洲的城市带来了与日俱增的风险。作为应对手段,提出一种整合性的洪水风险管理方法,该方法确保了洪水风险沟通在洪水风险管理战略中的重要地位。洪水的可视化作为洪水风险沟通的一种工具,在改变人们对洪水风险的观念方面有着强大的作用。它可以通过互动的方式,使当地的利益相关者了解洪水的剩余风险和未来风险。其中增强现实技术作为一种可视化手段,它的快速发展与应用为风景园林设计、规划与教育等领域提供了崭新的交互方式。首先,探讨增强现实技术（AR）在洪水风险沟通中的应用现状,并重点关注增强现实技术的2 个关键应用领域：对现场决策的支持和针对高层次设计的可视化与对景观干预的评估。随后,展示一种基于增强现实技术所开发的应用,该款创新性的应用为洪水风险沟通提供了一种轻量化的可视化手段。     

A framework for mapping,visualisation and automatic model creation of signal‐transduction networks

Intracellular signalling systems are highly complex. This complexity makes handling, analysis and visualisation of available knowledge a major challenge in current signalling research. Here, we present a novel framework for mapping signal‐transduction networks that avoids the combinatorial explosion by breaking down the network in reaction and contingency information. It provides two new visualisation methods and automatic export to mathematical models. We use this framework to compile the presently most comprehensive map of the yeast MAP kinase network. Our method improves previous strategies by combining (I) more concise mapping adapted to empirical data, (II) individual referencing for each piece of information, (III) visualisation without simplifications or added uncertainty, (IV) automatic visualisation in multiple formats, (V) automatic export to mathematical models and (VI) compatibility with established formats. The framework is supported by an open source software tool that facilitates integration of the three levels of network analysis: definition, visualisation and mathematical modelling. The framework is species independent and we expect that it will have wider impact in signalling research on any system.     

Application of an unsupervised artificial neural network technique to multivariant surface water quality data

Surface water contamination from agricultural and urban runoff and wastewater discharges from industrial and municipal activities is of major concern to people worldwide. Classical models can be insufficient to visualise the results because the water quality variables used to describe dynamic pollution sources are complex, multivariable, and nonlinearly related. Artificial intelligence techniques with the ability to analyse multivariant water quality data by means of a sophisticated visualisation capacity can offer an alternative to current models. In this study, the Kohonen self-organising feature maps (SOM) neural network was initially applied to analyse the complex nonlinear relationships among multivariable surface water quality variables using the component planes of the variables to determine the complex behaviour of water quality parameters. The dependencies between water quality variables were extracted and interpreted using the pattern analysis visualised in component planes. For further investigation, the k-means clustering algorithm was used to determine the optimal number of clusters by partitioning the maps and utilising the Davies–Bouldin clustering index, leading to seven groups or clusters corresponding to water quality variables. The results reveal that the concentrations of Na, K, Cl, NH₄-N, NO₂-N, o-PO₄, component planes of organic matter (pV), and dissolved oxygen (DO) were significantly affected by seasonal changes, and that the SOM technique is an efficient tool with which to analyse and determine the complex behaviour of multidimensional surface water quality data. These results suggest that this technique could also be applied to other environmentally sensitive areas such as air and groundwater pollution.     

Ecological land suitability analysis through spatial indicators: An application of the Analytic Network Process technique and Ordered Weighted Average approach

Multicriteria-Spatial Decision Support Systems (MC-SDSS) are increasingly popular tools in decision-making processes and in policy making, thanks to their significant new capabilities in the use of spatial or geospatial information.Many spatial problems are complex and require the use of integrated analysis and models. The present paper illustrates the development of a MC-SDSS approach for studying the ecological connectivity of the Piedmont Region in Italy. The MC-SDSS model considers ecological and environmental spatial indicators which are combined by integrating the Multicriteria Decision Aiding (MCDA) technique named Analytic Network Process (ANP) and the Ordered Weighted Average (OWA) approach. The ANP is used for the elicitation of attribute weights while the OWA operator function is used to generate a wide range of decision alternatives for addressing uncertainty associated with interaction between multiple criteria. The usefulness of the approach is illustrated by different OWA scenarios that report the ecological connectivity index on a scale between 0 and 1. The OWA scenarios are intended to quantify the level of risk taking (i.e., optimistic, pessimistic, and neutral) and to facilitate a better understanding of patterns that emerge from decision alternatives involved in the decision-making process.The purpose of the research is to generate a final map representing the ecological connectivity index of each area in the region under analysis, to be used as a decision variable in spatial planning. In particular, by using the resulting index map as a means of analysis, it is possible to identify, for the sake of nature conservation, some critical areas needing mitigation measures. In addition, areas with high ecological connectivity values can be identified and monitoring procedures can therefore be planned. The study concludes highlighting that the applied methodology is an effective tool in providing decision support for spatial planning and sustainability assessments.     

Comparative study of mannose-binding C-type lectin isolated from channel catfish (Ictalurus punctatus) and blue catfish (Ictalurus furcatus)

Mannose-binding C-type lectin (MBL) was isolated from channel catfish (Ictalurus punctatus) NWAC 102 and 103 strains, blue catfish (Ictalurus furcatus) D+B and Rio Grande strains, hybrid catfish (channel catfish female NWAC 103 x blue catfish male D+B) sera, and purified by affinity chromatography from channel catfish Norris strain serum. Reduction of purified channel catfish MBL with 2-ME yielded a single band of 62 kDa by SDS-PAGE and Western blot analysis using guinea pig anti-MBL IgG as primary antibody. Channel catfish NWAC 102 strain, channel catfish NWAC 103 strain and hybrid catfish sera had molecular masses of 63 kDa for MBL. Blue catfish (D+B strain) serum MBL had a molecular mass of 66 kDa. Rio Grande blue catfish serum MBL had a molecular mass of 65 kDa. Amino acid composition analysis (mol%) of the affinity-purified channel catfish MBL found a high content of serine present. Functional binding studies of channel catfish and blue catfish MBLs binding to Edwardsiella ictaluri were done using a dot-immunoblot ELISA method. A dot-immunoblot ELISA binding assay was done to compare nine different strains and species of channel catfish and blue catfish for their levels of serum MBL. Blue catfish had higher levels of MBL than did the various strains of channel catfish tested. MBL could be used as a genetic marker for selection of disease resistance in the different strains of catfish used in aquaculture. This study describes the presence of serum MBL in catfish and evidence for a C-type lectin complement pathway of innate immunity.     

webFOG: A web tool to map genomic features onto genes

A large number of new genomic features are being discovered using high throughput techniques. The next challenge is to automatically map them to the reference genome for further analysis and functional annotation. We have developed a tool that can be used to map important genomic features to the latest version of the human genome and also to annotate new features. These genomic features could be of many different source types, including miRNAs, microarray primers or probes, Chip-on-Chip data, CpG islands and SNPs to name a few. A standalone version and web interface for the tool can be accessed through: http://populationhealth.qimr.edu.au/cgi-bin/webFOG/index.cgi. The project details and source code is also available at http://www.bioinformatics.org/webfog.     

内蒙古草原植被覆盖度遥感估算

以内蒙古锡林浩特市南部中国科学院草原生态系统定位研究站周围的草场为研究对象, 分析比较了统计模型和亚像元分解模型进行草地植被覆盖度(vegetation coverage, VC)遥感估算的适用性。结果表明, 根据Landsat-5 TM影像数据计算的比值植被指数(simple ratio vegetation index, SR)与观测的VC的相关性最高(R² = 0.761); 统计模型和亚像元分解模型生成的VC空间分布特征相似, 但亚像元分解模型得到的VC平均值比统计模型的结果高0.091; 在VC的低值和高值区, 两种方法得到的VC结果相似; 但在VC的中值区, 亚像元模型得到的结果较统计模型的结果偏高。     

Enhancing the performance of hazard indexes in assessing hot spots of harbour areas by considering hydrodynamic parameters

The hazard assessment strategies for harbour areas usually rely on tools able to predict environmental threats posed by contaminated sediments, mostly based on biological and chemical parameters and distinctly less on hydrological factors. Although ports are considered semi-enclosed and low-energy systems with scarce capacity to disperse contaminants to the open sea, the hydrological pattern established within the port basin cannot be neglected, especially when the localisation of hot spots is required for clean-up and remediation actions. In the present study we considered both approaches (biological/chemical and hydrological) for assessing hot spots of harbour areas. In particular, the relationship between the sediment hazard assessment c_NWAC (cumulative Normalized and Weighted Average Concentration) index (which is based on chemical and biological data) and a properly selected hydrodynamic parameter (the bottom shear stress) of the port area was investigated. This study demonstrates that marine currents influence significantly the fine-grained fraction distribution of the surficial sediments, and thus, the spatial and temporal variability of contaminant concentration. The evaluation of hydrodynamic parameters enhances the performance of hazard tools in the localization of areas of most concern and thus a detailed knowledge of the hydrodynamic features of the port seabed is advisable before defining a proper characterisation strategy for the harbour area.     

Application of LANDSAT MSS Digital Image Processing Techniques in Investigation of Aquatic Plant Distribution in Honghu Lake

In this paper an experiment in the application of LANDSAT MSS digital image proces. sing technique to classify the aquatic plants in the Honghu Lake, China, as well as the necessary ground feature spectrum measurement and plant chlorophyll content determination techniques are introduced. In order to obtain the expected computer aided classification result different methods of digital image feature extraction have been tried, namely the ratio transformation, the biomass index transformation and the linear stretching of image intensity. The data from spectrum measurement and chlorophyll content determination were used to distinguish the attributions of different classes of aquatic plant associations from one another by comparing with their spectrum response intensity values on different LANDSAT band images. The original LANDSAT MSS images were digitally rectified by control points to a certain map projection system using a general polynomial approach scheme before the classifying activities, so that the classification result may be transfered to an existing map. In this paper the resulting colourassigued image and the thematic map of Honghu Lakes aquatic plant (association) distribution are included, the areas of different classes of aquatic plants are listed and the reliability of the resulting classification and pattern recognition are analysed. These results will provide useful informations for the investigation of the present situation as well as the historical succession of the Honghu Lake and its aquatic plant distribution, and also for the research works of the lake management.     

Experimental Study of Mobility and Kinetic Characterization of Trace Elements in Contaminated Sediments from a River Basin in Northern Peru

In the Jequetepeque basin (Peru), gold extraction activity has been performed in the last decades, leading to a release of metals and metalloids into the environment. Sediment samples were taken in the vicinity of two mines and analyzed. Extraction of metals and metalloids from sediments was carried out using single extraction procedures, acidic (HNO₃), and complexation (EDTA) leaching, in order to determine the mobility of trace elements. Results indicated that acidic extraction at low pH values increased the leachability of trace elements. EDTA showed a higher bioavailability of metals in sediments than acidic extraction under similar pH conditions because of its greater leaching capacity. This is an important issue in view of risk assessment analysis. The highest extractability was observed for Cd in all sediments with up to 90% of extraction after 1 h. The mobility index analysis indicated that faster kinetic leachability of some trace elements leads to a higher mobility in sediments, especially those near the active gold extraction mine. The ecological risk assessment suggested that the four river sediments were at high and very high risk levels, indicating that sediment contamination is an issue of environmental concern in the Jequetepeque basin of northern Peru.     

Novel application of a quantitative spatial comparison tool to species distribution data

Comparing geographically referenced maps has become an important aspect of spatial ecology (e.g. assessing change in distribution over time). Whilst humans are adept at recognising and extracting structure from maps (i.e. identifying spatial patterns), quantifying these structures can be difficult. Here, we show how the Structural Similarity (SSIM) index, a spatial comparison method adapted from techniques developed in computer science to determine the quality of image compression, can be used to extract additional information from spatial ecological data. We enhance the SSIM index to incorporate uncertainty from the underlying spatial models, and provide a software algorithm to correct for internal edge effects so that loss of spatial information from the map comparison is limited. The SSIM index uses a spatially-local window to calculate statistics based on local mean, variance, and covariance between the maps being compared. A number of statistics can be calculated using the SSIM index, ranging from a single summary statistic to quantify similarities between two maps, to maps of similarities in mean, variance, and covariance that can provide additional insight into underlying biological processes. We demonstrate the applicability of the SSIM approach using a case study of sperm whales in the Mediterranean Sea and identify areas where local-scale differences in space-use between groups and singleton whales occur. We show how novel insights into spatial structure can be extracted, which could not be obtained by visual inspection or cell-by-cell subtraction. As an approach, SSIM is applicable to a broad range of spatial ecological data, providing a novel, implementable tool for map comparison.     

Delimitation of kala-azar risk areas in the district of Vaishali in Bihar (India) using a geo-environmental approach

Remote sensing and geographical information technologies were used to discriminate areas of high and low risk for contracting kala-azar or visceral leishmaniasis. Satellite data were digitally processed to generate maps of land cover and spectral indices, such as the normalised difference vegetation index and wetness index. To map estimated vector abundance and indoor climate data, local polynomial interpolations were used based on the weightage values. Attribute layers were prepared based on illiteracy and the unemployed proportion of the population and associated with village boundaries. Pearson's correlation coefficient was used to estimate the relationship between environmental variables and disease incidence across the study area. The cell values for each input raster in the analysis were assigned values from the evaluation scale. Simple weighting/ratings based on the degree of favourable conditions for kala-azar transmission were used for all the variables, leading to geo-environmental risk model. Variables such as, land use/land cover, vegetation conditions, surface dampness, the indoor climate, illiteracy rates and the size of the unemployed population were considered for inclusion in the geo-environmental kala-azar risk model. The risk model was stratified into areas of "risk"and "non-risk"for the disease, based on calculation of risk indices. The described approach constitutes a promising tool for microlevel kala-azar surveillance and aids in directing control efforts.     

The metal ion theory of ageing: dietary target hazard quotients beyond radicals

Numerous theories of ageing exist and many are interconnected when viewed through a modern integrative biology perspective. Diet provides a link to a large number of the theories that prevail at the molecular levels. In particular, metal ions form key elements of the radical theory along with having established roles in several age-related neurodegenerative disorders. Lifetime exposure to metals has been linked to ageing by contributions to oxidative stress and neurodegenerative disorders. As many foodstuffs contain high levels and diverse profiles of metals, their cumulative effect on ageing warrants investigation. The cumulative level of concern from environmental exposure can be expressed as a dimensionless index of target hazard quotient (THQ) or for known carcinogens, the target cancer risk (TR). This paper posits that a quantifiable relationship exists between ageing and level of concern resulting from cumulated metal exposure; and that this relationship can be used to develop an ageing-related index of concern from chronic metal ion exposure. As individual differences may facilitate or moderate this cumulated exposure, the potential influence on ageing or on the development of neurodegenerative disorders should be included into the model.     

Linkage analysis in tetraploid potato and association of markers with quantitative resistance to late blight (Phytophthora infestans)

We have constructed a partial linkage map in tetraploid potato which integrates simplex, duplex and double-simplex AFLP markers. The map consists of 231 maternal and 106 paternal markers with total map lengths of 990.9?cM and 484.6?cM. The longer of the two cumulative map lengths represents approximately 25% coverage of the genome. In tetraploids, much of the polymorphism between parental clones is masked by `dosage' which significantly reduces the number of individual markers that can be scored in a population. Consequently, the major advantage of using AFLPs – their high multiplex ratio – is reduced to the point where the use of alternative multi-allelic marker types would be significantly more efficient. The segregation data and map information have been used in a QTL analysis of late blight resistance, and a multi-allelic locus at the proximal end of chromosome VIII has been identified which contributes significantly to the expression of resistance. No late blight resistance genes or QTLs have previously been mapped to this location.     

Recent variations in sediment organic carbon content in Lake Soyang (Korea)

Four gravity cores were taken from Lake Soyang, which was created by the construction of an artificial dam in 1973. The variation of organic carbon content of the bottom sediments since the construction was interpreted using a variety of sedimentological and geochemical measurements. Based on the textural properties of sediments and the total organic carbon (TOC) content, it is clear that sediment organic carbon has been deposited very consistently throughout the postconstruction period, except for local sudden inputs caused by summer flooding events near fish farms or farmland areas. The autochthonous input resulting from the enhanced primary production led by phytoplanktons each year is likely to become a major problem at downstream sites within Lake Soyang. The vertical variation of δ¹³C values of sediment organic matter also reflects the fact that the level of autochthonous supply of organic carbon becomes high downstream.An erratum to this article can be found at .     

Optimizing coastal and marine spatial planning through the use of high-resolution benthic sensitivity models

Effective management of coastal and marine resources requires knowledge of how community sensitivity varies spatially. With this in mind, we developed a benthic sensitivity index (SI), based on the distribution and abundance of five ecological groups that can be used to assess community tolerance to organic enrichment and other disturbances. The index, projected as a high-resolution map, ranks communities from those dominated by sensitive and ecologically important species (i.e. low SI values) to those composed mainly of tolerant and/or opportunistic species (i.e., high SI values). Applying our model to a multiple-use case study in southeast Brazil, we were able to show considerable variability in the sensitivity of communities across the study area that was relatively stable over time. This allowed us to evaluate the possible direct (i.e., spatially overlapping) and indirect effects (i.e., cumulative changes to the physical environment) of a range of activities on sensitive and ecologically diverse benthic communities. Our approach and the resulting high-resolution maps hold promise for a range of spatial planning applications, including the development of coastal infrastructure, assessments of the representativeness of marine protected areas and other activities such as the selection of appropriate locations for dredge spoil dumping. Overall, we present a novel and transparent way of extrapolating limited survey data to provide spatial and temporal information on the sensitivity of benthic communities in multiple-use coastal and marine areas.     

基于SolVES模型的关中-天水经济区生态系统文化服务评估

随着人类对于生态系统服务的需求持续增加,生态系统服务的评估逐渐成为研究热点。其中文化服务因其自身的无形性常在研究中被忽视且难以衡量。选取关中-天水经济区为研究区域,应用Sol VES模型并生成5种价值指数地图和价值总和地图来评估该区域生态系统的文化服务。结果表明:审美价值在秦岭山脉和城市公园等区域较高;娱乐价值在娱乐机会较多、交通便利的城市和秦岭北麓区域更高;文化与历史价值集中在历史文化底蕴深厚的城市地区;精神价值在与城市距离较近、有山川分布的森林公园更高。Sol VES模型在大范围区域的应用取得了较好的效果同时为政府进行生态建设和规划提供了科学依据。