Combining Existing Monitoring Sites with a Probability Survey Design-Examples from U.S. EPA’s National Coastal Assessment

U.S. Environmental Protection Agency’s (EPA’s) National Coastal Assessment was envisioned as a research effort led by EPA’s Office of Research and Development to evaluate assessment methods for ecosystem condition monitoring. The program was conducted through strategic partnerships with the coastal states. These states conducted the survey in their waters with a common set of indicators. The resources targeted for initial monitoring were estuarine waters. A flexible probability survey design was used to incorporate, to the extent possible, existing state monitoring program sites. Three criteria were developed to evaluate existing monitoring program sites in the northeastern United States for possible incorporation into the national design: (1) the sites were selected to be representative, (2) the variables sampled at the sites were similar in distribution with variables from a probability design, and (3) the correlation structure of variables was equivalent to that for a probability design. Detailed examples were presented for Long Island Sound water quality sites, New Jersey coastal water quality sites, and Casco Bay, ME, sediment sites to illustrate the approach

Restoring Cystic Fibrosis Transmembrane Conductance Regulator Function Reduces Airway Bacteria and Inflammation in People with Cystic Fibrosis and Chronic Lung Infections

Rationale: Previous work indicates that ivacaftor improves cystic fibrosis transmembrane conductance regulator (CFTR) activity and lung function in people with cystic fibrosis and G551D-CFTR mutations but does not reduce density of bacteria or markers of inflammation in the airway. These findings raise the possibility that infection and inflammation may progress independently of CFTR activity once cystic fibrosis lung disease is established. Objectives: To better understand the relationship between CFTR activity, airway microbiology and inflammation, and lung function in subjects with cystic fibrosis and chronic airway infections. Methods: We studied 12 subjects with G551D-CFTR mutations and chronic airway infections before and after ivacaftor. We measured lung function, sputum bacterial content, and inflammation, and obtained chest computed tomography scans. Measurements and Main Results: Ivacaftor produced rapid decreases in sputum Pseudomonas aeruginosa density that began within 48 hours and continued in the first year of treatment. However, no subject eradicated their infecting P. aeruginosa strain, and after the first year P. aeruginosa densities rebounded. Sputum total bacterial concentrations also decreased, but less than P. aeruginosa. Sputum inflammatory measures decreased significantly in the first week of treatment and continued to decline over 2 years. Computed tomography scans obtained before and 1 year after ivacaftor treatment revealed that ivacaftor decreased airway mucous plugging. Conclusions: Ivacaftor caused marked reductions in sputum P. aeruginosa density and airway inflammation and produced modest improvements in radiographic lung disease in subjects with G551D-CFTR mutations. However, P. aeruginosa airway infection persisted. Thus, measures that control infection may be required to realize the full benefits of CFTR-targeting treatments

Non-parametric class completeness estimators for collaborative knowledge graphs — the case of wikidata

Collaborative Knowledge Graph platforms allow humans and automated scripts to collaborate in creating, updating and interlinking entities and facts. To ensure both the completeness of the data as well as a uniform coverage of the different topics, it is crucial to identify underrepresented classes in the Knowledge Graph. In this paper, we tackle this problem by developing statistical techniques for class cardinality estimation in collaborative Knowledge Graph platforms. Our method is able to estimate the completeness of a class—as defined by a schema or ontology—hence can be used to answer questions such as “Does the knowledge base have a complete list of all {Beer Brands—Volcanos—Video Game Consoles}?” As a use-case, we focus on Wikidata, which poses unique challenges in terms of the size of its ontology, the number of users actively populating its graph, and its extremely dynamic nature. Our techniques are derived from species estimation and data-management methodologies, and are applied to the case of graphs and collaborative editing. In our empirical evaluation, we observe that i) the number and frequency of unique class instances drastically influence the performance of an estimator, ii) bursts of inserts cause some estimators to overestimate the true size of the class if they are not properly handled, and iii) one can effectively measure the convergence of a class towards its true size by considering the stability of an estimator against the number of available instances

Assessing Conservation Values: Biodiversity and Endemicity in Tropical Land Use Systems

Despite an increasing amount of data on the effects of tropical land use on continental forest fauna and flora, it is debatable whether the choice of the indicator variables allows for a proper evaluation of the role of modified habitats in mitigating the global biodiversity crisis. While many single-taxon studies have highlighted that species with narrow geographic ranges especially suffer from habitat modification, there is no multi-taxa study available which consistently focuses on geographic range composition of the studied indicator groups. We compiled geographic range data for 180 bird, 119 butterfly, 204 tree and 219 understorey plant species sampled along a gradient of habitat modification ranging from near-primary forest through young secondary forest and agroforestry systems to annual crops in the southwestern lowlands of Cameroon. We found very similar patterns of declining species richness with increasing habitat modification between taxon-specific groups of similar geographic range categories. At the 8 km2 spatial level, estimated richness of endemic species declined in all groups by 21% (birds) to 91% (trees) from forests to annual crops, while estimated richness of widespread species increased by +101% (trees) to +275% (understorey plants), or remained stable (- 2%, butterflies). Even traditional agroforestry systems lost estimated endemic species richness by - 18% (birds) to - 90% (understorey plants). Endemic species richness of one taxon explained between 37% and 57% of others (positive correlations) and taxon-specific richness in widespread species explained up to 76% of variation in richness of endemic species (negative correlations). The key implication of this study is that the range size aspect is fundamental in assessments of conservation value via species inventory data from modified habitats. The study also suggests that even ecologically friendly agricultural matrices may be of much lower value for tropical conservation than indicated by mere biodiversity value

Fish assemblage associated with aquatic macrophytes bank in mananged lakes of Central Amazon, Amazonas, Brazil

The co-management of fishery resources developed by Amazonian riverine people is concerned with the maintenance of suitable environments for fish stock conservation. This type of co-management strategy is based on rules of access and use for fishery resources. In this research we investigated the influence of using lakes (preserved and managed for subsistence) and its distance from the river (near and far) in the structure of the fish assemblages associated with floating meadows bank in floodplain lakes, Central Amazonian. Fish were caught during flood period using seine nets in six lakes in a distance ranging from 0.87 to 10.9 km from the river. In floating meadows bank were captured a total of 623 specimens of fish, over 56 species. The analysis of covariance (ANCOVA) indicates that the co-management of lakes and distance did not influence significantly the ecological attributes of fish assemblages (abundance, richness, total weight, Shannon-Weaver and Berger-Parker diversity, evenness and dominance). According to analysis of similarity (ANOSIM) there was no difference in species composition among the lakes. These results suggest other factors, such as: short time of effective management, the agriculture as the most important economic activity of subsistence, the lack of fisheries in large-scale which cause significant environmental changes and the existence of an ecological factor of great intensity, "the flood pulse", overlapping others of less intensity.O co-manejo dos recursos pesqueiros que vem sendo desenvolvido pelos ribeirinhos da Amazônia têm a preocupação de assegurar ambientes adequados para a conservação dos estoques. Esta estratégia de co-manejo é baseada em regras de acesso e uso dos recursos pesqueiros. Nesse estudo, foi investigada a influência do tipo de uso de lagos (preservados e manejados para subsistência) e a sua distância do rio (próximos e distantes) na estrutura das assembleias de peixes associadas aos bancos de macrófitas aquáticas em lagos de várzea, Amazônia Central. Os peixes foram capturados na cheia com rede de cerco em seis lagos com distância do rio variando de 0,87 a 10,9 km. Nas macrófitas aquáticas e capins flutuantes dos lagos foram capturados um total de 623 exemplares de peixes, distribuídos em 56 espécies. A análise de covariância (ANCOVA) indica que o co-manejo dos lagos e distância não influenciaram significativamente nos atributos ecológicos das assembleias (abundância, riqueza, peso total, diversidade de Shannon-Weaver, diversidade Berger-Parker, equitabilidade e dominância). A análise de similaridade (ANOSIM) também mostrou que não existe diferença na composição de espécies entre os tipos de lago. Estes resultados sugerem outros fatores, como o pouco tempo de manejo efetivo, a agricultura como sendo a principal atividade econômica de subsistência, inexistência de pescarias em larga escala que produzam alterações ambientais significativas e a existência de um fator ecológico de grande intensidade, o pulso de inundação, sobrepondo a outros de menor intensidade

A method to identify estuarine macroinvertebrate pollution indicator species in the Virginian Biogeographic Province

Macroinvertebrates are commonly used as biomonitors to detect pollution impacts in estuaries. The goal of this research was to identify estuarine benthic invertebrates that could be used as indicator species to detect presence or absence of pollution in the Virginian Biogeographic Province using available monitoring data from the U.S. Environmental Protection Agency\u27s Environmental Monitoring and Assessment Program. The data were first subdivided by habitat. Then we summarized the benthic community using principal coordinates analysis and projected the results onto a pollution gradient. Then we compared medians and corrected interquartile ranges to identify indicator species that were sensitive to pollution (or lack thereof) and showed low variation in response. Our data set was divided into smaller subsets that ranged from 108 to 532 stations per habitat. Out of 707 species in the Virginian Province, 67 were identified as pollution indicator species; 37 pollution sensitive taxa and 30 pollution tolerant taxa. The pollution sensitive taxa were represented by more phyla than were the pollution tolerant taxa. The pollution tolerant taxa were dominated by deposit feeders while the pollution sensitive taxa were not dominated by animals using any one feeding strategy. The pollution sensitive taxa included many crustaceans, known to be sensitive to pollution, while the pollution tolerant taxa included many tubificid oligochaetes, which are common indicators of pollution. Our empirically based results corresponded well with other studies that identified tolerance values or indicator species. One advantage of this technique is that it can be used on smaller data sets, assuming that there are not major habitat differences among the samples. We believe that this parsimonious technique can be applied to other coastal areas where mid-size (100-500 stations) monitoring data sets are available

The importance of physical and biotic scaling to the experimental simulation of a coastal marine ecosystem

A marine microcosm, consisting of a pelagic phase interacting with a benthic phase, is described. Variations in water turnover, turbulence, incident radiation and ratio of pelagic volume to benthic surface area are shown to have significant effects on the behavior of these microcosms. It is argued that the inclusion and accurate simulation of appropriate levels of these variables is important in microcosm studies designed to study the dynamics of natural systems. © 1977 Biologische Anstalt Helgoland