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Sample records for midrobial community analysis

  1. Wakefield: Community and Library Analysis.

    Trumpeter, Margo C.; Donahue, Mary Ellen

    This community analysis was conducted in order to characterize and identify the information needs of the Wakefield community, and library services and use were evaluated to determine how well the library meets these needs. The study included an examination of the history of the town and its physical characteristics, economic development, and…

  2. Seniors' Online Communities: A Quantitative Content Analysis

    Nimrod, Galit

    2010-01-01

    Purpose: To examine the contents and characteristics of seniors' online communities and to explore their potential benefits to older adults. Design and Methods: Quantitative content analysis of a full year's data from 14 leading online communities using a novel computerized system. The overall database included 686,283 messages. Results: There was…

  3. Chapter 11. Community analysis-based methods

    Cao, Y.; Wu, C.H.; Andersen, G.L.; Holden, P.A.

    2010-05-01

    Microbial communities are each a composite of populations whose presence and relative abundance in water or other environmental samples are a direct manifestation of environmental conditions, including the introduction of microbe-rich fecal material and factors promoting persistence of the microbes therein. As shown by culture-independent methods, different animal-host fecal microbial communities appear distinctive, suggesting that their community profiles can be used to differentiate fecal samples and to potentially reveal the presence of host fecal material in environmental waters. Cross-comparisons of microbial communities from different hosts also reveal relative abundances of genetic groups that can be used to distinguish sources. In increasing order of their information richness, several community analysis methods hold promise for MST applications: phospholipid fatty acid (PLFA) analysis, denaturing gradient gel electrophoresis (DGGE), terminal restriction fragment length polymorphism (TRFLP), cloning/sequencing, and PhyloChip. Specific case studies involving TRFLP and PhyloChip approaches demonstrate the ability of community-based analyses of contaminated waters to confirm a diagnosis of water quality based on host-specific marker(s). The success of community-based MST for comprehensively confirming fecal sources relies extensively upon using appropriate multivariate statistical approaches. While community-based MST is still under evaluation and development as a primary diagnostic tool, results presented herein demonstrate its promise. Coupled with its inherently comprehensive ability to capture an unprecedented amount of microbiological data that is relevant to water quality, the tools for microbial community analysis are increasingly accessible, and community-based approaches have unparalleled potential for translation into rapid, perhaps real-time, monitoring platforms.

  4. Microbial community analysis using MEGAN.

    Huson, Daniel H; Weber, Nico

    2013-01-01

    Metagenomics, the study of microbes in the environment using DNA sequencing, depends upon dedicated software tools for processing and analyzing very large sequencing datasets. One such tool is MEGAN (MEtaGenome ANalyzer), which can be used to interactively analyze and compare metagenomic and metatranscriptomic data, both taxonomically and functionally. To perform a taxonomic analysis, the program places the reads onto the NCBI taxonomy, while functional analysis is performed by mapping reads to the SEED, COG, and KEGG classifications. Samples can be compared taxonomically and functionally, using a wide range of different charting and visualization techniques. PCoA analysis and clustering methods allow high-level comparison of large numbers of samples. Different attributes of the samples can be captured and used within analysis. The program supports various input formats for loading data and can export analysis results in different text-based and graphical formats. The program is designed to work with very large samples containing many millions of reads. It is written in Java and installers for the three major computer operating systems are available from http://www-ab.informatik.uni-tuebingen.de.

  5. Social network analysis community detection and evolution

    Missaoui, Rokia

    2015-01-01

    This book is devoted to recent progress in social network analysis with a high focus on community detection and evolution. The eleven chapters cover the identification of cohesive groups, core components and key players either in static or dynamic networks of different kinds and levels of heterogeneity. Other important topics in social network analysis such as influential detection and maximization, information propagation, user behavior analysis, as well as network modeling and visualization are also presented. Many studies are validated through real social networks such as Twitter. This edit

  6. Metagenomic analysis of microbial communities and beyond

    Schreiber, Lars

    2014-01-01

    From small clone libraries to large next-generation sequencing datasets – the field of community genomics or metagenomics has developed tremendously within the last years. This chapter will summarize some of these developments and will also highlight pitfalls of current metagenomic analyses....... It will illustrate the general workflow of a metagenomic study and introduce the three different metagenomic approaches: (1) the random shotgun approach that focuses on the metagenome as a whole, (2) the targeted approach that focuses on metagenomic amplicon sequences, and (3) the function-driven approach that uses...... heterologous expression of metagenomic DNA fragments to discover novel metabolic functions. Lastly, the chapter will shortly discuss the meta-analysis of gene expression of microbial communities, more precisely metatranscriptomics and metaproteomics....

  7. Interspecific associations and community structure: A local survey and analysis in a grass community

    WenJun Zhang

    2014-09-01

    Full Text Available Interspecific associations in the plant community may help to understand the self-organizing assembly and succession of the community. In present study, Pearson correlation, net correlation, Spearman rank correlation, and point correlation were used to detect the interspecific (inter-family associations of grass species (families using the sampling data collected in a grass community of Zhuhai, China. We found that most associations between grass species (families were positive associations. The competition/interference/niche separation between grass species (families was not significant. A lot of pairs of grass species and families with statistically significant interspecific (inter-family associations based on four correlation measures were discovered. Cluster trees for grass species/families were obtained by using cluster analysis. Relationship among positive/negative associations, interspecific relationship and community succession/stability/robustness was discussed. I held that species with significant positive or negative associations are generally keystone species in the community. Although both negative and positive associations occur in the community succession, the adaptation and selection will finally result in the successful coexistence of the species with significant positive associations in the climax community. As the advance of community succession, the significant positive associations increase and maximize in climax community, and the significant negative associations increase to a maximum and then decline into climax community. Dominance of significant positive associations in the climax community means the relative stablility and equilibrium of the community. No significant associations usually account for the majority of possible interspecific associations at each phase of community succession. They guarantee the robustness of community. They are candidates of keystone species. Lose of some existing keystone species might be

  8. ANALYSIS OF VIRTUAL COMMUNITIES IN TOURISM

    Silvena DENCHEVA

    2014-01-01

    Full Text Available Internet has changed the way companies interact with customers. Customers have become the active part of the communication with business. Virtual communities are the most popular implication of the usage of Internet into business world. The article presents the nature of virtual communities and how they are functioning in the hospitality industry. The web site of hotel Dobruzda-Dobrich has been analyzed regarding its Internet presence. Internet marketing strategy for improving its internet presence is presented in the paper.

  9. Community Analysis of Global Financial Markets

    Irena Vodenska

    2016-05-01

    Full Text Available We analyze the daily returns of stock market indices and currencies of 56 countries over the period of 2002–2012. We build a network model consisting of two layers, one being the stock market indices and the other the foreign exchange markets. Synchronous and lagged correlations are used as measures of connectivity and causality among different parts of the global economic system for two different time intervals: non-crisis (2002–2006 and crisis (2007–2012 periods. We study community formations within the network to understand the influences and vulnerabilities of specific countries or groups of countries. We observe different behavior of the cross correlations and communities for crisis vs. non-crisis periods. For example, the overall correlation of stock markets increases during crisis while the overall correlation in the foreign exchange market and the correlation between stock and foreign exchange markets decrease, which leads to different community structures. We observe that the euro, while being central during the relatively calm period, loses its dominant role during crisis. Furthermore we discover that the troubled Eurozone countries, Portugal, Italy, Greece and Spain, form their own cluster during the crisis period.

  10. Metagenomic analysis of soil microbial communities

    Đokić Lidija

    2010-01-01

    Full Text Available Ramonda serbica and Ramonda nathaliae, rare resurrection plants growing in the Balkan Peninsula, produce a high amount of phenolic compounds as a response to stress. The composition and size of bacterial communities in two rhizosphere soil samples of these plants were analyzed using a metagenomic approach. Fluorescent in situ hybridization (FISH experiments together with DAPI staining showed that the metabolically active bacteria represent only a small fraction, approximately 5%, of total soil bacteria. Using universal bacteria - specific primers 16S rDNA genes were amplified directly from metagenomic DNAs and two libraries were constructed. The Restriction Fragment Length Polymorphism (RLFP method was used in library screening. Amongst 192 clones, 35 unique operational taxonomic units (OTUs were determined from the rhizosphere of R. nathaliae, and 13 OTUs out of 80 clones in total from the library of R. serbica. Representative clones from each OTU were sequenced. The majority of sequences from metagenomes showed very little similarity to any cultured bacteria. In conclusion, the bacterial communities in the studied soil samples showed quite poor diversity. .

  11. Community evolution mining and analysis in social network

    Liu, Hongtao; Tian, Yuan; Liu, Xueyan; Jian, Jie

    2017-03-01

    With the development of digital and network technology, various social platforms emerge. These social platforms have greatly facilitated access to information, attracting more and more users. They use these social platforms every day to work, study and communicate, so every moment social platforms are generating massive amounts of data. These data can often be modeled as complex networks, making large-scale social network analysis possible. In this paper, the existing evolution classification model of community has been improved based on community evolution relationship over time in dynamic social network, and the Evolution-Tree structure is proposed which can show the whole life cycle of the community more clearly. The comparative test result shows that the improved model can excavate the evolution relationship of the community well.

  12. Microbial communities of the Costa Rica Margin: contamination controls and community analysis

    Martino, A. J.; Biddle, J.; House, C. H.

    2013-12-01

    Most microbiology work in marine subsurface sediments has been focused in the upper 100-200 meters of sediment, as the switchover from advanced piston coring (APC) to extended core barrel coring (XCB) generally occurs around this depth. This leads to large increases in drilling-induced contamination and interferes in molecular studies. Here, we utilized deep 16S rRNA sequencing of DNA from both the subsurface sediments and the drilling fluid as a strategy for separating sequence information originating from drill-fluid contamination from that which represents the indigenous microbial communities of the sediments. This permitted a characterization of both sediment microbial communities and drilling-fluid communities that was thorough enough to confidently show the differences in the communities. Examination of the results suggests that sequences originating from drilling fluid may be only a minor portion of the data obtained from even the deepest XCB cores examined, and further that the different community composition of the drilling fluid should permit the subtraction of contaminating lineages from the analysis. As part of this work, we also show an extensive community composition analysis of multiple samples from two drilling sites of IODP Expedition 334, on the upper plate of the subduction zone between the Cocos plate and the Caribbean plate, off the Costa Rica Margin. Preliminary analysis of the sequence data suggests that the bacterial communities at both the upper slope site (1379) and the mid-slope site (1378) are dominated by Chloroflexi, Nitrospirae, Actinobacteria, Planctomycetes, and Proteobacteria, while Archaeal communities are dominated by the Miscellaneous Crenarchaeotal Group. Using universal primers revealed that the relative dominance of Bacteria to Archaea differs between the two sites, and the trends of increasing and decreasing abundance with depth are nearly opposite between the sites. At site 1379, the Bacterial to Archaeal relationship seems

  13. Bayesian model-based cluster analysis for predicting macrofaunal communities

    Braak, ter C.J.F.; Hoijtink, H.; Akkermans, W.; Verdonschot, P.F.M.

    2003-01-01

    To predict macrofaunal community composition from environmental data a two-step approach is often followed: (1) the water samples are clustered into groups on the basis of the macrofauna data and (2) the groups are related to the environmental data, e.g. by discriminant analysis. For the cluster ana

  14. Metagenomics meets time series analysis: unraveling microbial community dynamics

    Faust, K.; Lahti, L.M.; Gonze, D.; Vos, de W.M.; Raes, J.

    2015-01-01

    The recent increase in the number of microbial time series studies offers new insights into the stability and dynamics of microbial communities, from the world's oceans to human microbiota. Dedicated time series analysis tools allow taking full advantage of these data. Such tools can reveal periodic

  15. Exploring Twitter communication dynamics with evolving community analysis

    Konstantinos Konstantinidis

    2017-02-01

    Full Text Available Online Social Networks (OSNs have been widely adopted as a means of news dissemination, event reporting, opinion expression and discussion. As a result, news and events are being constantly reported and discussed online through OSNs such as Twitter. However, the variety and scale of all the information renders manual analysis extremely cumbersome, and therefore creating a storyline for an event or news story is an effort-intensive task. The main challenge pertains to the magnitude of data to be analyzed. To this end, we propose a framework for ranking the resulting communities and their metadata on the basis of structural, contextual and evolutionary characteristics such as community centrality, textual entropy, persistence and stability. We apply the proposed framework on three Twitter datasets and demonstrate that the analysis that followed enables the extraction of new insights with respect to influential user accounts, topics of discussion and emerging trends. These insights could primarily assist the work of social and political analysis scientists and the work of journalists in their own story telling, but also highlight the limitations of existing analysis methods and pose new research questions. To our knowledge, this study is the first to investigate the ranking of dynamic communities. In addition, our findings suggest future work regarding the determination of the general context of the communities based on structure and evolutionary behavior alone.

  16. Correlation network analysis applied to complex biofilm communities.

    Ana E Duran-Pinedo

    Full Text Available The complexity of the human microbiome makes it difficult to reveal organizational principles of the community and even more challenging to generate testable hypotheses. It has been suggested that in the gut microbiome species such as Bacteroides thetaiotaomicron are keystone in maintaining the stability and functional adaptability of the microbial community. In this study, we investigate the interspecies associations in a complex microbial biofilm applying systems biology principles. Using correlation network analysis we identified bacterial modules that represent important microbial associations within the oral community. We used dental plaque as a model community because of its high diversity and the well known species-species interactions that are common in the oral biofilm. We analyzed samples from healthy individuals as well as from patients with periodontitis, a polymicrobial disease. Using results obtained by checkerboard hybridization on cultivable bacteria we identified modules that correlated well with microbial complexes previously described. Furthermore, we extended our analysis using the Human Oral Microbe Identification Microarray (HOMIM, which includes a large number of bacterial species, among them uncultivated organisms present in the mouth. Two distinct microbial communities appeared in healthy individuals while there was one major type in disease. Bacterial modules in all communities did not overlap, indicating that bacteria were able to effectively re-associate with new partners depending on the environmental conditions. We then identified hubs that could act as keystone species in the bacterial modules. Based on those results we then cultured a not-yet-cultivated microorganism, Tannerella sp. OT286 (clone BU063. After two rounds of enrichment by a selected helper (Prevotella oris OT311 we obtained colonies of Tannerella sp. OT286 growing on blood agar plates. This system-level approach would open the possibility of

  17. Metagenomic analysis of the microbial community in kefir grains.

    Nalbantoglu, Ufuk; Cakar, Atilla; Dogan, Haluk; Abaci, Neslihan; Ustek, Duran; Sayood, Khalid; Can, Handan

    2014-08-01

    Kefir grains as a probiotic have been subject to microbial community identification using culture-dependent and independent methods that target specific strains in the community, or that are based on limited 16S rRNA analysis. We performed whole genome shotgun pyrosequencing using two Turkish Kefir grains. Sequencing generated 3,682,455 high quality reads for a total of ∼1.6 Gbp of data assembled into 6151 contigs with a total length of ∼24 Mbp. Species identification mapped 88.16% and 93.81% of the reads rendering 4 Mpb of assembly that did not show any homology to known bacterial sequences. Identified communities in the two grains showed high concordance where Lactobacillus was the most abundant genus with a mapped abundance of 99.42% and 99.79%. This genus was dominantly represented by three species Lactobacillus kefiranofaciens, Lactobacillus buchneri and Lactobacillus helveticus with a total mapped abundance of 97.63% and 98.74%. We compared and verified our findings with 16S pyrosequencing and model based 16S data analysis. Our results suggest that microbial community profiling using whole genome shotgun data is feasible, can identify novel species data, and has the potential to generate a more accurate and detailed assessment of the underlying bacterial community, especially for low abundance species.

  18. [A phylogenetic analysis of plant communities of Teberda Biosphere Reserve].

    Shulakov, A A; Egorov, A V; Onipchenko, V G

    2016-01-01

    Phylogenetic analysis of communities is based on the comparison of distances on the phylogenetic tree between species of a community under study and those distances in random samples taken out of local flora. It makes it possible to determine to what extent a community composition is formed by more closely related species (i.e., "clustered") or, on the opposite, it is more even and includes species that are less related with each other. The first case is usually interpreted as a result of strong influence caused by abiotic factors, due to which species with similar ecology, a priori more closely related, would remain: In the second case, biotic factors, such as competition, may come to the fore and lead to forming a community out of distant clades due to divergence of their ecological niches: The aim of this' study Was Ad explore the phylogenetic structure in communities of the northwestern Caucasus at two spatial scales - the scale of area from 4 to 100 m2 and the smaller scale within a community. The list of local flora of the alpine belt has been composed using the database of geobotanic descriptions carried out in Teberda Biosphere Reserve at true altitudes exceeding.1800 m. It includes 585 species of flowering plants belonging to 57 families. Basal groups of flowering plants are.not represented in the list. At the scale of communities of three classes, namely Thlaspietea rotundifolii - commumties formed on screes and pebbles, Calluno-Ulicetea - alpine meadow, and Mulgedio-Aconitetea subalpine meadows, have not demonstrated significant distinction of phylogenetic structure. At intra level, for alpine meadows the larger share of closely related species. (clustered community) is detected. Significantly clustered happen to be those communities developing on rocks (class Asplenietea trichomanis) and alpine (class Juncetea trifidi). At the same time, alpine lichen proved to have even phylogenetic structure at the small scale. Alpine (class Salicetea herbaceae) that

  19. Metagenomics meets time series analysis: unraveling microbial community dynamics.

    Faust, Karoline; Lahti, Leo; Gonze, Didier; de Vos, Willem M; Raes, Jeroen

    2015-06-01

    The recent increase in the number of microbial time series studies offers new insights into the stability and dynamics of microbial communities, from the world's oceans to human microbiota. Dedicated time series analysis tools allow taking full advantage of these data. Such tools can reveal periodic patterns, help to build predictive models or, on the contrary, quantify irregularities that make community behavior unpredictable. Microbial communities can change abruptly in response to small perturbations, linked to changing conditions or the presence of multiple stable states. With sufficient samples or time points, such alternative states can be detected. In addition, temporal variation of microbial interactions can be captured with time-varying networks. Here, we apply these techniques on multiple longitudinal datasets to illustrate their potential for microbiome research.

  20. Matrix composition and community structure analysis of a novel bacterial pyrite leaching community.

    Ziegler, Sibylle; Ackermann, Sonia; Majzlan, Juraj; Gescher, Johannes

    2009-09-01

    Here we describe a novel bacterial community that is embedded in a matrix of carbohydrates and bio/geochemical products of pyrite (FeS(2)) oxidation. This community grows in stalactite-like structures--snottites--on the ceiling of an abandoned pyrite mine at pH values of 2.2-2.6. The aqueous phase in the matrix contains 200 mM of sulfate and total iron concentrations of 60 mM. Micro-X-ray diffraction analysis showed that jarosite [(K,Na,H(3)O)Fe(3)(SO(4))(2)(OH)(6)] is the major mineral embedded in the snottites. X-ray absorption near-edge structure experiments revealed three different sulfur species. The major signal can be ascribed to sulfate, and the other two features may correspond to thiols and sulfoxides. Arabinose was detected as the major sugar component in the extracellular polymeric substance. Via restriction fragment length polymorphism analysis, a community was found that mainly consists of iron oxidizing Leptospirillum and Ferrovum species but also of bacteria that could be involved in dissimilatory sulfate and dissimilatory iron reduction. Each snottite can be regarded as a complex, self-contained consortium of bacterial species fuelled by the decomposition of pyrite.

  1. Analysis of the communities of an urban mobile phone network

    Botta, Federico; del Genio, Charo I.

    2017-01-01

    Being able to characterise the patterns of communications between individuals across different time scales is of great importance in understanding people’s social interactions. Here, we present a detailed analysis of the community structure of the network of mobile phone calls in the metropolitan area of Milan revealing temporal patterns of communications between people. We show that circadian and weekly patterns can be found in the evolution of communities, presenting evidence that these cycles arise not only at the individual level but also at that of social groups. Our findings suggest that these trends are present across a range of time scales, from hours to days and weeks, and can be used to detect socially relevant events. PMID:28334003

  2. Determining patterns of variability in ecological communities: time lag analysis revisited

    Kampichler, C.; Van der Jeugd, H.P.

    2013-01-01

    All ecological communities experience change over time. One method to quantify temporal variation in the patterns of relative abundance of communities is time lag analysis (TLA). It uses a distance-based approach to study temporal community dynamics by regressing community dissimilarity over increas

  3. Microbial community analysis in biotrickling filters treating isopropanol air emissions.

    Pérez, M Carmen; Alvarez-Hornos, F Javier; San-Valero, Pau; Marzal, Paula; Gabaldón, Carmen

    2013-01-01

    The evolution of the microbial community was analysed over one year in two biotrickling filters operating under intermittent feeding conditions and treating isopropanol emissions, a pollutant typically found in the flexography sector. Each reactor was packed with one media: plastic cross-flow-structured material or polypropylene rings. The communities were monitored by fluorescence in situ hybridization (FISH) and denaturing gradient gel electrophoresis (DGGE) analysis of the 16S rRNA region. After inoculation with activated sludge, the biotrickling filters were operated using inlet loads (ILs) from 20 to 65 g C m(-3) h(-1) and empty-bed residence times (EBRTs) from 14 to 160 s. Removal efficiencies higher than 80% were obtained with ILs up to 35 g C m(-3) h(-1) working at EBRTs as low as 24 s. There was an increase in the total percentage of the target domains of up to around 80% at the end of the experiment. Specifically, the Gammaproteobacteria domain group, which includes the well-known volatile organic compound (VOC)-degrading species such as Pseudomonas putida, showed a noticeable rise in the two biotrickling filters of 26% and 27%, respectively. DGGE pattern band analysis revealed a stable band of Pseudomonas putida in all the samples monitored, even in the lower diversity communities. In addition, at similar operational conditions, the biotrickling filter with a greater relative abundance of Pseudomonas sp. (19.2% vs. 8%) showed higher removal efficiency (90% vs. 79%). Results indicate the importance of undertaking a further in-depth study of the involved species in the biofiltration process and their specific function.

  4. CORSSA: The Community Online Resource for Statistical Seismicity Analysis

    Michael, Andrew J.; Wiemer, Stefan

    2010-01-01

    Statistical seismology is the application of rigorous statistical methods to earthquake science with the goal of improving our knowledge of how the earth works. Within statistical seismology there is a strong emphasis on the analysis of seismicity data in order to improve our scientific understanding of earthquakes and to improve the evaluation and testing of earthquake forecasts, earthquake early warning, and seismic hazards assessments. Given the societal importance of these applications, statistical seismology must be done well. Unfortunately, a lack of educational resources and available software tools make it difficult for students and new practitioners to learn about this discipline. The goal of the Community Online Resource for Statistical Seismicity Analysis (CORSSA) is to promote excellence in statistical seismology by providing the knowledge and resources necessary to understand and implement the best practices, so that the reader can apply these methods to their own research. This introduction describes the motivation for and vision of CORRSA. It also describes its structure and contents.

  5. Using Social Network Analysis to Evaluate Community Capacity Building of a Regional Community Cancer Network

    Luque, John; Tyson, Dinorah Martinez; Lee, Ji-Hyun; Gwede, Clement; Vadaparampil, Susan; Noel-Thomas, Shalewa; Meade, Cathy

    2010-01-01

    The Tampa Bay Community Cancer Network (TBCCN) is one of 25 Community Network Programs funded by the National Cancer Institute's (NCI's) Center to Reduce Cancer Health Disparities with the objectives to create a collaborative infrastructure of academic and community based organizations and to develop effective and sustainable interventions to…

  6. The local community development and the community-based tourism : a comparative conceptual analysis

    Sylvie PARENT

    2009-01-01

    Full Text Available According to the authors of this paper, mass tourism does not generate the development of local communities but rather their devitalization. This paper presents a cross-literature survey on community-based tourism and local community development. It proposes some links between these two approaches and asserts that community-based tourism can be a strategy to trigger local community development. It address the conditions under which the convergence of these two approaches may allow the launching of development initiatives liable to counter the devitalization and impoverishment process which characterizes certain mass tourism oriented places.

  7. Pyrosequencing Based Microbial Community Analysis of Stabilized Mine Soils

    Park, J. E.; Lee, B. T.; Son, A.

    2015-12-01

    Heavy metals leached from exhausted mines have been causing severe environmental problems in nearby soils and groundwater. Environmental mitigation was performed based on the heavy metal stabilization using Calcite and steel slag in Korea. Since the soil stabilization only temporarily immobilizes the contaminants to soil matrix, the potential risk of re-leaching heavy metal still exists. Therefore the follow-up management of stabilized soils and the corresponding evaluation methods are required to avoid the consequent contamination from the stabilized soils. In this study, microbial community analysis using pyrosequencing was performed for assessing the potential leaching of the stabilized soils. As a result of rarefaction curve and Chao1 and Shannon indices, the stabilized soil has shown lower richness and diversity as compared to non-contaminated negative control. At the phyla level, as the degree of contamination increases, most of phyla decreased with only exception of increased proteobacteria. Among proteobacteria, gamma-proteobacteria increased against the heavy metal contamination. At the species level, Methylobacter tundripaludum of gamma-proteobacteria showed the highest relative portion of microbial community, indicating that methanotrophs may play an important role in either solubilization or immobilization of heavy metals in stabilized soils.

  8. Microbial community analysis of a full-scale DEMON bioreactor.

    Gonzalez-Martinez, Alejandro; Rodriguez-Sanchez, Alejandro; Muñoz-Palazon, Barbara; Garcia-Ruiz, Maria-Jesus; Osorio, Francisco; van Loosdrecht, Mark C M; Gonzalez-Lopez, Jesus

    2015-03-01

    Full-scale applications of autotrophic nitrogen removal technologies for the treatment of digested sludge liquor have proliferated during the last decade. Among these technologies, the aerobic/anoxic deammonification process (DEMON) is one of the major applied processes. This technology achieves nitrogen removal from wastewater through anammox metabolism inside a single bioreactor due to alternating cycles of aeration. To date, microbial community composition of full-scale DEMON bioreactors have never been reported. In this study, bacterial community structure of a full-scale DEMON bioreactor located at the Apeldoorn wastewater treatment plant was analyzed using pyrosequencing. This technique provided a higher-resolution study of the bacterial assemblage of the system compared to other techniques used in lab-scale DEMON bioreactors. Results showed that the DEMON bioreactor was a complex ecosystem where ammonium oxidizing bacteria, anammox bacteria and many other bacterial phylotypes coexist. The potential ecological role of all phylotypes found was discussed. Thus, metagenomic analysis through pyrosequencing offered new perspectives over the functioning of the DEMON bioreactor by exhaustive identification of microorganisms, which play a key role in the performance of bioreactors. In this way, pyrosequencing has been proven as a helpful tool for the in-depth investigation of the functioning of bioreactors at microbiological scale.

  9. A Comparative Analysis of Community Wind Power DevelopmentModels

    Bolinger, Mark; Wiser, Ryan; Wind, Tom; Juhl, Dan; Grace, Robert; West, Peter

    2005-05-20

    For years, farmers in the United States have looked with envy on their European counterparts ability to profitably farm the wind through ownership of distributed, utility-scale wind projects. Only within the past few years, however, has farmer- or community-owned windpower development become a reality in the United States. The primary hurdle to this type of development in the United States has been devising and implementing suitable business and legal structures that enable such projects to take advantage of tax-based federal incentives for windpower. This article discusses the limitations of such incentives in supporting farmer- or community-owned wind projects, describes four ownership structures that potentially overcome such limitations, and finally conducts comparative financial analysis on those four structures, using as an example a hypothetical 1.5 MW farmer-owned project located in the state of Oregon. We find that material differences in the competitiveness of each structure do exist, but that choosing the best structure for a given project will largely depend on the conditions at hand; e.g., the ability of the farmer(s) to utilize tax credits, preference for individual versus cooperative ownership, and the state and utility service territory in which the project will be located.

  10. GeoChips for Analysis of Microbial Functional Communities

    Van Nostrand, Joy D.; Wu, Liyou; He, Zhili; Zhou, Jizhong

    2008-09-30

    Functional gene arrays (FGA) are microarrays that contain probes for genes encoding proteins or enzymes involved in functions of interest and allow for the study of thousands of genes at one time. The most comprehensive FGA to date is the GeoChip, which contains ~;;24,000 probes for ~;;10,000 genes involved in the geochemical cycling of C, N, P, and S, as well as genes involved in metal resistance and reduction and contaminant degradation. This chapter details the methods necessary for GeoChip analysis. Methods covered include preparation of DNA (whole community genome amplification and labeling), array setup (prehybridization steps), hybridization (sample and hybridization buffers), and post hybridization steps (slide washing and array scanning).

  11. Integrating software architectures for distributed simulations and simulation analysis communities.

    Goldsby, Michael E.; Fellig, Daniel; Linebarger, John Michael; Moore, Patrick Curtis; Sa, Timothy J.; Hawley, Marilyn F.

    2005-10-01

    The one-year Software Architecture LDRD (No.79819) was a cross-site effort between Sandia California and Sandia New Mexico. The purpose of this research was to further develop and demonstrate integrating software architecture frameworks for distributed simulation and distributed collaboration in the homeland security domain. The integrated frameworks were initially developed through the Weapons of Mass Destruction Decision Analysis Center (WMD-DAC), sited at SNL/CA, and the National Infrastructure Simulation & Analysis Center (NISAC), sited at SNL/NM. The primary deliverable was a demonstration of both a federation of distributed simulations and a federation of distributed collaborative simulation analysis communities in the context of the same integrated scenario, which was the release of smallpox in San Diego, California. To our knowledge this was the first time such a combination of federations under a single scenario has ever been demonstrated. A secondary deliverable was the creation of the standalone GroupMeld{trademark} collaboration client, which uses the GroupMeld{trademark} synchronous collaboration framework. In addition, a small pilot experiment that used both integrating frameworks allowed a greater range of crisis management options to be performed and evaluated than would have been possible without the use of the frameworks.

  12. Community College Student Mental Health: A Comparative Analysis

    Katz, Daniel Seth; Davison, Karen

    2014-01-01

    This study explores community college student mental health by comparing the responses of California community college and traditional university students on the American College Health Association-National College Health Assessment II (ACHA-NCHA II). Using MANOVA, we compared community college and traditional university students, examining…

  13. Feature Analysis and Modeling of the Network Community Structure

    袁超; 柴毅; 魏善碧

    2012-01-01

    Community structure has an important influence on the structural and dynamic characteristics of the complex systems.So it has attracted a large number of researchers.However,due to its complexity,the mechanism of action of the community structure is still not clear to this day.In this paper,some features of the community structure have been discussed.And a constraint model of the community has been deduced.This model is effective to identify the communities.And especially,it is effective to identify the overlapping nodes between the communities.Then a community detection algorithm,which has linear time complexity,is proposed based on this constraint model,a proposed node similarity model and the Modularity Q.Through some experiments on a series of real-world and synthetic networks,the high performances of the algorithm and the constraint model have been illustrated.

  14. Networked Community Change: Understanding Community Systems Change through the Lens of Social Network Analysis.

    Lawlor, Jennifer A; Neal, Zachary P

    2016-06-01

    Addressing complex problems in communities has become a key area of focus in recent years (Kania & Kramer, 2013, Stanford Social Innovation Review). Building on existing approaches to understanding and addressing problems, such as action research, several new approaches have emerged that shift the way communities solve problems (e.g., Burns, 2007, Systemic Action Research; Foth, 2006, Action Research, 4, 205; Kania & Kramer, 2011, Stanford Social Innovation Review, 1, 36). Seeking to bring clarity to the emerging literature on community change strategies, this article identifies the common features of the most widespread community change strategies and explores the conditions under which such strategies have the potential to be effective. We identify and describe five common features among the approaches to change. Then, using an agent-based model, we simulate network-building behavior among stakeholders participating in community change efforts using these approaches. We find that the emergent stakeholder networks are efficient when the processes are implemented under ideal conditions.

  15. Metagenomic analysis of microbial community in uranium-contaminated soil.

    Yan, Xun; Luo, Xuegang; Zhao, Min

    2016-01-01

    Uranium tailing is a serious pollution challenge for the environment. Based on metagenomic sequencing analysis, we explored the functional and structural diversity of the microbial community in six soil samples taken at different soil depths from uranium-contaminated and uncontaminated areas. Kyoto Encyclopedia of Genes and Genomes Orthology (KO) groups were obtained using a Basic Local Alignment Search Tool search based on the universal protein resource database. The KO-pathway network was then constructed using the selected KOs. Finally, alpha and beta diversity analyses were performed to explore the differences in soil bacterial diversity between the radioactive soil and uncontaminated soil. In total, 30-68 million high-quality reads were obtained. Sequence assembly yielded 286,615 contigs; and these contigs mostly annotated to 1699 KOs. The KO distributions were similar among the six soil samples. Moreover, the proportion of the metabolism of other amino acids (e.g., beta-alanine, taurine, and hypotaurine) and signal transduction was significantly lower in radioactive soil than in uncontaminated soil, whereas the proportion of membrane transport and carbohydrate metabolism was higher. Additionally, KOs were mostly enriched in ATP-binding cassette transporters and two-component systems. According to diversity analyses, Actinobacteria and Proteobacteria were the dominant phyla in radioactive and uncontaminated soil, and Robiginitalea, Microlunatus, and Alicyclobacillus were the dominant genera in radioactive soil. Taken together, these results demonstrate that soil microbial community, structure, and functions show significant changes in uranium-contaminated soil. The dominant categories such as Actinobacteria and Proteobacteria may be applied in environmental governance for uranium-contaminated soil in southern China.

  16. Community-enhanced Network Representation Learning for Network Analysis

    Tu, Cunchao; Zeng, Xiangkai; Liu, Zhiyuan; Sun, Maosong

    2016-01-01

    Network representation learning (NRL) aims to build low-dimensional vectors for vertices in a network. Most existing NRL methods focus on learning representations from local context of vertices (such as their neighbors). Nevertheless, vertices in many complex networks also exhibit significant global patterns widely known as communities. It's a common sense that vertices in the same community tend to connect densely, and usually share common attributes. These patterns are expected to improve NRL and benefit relevant evaluation tasks, such as link prediction and vertex classification. In this work, we propose a novel NRL model by introducing community information of vertices to learn more discriminative network representations, named as Community-enhanced Network Representation Learning (CNRL). CNRL simultaneously detects community distribution of each vertex and learns embeddings of both vertices and communities. In this way, we can obtain more informative representation of a vertex accompanying with its commu...

  17. Bacterial community analysis of Tatsoi cultivated by hydroponics.

    Koo, Ok K; Kim, Hun; Kim, Hyun J; Baker, Christopher A; Ricke, Steven C

    2016-07-02

    Tatsoi (Brassica narinosa) is a popular Asian salad green that is mostly consumed as a source of fresh produce. The purpose of this study was to assess the microbial diversity of Tatsoi cultivated in a hydroponic system and of its ecosystem. Tatsoi leaves, nutrient solution, and perlite/earth samples from a trickle feed system (TFS) and an ebb-and-flow system (EFS) were collected and their microbial communities were analyzed by pyrosequencing analysis. The results showed that most bacteria in the leaves from the TFS contained genus Sporosarcina (99.6%), while Rhizobium (60.4%) was dominant in the leaves from the EFS. Genus Paucibacter (18.21%) and Pelomonas (12.37%) were the most abundant microbiota in the nutrient solution samples of the TFS. In the EFS, the nutrient solution samples contained mostly genus Rhodococcus and Acinetobacter. Potential microbial transfer between the leaves and the ecosystem was observed in the EFS, while samples in the TFS were found to share only one species between the leaves, nutrient solution, and earth. Together, these results show that the bacterial populations in Tatsoi and in its ecosystem are highly diverse based on the cultivation system.

  18. Designing healthy communities: A walkability analysis of LEED-ND

    Adriana A. Zuniga-Teran

    2016-12-01

    Full Text Available Prevailing city design in many countries has created sedentary societies that depend on automobile use. Consequently, architects, urban designers, and land planners have developed new urban design theories, which have been incorporated into the Leadership in Energy and Environmental Design for Neighborhood Development (LEED-ND certification system. The LEED-ND includes design elements that improve human well-being by facilitating walking and biking, a concept known as walkability. Despite these positive developments, relevant research findings from other fields of study have not been fully integrated into the LEED-ND. According to Zuniga-Teran (2015, relevant walkability research findings from multiple disciplines were organized into a walkability framework (WF that organizes design elements related to physical activity into nine categories, namely, connectivity, land use, density, traffic safety, surveillance, parking, experience, greenspace, and community. In this study, we analyze walkability in the LEED-ND through the lens of the nine WF categories. Through quantitative and qualitative analyses, we identify gaps and strengths in the LEED-ND and propose potential enhancements to this certification system that reflects what is known about enhancing walkability more comprehensively through neighborhood design analysis. This work seeks to facilitate the translation of research into practice, which can ultimately lead to more active and healthier societies.

  19. A Political Analysis of Community Influence over School Closure

    Finnigan, Kara S.; Lavner, Mark

    2012-01-01

    This study seeks to understand community member participation in and influence over an urban school district's school closure process. Data from interviews with School Board members, district administrators, and community members, as well as district documents and newspaper articles suggest that district administrators limited participation…

  20. George Washington Community High School: analysis of a partnership network.

    Bringle, Robert G; Officer, Starla D H; Grim, Jim; Hatcher, Julie A

    2009-01-01

    After five years with no public schools in their community, residents and neighborhood organizations of the Near Westside of Indianapolis advocated for the opening of George Washington Community High School (GWCHS). As a neighborhood in close proximity to the campus of Indiana University-Purdue University Indianapolis, the Near Westside and campus worked together to address this issue and improve the educational success of youth. In fall 2000, GWCHS opened as a community school and now thrives as a national model, due in part to its network of community relationships. This account analyzes the development of the school by focusing on the relationships among the university, the high school, community organizations, and the residents of the Near Westside and highlights the unique partnership between the campus and school by defining the relational qualities and describing the network created to make sustainable changes with the high school.

  1. Illusions of Resilience? An Analysis of Community Responses to Change in Northern Norway.

    Helene Amundsen

    2012-12-01

    Full Text Available This article contributes to our understanding of community resilience. Community resilience is the ability of a community to cope and adjust to stresses caused by social, political, and environmental change and to engage community resources to overcome adversity and take advantage of opportunities in response to change. Through an analysis of local responses to multiple challenges, six dimensions of community resilience were found in one village in northern Norway. These dimensions; community resources, community networks, institutions and services, people-place connections, active agents, and learning; are activated in processes and activities in the village to respond to current challenges. Although this corroborates findings from other community resilience research, this research suggests that community resilience is both complex and dynamic over time. Although communities may consider themselves resilient to today's challenges, the rate and magnitude of expected systemic global changes, especially climate change, means that future resilience cannot be taken for granted. This work concludes that there is a risk that community resilience may be an illusion, leading to complacency about the need for adaption to multiple factors of change. Hence, the ability of communities to actively engage in reflexive learning processes is of importance for both adaptation and future resilience.

  2. Molecular analysis of microbial communities in endotracheal tube biofilms.

    Scott Cairns

    Full Text Available BACKGROUND: Ventilator-associated pneumonia is the most prevalent acquired infection of patients on intensive care units and is associated with considerable morbidity and mortality. Evidence suggests that an improved understanding of the composition of the biofilm communities that form on endotracheal tubes may result in the development of improved preventative strategies for ventilator-associated pneumonia. METHODOLOGY/PRINCIPAL FINDINGS: The aim of this study was to characterise microbial biofilms on the inner luminal surface of extubated endotracheal tubes from ICU patients using PCR and molecular profiling. Twenty-four endotracheal tubes were obtained from twenty mechanically ventilated patients. Denaturing gradient gel electrophoresis (DGGE profiling of 16S rRNA gene amplicons was used to assess the diversity of the bacterial population, together with species specific PCR of key marker oral microorganisms and a quantitative assessment of culturable aerobic bacteria. Analysis of culturable aerobic bacteria revealed a range of colonisation from no growth to 2.1×10(8 colony forming units (cfu/cm(2 of endotracheal tube (mean 1.4×10(7 cfu/cm(2. PCR targeting of specific bacterial species detected the oral bacteria Streptococcus mutans (n = 5 and Porphyromonas gingivalis (n = 5. DGGE profiling of the endotracheal biofilms revealed complex banding patterns containing between 3 and 22 (mean 6 bands per tube, thus demonstrating the marked complexity of the constituent biofilms. Significant inter-patient diversity was evident. The number of DGGE bands detected was not related to total viable microbial counts or the duration of intubation. CONCLUSIONS/SIGNIFICANCE: Molecular profiling using DGGE demonstrated considerable biofilm compositional complexity and inter-patient diversity and provides a rapid method for the further study of biofilm composition in longitudinal and interventional studies. The presence of oral microorganisms in

  3. Molecular Analysis Research at Community College of Philadelphia

    2015-09-21

    institutions. The project aims to validate the work of current graduate students and continue on Dr. Salerno’s postdoctoral project (Salerno et al., 2012...essential tool in completing this research project. Funds for training students on the V3 Western Workflow were obtained through a Community College ...partnership in proteomics research between The Community College of Philadelphia and Philadelphia University. Training Component: 4-5 students

  4. Funding Ohio Community Colleges: An Analysis of the Performance Funding Model

    Krueger, Cynthia A.

    2013-01-01

    This study examined Ohio's community college performance funding model that is based on seven student success metrics. A percentage of the regular state subsidy is withheld from institutions; funding is earned back based on the three-year average of success points achieved in comparison to other community colleges in the state. Analysis of…

  5. Using Social Network Analysis to Understand Sense of Community in an Online Learning Environment

    Shen, Demei; Nuankhieo, Piyanan; Huang, Xinxin; Amelung, Christopher; Laffey, James

    2008-01-01

    This study uses social network analysis (SNA) in an innovative way to describe interaction and explain how interaction influences sense of community of students in online learning environments. The findings reveal differences on sense of community between two similarly structured online courses, and show unique interaction patterns for students in…

  6. Impact of plant invasions on local arthropod communities: a meta-analysis

    van Hengstum, T.; Hooftman, D.A.P.; Oostermeijer, J.G.B.; van Tienderen, P.H.

    2014-01-01

    1. Invasive plants can have a major impact on local plant and animal communities. However, effects of plant invasions on arthropod communities and the potential drivers have rarely been studied. 2. We present a meta-analysis of 56 studies on the impact of plant invasions on abundance and richness of

  7. Newspaper Content Analysis in Evaluation of a Community-Based Participatory Project to Increase Physical Activity

    Granner, Michelle L.; Sharpe, Patricia A.; Burroughs, Ericka L.; Fields, Regina; Hallenbeck, Joyce

    2010-01-01

    This study conducted a newspaper content analysis as part of an evaluation of a community-based participatory research project focused on increasing physical activity through policy and environmental changes, which included activities related to media advocacy and media-based community education. Daily papers (May 2003 to December 2005) from both…

  8. Course-Shopping in the Urban Community Colleges: An Analysis of Student Drop and Add Activities.

    Hagedorn, Linda Serra; Maxwell, William B.; Cypers, Scott; Moon, Hye Sun; Lester, Jaime

    This study examines the course shopping behaviors of approximately 5,000 community college students enrolled across the nine campuses of the Los Angeles Community College District in spring 2001. The sample students are representative of the district. For the purpose of this analysis, the authors define course shopping as: (1) cyclic shopping, the…

  9. Principal response curves: analysis of time-dependent multivariate responses of biological community to stress

    Brink, van den P.J.; Braak, ter C.J.F.

    1999-01-01

    In this paper a novel multivariate method is proposed for the analysis of community response data from designed experiments repeatedly sampled in time. The long-term effects of the insecticide chlorpyrifos on the invertebrate community and the dissolved oxygen (DO)–pH–alkalinity–conductivity syndrom

  10. Analysis of community-level mesocosm data based on ecologically meaningful dissimilarity measures and data transformation

    Tebby, Cleo; Joachim, Sandrine; Brink, Van den Paul J.; Porcher, Jean Marc; Beaudouin, Rémy

    2017-01-01

    The principal response curve (PRC) method is a constrained ordination method developed specifically for the analysis of community data collected in mesocosm experiments, which provides easily understood summaries and graphical representations of community response to stress. It is a redundancy an

  11. Shared Governance in the Community College: An Analysis of Formal Authority in Collective Bargaining Agreements

    McDermott, Linda A.

    2012-01-01

    This qualitative study examines shared governance in Washington State's community and technical colleges and provides an analysis of faculty participation in governance based on formal authority in collective bargaining agreements. Contracts from Washington's thirty community and technical college districts were reviewed in order to identify in…

  12. University-Community Engagement: A grid-group analysis

    David Low

    2008-09-01

    Full Text Available University-community engagement involves complex issues, entangling multiple and interacting points of view, all of which operate in a wider dynamic evolving social environment. For this reason, there is often disagreement about why engagement is necessary or desirable, and whether there is one optimal method to practice it. To address this issue, I argue that university-community engagement can be examined as a form of enquiry. In this view, engagement is viewed as a system that arises through the recognition of the dissent it embodies. As such, enquiry functions to process disagreements into diverse methods of communication. Most of the disagreements utilised by universities are derived from external sources, thus university-based enquiry must necessarily involve a dialogue with a broader community or environment. In this sense, university-community engagement can be viewed most generally as a method that processes disagreements into shared understandings through enquiry. To demonstrate how university-community engagement functions from an enquiry point of view, I use Mary Douglas’ grid-group diagramming method to develop a critical typology for classifying university-community engagement. My modified grid-group diagram provides a structured typological space within which four distinct methods of university-community engagement can be identified and discussed – both in relation to their internal communicational characteristics, and in relation to each other. The university-engagement grid-group diagram is constructed by locating each of Douglas’ four quadrants within Charles Peirce’s four methods of enquiry. Peirce’s work is introduced because each of his four methods of enquiry deals specifically with how disagreements are processed and resolved. When Peirce’s methods for fixing belief are located in Douglas’ grid-group diagram, they create a sense-making framework for university-community engagement. It is argued

  13. Community violence and urban childhood asthma: a multilevel analysis.

    Sternthal, M J; Jun, H-J; Earls, F; Wright, R J

    2010-12-01

    We examined the association between community violence exposure and childhood asthma risk in a multilevel, multimethod, longitudinal study controlling for individual- and neighbourhood-level confounders and pathway variables. Analyses included 2,071 children aged 0-9 yrs at enrolment from the Project on Human Development in Chicago Neighborhoods. Multilevel logistic regression models estimated the likelihood of asthma, controlling for individual-level (child's age, sex, race/ethnicity, maternal asthma, socioeconomic status and family violence in the home) and neighbourhood-level confounders (concentrated disadvantage, collective efficacy and social disorder), and pathway variables (maternal smoking, breastfeeding). In adjusted analyses, medium (OR 1.60, 95% CI 1.17-2.19) and high levels (OR 1.56, 95% CI 1.12-2.18) of community violence were associated with increased asthma risk, relative to low levels. The increased asthma risk remained for African Americans when models included community violence and all other individual-level covariates, but attenuated to borderline nonsignificance when further adjusting for collective efficacy. Community violence is associated with asthma risk when controlling for individual- and neighborhood-level confounders. Neither community violence, nor the other individual-level factors, fully accounted for the excess asthma burden among African Americans. These data suggest that public health interventions outside the biomedical model may be needed to reduce asthma in disadvantaged populations.

  14. Perspective for Aquaponic Systems: "Omic" Technologies for Microbial Community Analysis.

    Munguia-Fragozo, Perla; Alatorre-Jacome, Oscar; Rico-Garcia, Enrique; Torres-Pacheco, Irineo; Cruz-Hernandez, Andres; Ocampo-Velazquez, Rosalia V; Garcia-Trejo, Juan F; Guevara-Gonzalez, Ramon G

    2015-01-01

    Aquaponics is the combined production of aquaculture and hydroponics, connected by a water recirculation system. In this productive system, the microbial community is responsible for carrying out the nutrient dynamics between the components. The nutrimental transformations mainly consist in the transformation of chemical species from toxic compounds into available nutrients. In this particular field, the microbial research, the "Omic" technologies will allow a broader scope of studies about a current microbial profile inside aquaponics community, even in those species that currently are unculturable. This approach can also be useful to understand complex interactions of living components in the system. Until now, the analog studies were made to set up the microbial characterization on recirculation aquaculture systems (RAS). However, microbial community composition of aquaponics is still unknown. "Omic" technologies like metagenomic can help to reveal taxonomic diversity. The perspectives are also to begin the first attempts to sketch the functional diversity inside aquaponic systems and its ecological relationships. The knowledge of the emergent properties inside the microbial community, as well as the understanding of the biosynthesis pathways, can derive in future biotechnological applications. Thus, the aim of this review is to show potential applications of current "Omic" tools to characterize the microbial community in aquaponic systems.

  15. A Comparative Analysis of Community Detection Algorithms on Artificial Networks

    Yang, Zhao; Tessone, Claudio Juan

    2016-01-01

    Many community detection algorithms have been developed to uncover the mesoscopic properties of complex networks. However how good an algorithm is, in terms of accuracy and computing time, remains still open. Testing algorithms on real-world network has certain restrictions which made their insights potentially biased: the networks are usually small, and the underlying communities are not defined objectively. In this study, we employ the Lancichinetti-Fortunato-Radicchi benchmark graph to test eight state-of-the-art algorithms. We quantify the accuracy using complementary measures and algorithms' computing time. Based on simple network properties and the aforementioned results, we provide guidelines that help to choose the most adequate community detection algorithm for a given network. Moreover, these rules allow uncovering limitations in the use of specific algorithms given macroscopic network properties. Our contribution is threefold: firstly, we provide actual techniques to determine which is the most sui...

  16. Conceptualizing age-friendly community characteristics in a sample of urban elders: an exploratory factor analysis.

    Smith, Richard J; Lehning, Amanda J; Dunkle, Ruth E

    2013-01-01

    Accurate conceptualization and measurement of age-friendly community characteristics would help to reduce barriers to documenting the effects on elders of interventions to create such communities. This article contributes to the measurement of age-friendly communities through an exploratory factor analysis of items reflecting an existing US Environmental Protection Agency policy framework. From a sample of urban elders (n = 1,376), we identified 6 factors associated with demographic and health characteristics: access to business and leisure, social interaction, access to health care, neighborhood problems, social support, and community engagement. Future research should explore the effects of these factors across contexts and populations.

  17. Understanding interactions in virtual HIV communities: a social network analysis approach.

    Shi, Jingyuan; Wang, Xiaohui; Peng, Tai-Quan; Chen, Liang

    2017-02-01

    This study investigated the driving mechanism of building interaction ties among the people living with HIV/AIDS in one of the largest virtual HIV communities in China using social network analysis. Specifically, we explained the probability of forming interaction ties with homophily and popularity characteristics. The exponential random graph modeling results showed that members in this community tend to form homophilous ties in terms of shared location and interests. Moreover, we found a tendency away from popularity effect. This suggests that in this community, resources and information were not disproportionally received by a few of members, which could be beneficial to the overall community.

  18. Analysis of Computer Science Communities Based on DBLP

    Biryukov, Maria; 10.1007/978-3-642-15464-5_24

    2010-01-01

    It is popular nowadays to bring techniques from bibliometrics and scientometrics into the world of digital libraries to analyze the collaboration patterns and explore mechanisms which underlie community development. In this paper we use the DBLP data to investigate the author's scientific career and provide an in-depth exploration of some of the computer science communities. We compare them in terms of productivity, population stability and collaboration trends.Besides we use these features to compare the sets of topranked conferences with their lower ranked counterparts.

  19. SmashCommunity: A metagenomic annotation and analysis tool

    Arumugam, Manimozhiyan; Harrington, Eoghan D; Foerstner, Konrad U;

    2010-01-01

    the quantitative phylogenetic and functional compositions of metagenomes, to compare compositions of multiple metagenomes and to produce intuitive visual representations of such analyses. AVAILABILITY: SmashCommunity is freely available at http://www.bork.embl.de/software/smash CONTACT: bork@embl.de....

  20. Professional communities and student achievement - a meta-analysis

    Lomos, Catalina; Hofman, Roelande H.; Bosker, Roel J.

    2011-01-01

    In the past 3 decades, the concept of professional community has gained considerable momentum in the theoretical and empirical studies in this field. At the same time, the concept has faced conceptual and methodological difficulties in that as yet no universal definition has been formulated and that

  1. Pyrosequencing analysis of the bacterial community in drinking water wells.

    Navarro-Noya, Yendi E; Suárez-Arriaga, Mayra C; Rojas-Valdes, Aketzally; Montoya-Ciriaco, Nina M; Gómez-Acata, Selene; Fernández-Luqueño, Fabián; Dendooven, Luc

    2013-07-01

    Wells used for drinking water often have a large biomass and a high bacterial diversity. Current technologies are not always able to reduce the bacterial population, and the threat of pathogen proliferation in drinking water sources is omnipresent. The environmental conditions that shape the microbial communities in drinking water sources have to be elucidated, so that pathogen proliferation can be foreseen. In this work, the bacterial community in nine water wells of a groundwater aquifer in Northern Mexico were characterized and correlated to environmental characteristics that might control them. Although a large variation was observed between the water samples, temperature and iron concentration were the characteristics that affected the bacterial community structure and composition in groundwater wells. Small increases in the concentration of iron in water modified the bacterial communities and promoted the growth of the iron-oxidizing bacteria Acidovorax. The abundance of the genera Flavobacterium and Duganella was correlated positively with temperature and the Acidobacteria Gp4 and Gp1, and the genus Acidovorax with iron concentrations in the well water. Large percentages of Flavobacterium and Pseudomonas bacteria were found, and this is of special concern as bacteria belonging to both genera are often biofilm developers, where pathogens survival increases.

  2. A Learning Community's Potential Academic Impact: A Qualitative Analysis

    Firmin, Michael W.; Warner, Susan C.; Rose, Stephanie Firebaugh; Johnson, Courtney B.; Firmin, Ruth L.

    2012-01-01

    Learning Communities (LC) in higher education can serve as powerful connectors among individuals, particularly when integrating minority and White students. We conducted 24 in-depth interviews, using qualitative research methodology, with the 2004 cohort of LC students from a private, selective, Midwest university. Seniors at the time of…

  3. Defining Campus Violence: A Phenomenological Analysis of Community Stakeholder Perspectives

    Mayhew, Matthew J.; Caldwell, Rebecca J.; Goldman, Emily Grey

    2011-01-01

    The purpose of this study was to derive an empirically based understanding of campus violence. Grounded in a communication paradigm offered by sociolinguistic scholars, we adopted a phenomenological approach for conducting and analyzing 23 interviews from campus community stakeholders, including students, staff, faculty, administrators, and…

  4. Community College Mission Influence on Culture: An Organizational Analysis

    Stephens, E. Gerome

    2013-01-01

    Strong agreement of mission and culture has been found in more effective colleges (Fjortoft & Smart, 1994). For leaders, the culture of an organization provides the context for which decisions about organizational change processes can be made (Malm, 2008). The purpose of this study was to explore the culture present within a community college…

  5. Using Analysis of Governance to Unpack Community-Based Conservation: A Case Study from Tanzania.

    Robinson, Lance W; Makupa, Enock

    2015-11-01

    Community-based conservation policies and programs are often hollow with little real devolution. But to pass a judgment of community-based or not community-based on such initiatives and programs obscures what is actually a suite of attributes. In this paper, we analyze governance around a specific case of what is nominally community-based conservation-Ikona Wildlife Management Area (WMA) in Tanzania-using two complementary sets of criteria. The first relates to governance "powers": planning powers, regulatory powers, spending powers, revenue-generating powers, and the power to enter into agreements. The second set of criteria derive from the understanding of governance as a set of social functions: social coordination, shaping power, setting direction, and building community. The analysis helps to detail ways in which the Tanzanian state through policy and regulations has constrained the potential for Ikona WMA to empower communities and community actors. Although it has some features of community-based conservation, community input into how the governance social functions would be carried out in the WMA was constrained from the start and is now largely out of community hands. The two governance powers that have any significant community-based flavor-spending powers and revenue-generating powers-relate to the WMA's tourism activities, but even here the picture is equivocal at best. The unpacking of governance that we have done, however, reveals that community empowerment through the processes associated with creating and recognizing indigenous and community-conserved areas is something that can be pursued through multiple channels, some of which might be more strategic than others.

  6. Multiplex social ecological network analysis reveals how social changes affect community robustness more than resource depletion.

    Baggio, Jacopo A; BurnSilver, Shauna B; Arenas, Alex; Magdanz, James S; Kofinas, Gary P; De Domenico, Manlio

    2016-11-29

    Network analysis provides a powerful tool to analyze complex influences of social and ecological structures on community and household dynamics. Most network studies of social-ecological systems use simple, undirected, unweighted networks. We analyze multiplex, directed, and weighted networks of subsistence food flows collected in three small indigenous communities in Arctic Alaska potentially facing substantial economic and ecological changes. Our analysis of plausible future scenarios suggests that changes to social relations and key households have greater effects on community robustness than changes to specific wild food resources.

  7. Community analysis of biting midges (Culicoides Latr.) on livestock farms in Denmark

    Nielsen, S. A.; Banta, G.; Rasmussen, Anne-Marie;

    2014-01-01

    This study presents descriptive statistics and community analysis of adult biting midges trapped at 16 livestock farms by means of light traps on Zealand and Lolland-Falster, Denmark. A total of 9,047 male and female Culicoides divided into 24 species, were caught. Biotic and abiotic factors...... ranging from presence of different host species (cattle or sheep/goats), presence of small woody areas or wetlands in the surrounding landscape, and agricultural practice (organic or conventional) were included in the community analysis. Only differences in the Culicoides communities between conventional...

  8. Evaluation of next generation sequencing for the analysis of Eimeria communities in wildlife.

    Vermeulen, Elke T; Lott, Matthew J; Eldridge, Mark D B; Power, Michelle L

    2016-05-01

    Next-generation sequencing (NGS) techniques are well-established for studying bacterial communities but not yet for microbial eukaryotes. Parasite communities remain poorly studied, due in part to the lack of reliable and accessible molecular methods to analyse eukaryotic communities. We aimed to develop and evaluate a methodology to analyse communities of the protozoan parasite Eimeria from populations of the Australian marsupial Petrogale penicillata (brush-tailed rock-wallaby) using NGS. An oocyst purification method for small sample sizes and polymerase chain reaction (PCR) protocol for the 18S rRNA locus targeting Eimeria was developed and optimised prior to sequencing on the Illumina MiSeq platform. A data analysis approach was developed by modifying methods from bacterial metagenomics and utilising existing Eimeria sequences in GenBank. Operational taxonomic unit (OTU) assignment at a high similarity threshold (97%) was more accurate at assigning Eimeria contigs into Eimeria OTUs but at a lower threshold (95%) there was greater resolution between OTU consensus sequences. The assessment of two amplification PCR methods prior to Illumina MiSeq, single and nested PCR, determined that single PCR was more sensitive to Eimeria as more Eimeria OTUs were detected in single amplicons. We have developed a simple and cost-effective approach to a data analysis pipeline for community analysis of eukaryotic organisms using Eimeria communities as a model. The pipeline provides a basis for evaluation using other eukaryotic organisms and potential for diverse community analysis studies.

  9. High-Resolution Melt Analysis for Rapid Comparison of Bacterial Community Compositions

    Hjelmsø, Mathis Hjort; Hansen, Lars Hestbjerg; Bælum, Jacob

    2014-01-01

    and fertilization treatments. The HRM analysis identified a shift in the bacterial community composition in two of the treatments, both including the soil fumigant Basamid GR. These results were confirmed with both denaturing gradient gel electrophoresis (DGGE) analysis and 454-based 16S rRNA gene amplicon......In the study of bacterial community composition, 16S rRNA gene amplicon sequencing is today among the preferred methods of analysis. The cost of nucleotide sequence analysis, including requisite computational and bioinformatic steps, however, takes up a large part of many research budgets. High......-resolution melt (HRM) analysis is the study of the melt behavior of specific PCR products. Here we describe a novel high-throughput approach in which we used HRM analysis targeting the 16S rRNA gene to rapidly screen multiple complex samples for differences in bacterial community composition. We hypothesized...

  10. Newcomer Integration in Online Knowledge Building Communities: Automated Dialogue Analysis in Integrative vs. Non-Integrative Blogger Communities

    Nicolae Nistor

    2014-11-01

    Full Text Available Online knowledge building communities (OKBC reunite participants engaged in collaborative discourse. OKBCs can be made „smart“ by adding tools that predict how likely an OKBC is to integrate newcomers in existing dialogues and socio-cognitive structures. Starting from Bakhtin’s dialogical approach and polyphony theory, and building on the concept of inter- animation of voices, this study explores the relationship between newcomer integration and dialogue quality in OKBCs. The automated analysis tool “Important Moments” was employed to compare two dialogues, from an integrative and from a non-integrative blog-based OKBC. In the former, the concepts, lexical chains and inter-animation moments occurred more frequently than in the latter. Also, newcomer comments were linked to less lexical chains in the integrative community than in the non-integrative OKBC. These findings suggest close relationships between dialogue quality and newcomer integration, which can be used for designing smart OKBCs.

  11. Analysis of Community Detection Algorithms for Large Scale Cyber Networks

    Mane, Prachita; Shanbhag, Sunanda; Kamath, Tanmayee; Mackey, Patrick S.; Springer, John

    2016-09-30

    The aim of this project is to use existing community detection algorithms on an IP network dataset to create supernodes within the network. This study compares the performance of different algorithms on the network in terms of running time. The paper begins with an introduction to the concept of clustering and community detection followed by the research question that the team aimed to address. Further the paper describes the graph metrics that were considered in order to shortlist algorithms followed by a brief explanation of each algorithm with respect to the graph metric on which it is based. The next section in the paper describes the methodology used by the team in order to run the algorithms and determine which algorithm is most efficient with respect to running time. Finally, the last section of the paper includes the results obtained by the team and a conclusion based on those results as well as future work.

  12. Boston Community Energy Study - Zonal Analysis for Urban Microgrids

    2016-04-05

    Hatziargyriou, H. Asano, R. Iravani, and C. Marnay, “Microgrids,” Power and Energy Magazine , IEEE 5(4), 78–94 (2007). [18] M. Stadler, “Effect of Heat and...markets. These microgrids typically exploit combined heat and power (CHP) systems to increase the overall energy efficiency, while increasing grid...simulation. The community energy simulation reflects certain policies of the City of Boston, including increasing affordability, increasing power grid

  13. Perceived community environmental influences on eating behaviors: A Photovoice analysis.

    Belon, Ana Paula; Nieuwendyk, Laura M; Vallianatos, Helen; Nykiforuk, Candace I J

    2016-12-01

    People's perceptions of local food environments influence their abilities to eat healthily. PhotoVoice participants from four communities in Alberta, Canada took pictures of barriers and opportunities for healthy eating and shared their stories in one-on-one semi-structured interviews. Using a socioecological framework, emergent themes were organized by type and size of environment. Findings show that, while availability and access to food outlets influence healthy eating practices, these factors may be eclipsed by other non-physical environmental considerations, such as food regulations and socio-cultural preferences. This study identifies a set of meta-themes that summarize and illustrate the interrelationships between environmental attributes, people's perceptions, and eating behaviors: a) availability and accessibility are interrelated and only part of the healthy eating equation; b) local food is synonymous with healthy eating; c) local food places for healthy eating help define community identity; d) communal dining (commensality) does not necessarily mean healthy eating; e) rewarding an achievement or celebrating special occasions with highly processed foods is socially accepted; f) food costs seemed to be driving forces in food decisions; g) macro-environmental influences are latent in food decisions. Recognizing the interrelationship among multiple environmental factors may help efforts to design effective community-based interventions and address knowledge gaps on how sociocultural, economic, and political environments intersect with physical worlds.

  14. AN ANALYSIS OF PHARMACY SERVICES BY PHARMACIST IN COMMUNITY PHARMACY

    Max Joseph Herman

    2013-03-01

    Full Text Available ABSTRACT Background: Up to now there are more than 60 schools of pharmacy with a variety of accreditation level in lndonesia. Previous study found that the standard of pharmaceutical services at various service facilities (hospitals, primary health care and community pharmacy can not be fully implemented because of the limited competency of pharmacist. This study was conducted to identify the qualification of pharmacist who delivers services in community pharmacy in compliance with the Indonesian Health Law No. 36 of 2009. As mandated in the Health Law No. 36 of 2009, the government is obliged to establish minimum requirements that must be possessed. Methods: This cross sectional study was conducted in 2010 at 2 community pharmacies in each of 3 cities, i.e. Bandung, DI Yogyakarta and Surabaya. Other than ten pharmacists delivering services in community pharmacies, there were pharmacists as informants from 4 institutions in each city selected, i.e. six pharmacists from two Schools of Pharmacy, three pharmacists from three Regional Indonesian Pharmacists Association,six pharmacists from three District Health Offices and three Provincial Health Offices. Primary data collection through in-depth interviews and observation as well as secondary data collection concerning standard operating procedures, monitoring documentation and academic curricula has been used. Descriptive data were analysed qualitatively Results: The findings indicate that pharmacists' qualification to deliver services in a community pharmacy in accordance with the Government Regulation No. 51 of 2009, Standards of Pharmacy Services in Community Pharmacy and Good Pharmaceutical Practices (GPP was varied. Most pharmacists have already understood their roles in pharmacy service, but to practice it in accordance with the standards or guidelines they are still having problems. It is also acknowledged by pharmacists in other institutions, including School of Pharmacy, Regional

  15. Organizational analysis of three community support program models.

    Reinke, B; Greenley, J R

    1986-06-01

    Little attention has been paid to the organizational and administrative characteristics of effective community support programs for the chronic mentally ill. The authors analyzed three successful support programs in Wisconsin that employ three different models of service delivery: one provides services through caseworkers who carry specialized caseloads, another through local nonprofessionals who work with a centrally located program coordinator, and the third through a team of various mental health workers. Each program has tailored its organizational process to suit the types of clients it sees, the size of its catchment area, and the availability of other professional resources. The interrelated strengths and weaknesses of each model are discussed.

  16. Microbial community analysis of anaerobic reactors treating soft drink wastewater.

    Takashi Narihiro

    Full Text Available The anaerobic packed-bed (AP and hybrid packed-bed (HP reactors containing methanogenic microbial consortia were applied to treat synthetic soft drink wastewater, which contains polyethylene glycol (PEG and fructose as the primary constituents. The AP and HP reactors achieved high COD removal efficiency (>95% after 80 and 33 days of the operation, respectively, and operated stably over 2 years. 16S rRNA gene pyrotag analyses on a total of 25 biofilm samples generated 98,057 reads, which were clustered into 2,882 operational taxonomic units (OTUs. Both AP and HP communities were predominated by Bacteroidetes, Chloroflexi, Firmicutes, and candidate phylum KSB3 that may degrade organic compound in wastewater treatment processes. Other OTUs related to uncharacterized Geobacter and Spirochaetes clades and candidate phylum GN04 were also detected at high abundance; however, their relationship to wastewater treatment has remained unclear. In particular, KSB3, GN04, Bacteroidetes, and Chloroflexi are consistently associated with the organic loading rate (OLR increase to 1.5 g COD/L-d. Interestingly, KSB3 and GN04 dramatically decrease in both reactors after further OLR increase to 2.0 g COD/L-d. These results indicate that OLR strongly influences microbial community composition. This suggests that specific uncultivated taxa may take central roles in COD removal from soft drink wastewater depending on OLR.

  17. Is the contribution of community forest users financially efficient? A household level benefit-cost analysis of community forest management in Nepal

    Rajesh Kumar Rai

    2016-02-01

    Full Text Available Community forestry in Nepal is considered an exemplary forest management regime. However, the economics behind managing a community forest is not fully studied. This study examines whether the benefits generated from community forest management justify the contributions of forest users. The study is based on a survey of community forest users in Chitwan, Nepal. A household level benefit-cost analysis was performed to quantify and compare the costs and benefits from community forest management. Only direct benefits were included in the analysis. The study shows that older forest user groups derive more benefits to households compared to more recently established ones. The extent of timber harvesting also substantially influences the size of the household benefits. In addition, redistribution of benefits at the household level, in terms of income generating activities and payment for involvement in forest management activities, also enhances household benefits. Sensitivity analysis suggests that the current practice of community forest management enhances the welfare of rural households in this subsistence community. However, this finding is sensitive to assumptions regarding the opportunity cost of time. The study also found that the household costs of community forest management depend upon two factors – the area of community forest and the size of the forest area relative to the number of households.

  18. Analysis of oxygen reduction and microbial community of air-diffusion biocathode in microbial fuel cells.

    Wang, Zejie; Zheng, Yue; Xiao, Yong; Wu, Song; Wu, Yicheng; Yang, Zhaohui; Zhao, Feng

    2013-09-01

    Microbes play irreplaceable role in oxygen reduction reaction of biocathode in microbial fuel cells (MFCs). In this study, air-diffusion biocathode MFCs were set up for accelerating oxygen reduction and microbial community analysis. Linear sweep voltammetry and Tafel curve confirmed the function of cathode biofilm to catalyze oxygen reduction. Microbial community analysis revealed higher diversity and richness of community in plankton than in biofilm. Proteobacteria was the shared predominant phylum in both biofilm and plankton (39.9% and 49.8%) followed by Planctomycetes (29.9%) and Bacteroidetes (13.3%) in biofilm, while Bacteroidetes (28.2%) in plankton. Minor fraction (534, 16.4%) of the total operational taxonomic units (3252) was overlapped demonstrating the disproportionation of bacterial distribution in biofilm and plankton. Pseudomonadales, Rhizobiales and Sphingobacteriales were exoelectrogenic orders in the present study. The research obtained deep insight of microbial community and provided more comprehensive information on uncultured rare bacteria.

  19. Bioconductor workflow for microbiome data analysis: from raw reads to community analyses

    Callahan, Ben J.; Sankaran, Kris; Fukuyama, Julia A.; McMurdie, Paul J.; Holmes, Susan P; Garud, Nandita R.; Charlop-Powers, Zachary; Lahti, Leo

    2016-01-01

    High-throughput sequencing of PCR-amplified taxonomic markers (like the 16S rRNA gene) has enabled a new level of analysis of complex bacterial communities known as microbiomes. Many tools exist to quantify and compare abundance levels or microbial composition of communities in different conditions. The sequencing reads have to be denoised and assigned to the closest taxa from a reference database. Common approaches use a notion of 97% similarity and normalize the data by subsampling to equal...

  20. Characterization of Antimicrobial Resistance Dissemination across Plasmid Communities Classified by Network Analysis

    Akifumi Yamashita

    2014-04-01

    Full Text Available The global clustering of gene families through network analysis has been demonstrated in whole genome, plasmid, and microbiome analyses. In this study, we carried out a plasmidome network analysis of all available complete bacterial plasmids to determine plasmid associations. A blastp clustering search at 100% aa identity cut-off and sharing at least one gene between plasmids, followed by a multilevel community network analysis revealed that a surprisingly large number of the plasmids were connected by one largest connected component (LCC, with dozens of community sub-groupings. The LCC consisted mainly of Bacilli and Gammaproteobacteria plasmids. Intriguingly, horizontal gene transfer (HGT was noted between different phyla (i.e., Staphylococcus and Pasteurellaceae, suggesting that Pasteurellaceae can acquire antimicrobial resistance (AMR genes from closely contacting Staphylococcus spp., which produce the external supplement of V-factor (NAD. Such community network analysis facilitate displaying possible recent HGTs like a class 1 integron, str and tet resistance markers between communities. Furthermore, the distribution of the Inc replicon type and AMR genes, such as the extended-spectrum ß-lactamase (ESBL CTX-M or the carbapenemases KPC NDM-1, implies that such genes generally circulate within limited communities belonging to typical bacterial genera. Thus, plasmidome network analysis provides a remarkable discriminatory power for plasmid-related HGT and evolution.

  1. Development and application of functional gene arrays for microbial community analysis

    Z.L.HE; J.D.VAN NOSTRAND; L.Y.WU; J.Z.ZHOU

    2008-01-01

    Functional gene markers can provide important information about functional gene diversity and potential activity of microbial communities.Although microarray technology has been successfully applied to study gene expression for pure cultures,simple,and artificial microbial communities,adapting such a technology to analyze complex microbial communities still presents a lot of challenges in terms of design,sample preparation,and data analysis.This work is focused on the development and application of functional gene arrays (FGAs) to target key functional gene markers for microbial community studies.A few key issues specifically related to FGAs,such as oligonucleotide probe design,nucleic acid extraction and purification,data analysis,specificity,sensitivity,and quantitative capability are discussed in detail.Recent studies have demonstrated that FGAs can provide specific,sensitive,and potentially quantitative information about microbial communities from a variety of natural environments and controlled ecosystems.This technology is expected to revolutionize the analysis of microbial communities,and link microbial structure to ecosystem functioning.

  2. Applying information network analysis to fire-prone landscapes: implications for community resilience

    Derric B. Jacobs

    2017-03-01

    Full Text Available Resilient communities promote trust, have well-developed networks, and can adapt to change. For rural communities in fire-prone landscapes, current resilience strategies may prove insufficient in light of increasing wildfire risks due to climate change. It is argued that, given the complexity of climate change, adaptations are best addressed at local levels where specific social, cultural, political, and economic conditions are matched with local risks and opportunities. Despite the importance of social networks as key attributes of community resilience, research using social network analysis on coupled human and natural systems is scarce. Furthermore, the extent to which local communities in fire-prone areas understand climate change risks, accept the likelihood of potential changes, and have the capacity to develop collaborative mitigation strategies is underexamined, yet these factors are imperative to community resiliency. We apply a social network framework to examine information networks that affect perceptions of wildfire and climate change in Central Oregon. Data were collected using a mailed questionnaire. Analysis focused on the residents' information networks that are used to gain awareness of governmental activities and measures of community social capital. A two-mode network analysis was used to uncover information exchanges. Results suggest that the general public develops perceptions about climate change based on complex social and cultural systems rather than as patrons of scientific inquiry and understanding. It appears that perceptions about climate change itself may not be the limiting factor in these communities' adaptive capacity, but rather how they perceive local risks. We provide a novel methodological approach in understanding rural community adaptation and resilience in fire-prone landscapes and offer a framework for future studies.

  3. Investigating Student Communities with Network Analysis of Interactions in a Physics Learning Center

    Brewe, Eric; Sawtelle, Vashti

    2011-01-01

    Developing a sense of community among students is one of the three pillars of an overall reform effort to increase participation in physics, and the sciences more broadly, at Florida International University. The emergence of a research and learning community, embedded within a course reform effort, has contributed to increased recruitment and retention of physics majors. Finn and Rock [1] link the academic and social integration of students to increased rates of retention. We utilize social network analysis to quantify interactions in Florida International University's Physics Learning Center (PLC) that support the development of academic and social integration,. The tools of social network analysis allow us to visualize and quantify student interactions, and characterize the roles of students within a social network. After providing a brief introduction to social network analysis, we use sequential multiple regression modeling to evaluate factors which contribute to participation in the learning community. ...

  4. A SOCIAL NETWORK ANALYSIS APPROACH TO UNDERSTAND CHANGES IN A CANCER DISPARITIES COMMUNITY PARTNERSHIP NETWORK.

    Luque, John S; Tyson, Dinorah Martinez; Bynum, Shalanda A; Noel-Thomas, Shalewa; Wells, Kristen J; Vadaparampil, Susan T; Gwede, Clement K; Meade, Cathy D

    2011-11-01

    The Tampa Bay Community Cancer Network (TBCCN) is one of the Community Network Program sites funded (2005-10) by the National Cancer Institute's Center to Reduce Cancer Health Disparities. TBCCN was tasked to form a sustainable, community-based partnership network focused on the goal of reducing cancer health disparities among racial-ethnic minority and medically underserved populations. This article reports evaluation outcome results from a social network analysis and discusses the varying TBCCN partner roles-in education, training, and research-over a span of three years (2007-09). The network analysis included 20 local community partner organizations covering a tricounty area in Southwest Florida. In addition, multiple externally funded, community-based participatory research pilot projects with community-academic partners have either been completed or are currently in progress, covering research topics including culturally targeted colorectal and prostate cancer screening education, patient navigation focused on preventing cervical cancer in rural Latinas, and community perceptions of biobanking. The social network analysis identified a trend toward increased network decentralization based on betweenness centrality and overall increase in number of linkages, suggesting network sustainability. Degree centrality, trust, and multiplexity exhibited stability over the three-year time period. These results suggest increased interaction and interdependence among partner organizations and less dependence on the cancer center. Social network analysis enabled us to quantitatively evaluate partnership network functioning of TBCCN in terms of network structure and information and resources flows, which are integral to understanding effective coalition practice based on Community Coalition Action Theory ( Butterfoss and Kegler 2009). Sharing the results of the social network analysis with the partnership network is an important component of our coalition building efforts. A

  5. Regional-scale analysis of subtidal rocky shore community

    Derrien-Courtel, Sandrine; Le Gal, Aodren; Grall, Jacques

    2013-12-01

    The French monitoring network, REseau BENThique (REBENT), was launched by the Ministry of the Environment in 2003 following the 1999 Erika oil spill. REBENT aimed to acquire baseline knowledge of coastal benthic habitat distributions with a special focus on biological diversity. This study analyzed data from 38 subtidal rocky reef sites collected by a single diving team of marine biologists along the coast of Brittany from 2004 to 2010. At each site, the depth limits of the algal belts were determined between 0 and -40 m Chart Datum (CD); the flora and fauna compositions and abundances were sampled at -3 and -8 m CD. A total of 364 taxa (156 flora and 208 fauna), belonging to 12 phyla, were identified. The results showed that the depth limit and density of kelp beds increased as water turbidity decreased; moreover, several changes in community structure could be related to water turbidity and temperature. Thus, northern and southern Brittany showed strong differences in diversity and structure of the dominant kelp species ( Laminaria hyperborea and Saccorhiza polyschides). The results from this kelp habitat composition survey (dominant kelp species and indicator species) provided important information for local pressure assessments, like increases in turbidity. The data also provided a reference that could be useful for detecting changes in coastal water temperatures due to global warming.

  6. Spatial and seasonal variations in bacterial communities of the Yellow Sea by T-RFLP analysis

    Hongyuan WANG; Xiaolu JIANG; Ya HE; Huashi GUAN

    2009-01-01

    Four typical coastal sites (rocky shore, sandy shore, mud flat shore, and artificial harbor) at the Yellow Sea were chosen to investigate the spatial and seasonal variations in bacterial communities. This was accomplished by using terminal restriction fragment length polymorphism (T-RFLP) analysis of PCR amplified 16S rDNA fragments. Two kinds of tetrameric restriction enzymes, HhaI and MspI, were used in the experiment to depict the bacterial community diversity in different marine environments. It was found that the community compositions digested by the two enzymes separately were different. However, the results of bacterial community diversity derived from them were similar. The MDA analysis results of T-RFLP profiles coming from HhaI and MspI both exhibited a significant seasonal community shift for bacteria and a relatively low spatial variation among the four locations. With HhaI as the sample, the pair wise T-tests also revealed that variations were minor between each pair of marine environments, with R ranging from 0.198 to 0.349. However, the bacterial community structure in the mud flat site depicted a larger difference than each of the other three sites (R ranging from 0.282 to 0.349).

  7. Characterization of chlorinated and chloraminated drinking water microbial communities in a distribution system simulator using pyrosequencing data analysis

    The molecular analysis of drinking water microbial communities has focused primarily on 16S rRNA gene sequence analysis. Since this approach provides limited information on function potential of microbial communities, analysis of whole-metagenome pyrosequencing data was used to...

  8. Analysis Grid for Environments Linked to Obesity (ANGELO) framework to develop community-driven health programmes in an Indigenous community in Canada.

    Willows, Noreen; Dyck Fehderau, David; Raine, Kim D

    2016-09-01

    Indigenous First Nations people in Canada have high chronic disease morbidity resulting in part from enduring social inequities and colonialism. Obesity prevention strategies developed by and for First Nations people are crucial to improving the health status of this group. The research objective was to develop community-relevant strategies to address childhood obesity in a First Nations community. Strategies were derived from an action-based workshop based on the Analysis Grid for Environments Linked to Obesity (ANGELO) framework. Thirteen community members with wide-ranging community representation took part in the workshop. They combined personal knowledge and experience with community-specific and national research to dissect the broad array of environmental factors that influenced childhood obesity in their community. They then developed community-specific action plans focusing on healthy eating and physical activity for children and their families. Actions included increasing awareness of children's health issues among the local population and community leadership, promoting nutrition and physical activity at school, and improving recreation opportunities. Strengthening children's connection to their culture was considered paramount to improving their well-being; thus, workshop participants developed programmes that included elders as teachers and reinforced families' acquaintance with First Nations foods and activities. The research demonstrated that the ANGELO framework is a participatory way to develop community-driven health programmes. It also demonstrated that First Nations people involved in the creation of solutions to health issues in their communities may focus on decolonising approaches such as strengthening their connection to indigenous culture and traditions. External funds were not available to implement programmes and there was no formal follow-up to determine if community members implemented programmes. Future research needs to examine the

  9. The role of reflection in the effects of community service on adolescent development: A meta-analysis

    Van Goethem, Anne A J; Van Hoof, Anne; Orobio De Castro, Bram; Van Aken, Marcel A G; Hart, Daniel A.; Leerstoel Aken; Leerstoel Orobio de Castro; Faculteit Sociale Wetenschappen

    2014-01-01

    This meta-analysis assessed the effect of community service on adolescent development and the moderation of this effect by reflection, community service, and adolescent characteristics to explicate the mechanisms underlying community service effects. Random effects analyses, based on 49 studies (24,

  10. The Role of Reflection in the Effects of Community Service on Adolescent Development : A Meta-Analysis

    Van Goethem, Anne; Van Hoof, Anne; Orobio de Castro, Bram; Van Aken, Marcel; Hart, Daniel

    2015-01-01

    This meta-analysis assessed the effect of community service on adolescent development and the moderation of this effect by reflection, community service, and adolescent characteristics to explicate the mechanisms underlying community service effects. Random effects analyses, based on 49 studies (24,

  11. Community Schools. NAESP School Leadership Digest Series, Number Four. ERIC/CEM Research Analysis Series, Number Six.

    Schofield, Dee

    By making educational opportunities available to all segments of society, the community school narrows the gap between "in school" experience and "real world" experience. This analysis of the research outlines the history and implementation of the community school concept and its relationship to that of community education. Ways to insure full…

  12. Studying the Complex Communities of Ants and Their Symbionts Using Ecological Network Analysis.

    Ivens, Aniek B F; von Beeren, Christoph; Blüthgen, Nico; Kronauer, Daniel J C

    2016-01-01

    Ant colonies provide well-protected and resource-rich environments for a plethora of symbionts. Historically, most studies of ants and their symbionts have had a narrow taxonomic scope, often focusing on a single ant or symbiont species. Here we discuss the prospects of studying these assemblies in a community ecology context using the framework of ecological network analysis. We introduce three basic network metrics that we consider particularly relevant for improving our knowledge of ant-symbiont communities: interaction specificity, network modularity, and phylogenetic signal. We then discuss army ant symbionts as examples of large and primarily parasitic communities, and symbiotic sternorrhynchans as examples of generally smaller and primarily mutualistic communities in the context of these network analyses. We argue that this approach will provide new and complementary insights into the evolutionary and ecological dynamics between ants and their many associates, and will facilitate comparisons across different ant-symbiont assemblages as well as across different types of ecological networks.

  13. The voluntary community health movement in India: a strengths, weaknesses, opportunities, and threats (SWOT) analysis.

    Sharma, M; Bhatia, G

    1996-12-01

    There has been a prolific growth of voluntary organizations in India since independence in 1947. One of the major areas of this growth has been in the field of community health. The purpose of this article is to historically trace the voluntary movement in community health in India, analyze the current status, and predict future trends of voluntary efforts. A review of the literature in the form of a Strengths, Weaknesses, Opportunities, and Threats (SWOT) analysis was the method of this study. Some of the key trends which emerged as the priority areas for progress and for strengthening voluntary organizations in the future were enhancing linkages between health and development; building upon collective force; greater utilization of participatory training; establishing egalitarian and effectual linkages for decision making at the international level; developing self-reliant community-based models; and the need for attaining holistic empowerment at individual, organizational, and community levels through "duty consciousness" as opposed to merely asking for rights.

  14. Quantitative Analysis on Economic Contribution of Community Health Service in China

    张新平; 王铁军

    2004-01-01

    Summary: In China, the implementation of community health service shows that the prevention is an essential and important part of our national health system and is helpful to decrease the medical expenditure gradually. According to the data from Health Statistic Information Center of Ministry of Health in China, we calculated that the total health expenditure of China would be decreased 8000. 0 million yuan only in 2001, among which, 1188.3 million, 1953.9 million and 4833.0 million yuan were respectively saved for the government budget, the society and resident if implementing the policy of community health service powerfully. And every outpatient can save 15.46 yuan per time. By the quantitative analysis on the economic contribution of community health service, it can be proved that a great economic benefit could be gotten from the implementation of community health service.

  15. The Northwest Indiana Center for Data and Analysis: A Case Study of Academic Library Community Engagement

    Sandberg, Scott; Morris, Cele; Sutherland, Timothy

    2013-01-01

    This paper details community engagement activity of an academic library coordinated within a broader university strategic plan. The Anderson Library at Indiana University Northwest (IU-Northwest) supports a service called the Northwest Indiana Center for Data and Analysis. Created in 1996 with funding made available from the Indiana University…

  16. A Discourse Analysis of Collaboration between Academic and Student Affairs in Community Colleges

    Gulley, Needham Yancey

    2016-01-01

    The purpose of this study was to understand the nature of collaboration between academic affairs and student affairs units in the community college context from a qualitative perspective. A discourse analysis study was conducted to explore the ways in which collaborative practice was discussed and understood by chief and midlevel academic and…

  17. Chapter 2: Predicting Newcomer Integration in Online Knowledge Communities by Automated Dialog Analysis

    Nistor, Nicolae; Dascalu, Mihai; Stavarache, Lucia; Tarnai, Christian; Trausan-Matu, Stefan

    2016-01-01

    Nistor, N., Dascalu, M., Stavarache, L.L., Tarnai, C., & Trausan-Matu, S. (2015). Predicting Newcomer Integration in Online Knowledge Communities by Automated Dialog Analysis. In Y. Li, M. Chang, M. Kravcik, E. Popescu, R. Huang, Kinshuk & N.-S. Chen (Eds.), State-of-the-Art and Future Directions of

  18. A Social Network Analysis of Teaching and Research Collaboration in a Teachers' Virtual Learning Community

    Lin, Xiaofan; Hu, Xiaoyong; Hu, Qintai; Liu, Zhichun

    2016-01-01

    Analysing the structure of a social network can help us understand the key factors influencing interaction and collaboration in a virtual learning community (VLC). Here, we describe the mechanisms used in social network analysis (SNA) to analyse the social network structure of a VLC for teachers and discuss the relationship between face-to-face…

  19. Critical Social Network Analysis in Community Colleges: Peer Effects and Credit Attainment

    González Canché, Manuel S.; Rios-Aguilar, Cecilia

    2014-01-01

    This chapter discusses the importance of conducting critical social network analysis (CSNA) in higher education. To illustrate the benefits of CSNA, the authors use existing institutional data to examine peer effects in community colleges. The chapter ends with a discussion of the implications of using a CSNA approach to measure inequities in…

  20. Research Trends in the Study of ICT Based Learning Communities: A Bibliometric Analysis

    Hernández, Jonathan Bermúdez; Chalela, Salim; Arias, Jackeline Valencia; Arias, Alejandro Valencia

    2017-01-01

    The current opportunities to develop and acquire knowledge in the network, Information and Communications Technology (ICT) play a major role in the learning process. This research offers a bibliometric analysis in order to examine the state of the research activity carried out in relation to the learning communities based on ICT. The indicators…

  1. Confirmatory Factor Analysis of the Career Factors Inventory on a Community College Sample

    Simon, Merril A.; Tovar, Esau

    2004-01-01

    A confirmatory factor analysis was conducted using AMOS 4.0 to validate the 21-item Career Factors Inventory on a community college student sample. The multidimensional inventory assesses types and levels of career indecision antecedents. The sample consisted of 512 ethnically diverse freshmen students; 46% were men and 54% were women.…

  2. Metagenomic Analysis of Bacterial Communities of Antarctic Surface Snow.

    Lopatina, Anna; Medvedeva, Sofia; Shmakov, Sergey; Logacheva, Maria D; Krylenkov, Vjacheslav; Severinov, Konstantin

    2016-01-01

    The diversity of bacteria present in surface snow around four Russian stations in Eastern Antarctica was studied by high throughput sequencing of amplified 16S rRNA gene fragments and shotgun metagenomic sequencing. Considerable class- and genus-level variation between the samples was revealed indicating a presence of inter-site diversity of bacteria in Antarctic snow. Flavobacterium was a major genus in one sampling site and was also detected in other sites. The diversity of flavobacterial type II-C CRISPR spacers in the samples was investigated by metagenome sequencing. Thousands of unique spacers were revealed with less than 35% overlap between the sampling sites, indicating an enormous natural variety of flavobacterial CRISPR spacers and, by extension, high level of adaptive activity of the corresponding CRISPR-Cas system. None of the spacers matched known spacers of flavobacterial isolates from the Northern hemisphere. Moreover, the percentage of spacers with matches with Antarctic metagenomic sequences obtained in this work was significantly higher than with sequences from much larger publically available environmental metagenomic database. The results indicate that despite the overall very high level of diversity, Antarctic Flavobacteria comprise a separate pool that experiences pressures from mobile genetic elements different from those present in other parts of the world. The results also establish analysis of metagenomic CRISPR spacer content as a powerful tool to study bacterial populations diversity.

  3. Metagenomic Analysis of Bacterial Communities of Antarctic Surface Snow

    Anna eLopatina

    2016-03-01

    Full Text Available The diversity of bacteria present in surface snow around four Russian stations in Eastern Antarctica was studied by high throughput sequencing of amplified 16S rRNA gene fragments and shotgun metagenomic sequencing. Considerable class- and genus-level variation between the samples was revealed indicating a presence of inter-site diversity of bacteria in Antarctic snow. Flavobacterium was a major genus in one sampling site and was also detected in other sites. The diversity of flavobacterial type II-C CRISPR spacers in the samples was investigated by metagenome sequencing. Thousands of unique spacers were revealed with less than 35% overlap between the sampling sites, indicating an enormous natural variety of flavobacterial CRISPR spacers and, by extension, high level of adaptive activity of the corresponding CRISPR-Cas system. None of the spacers matched known spacers of flavobacterial isolates from the Northern hemisphere. Moreover, the percentage of spacers with matches with Antarctic metagenomic sequences obtained in this work was significantly higher than with sequences from much larger publically available environmental metagenomic database. The results indicate that despite the overall very high level of diversity, Antarctic Flavobacteria comprise a separate pool that experiences pressures from mobile genetic elements different from those present in other parts of the world. The results also establish analysis of metagenomic CRISPR spacer content as a powerful tool to study bacterial populations diversity.

  4. Trenton ICES: demonstration of a grid-connected integrated community energy system. Phase II. Volumes 1 and 2. Preliminary design of ICES system and analysis of community ownership

    1978-03-22

    Preliminary design and evaluation for the system has been carried out. The findings of this study are: (1) it is technically feasible, utilizing commercially available hardware; (2) under utility ownership and operation, it will not be economically competitive with conventional alternatives for heating and cooling buildings (analysis contained in companion report under separate cover); (3) under utility ownership and operation, no restrictions have been identified that would prevent the project from proceeding; (4) under community ownership, preliminary analysis indicates that thermal energy produced by Trenton ICES will be approximately 12 percent less expensive than thermal energy produced by oil-fired boilers; and (5) a review and update of institutional analyses performed during Phase 2 has identified no factors that would preclude community ownership and operation of the Trenton ICES. The background data produced for the analysis of the Trenton ICES based on utility ownership and operation can, in large part, be used as the bases for a detailed analysis of community ownership.

  5. Preparation of microbial community cDNA for metatranscriptomic analysis in marine plankton.

    Stewart, Frank J

    2013-01-01

    High-throughput sequencing and analysis of microbial community cDNA (metatranscriptomics) are providing valuable insight into in situ microbial activity and metabolism in the oceans. A critical first step in metatranscriptomic studies is the preparation of high-quality cDNA. At the minimum, preparing cDNA for sequencing involves steps of biomass collection, RNA preservation, total RNA extraction, and cDNA synthesis. Each of these steps may present unique challenges for marine microbial samples, particularly for deep-sea samples whose transcriptional profiles may change between water collection and RNA preservation. Because bacterioplankton community RNA yields may be relatively low (microbiology research.

  6. [Analysis of abortions at a community maternity hospital in Bangui].

    Sepou, A; Ngbale, R; Yanza, M C; Domande-Modanga, Z; Nguembi, E

    2004-01-01

    Abortion, i.e., early termination of pregnancy, has few complications when it occurs spontaneously. However self-inflicted abortion (SIA) often leads to more or less serious complications. In view of the increasing number of abortion cases in our department, we undertook this yearlong transversal study to evaluate the incidence of SIA in the department, determine the demographic characteristics of the women that practiced SIA, and identify the complications of SIA. Only ongoing or incomplete abortions were studied. Amenorrhea not related to pregnancy or associated with ectopic pregnancy was excluded from study. Clinical and demographic data were noted on forms specially designed by the research team. Data analysis yielded the following findings. Abortion accounted for 719 of the 5292 hospitalizations (13.6%) in gynecology unit, including 43.4% of SIA. Mean patient age was 24.7 years (range, 13 to 39). Spontaneous abortion was more likely to be observed in married women than in students who usually presented SIA. Wanted pregnancy was more likely to be reported by married women than by single woman who posed the problem of unwanted pregnancy. Students had more SIA. The main reasons for practicing SIA were financial (61.5%). The most common methods used for SIA were drug combinations (39.1%) and mechanical tools (26.0%). All severe complications such as infection and death were observed in women who practiced SIA. The high incidence of SIA in the department was especially disturbing due to the young age of the women involved and the severity of the complications. More action is needed to spread information on contraceptive methods in schools and universities to avoid unintended pregnancies that drive young people to practice SIA.

  7. Seasonal changes in the microbial community of a salt marsh, measured by phospholipid fatty acid analysis

    Keith-Roach, Miranda; Bryan, N.D.; Bardgett, R.D.;

    2002-01-01

    to characterise biogeochemical processes occurring at this site. Phospholipid fatty acid (PLFA) analysis of sediment samples collected at monthly intervals was used to measure seasonal changes in microbial biomass and community structure. The PLFA data were analysed using multivariate techniques (Ward's method...... defined, showing differences in the community structure over the course of a year. At all times, the microbial community was dominated by PLFA associated with aerobic bacteria, but this was most pronounced in summer (August). The abundance of branched fatty acids, a measure of the biomass of anaerobes......, started to increase later in the year than did those associated with aerobes and the fungal biomarker 18:2omega6 showed a brief late-summer peak. The salt marsh remained mildly oxic throughout the year despite the increase in microbial respiration, suggested by the large increases in the abundance of PLFA...

  8. Habitat niche community-level analysis of an amphibian assemblage at Lake Nabugabo, Uganda

    M. Behangana

    2008-11-01

    Full Text Available Community structure was studied across six different habitat types in an amphibian assemblage constituted by 24 species belonging to five families, from Lake Nabugabo, Uganda. We employed a suite of different statistical methods, including univariate, multivariate, and Monte Carlo procedures to investigate the randomness/nonrandomness and the seasonal effects (wet versus dry season of the community assembly. We calculated for each species in each habitat type an index of relative abundance by using a time constrained counting technique, with 48 1-h counts for each habitat type. Co-occurrence was analysed by C score with 30 000 simulations; resource partitioning patterns by RA2 and RA3 algorithms with 30 000 simulations; and apparent dissimilarity among species in terms of habitat use by UPGMA dendrograms. After pooling data from wet and dry seasons, it resulted that the amphibian community was non-randomly assembled according to C-score analyses, but both RA2 and RA3 were unable to uncover any competitive structure for the dataset. Seasonal effects were evident, and although C score analyses confirmed a nonrandom structure for the community under study (particularly in wet season, RA3 showed that species with high relative abundance tended to significantly concentrate in one habitat type (swamp forest rather than to partition the habitat resource. UPGMA dendrograms grouped the species differently in dry versus wet seasons. Overall, the comparative evidence of 1 non-random community structure according to C-score analysis, and 2 absence of resource partitioning according to niche overlap null models analysis, suggests that community organization in Lake Nabugabo amphibians is generated by habitat affinities rather than by interspecific competition.

  9. Sensitivity analysis in the WWTP modelling community – new opportunities and applications

    Sin, Gürkan; Ruano, M.V.; Neumann, Marc B.

    2010-01-01

    design (BSM1 plant layout) using Standardized Regression Coefficients (SRC) and (ii) Applying sensitivity analysis to help fine-tuning a fuzzy controller for a BNPR plant using Morris Screening. The results obtained from each case study are then critically discussed in view of practical applications......A mainstream viewpoint on sensitivity analysis in the wastewater modelling community is that it is a first-order differential analysis of outputs with respect to the parameters – typically obtained by perturbing one parameter at a time with a small factor. An alternative viewpoint on sensitivity...

  10. Community occupancy before-after-control-impact (CO-BACI) analysis of Hurricane Gudrun on Swedish forest birds.

    Russell, James C; Stjernman, Martin; Lindström, Åke; Smith, Henrik G

    2015-04-01

    Resilience of ecological communities to perturbation is important in the face of increased global change from anthropogenic stressors. Monitoring is required to detect the impact of, and recovery from, perturbations, and before-after-control-impact (BACI) analysis provides a powerful framework in this regard. However, species in a community are not observed with perfect detection, and occupancy analysis is required to correct for imperfect detectability of species. We present a Bayesian community occupancy before-after-control-impact (CO-BACI) framework to monitor ecological community response to perturbation when constituent species are imperfectly detected. We test the power of the model to detect changes in community composition following an acute perturbation with simulation. We then apply the model to a study of the impact of a large hurricane on the forest bird community of Sweden, using data from the national bird survey scheme. Although simulation shows the model can detect changes in community occupancy following an acute perturbation, application to a Swedish forest bird community following a major hurricane detected no change in community occupancy despite widespread forest loss. Birds with landscape occupancy less than 50% required correcting for detectability. We conclude that CO-BACI analysis is a useful tool that can incorporate rare species in analyses and detect occupancy changes in ecological communities following perturbation, but, because it does not include abundance, some impacts may be overlooked.

  11. Phylogenetic analysis of bacterial community in deep-sea sediment from the western Pacific "warm pool"

    2005-01-01

    A depth profile of bacterial community structure in one deep-sea sediment core of the western Pacific "warm pool" (WP) was investigated and compared with that in a sediment sample from the eastern Pacific (EP) by phylogenetic analysis of 16S rDNA fragments.Five bacterial 16S rDNA clone libraries were constructed, and t33 clones with different restriction fragment length polymorphism(RFLP) patterns were sequenced. A phylogenetic analysis of these sequences revealed that the bacterial diversity in a sample from the WP was more abundant than that in the EP sample. The bacterial population in the sediment core of WP was composed of eight major lineages of the domain bacteria. Among them the γ-Proteobacteria was the predominant and most diverse group in each section of WP sediment core, followed by the α-Proteobacteria. The genus Colwellia belonging to γ-Proteobacteria was predominant in this sample.The shift of bacterial communities among different sections of the WP sediment core was δ-, ε-Proteobacteria, and Cytopahga-Flexibacteria-Bacteroides (CFB) group. The ratios between them in the bacterial communities all showed inversely proportional to the depth of sediment. The sequences related to sulphate reducing bacteria (SRB) were detected in every section. The bacterial community structure in this sediment core might be related to the environmental characteristics of the surface seawater of the western Pacific WP.

  12. Stable isotope analysis as an early monitoring tool for community-scale effects of rat eradication

    Nigro, Katherine M.; Hathaway, Stacie A.; Wegmann, Alex; Miller-ter Kuile, Ana; Fisher, Robert N.; Young, Hillary S.

    2017-01-01

    Invasive rats have colonized most of the islands of the world, resulting in strong negative impacts on native biodiversity and on ecosystem functions. As prolific omnivores, invasive rats can cause local extirpation of a wide range of native species, with cascading consequences that can reshape communities and ecosystems. Eradication of rats on islands is now becoming a widespread approach to restore ecosystems, and many native island species show strong numerical responses to rat eradication. However, the effect of rat eradication on other consumers can extend beyond direct numerical effects, to changes in behavior, dietary composition, and other ecological parameters. These behavioral and trophic effects may have strong cascading impacts on the ecology of restored ecosystems, but they have rarely been examined. In this study, we explore how rat eradication has affected the trophic ecology of native land crab communities. Using stable isotope analysis of rats and crabs, we demonstrate that the diet or trophic position of most crabs changed subsequent to rat eradication. Combined with the numerical recovery of two carnivorous land crab species (Geograpsus spp.), this led to a dramatic widening of the crab trophic niche following rat eradication. Given the established importance of land crabs in structuring island communities, particularly plants, this suggests an unappreciated mechanism by which rat eradication may alter island ecology. This study also demonstrates the potential for stable isotope analysis as a complementary monitoring tool to traditional techniques, with the potential to provide more nuanced assessments of the community- and ecosystem-wide effects of restoration.

  13. Zooplankton diversity analysis through single-gene sequencing of a community sample

    Nishida Mutsumi

    2009-09-01

    Full Text Available Abstract Background Oceans cover more than 70% of the earth's surface and are critical for the homeostasis of the environment. Among the components of the ocean ecosystem, zooplankton play vital roles in energy and matter transfer through the system. Despite their importance, understanding of zooplankton biodiversity is limited because of their fragile nature, small body size, and the large number of species from various taxonomic phyla. Here we present the results of single-gene zooplankton community analysis using a method that determines a large number of mitochondrial COI gene sequences from a bulk zooplankton sample. This approach will enable us to estimate the species richness of almost the entire zooplankton community. Results A sample was collected from a depth of 721 m to the surface in the western equatorial Pacific off Pohnpei Island, Micronesia, with a plankton net equipped with a 2-m2 mouth opening. A total of 1,336 mitochondrial COI gene sequences were determined from the cDNA library made from the sample. From the determined sequences, the occurrence of 189 species of zooplankton was estimated. BLASTN search results showed high degrees of similarity (>98% between the query and database for 10 species, including holozooplankton and merozooplankton. Conclusion In conjunction with the Census of Marine Zooplankton and Barcode of Life projects, single-gene zooplankton community analysis will be a powerful tool for estimating the species richness of zooplankton communities.

  14. Zooplankton community analysis in the Changjiang River estuary by single-gene-targeted metagenomics

    Cheng, Fangping; Wang, Minxiao; Li, Chaolun; Sun, Song

    2014-07-01

    DNA barcoding provides accurate identification of zooplankton species through all life stages. Single-gene-targeted metagenomic analysis based on DNA barcode databases can facilitate longterm monitoring of zooplankton communities. With the help of the available zooplankton databases, the zooplankton community of the Changjiang (Yangtze) River estuary was studied using a single-gene-targeted metagenomic method to estimate the species richness of this community. A total of 856 mitochondrial cytochrome oxidase subunit 1 (cox1) gene sequences were determined. The environmental barcodes were clustered into 70 molecular operational taxonomic units (MOTUs). Forty-two MOTUs matched barcoded marine organisms with more than 90% similarity and were assigned to either the species (similarity>96%) or genus level (similaritymorphological methods were identified by molecular methods, especially gelatinous zooplankton and merozooplankton that were likely sampled at different life history phases. Zooplankton community structures differed significantly among all of the samples. The MOTU spatial distributions were influenced by the ecological habits of the corresponding species. In conclusion, single-gene-targeted metagenomic analysis is a useful tool for zooplankton studies, with which specimens from all life history stages can be identified quickly and effectively with a comprehensive database.

  15. A causal loop analysis of the sustainability of integrated community case management in Rwanda.

    Sarriot, Eric; Morrow, Melanie; Langston, Anne; Weiss, Jennifer; Landegger, Justine; Tsuma, Laban

    2015-04-01

    Expansion of community health services in Rwanda has come with the national scale up of integrated Community Case Management (iCCM) of malaria, pneumonia and diarrhea. We used a sustainability assessment framework as part of a large-scale project evaluation to identify factors affecting iCCM sustainability (2011). We then (2012) used causal-loop analysis to identify systems determinants of iCCM sustainability from a national systems perspective. This allows us to develop three high-probability future scenarios putting the achievements of community health at risk, and to recommend mitigating strategies. Our causal loop diagram highlights both balancing and reinforcing loops of cause and effect in the national iCCM system. Financial, political and technical scenarios carry high probability for threatening the sustainability through: (1) reduction in performance-based financing resources, (2) political shocks and erosion of political commitment for community health, and (3) insufficient progress in resolving district health systems--"building blocks"--performance gaps. In a complex health system, the consequences of choices may be delayed and hard to predict precisely. Causal loop analysis and scenario mapping make explicit complex cause-and-effects relationships and high probability risks, which need to be anticipated and mitigated.

  16. Integrative microbial community analysis reveals full-scale enhanced biological phosphorus removal under tropical conditions

    Law, Yingyu; Kirkegaard, Rasmus Hansen; Cokro, Angel Anisa; Liu, Xianghui; Arumugam, Krithika; Xie, Chao; Stokholm-Bjerregaard, Mikkel; Drautz-Moses, Daniela I.; Nielsen, Per Halkjær; Wuertz, Stefan; Williams, Rohan B. H.

    2016-05-01

    Management of phosphorus discharge from human waste is essential for the control of eutrophication in surface waters. Enhanced biological phosphorus removal (EBPR) is a sustainable, efficient way of removing phosphorus from waste water without employing chemical precipitation, but is assumed unachievable in tropical temperatures due to conditions that favour glycogen accumulating organisms (GAOs) over polyphosphate accumulating organisms (PAOs). Here, we show these assumptions are unfounded by studying comparative community dynamics in a full-scale plant following systematic perturbation of operational conditions, which modified community abundance, function and physicochemical state. A statistically significant increase in the relative abundance of the PAO Accumulibacter was associated with improved EBPR activity. GAO relative abundance also increased, challenging the assumption of competition. An Accumulibacter bin-genome was identified from a whole community metagenomic survey, and comparative analysis against extant Accumulibacter genomes suggests a close relationship to Type II. Analysis of the associated metatranscriptome data revealed that genes encoding proteins involved in the tricarboxylic acid cycle and glycolysis pathways were highly expressed, consistent with metabolic modelling results. Our findings show that tropical EBPR is indeed possible, highlight the translational potential of studying competition dynamics in full-scale waste water communities and carry implications for plant design in tropical regions.

  17. Application of Nonlinear Analysis Methods for Identifying Relationships Between Microbial Community Structure and Groundwater Geochemistry

    Schryver, Jack C.; Brandt, Craig C.; Pfiffner, Susan M.; Palumbo, A V.; Peacock, Aaron D.; White, David C.; McKinley, James P.; Long, Philip E.

    2006-02-01

    The relationship between groundwater geochemistry and microbial community structure can be complex and difficult to assess. We applied nonlinear and generalized linear data analysis methods to relate microbial biomarkers (phospholipids fatty acids, PLFA) to groundwater geochemical characteristics at the Shiprock uranium mill tailings disposal site that is primarily contaminated by uranium, sulfate, and nitrate. First, predictive models were constructed using feedforward artificial neural networks (NN) to predict PLFA classes from geochemistry. To reduce the danger of overfitting, parsimonious NN architectures were selected based on pruning of hidden nodes and elimination of redundant predictor (geochemical) variables. The resulting NN models greatly outperformed the generalized linear models. Sensitivity analysis indicated that tritium, which was indicative of riverine influences, and uranium were important in predicting the distributions of the PLFA classes. In contrast, nitrate concentration and inorganic carbon were least important, and total ionic strength was of intermediate importance. Second, nonlinear principal components (NPC) were extracted from the PLFA data using a variant of the feedforward NN. The NPC grouped the samples according to similar geochemistry. PLFA indicators of Gram-negative bacteria and eukaryotes were associated with the groups of wells with lower levels of contamination. The more contaminated samples contained microbial communities that were predominated by terminally branched saturates and branched monounsaturates that are indicative of metal reducers, actinomycetes, and Gram-positive bacteria. These results indicate that the microbial community at the site is coupled to the geochemistry and knowledge of the geochemistry allows prediction of the community composition.

  18. New Primers for Denaturing Gradient Gel Electrophoresis Analysis of Nitrate-Reducing Bacterial Community in Soil

    R.PASTORELLI; R.PICCOLO; S.SIMONCINI; S.LANDI

    2013-01-01

    The narG gene is frequently used as a molecular marker for bacterial nitrate-reducing community analysis.In this study,a new set of primers targeting the narG gene was designed and applied to semi-nested polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) assay.The potential of the new primers was verified on DNA directly extracted from soils from five different experimental sites distributed in Central and Southern Italy.Specificity of the primers was determined by excision,amplification,and sequencing of bands resolved by DGGE.A phylogenetic analysis showed the correlation between the sequences retrieved from the soils studied and the narG sequences from β and γ-Proteobacteria.These primers expanded the existing molecular tools for ecological study on the size and diversity of nitrate-reducing bacterial community in soil.

  19. Integrated community case management in Malawi: an analysis of innovation and institutional characteristics for policy adoption.

    Rodríguez, Daniela C; Banda, Hastings; Namakhoma, Ireen

    2015-12-01

    In 2007, Malawi became an early adopter of integrated community case management for childhood illnesses (iCCM), a policy aimed at community-level treatment for malaria, diarrhoea and pneumonia for children below 5 years. Through a retrospective case study, this article explores critical issues in implementation that arose during policy formulation through the lens of the innovation (i.e. iCCM) and of the institutions involved in the policy process. Data analysis is founded on a documentary review and 21 in-depth stakeholder interviews across institutions in Malawi. Findings indicate that the characteristics of iCCM made it a suitable policy to address persistent challenges in child mortality, namely that ill children were not interacting with health workers on a timely basis and consequently were dying in their communities. Further, iCCM was compatible with the Malawian health system due to the ability to build on an existing community health worker cadre of health surveillance assistants (HSAs) and previous experiences with treatment provision at the community level. In terms of institutions, the Ministry of Health (MoH) demonstrated leadership in the overall policy process despite early challenges of co-ordination within the MoH. WHO, United Nations Children's Fund (UNICEF) and implementing organizations played a supportive role in their position as knowledge brokers. Greater challenges were faced in the organizational capacity of the MoH. Regulatory issues around HSA training as well as concerns around supervision and overburdening of HSAs were discussed, though not fully addressed during policy development. Similarly, the financial sustainability of iCCM, including the mechanisms for channelling funding flows, also remains an unresolved issue. This analysis highlights the role of implementation questions during policy development. Despite several outstanding concerns, the compatibility between iCCM as a policy alternative and the local context laid the

  20. Microbial community analysis of soils contaminated with lead, chromium and petroleum hydrocarbons.

    Joynt, Janet; Bischoff, Marianne; Turco, Ron; Konopka, Allan; Nakatsu, Cindy H

    2006-02-01

    The impact on the microbial community of long-term environmental exposure to metal and organic contamination was investigated. Twenty-four soil samples were collected along a transect dug in soils contaminated with road paint and paint solvents, mainly toluene. Chemical analysis along the transect revealed a range from high to low concentrations of metals (lead and chromium) and organic solvent compounds. Principal components analysis of microbial community structure based on denaturing gradient gel electrophoresis of the V3 region of the 16S rRNA gene and fatty acid methyl esters derived from phospholipids (phospholipid fatty acid analysis) showing samples with similar fingerprints also had similar contaminant concentrations. There was also a weak positive correlation between microbial biomass and the organic carbon concentration. Results indicated that microbial populations are present despite some extreme contaminant levels in this mixed-waste contaminated site. Nucleotide sequence determination of the 16S rRNA gene indicated the presence of phylogenetically diverse bacteria belonging to the alpha-, beta-, gamma-, and delta-Proteobacteria, the high and low G + C Gram-positive bacteria, green nonsulfur, OP8, and others that did not group within a described division. This indicates that soils contaminated with both heavy metals and hydrocarbons for several decades have undergone changes in community composition, but still contain a phylogenetically diverse group of bacteria (including novel phylotypes) that warrant further investigation.

  1. Unravelling the community structure of the climate system by using lags and symbolic time-series analysis

    Tirabassi, Giulio; Masoller, Cristina

    2016-07-01

    Many natural systems can be represented by complex networks of dynamical units with modular structure in the form of communities of densely interconnected nodes. Unraveling this community structure from observed data requires the development of appropriate tools, particularly when the nodes are embedded in a regular space grid and the datasets are short and noisy. Here we propose two methods to identify communities, and validate them with the analysis of climate datasets recorded at a regular grid of geographical locations covering the Earth surface. By identifying mutual lags among time-series recorded at different grid points, and by applying symbolic time-series analysis, we are able to extract meaningful regional communities, which can be interpreted in terms of large-scale climate phenomena. The methods proposed here are valuable tools for the study of other systems represented by networks of dynamical units, allowing the identification of communities, through time-series analysis of the observed output signals.

  2. QUALIMETRIC ESTIMATION OF INTEGRATION OF RESEARCHERS INTO THE SCIENTIFIC COMMUNITY, BASED ON THE ANALYSIS OF CITATIONS

    Loyko V. I.

    2016-04-01

    Full Text Available The article presents the criteria for evaluating the integration of researchers in the scientific community, based on an analysis of its citations. It is known, that one of the major components of interscientific communication (communication in the scientific community is a citation of scientific publications (monographs, articles, etc.. According to the sociological approach, a scientist is a part of society, ie, scientific community; under scientific community we understand scientific mega environment (opposed to research groups of institutions and their structural units. Integration of a researcher to the community has many aspects: on the one hand, it is - the importance of his work to the scientific community, on the other hand, it is - the use of a scientist social mega environment for building for their personal and professional development to improve their research and improve the quality of its results (in the context of the article we will consider the second aspect. Methodological bases of the research: systematic, competence, sociological, and mega-system qualimetric approaches. Methods: modeling, methods of quality control, methods of set theory, relations and graphs. Evaluation (diagnostics involvement of scientists in the scientific community - is more complicated metrology task than the evaluation of the significance of the results of its research activities. For the authors it is clear that a mature scientist (with a high level of research competence should intensively use the potential of the social and the cultural science international environment (community for their personal and professional development, to improve the efficiency of this research activities and the quality of this results. The proposed indicators can be considered as group indicator variables reflecting the level of the behavioral component of the research competence (scientist. Using social media for researcher’s potential – it is necessary, but not

  3. Multistage A-O Activated Sludge Process for Paraformaldehyde Wastewater Treatment and Microbial Community Structure Analysis

    Danyang Zheng

    2016-01-01

    Full Text Available In recent years, the effect of formaldehyde on microorganisms and body had become a global public health issue. The multistage combination of anaerobic and aerobic process was adopted to treat paraformaldehyde wastewater. Microbial community structure in different reaction stages was analyzed through high-throughput sequencing. Results showed that multistage A-O activated sludge process positively influenced polyformaldehyde wastewater. The removal rates of formaldehyde were basically stable at more than 99% and those of COD were about 89%. Analysis of the microbial diversity index indicated that the microbial diversity of the reactor was high, and the treatment effect was good. Moreover, microbial community had certain similarity in the same system. Microbial communities in different units also showed typical representative characteristics affected by working conditions and influent concentrations. Proteobacteria, Firmicutes, and Bacteroidetes were the dominant fungal genera in the phylum level of community composition. As to family and genus levels, Peptostreptococcaceae was distributed at various stages and the dominant in this system. This bacterium also played an important role in organic matter removal, particularly decomposition of the acidified middle metabolites. In addition, Rhodobacteraceae and Rhodocyclaceae were the formaldehyde-degrading bacteria found in the reactor.

  4. Microbial community analysis of pH 4 thermal springs in Yellowstone National Park.

    Jiang, Xiaoben; Takacs-Vesbach, Cristina D

    2017-01-01

    The pH of the majority of thermal springs in Yellowstone National Park (YNP) is from 1 to 3 and 6 to 10; relatively few springs (~5%) have a pH range of 4-5. We used 16S rRNA gene pyrosequencing to investigate microbial communities sampled from four pH 4 thermal springs collected from four regions of YNP that differed in their fluid temperature and geochemistry. Our results revealed that the composition of bacterial communities varied among the sites, despite sharing similar pH values. The taxonomic composition and metabolic functional potential of the site with the lowest temperature (55 °C), a thermal spring from the Seven Mile Hole (SMH) area, were further investigated using shotgun metagenome sequencing. The taxonomic classification, based on 372 Mbp of unassembled metagenomic reads, indicated that this community included a high proportion of Chloroflexi, Bacteroidetes, Proteobacteria, and Firmicutes. Functional comparison with other YNP thermal spring metagenomes indicated that the SMH metagenome was enriched in genes related to energy production and conversion, transcription, and carbohydrate transport. Analysis of genes involved in nitrogen metabolism revealed assimilatory and dissimilatory nitrate reduction pathways, whereas the majority of genes involved in sulfur metabolism were related to the reduction of sulfate to adenylylsulfate, sulfite, and H2S. Given that pH 4 thermal springs are relatively less common in YNP and thermal areas worldwide, they may harbor novel microbiota and the communities that inhabit them deserve further investigation.

  5. Culture-dependent and -independent molecular analysis of the bacterial community within uranium ore.

    Islam, Ekramul; Sar, Pinaki

    2011-08-01

    The bacterial community structure within a uranium ore was investigated using culture-dependent and -independent clone library analysis and denaturing gradient gel electrophoresis of 16S rRNA genes. The major aerobic heterotrophic bacteria were isolated and identified, and their resistance to uranium and other heavy metals was characterized. Together with near neutral pH, moderate organic carbon content, elevated U and other heavy metals (V, Ni, Mn, Cu, etc.), the ore showed high microbial counts and phylotype richness. The bacterial community mainly consisted of uncultured Proteobacteria, with the predominance of γ - over β - and α -subdivisions, along with Actinobacteria and Firmicutes. A phylogenetic study revealed that nearly one-third of the community was affiliated to as yet uncultured and unidentified bacteria having a closer relationship to Pseudomonas. Lineages of Burkholderiaceae and Moraxellaceae were relatively more abundant in the total community, while genera affiliated to Xanthomonadaceae and Microbacteriaceae and Exiguobacterium were detected in the culturable fraction. More than 50% of the bacterial isolates affiliated to Stenotrophomonas, Microbacterium, Acinetobacter, Pseudomonas and Enterobacter showed resistance to uranium and other heavy metals. The study showed for the first time that uranium ore harbors major bacterial groups related to organisms having a wide range of environmentally significant functional attributes, and the most abundant members are possibly new groups/taxa. These findings provide new insights into U-ore geomicrobiology that could be useful in biohydrometallurgy and bioremediation applications.

  6. Molecular Analysis of the Bacterial Communities in Crude Oil Samples from Two Brazilian Offshore Petroleum Platforms

    Elisa Korenblum

    2012-01-01

    Full Text Available Crude oil samples with high- and low-water content from two offshore platforms (PA and PB in Campos Basin, Brazil, were assessed for bacterial communities by 16S rRNA gene-based clone libraries. RDP Classifier was used to analyze a total of 156 clones within four libraries obtained from two platforms. The clone sequences were mainly affiliated with Gammaproteobacteria (78.2% of the total clones; however, clones associated with Betaproteobacteria (10.9%, Alphaproteobacteria (9%, and Firmicutes (1.9% were also identified. Pseudomonadaceae was the most common family affiliated with these clone sequences. The sequences were further analyzed by MOTHUR, yielding 81 operational taxonomic units (OTUs grouped at 97% stringency. Richness estimators also calculated by MOTHUR indicated that oil samples with high-water content were the most diverse. Comparison of bacterial communities present in these four samples using LIBSHUFF and Principal Component Analysis (PCA indicated that the water content significantly influenced the community structure only of crude oil obtained from PA. Differences between PA and PB libraries were observed, suggesting the importance of the oil field as a driver of community composition in this habitat.

  7. Bacterioplankton community analysis in tilapia ponds by Illumina high-throughput sequencing.

    Fan, Li Min; Barry, Kamira; Hu, Geng Dong; Meng, Shun long; Song, Chao; Wu, Wei; Chen, Jia Zhang; Xu, Pao

    2016-01-01

    The changes of microbial community in aquaculture systems under the effects of stocking densities and seasonality were investigated in tilapia ponds. Total DNAs were extracted from the water samples, 16S rRNA gene was amplified and the bacterial community analyzed by Illumina high-throughput sequencing obtaining 3486 OTUs, from a total read of 715,842 sequences. Basing on the analysis of bacterial compositions, richness, diversity, bacterial 16S rRNA gene abundance, water sample comparisons and existence of specific bacterial taxa within three fish ponds in a 4 months period, the study conclusively observed that the dominant phylum in all water samples were similar, and they included; Proteobacteria, Cyanobacteria, Bacteroidetes, Actinobacteria, Planctomycetes and Chlorobi, distributed in different proportions in the different months and ponds. The seasonal changes had a more pronounced effect on the bacterioplankton community than the stocking densities; however some differences between the ponds were more likely caused by feed coefficient than by stocking densities. At the same time, most bacterial communities were affected by the nutrient input except phylum Cyanobacteria that was also affected by the feed control of tilapia.

  8. Relative diversity and community structure analysis of rumen protozoa according to T-RFLP and microscopic methods.

    Tymensen, Lisa; Barkley, Cindy; McAllister, Tim A

    2012-01-01

    Protozoa are common inhabitants of the rumen where they play roles in host nutrition and methanogenesis. Knowledge of how changes in the composition of protozoa communities affect these processes is limited in part due to a lack of efficient methods for protozoa community analysis. In this study, a terminal-restriction fragment length polymorphism (T-RFLP) assay targeting the 18S rRNA gene was developed for comparative analysis of rumen protozoa communities. Comparison of diversity and structure of protozoa communities from hay-fed versus silage/grain-fed cattle via T-RFLP analysis yielded similar overall results to microscopy analysis. According to both methods, Entodinium spp. were more abundant in the silage/grain-fed cattle and protozoa diversity (as calculated using the Shannon index) was higher for the hay-fed cattle due to greater species evenness. Type B protozoa were more prevalent in the hay-fed cattle, whereas Type A protozoa were more prevalent in the silage/grain-fed cattle. Analysis of similarity (ANOSIM) indicated that the protozoa communities from hay-fed and silage/grain-fed cattle were different, and multivariate analysis indicated that pen mates (i.e., cattle fed the same diet and housed together) tended to have similar protozoa communities types. In summary, we present a T-RFLP method for analyzing rumen protozoa communities which complements traditional microscopy approaches but has the advantage of being amenable to high-throughput.

  9. MG-RAST, a Metagenomics Service for Analysis of Microbial Community Structure and Function.

    Keegan, Kevin P; Glass, Elizabeth M; Meyer, Folker

    2016-01-01

    Approaches in molecular biology, particularly those that deal with high-throughput sequencing of entire microbial communities (the field of metagenomics), are rapidly advancing our understanding of the composition and functional content of microbial communities involved in climate change, environmental pollution, human health, biotechnology, etc. Metagenomics provides researchers with the most complete picture of the taxonomic (i.e., what organisms are there) and functional (i.e., what are those organisms doing) composition of natively sampled microbial communities, making it possible to perform investigations that include organisms that were previously intractable to laboratory-controlled culturing; currently, these constitute the vast majority of all microbes on the planet. All organisms contained in environmental samples are sequenced in a culture-independent manner, most often with 16S ribosomal amplicon methods to investigate the taxonomic or whole-genome shotgun-based methods to investigate the functional content of sampled communities. Metagenomics allows researchers to characterize the community composition and functional content of microbial communities, but it cannot show which functional processes are active; however, near parallel developments in transcriptomics promise a dramatic increase in our knowledge in this area as well. Since 2008, MG-RAST (Meyer et al., BMC Bioinformatics 9:386, 2008) has served as a public resource for annotation and analysis of metagenomic sequence data, providing a repository that currently houses more than 150,000 data sets (containing 60+ tera-base-pairs) with more than 23,000 publically available. MG-RAST, or the metagenomics RAST (rapid annotation using subsystems technology) server makes it possible for users to upload raw metagenomic sequence data in (preferably) fastq or fasta format. Assessments of sequence quality, annotation with respect to multiple reference databases, are performed automatically with minimal

  10. What reassurances do the community need regarding life extension? Evidence from studies of community attitudes and an analysis of film portrayals.

    Underwood, Mair

    2014-04-01

    It is increasingly recognized that community attitudes impact on the research trajectory, entry, and reception of new biotechnologies. Yet biogerontologists have generally been dismissive of public concerns about life extension. There is some evidence that biogerontological research agendas have not been communicated effectively, with studies finding that most community members have little or no knowledge of life extension research. In the absence of knowledge, community members' attitudes may well be shaped by issues raised in popular portrayals of life extension (e.g., in movies). To investigate how popular portrayals of life extension may influence community attitudes, I conducted an analysis of 19 films depicting human life extension across different genres. I focussed on how the pursuit of life extension was depicted, how life extension was achieved, the levels of interest in life extension shown by characters in the films, and the experiences of extended life depicted both at an individual and societal level. This paper compares the results of this analysis with the literature on community attitudes to life extension and makes recommendations about the issues in which the public may require reassurance if they are to support and accept life extension technologies.

  11. Analysis of the microbial community in moderately acidic drainage from the Yanahara pyrite mine in Japan.

    Wang, Yang; Yasuda, Takashi; Sharmin, Sultana; Kanao, Tadayoshi; Kamimura, Kazuo

    2014-01-01

    Acid rock drainage (ARD) originating from the Yasumi-ishi tunnel near the main tunnel of the Yanahara mine in Japan was characterized to be moderately acidic (pH 4.1) and contained iron at a low concentration (51 mg/L). The composition of the microbial community was determined by sequence analysis of 16S rRNA genes using PCR and denaturing gradient gel electrophoresis. The analysis of the obtained sequences showed their similarity to clones recently detected in other moderately acidic mine drainages. Uncultured bacteria related to Ferrovum- and Gallionella-like clones were dominant in the microbial community. Analyses using specific primers for acidophilic iron- or sulfur-oxidizing bacteria, Acidithiobacillus ferrooxidans, Leptospirillum spp., Acidithiobacillus caldus, Acidithiobacillus thiooxidans, and Sulfobacillus spp. revealed the absence of these bacteria in the microbial community in ARD from the Yasumi-ishi tunnel. Clones affiliated with a member of the order Thermoplasmatales were detected as the dominant archaea in the ARD microbial population.

  12. Use of multi-criteria analysis (MCA for supporting community forest management

    Khadka C

    2012-04-01

    Full Text Available Sustainable forest management usually involves the use of criteria and indicators (C&I allowing the monitoring, reporting and assessment of management activities at national, regional and forest management unit levels. Experiences of such concepts are scarce in Nepal, particularly with regard to the evaluation of management activities within a Multi-Criteria Analysis (MCA framework. In this contribution we describe how a MCA approach can be used to efficiently exploit information, knowledge, and preferences of stakeholders to address community forest management problems. Beside rating and ranking techniques, the Analytic Hierarchy Process (AHP is used to examine the importance of six criteria and forty-four indicators in a sustainable forest management context with a broad range of stakeholder groups. An evaluation of four management strategies in the Shree Gyneshwar community forest user group allows to demonstrate the relevance of changing priorities for different criteria. A passive adaptive management strategy focusing on a multiple use of natural resources and the introduction of production-oriented measures were identified as the most preferable option. The results of this study show that the multi-criteria analysis approach, and in particular the AHP, can assist decision-makers in efficiently evaluating management problems and generating ideas for the long-term strategic planning process of community forest management, even under complex socio-economic and ecological conditions. In that context, compromise solutions enjoy a higher possibility of being successful, taking into account the different views of stakeholder groups.

  13. A Policy Analysis of Missouri Community College Residence Hall Discipline Policies with an Analysis of Changes in the State Fair Community College Residence Hall Policy

    Gilgour, Joseph G.

    2012-01-01

    Community colleges in the United States have long been known as institutions of equal opportunity and affordable education. One facet of student life appearing at more and more community colleges is the addition of residence halls. Still, the number of community colleges with on-campus living is relatively small, and for the campuses with…

  14. High-throughput metagenomic technologies for complex microbial community analysis: open and closed formats.

    Zhou, Jizhong; He, Zhili; Yang, Yunfeng; Deng, Ye; Tringe, Susannah G; Alvarez-Cohen, Lisa

    2015-01-27

    Understanding the structure, functions, activities and dynamics of microbial communities in natural environments is one of the grand challenges of 21st century science. To address this challenge, over the past decade, numerous technologies have been developed for interrogating microbial communities, of which some are amenable to exploratory work (e.g., high-throughput sequencing and phenotypic screening) and others depend on reference genes or genomes (e.g., phylogenetic and functional gene arrays). Here, we provide a critical review and synthesis of the most commonly applied "open-format" and "closed-format" detection technologies. We discuss their characteristics, advantages, and disadvantages within the context of environmental applications and focus on analysis of complex microbial systems, such as those in soils, in which diversity is high and reference genomes are few. In addition, we discuss crucial issues and considerations associated with applying complementary high-throughput molecular technologies to address important ecological questions.

  15. Mean-variance portfolio analysis data for optimizing community-based photovoltaic investment.

    Shakouri, Mahmoud; Lee, Hyun Woo

    2016-03-01

    The amount of electricity generated by Photovoltaic (PV) systems is affected by factors such as shading, building orientation and roof slope. To increase electricity generation and reduce volatility in generation of PV systems, a portfolio of PV systems can be made which takes advantages of the potential synergy among neighboring buildings. This paper contains data supporting the research article entitled: PACPIM: new decision-support model of optimized portfolio analysis for community-based photovoltaic investment [1]. We present a set of data relating to physical properties of 24 houses in Oregon, USA, along with simulated hourly electricity data for the installed PV systems. The developed Matlab code to construct optimized portfolios is also provided in . The application of these files can be generalized to variety of communities interested in investing on PV systems.

  16. Analysis of bacterial community in bulking sludge using culture-dependent and -independent approaches

    Decai Jin; Ping Wang; Zhihui Bai; Xinxin Wang; Hong Peng; Rong Qi; Zhisheng Yu; Guoqiang Zhuang

    2011-01-01

    The bacterial community of a bulking sludge from a municipal wastewater treatment plant with anoxic-anaerobic-oxic process was investigated by combination of cultivation and 16S rRNA gene clone library analysis for understanding the causes of bulking.A total of 28 species were obtained from 63 isolates collected from six culture media.The most cultivable species belonged to γ-Proteobacteria including Klebsiella sp.,Pseudomonas sp.,Aeromonas sp.and Acinetobacter sp.Further analysis of these strains by repetitive sequence based on polymerase chain reaction (rep-PCR) technology showed that rep-PCR yielded discriminatory banding patterns within the same genus using REP and BOX primer sets.While the culture-independent assessment revealed that β-Proteobacteria was the dominant group in the bulking sample.Sequence analysis revealed that the highest proportion (14.7%) of operational taxonomic units was 98% similar to Candidatus Accumulibacter phosphatis,which is used to remove phosphorous from wastewater.Our results indicated that combining different approaches can produce complementary information,thus generate a more accurate view of microbial community in bulking sludge.

  17. Strainer: software for analysis of population variation in community genomic datasets

    Tyson Gene W

    2007-10-01

    Full Text Available Abstract Background Metagenomic analyses of microbial communities that are comprehensive enough to provide multiple samples of most loci in the genomes of the dominant organism types will also reveal patterns of genetic variation within natural populations. New bioinformatic tools will enable visualization and comprehensive analysis of this sequence variation and inference of recent evolutionary and ecological processes. Results We have developed a software package for analysis and visualization of genetic variation in populations and reconstruction of strain variants from otherwise co-assembled sequences. Sequencing reads can be clustered by matching patterns of single nucleotide polymorphisms to generate predicted gene and protein variant sequences, identify conserved intergenic regulatory sequences, and determine the quantity and distribution of recombination events. Conclusion The Strainer software, a first generation metagenomic bioinformatics tool, facilitates comprehension and analysis of heterogeneity intrinsic in natural communities. The program reveals the degree of clustering among closely related sequence variants and provides a rapid means to generate gene and protein sequences for functional, ecological, and evolutionary analyses.

  18. agriGO: a GO analysis toolkit for the agricultural community.

    Du, Zhou; Zhou, Xin; Ling, Yi; Zhang, Zhenhai; Su, Zhen

    2010-07-01

    Gene Ontology (GO), the de facto standard in gene functionality description, is used widely in functional annotation and enrichment analysis. Here, we introduce agriGO, an integrated web-based GO analysis toolkit for the agricultural community, using the advantages of our previous GO enrichment tool (EasyGO), to meet analysis demands from new technologies and research objectives. EasyGO is valuable for its proficiency, and has proved useful in uncovering biological knowledge in massive data sets from high-throughput experiments. For agriGO, the system architecture and website interface were redesigned to improve performance and accessibility. The supported organisms and gene identifiers were substantially expanded (including 38 agricultural species composed of 274 data types). The requirement on user input is more flexible, in that user-defined reference and annotation are accepted. Moreover, a new analysis approach using Gene Set Enrichment Analysis strategy and customizable features is provided. Four tools, SEA (Singular enrichment analysis), PAGE (Parametric Analysis of Gene set Enrichment), BLAST4ID (Transfer IDs by BLAST) and SEACOMPARE (Cross comparison of SEA), are integrated as a toolkit to meet different demands. We also provide a cross-comparison service so that different data sets can be compared and explored in a visualized way. Lastly, agriGO functions as a GO data repository with search and download functions; agriGO is publicly accessible at http://bioinfo.cau.edu.cn/agriGO/.

  19. Bioconductor workflow for microbiome data analysis: from raw reads to community analyses.

    Callahan, Ben J; Sankaran, Kris; Fukuyama, Julia A; McMurdie, Paul J; Holmes, Susan P

    2016-01-01

    High-throughput sequencing of PCR-amplified taxonomic markers (like the 16S rRNA gene) has enabled a new level of analysis of complex bacterial communities known as microbiomes. Many tools exist to quantify and compare abundance levels or microbial composition of communities in different conditions. The sequencing reads have to be denoised and assigned to the closest taxa from a reference database. Common approaches use a notion of 97% similarity and normalize the data by subsampling to equalize library sizes. In this paper, we show that statistical models allow more accurate abundance estimates. By providing a complete workflow in R, we enable the user to do sophisticated downstream statistical analyses, including both parameteric and nonparametric methods. We provide examples of using the R packages dada2, phyloseq, DESeq2, ggplot2 and vegan to filter, visualize and test microbiome data. We also provide examples of supervised analyses using random forests, partial least squares and linear models as well as nonparametric testing using community networks and the ggnetwork package.

  20. Quantitative Analysis of Lung Ultrasonography for the Detection of Community-Acquired Pneumonia: A Pilot Study

    Francesco Corradi

    2015-01-01

    Full Text Available Background and Objective. Chest X-ray is recommended for routine use in patients with suspected pneumonia, but its use in emergency settings is limited. In this study, the diagnostic performance of a new method for quantitative analysis of lung ultrasonography was compared with bedside chest X-ray and visual lung ultrasonography for detection of community-acquired pneumonia, using thoracic computed tomography as a gold standard. Methods. Thirty-two spontaneously breathing patients with suspected community-acquired pneumonia, undergoing computed tomography examination, were consecutively enrolled. Each hemithorax was evaluated for the presence or absence of abnormalities by chest X-ray and quantitative or visual ultrasonography. Results. Quantitative ultrasonography showed higher sensitivity (93%, specificity (95%, and diagnostic accuracy (94% than chest X-ray (64%, 80%, and 69%, resp., visual ultrasonography (68%, 95%, and 77%, resp., or their combination (77%, 75%, and 77%, resp.. Conclusions. Quantitative lung ultrasonography was considerably more accurate than either chest X-ray or visual ultrasonography in the diagnosis of community-acquired pneumonia and it may represent a useful first-line approach for confirmation of clinical diagnosis in emergency settings.

  1. Sourdough microbial community dynamics: An analysis during French organic bread-making processes.

    Lhomme, Emilie; Urien, Charlotte; Legrand, Judith; Dousset, Xavier; Onno, Bernard; Sicard, Delphine

    2016-02-01

    Natural sourdoughs are commonly used in bread-making processes, especially for organic bread. Despite its role in bread flavor and dough rise, the stability of the sourdough microbial community during and between bread-making processes is debated. We investigated the dynamics of lactic acid bacteria (LAB) and yeast communities in traditional organic sourdoughs of five French bakeries during the bread-making process and several months apart using classical and molecular microbiology techniques. Sourdoughs were sampled at four steps of the bread-making process with repetition. The analysis of microbial density over 68 sourdough/dough samples revealed that both LAB and yeast counts changed along the bread-making process and between bread-making runs. The species composition was less variable. A total of six LAB and nine yeast species was identified from 520 and 1675 isolates, respectively. The dominant LAB species was Lactobacillus sanfranciscensis, found for all bakeries and each bread-making run. The dominant yeast species changed only once between bread-making processes but differed between bakeries. They mostly belonged to the Kazachstania clade. Overall, this study highlights the change of population density within the bread-making process and between bread-making runs and the relative stability of the sourdough species community during bread-making process.

  2. AN ANALYSIS OF THE ROMANIAN FISHERY SECTOR IN THE EUROPEAN COMMUNITY CONTEXT

    Silvius STANCIU

    2015-12-01

    Full Text Available The development of the fishery sector represents one of the European Union’s priorities due to the positive impact it has on food security and to its potential to ensure nutritious and quality food at an affordable price as compared to other animal-origin resources. The Community policy in the fishery sector focuses on reducing the Community market dependence on imports and on the sustainable development of business in this domain. Romania aligned with the Community policies and, therefore, important funds were allocated to the national fishery sector. The diversified natural resources, the possibility to use friendly technologies, the qualified staff, the tradition in the domain, and the existence of a number of niche markets all represent motivations for the development of the Romanian fishery sector. The present paper proposes an analysis of the Romanian fishery production and of the European financing effects on the specialized companies. Despite the fact that there have been important resources allocated to the sector and there is a slight positive evolution, the absorption of funds was difficult. The results of the investment may be observed after a long period of time, this is why Romania is still dependent on fishery product imports. Aquaculture represents the main segment towards which the European funds were directed, including in our country, thus providing the greatest part of the income and employment in the domain.

  3. Analysis of culturable and unculturable microbial community in bensulfuron-methyl contaminated paddy soils

    LIN Xiaoyan; ZHAO Yuhua; FU Qinglin; M. L. Umashankara; FENG Zhihong

    2008-01-01

    To investigate the influence of bensulfuron-methyl (BSM) on culturable microbial quantities and unculturable microbial community structures, conventional and molecular biological methods were employed in five BSM treated soils with three replications, respectively. The results obtained with traditional culture-dependent methods showed that a low-level of BSM had slight and transient effects on culturable microorganisms; nevertheless, high concentration of BSM resulted in a dramatic decrease in bacterial colony forming units (cfus). The result obtained using denaturing gradient gel electrophoresis (DGGE) revealed that more than 17 bands were observed in low BSM contaminated soil samples and only 10 bands were detected in samples with high BSM contamination. In other words, the diversity of soil community structure is related to the concentration of BSM. Cluster analysis showed that the community structure under low level of contamination was more similar to that of the control, while heavy contaminated amendments were far away from the above group. In a sense, the cooperation of the traditional method and the molecular biological method is more powerful to study the soil microbial information in contaminated ecosystem.

  4. Ecomorphological analysis of trophic niche partitioning in a tropical savannah bat community.

    Aguirre, Luis F; Herrel, Anthony; van Damme, R; Matthysen, E

    2002-01-01

    The exceptional diversity of neotropical bat communities is sustained by an intricate partitioning of available resources among the member species. Trophical specialization is considered an important evolutionary avenue towards niche partitioning in neotropical phyllostomid bats. From an ancestral insectivorous condition, phyllostomids evolved into highly specialized frugivorous, carnivorous, nectarivorous, piscivorous and even sanguivorous species. Previously, correlations between cranial morphology and trophic ecology within this group have been documented. Here, we examine the evolutionary relationships between bite force and head shape in over 20 species of bats from a single tropical savannah bat community. The results show that bite force increases exponentially with body size across all species examined. Despite the significant differences between large dietary groups using traditional analysis (i.e. non-phylogenetic) and the strong evolutionary correlations between body mass and bite force, phylogenetic analyses indicated no differences in bite performance between insectivorous, omnivorous and frugivorous bats. Comparisons of three species with highly specialized feeding habits (nectarivory, piscivory and sanguivory) with the rest of the species in the community indicate that specialization into these niches comes at the expense of bite performance and, hence, may result in a reduction of the trophic niche breadth. PMID:12065044

  5. Comparative pyrosequencing analysis of bacterial community change in biofilm formed on seawater reverse osmosis membrane.

    Kim, In S; Lee, Jinwook; Kima, Sung-Jo; Yu, Hye-Weon; Jang, Am

    2014-01-01

    The change in bacterial community structure induced by bacterial competition and succession was investigated during seawater reverse osmosis (SWRO) in order to elucidate a possible link between the bacterial consortium on SWRO membranes and biofouling. To date, there has been no definitive characterization of the microbial diversity in SWRO in terms of distinguishing time-dependent changes in the richness or abundance of bacterial species. For bacterial succession within biofilms on the membrane surface, SWRO using a cross-flow filtration membrane test unit was operated for 5 and 100h, respectively. As results of the pyrosequencing analysis, bacterial communities differed considerably among seawater and the 5 and 100 h samples. From a total of 33,876 pyrosequences (using a 95% sequence similarity), there were less than 1% of shared species, confirming the influence of the operational time factor and lack of similarity of these communities. During SWRO operation, the abundance of Pseudomonas stutzeri BBSPN3 (GU594474) belonging to gamma-Proteobacteria suggest that biofouling of SWRO membrane might be driven by the dominant influence of a specific species. In addition, among the bacterial competition of five bacterial species (Pseudomonas aeruginosa, Bacillus sp., Rhodobacter sp., Flavobacterium sp., and Mycobacterium sp.) competing for bacterial colonization on the SWRO membrane surfaces, it was exhibited that Bacillus sp. was the most dominant. The dominant influences ofPseudomonas sp. and Bacillus sp. on biofouling during actual SWRO is decisive depending on higher removal efficiency of the seawater pretreatment.

  6. Community structure analysis of soil ammonia oxidizers during vegetation restoration in southwest China.

    Liang, Yueming; He, Xunyang; Liang, Shichu; Zhang, Wei; Chen, Xiangbi; Feng, Shuzheng; Su, Yirong

    2014-03-01

    Soil ammonia oxidizers play a critical role in nitrogen cycling and ecological restoration. The composition and structure of soil ammonia oxidizers and their impacting factors were studied in four typical ecosystem soils, tussock (T), shrub (S), secondary forest (SF), and primary forest (PF), during vegetation restoration in the Karst region of Southwest China. The composition and structure of the ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA) communities were characterized by sequencing the amoA and arch-amoA genes, respectively. The diversity of soil ammonia oxidizers (except in S) and plant Shannon diversity index gradually increased with vegetation restoration, and the ammonia oxidizer communities differed significantly (p soils. AOB Nitrosospira cluster 3b only appeared in PF and SF soils, while Nitrosospira cluster 3a species were found in all soils. Changes in AOB paralleled the changes in soil ammonium content that occurred with vegetation restoration. Redundancy analysis showed that the distribution of dominant AOB species was linked to pH, soil urease activity, and soil C/N ratio, whereas the distribution of dominant AOA species was mainly influenced by litter nitrogen content and C/N ratio. These results suggested that the composition and structure of the AOB community were more sensitive to changes in vegetation and soil ammonium content, and may be an important indicator of nitrogen availability in Karst ecosystem soils.

  7. Molecular Analysis of Bacterial Communities in Biofilms of a Drinking Water Clearwell

    Zhang, Minglu; Liu, Wenjun; Nie, Xuebiao; Li, Cuiping; Gu, Junnong; Zhang, Can

    2012-01-01

    Microbial community structures in biofilms of a clearwell in a drinking water supply system in Beijing, China were examined by clone library, terminal restriction fragment length polymorphism (T-RFLP) and 454 pyrosequencing of the amplified 16S rRNA gene. Six biofilm samples (designated R1–R6) collected from six locations (upper and lower sites of the inlet, middle and outlet) of the clearwell revealed similar bacterial patterns by T-RFLP analysis. With respect to the dominant groups, the phy...

  8. Community analysis of a full-scale anaerobic bioreactor treating paper mill wastewater.

    Roest, Kees; Heilig, Hans G H J; Smidt, Hauke; de Vos, Willem M; Stams, Alfons J M; Akkermans, Antoon D L

    2005-03-01

    To get insight into the microbial community of an Upflow Anaerobic Sludge Blanket reactor treating paper mill wastewater, conventional microbiological methods were combined with 16S rRNA gene analyses. Particular attention was paid to microorganisms able to degrade propionate or butyrate in the presence or absence of sulphate. Serial enrichment dilutions allowed estimating the number of microorganisms per ml sludge that could use butyrate with or without sulphate (10(5)), propionate without sulphate (10(6)), or propionate and sulphate (10(8)). Quantitative RNA dot-blot hybridisation indicated that Archaea were two-times more abundant in the microbial community of anaerobic sludge than Bacteria. The microbial community composition was further characterised by 16S rRNA-gene-targeted Denaturing Gradient Gel Electrophoresis (DGGE) fingerprinting, and via cloning and sequencing of dominant amplicons from the bacterial and archaeal patterns. Most of the nearly full length (approximately 1.45 kb) bacterial 16S rRNA gene sequences showed less than 97% similarity to sequences present in public databases, in contrast to the archaeal clones (approximately. 1.3 kb) that were highly similar to known sequences. While Methanosaeta was found as the most abundant genus, also Crenarchaeote-relatives were identified. The microbial community was relatively stable over a period of 3 years (samples taken in July 1999, May 2001, March 2002 and June 2002) as indicated by the high similarity index calculated from DGGE profiles (81.9+/-2.7% for Bacteria and 75.1+/-3.1% for Archaea). 16S rRNA gene sequence analysis indicated the presence of unknown and yet uncultured microorganisms, but also showed that known sulphate-reducing bacteria and syntrophic fatty acid-oxidising microorganisms dominated the enrichments.

  9. Development of a cost-effective metabarcoding strategy for analysis of the marine phytoplankton community.

    Yoon, Tae-Ho; Kang, Hye-Eun; Kang, Chang-Keun; Lee, Sang Heon; Ahn, Do-Hwan; Park, Hyun; Kim, Hyun-Woo

    2016-01-01

    We developed a cost-effective metabarcoding strategy to analyze phytoplankton community structure using the Illumina MiSeq system. The amplicons (404-411 bp) obtained by end-pairing of two reads were sufficiently long to distinguish algal species and provided barcode data equivalent to those generated with the Roche 454 system, but at less than 1/20th of the cost. The original universal primer sequences targeting the 23S rDNA region and the PCR strategy were both modified, and this resulted in higher numbers of eukaryotic algal sequences by excluding non-photosynthetic proteobacterial sequences supporting effectiveness of this strategy. The novel strategy was used to analyze the phytoplankton community structure of six water samples from the East/Japan Sea: surface and 50 m depths at coastal and open-sea sites, with collections in May and July 2014. In total, 345 operational taxonomic units (OTUs) were identified, which covered most of the prokaryotic and eukaryotic algal phyla, including Dinophyta, Rhodophyta, Ochrophyta, Chlorophyta, Streptophyta, Cryptophyta, Haptophyta, and Cyanophyta. This highlights the importance of plastid 23S primers, which perform better than the currently used 16S primers for phytoplankton community surveys. The findings also revealed that more efforts should be made to update 23S rDNA sequences as well as those of 16S in the databases. Analysis of algal proportions in the six samples showed that community structure differed depending on location, depth and season. Across the six samples evaluated, the numbers of OTUs in each phylum were similar but their relative proportions varied. This novel strategy would allow laboratories to analyze large numbers of samples at reasonable expense, whereas this has not been possible to date due to cost and time. In addition, we expect that this strategy will generate a large amount of novel data that could potentially change established methods and tools that are currently used in the realms of

  10. Development of a cost-effective metabarcoding strategy for analysis of the marine phytoplankton community

    Tae-Ho Yoon

    2016-06-01

    Full Text Available We developed a cost-effective metabarcoding strategy to analyze phytoplankton community structure using the Illumina MiSeq system. The amplicons (404–411 bp obtained by end-pairing of two reads were sufficiently long to distinguish algal species and provided barcode data equivalent to those generated with the Roche 454 system, but at less than 1/20th of the cost. The original universal primer sequences targeting the 23S rDNA region and the PCR strategy were both modified, and this resulted in higher numbers of eukaryotic algal sequences by excluding non-photosynthetic proteobacterial sequences supporting effectiveness of this strategy. The novel strategy was used to analyze the phytoplankton community structure of six water samples from the East/Japan Sea: surface and 50 m depths at coastal and open-sea sites, with collections in May and July 2014. In total, 345 operational taxonomic units (OTUs were identified, which covered most of the prokaryotic and eukaryotic algal phyla, including Dinophyta, Rhodophyta, Ochrophyta, Chlorophyta, Streptophyta, Cryptophyta, Haptophyta, and Cyanophyta. This highlights the importance of plastid 23S primers, which perform better than the currently used 16S primers for phytoplankton community surveys. The findings also revealed that more efforts should be made to update 23S rDNA sequences as well as those of 16S in the databases. Analysis of algal proportions in the six samples showed that community structure differed depending on location, depth and season. Across the six samples evaluated, the numbers of OTUs in each phylum were similar but their relative proportions varied. This novel strategy would allow laboratories to analyze large numbers of samples at reasonable expense, whereas this has not been possible to date due to cost and time. In addition, we expect that this strategy will generate a large amount of novel data that could potentially change established methods and tools that are currently used in

  11. Evaluation of SOVAT: An OLAP-GIS decision support system for community health assessment data analysis

    Parmanto Bambang

    2008-06-01

    Full Text Available Abstract Background Data analysis in community health assessment (CHA involves the collection, integration, and analysis of large numerical and spatial data sets in order to identify health priorities. Geographic Information Systems (GIS enable for management and analysis using spatial data, but have limitations in performing analysis of numerical data because of its traditional database architecture. On-Line Analytical Processing (OLAP is a multidimensional datawarehouse designed to facilitate querying of large numerical data. Coupling the spatial capabilities of GIS with the numerical analysis of OLAP, might enhance CHA data analysis. OLAP-GIS systems have been developed by university researchers and corporations, yet their potential for CHA data analysis is not well understood. To evaluate the potential of an OLAP-GIS decision support system for CHA problem solving, we compared OLAP-GIS to the standard information technology (IT currently used by many public health professionals. Methods SOVAT, an OLAP-GIS decision support system developed at the University of Pittsburgh, was compared against current IT for data analysis for CHA. For this study, current IT was considered the combined use of SPSS and GIS ("SPSS-GIS". Graduate students, researchers, and faculty in the health sciences at the University of Pittsburgh were recruited. Each round consisted of: an instructional video of the system being evaluated, two practice tasks, five assessment tasks, and one post-study questionnaire. Objective and subjective measurement included: task completion time, success in answering the tasks, and system satisfaction. Results Thirteen individuals participated. Inferential statistics were analyzed using linear mixed model analysis. SOVAT was statistically significant (α = .01 from SPSS-GIS for satisfaction and time (p Conclusion Using SOVAT, tasks were completed more efficiently, with a higher rate of success, and with greater satisfaction, than the

  12. Hygiene and sanitation promotion strategies among ethnic minority communities in northern Vietnam: a stakeholder analysis.

    Rheinländer, Thilde; Xuan, Le Thi Thanh; Hoat, Luu Ngoc; Dalsgaard, Anders; Konradsen, Flemming

    2012-10-01

    Effective rural hygiene and sanitation promotion (RHSP) is a major challenge for many low-income countries. This paper investigates strategies and stakeholders' roles and responsibilities in RHSP implementation in a multi-ethnic area of northern Vietnam, in order to identify lessons learned for future RHSP. A stakeholder analysis was performed, based on 49 semi-structured individual interviews and one group interview with stakeholders in RHSP in a northern province of Vietnam. Participants came from three sectors (agriculture, health and education), unions supported by the Vietnamese government and from four administrative levels (village, commune, district and province). The study villages represented four ethnic minority groups including lowland and highland communities. Stakeholders' roles, responsibilities and promotion methods were outlined, and implementation constraints and opportunities were identified and analysed using thematic content analysis. Effective RHSP in Vietnam is severely constrained despite supporting policies and a multi-sectorial and multi-level framework. Four main barriers for effective implementation of RHSP were identified: (1) weak inter-sectorial collaborations; (2) constraints faced by frontline promoters; (3) almost exclusive information-based and passive promotion methods applied; and (4) context unadjusted promotion strategies across ethnic groups, including a limited focus on socio-economic differences, language barriers and gender roles in the target groups. Highland communities were identified as least targeted and clearly in need of more intensive and effective RHSP. It is recommended that the Vietnamese government gives priority to increasing capacities of and collaboration among stakeholders implementing RHSP activities. This should focus on frontline promoters to perform effective behaviour change communication. It is also recommended to support more participatory and community-based initiatives, which can address the

  13. FoodMicrobionet: A database for the visualisation and exploration of food bacterial communities based on network analysis.

    Parente, Eugenio; Cocolin, Luca; De Filippis, Francesca; Zotta, Teresa; Ferrocino, Ilario; O'Sullivan, Orla; Neviani, Erasmo; De Angelis, Maria; Cotter, Paul D; Ercolini, Danilo

    2016-02-16

    Amplicon targeted high-throughput sequencing has become a popular tool for the culture-independent analysis of microbial communities. Although the data obtained with this approach are portable and the number of sequences available in public databases is increasing, no tool has been developed yet for the analysis and presentation of data obtained in different studies. This work describes an approach for the development of a database for the rapid exploration and analysis of data on food microbial communities. Data from seventeen studies investigating the structure of bacterial communities in dairy, meat, sourdough and fermented vegetable products, obtained by 16S rRNA gene targeted high-throughput sequencing, were collated and analysed using Gephi, a network analysis software. The resulting database, which we named FoodMicrobionet, was used to analyse nodes and network properties and to build an interactive web-based visualisation. The latter allows the visual exploration of the relationships between Operational Taxonomic Units (OTUs) and samples and the identification of core- and sample-specific bacterial communities. It also provides additional search tools and hyperlinks for the rapid selection of food groups and OTUs and for rapid access to external resources (NCBI taxonomy, digital versions of the original articles). Microbial interaction network analysis was carried out using CoNet on datasets extracted from FoodMicrobionet: the complexity of interaction networks was much lower than that found for other bacterial communities (human microbiome, soil and other environments). This may reflect both a bias in the dataset (which was dominated by fermented foods and starter cultures) and the lower complexity of food bacterial communities. Although some technical challenges exist, and are discussed here, the net result is a valuable tool for the exploration of food bacterial communities by the scientific community and food industry.

  14. Lipid and Phylogenetic Analysis of a Gypsum-hosted Endoevaporitic Microbial Community

    Turk, K. A.; Jahnke, L. L.; Green, S. J.; Kubo, M. D.; Vogel, M. B.; Des Marais, D. J.

    2007-12-01

    Gypsum evaporites host diverse, productive and volumetrically significant microbial communities and are relevant modern-day analogs to both Precambrian sabkha deposits and, potentially, Martian evaporites. Extensive evaporites form in subaqueous environments of high salinity ponds (>150 permil) maintained by the Exportadora de Sal, S. A. (ESSA) in Guerrero Negro, B.C.S., Mexico. A gypsarenite (reworked clastic gypsum) crust found along the southeast margin of ESSA's Pond 9 was collected in February 2004 and each vibrantly colored layer in the top centimeter was sampled. Extant microbial communities from each layer were characterized using complementary culture-independent molecular techniques, lipid biomarker analysis, and compound specific isotopic analysis. Coupling molecular analysis with lipid biomarker analysis revealed that oxygenic photosynthetic organisms dominate the surface layers (top 3 mm). Polar lipids from the surface layers consisted predominantly of glycolipids, which are characteristic of algae, cyanobacteria and green anoxygenic photosynthetic bacteria. Consistent with prior analyses of gypsum evaporites, 16S rRNA gene clone libraries indicate that cyanobacterial populations belong primarily to the genus Cyanothece. The bacterial community below the surface layers is more diverse and dominated by anaerobic organisms. Phototrophic purple sulfur bacteria, sulfate-reducing bacteria (SRB), and Bacteroidetes were particularly abundant. The relative abundances of SRB increased with depth; Desulfobacteraceae clones were distributed throughout the crust, but not at the surface, while Desulfovibrionaceae clones were found predominantly in the deepest layers. These molecular results are consistent with fatty acid biomarker analysis. δ13C values of major lipid classes in the crust and sediment range from 14 to 36‰, which is considerably lower than corresponding values for benthic Microcoleus-dominated cyanobacterial mats found at lower salinities at ESSA

  15. Metabolomic analysis of human fecal microbiota: a comparison of feces-derived communities and defined mixed communities.

    Yen, Sandi; McDonald, Julie A K; Schroeter, Kathleen; Oliphant, Kaitlyn; Sokolenko, Stanislav; Blondeel, Eric J M; Allen-Vercoe, Emma; Aucoin, Marc G

    2015-03-01

    The extensive impact of the human gut microbiota on its human host calls for a need to understand the types of communication that occur among the bacteria and their host. A metabolomics approach can provide a snapshot of the microbe-microbe interactions occurring as well as variations in the microbes from different hosts. In this study, metabolite profiles from an anaerobic continuous stirred-tank reactors (CSTR) system supporting the growth of several consortia of bacteria representative of the human gut were established and compared. Cell-free supernatant samples were analyzed by 1D (1)H nuclear magnetic resonance (NMR) spectroscopy, producing spectra representative of the metabolic activity of a particular community at a given time. Using targeted profiling, specific metabolites were identified and quantified on the basis of NMR analyses. Metabolite profiles discriminated each bacterial community examined, demonstrating that there are significant differences in the microbiota metabolome between each cultured community. We also found unique compounds that were identifying features of individual bacterial consortia. These findings are important because they demonstrate that metabolite profiles of gut microbial ecosystems can be constructed by targeted profiling of NMR spectra. Moreover, examination of these profiles sheds light on the type of microbes present in the gut and their metabolic interactions.

  16. Integrated Community Energy Systems: engineering analysis and design bibliography. [368 citations

    Calm, J.M.; Sapienza, G.R.

    1979-05-01

    This bibliography cites 368 documents that may be helpful in the planning, analysis, and design of Integrated Community Energy Systems. It has been prepared for use primarily by engineers and others involved in the development and implementation of ICES concepts. These documents include products of a number of Government research, development, demonstration, and commercialization programs; selected studies and references from the literature of various technical societies and institutions; and other selected material. The key programs which have produced cited reports are the Department of Energy Community Systems Program (DOE/CSP), the Department of Housing and Urban Development Modular Integrated Utility Systems Program (HUD/MIUS), and the Department of Health, Education, and Welfare Integrated Utility Systems Program (HEW/IUS). The cited documents address experience gained both in the U.S. and in other countries. Several general engineering references and bibliographies pertaining to technologies or analytical methods that may be helpful in the analysis and design of ICES are also included. The body of relevant literature is rapidly growing and future updates are therefore planned. Each citation includes identifying information, a source, descriptive information, and an abstract. The citations are indexed both by subjects and authors, and the subject index is extensively cross-referenced to simplify its use.

  17. Numeric syntaxonomical analysis of communities of the Molinia caerulea complex in Southwestern of Ukraine

    Budzhak Vasyl V.

    2016-12-01

    Full Text Available The aims of the paper are: i to establish the coenotic affinity of each species of the Molinia caerulea complex in the southwest of Ukraine, ii to present the results of a comparative analysis of the syntaxa in which include Molinia, iii to explain possible reasons for the expansion of Molinia caerulea in the studied area. The study area ranges from the basins of the Upper Prut River to the Upper Siret River in Ukraine. To determine the coenotical affinity of the studied species, 134 relevés were analysed. The data analysis was carried out using the Modified TWINSPAN algorithm provided by the JUICE software. Ecological features of the communities were analyzed by means of a DCA-ordination and phytoindication assessment. It was revealed that in the studied region the species of the Molinia caerulea complex are characterized by a relatively wide coenotic and ecological range and that they can be attributed to different communities of 4 vegetation classes: Molinio-Arrhenatheretea (Polygono bistortae-Trisetion flavescentis, Molinion cearuleae, Arrhenatherion elatioris alliances, Festuco-Brometea (Bromion erecti alliance, Mulgedio-Aconitetea (Calamagrostion villosae alliance, Oxycocco-Sphagnetea (Sphagnion magellanici alliance. This paper presents the results of the floristic composition analyses outlines some ecological peculiarities and discusses the conservational values of the identified syntaxa.

  18. Metagenomic analysis reveals symbiotic relationship among bacteria in Microcystis-dominated community

    Meili eXie

    2016-02-01

    Full Text Available Microcystis bloom, a cyanobacterial mass occurrence often found in eutrophicated water bodies, is one of the most serious threats to freshwater ecosystems worldwide. In nature, Microcystis forms aggregates or colonies that contain heterotrophic bacteria. The Microcystis-bacteria colonies were persistent even when they were maintained in lab culture for a long period. The relationship between Microcystis and the associated bacteria was investigated by a metagenomic approach in this study. We developed a visualization-guided method of binning for genome assembly after total colony DNA sequencing. We found that the method was effective in grouping sequences and it did not require reference genome sequence. Individual genomes of the colony bacteria were obtained and they provided valuable insights into microbial community structures. Analysis of metabolic pathways based on these genomes revealed that while all heterotrophic bacteria were dependent upon Microcystis for carbon and energy, Vitamin B12 biosynthesis, which is required for growth by Microcystis, was accomplished in a cooperative fashion among the bacteria. Our analysis also suggests that individual bacteria in the colony community contributed a complete pathway for degradation of benzoate, which is inhibitory to the cyanobacterial growth, and its ecological implication for Microcystis bloom is discussed.

  19. Microbial community analysis of shallow subsurface samples with PCR-DGGE

    Itaevaara, M.; Suihko, M.-L.; Kapanen, A.; Piskonen, R.; Juvonen, R. [VTT Biotechnology, Espoo (Finland)

    2005-11-15

    bacteria (SRB) indicating low redox potential of the samples. In addition phylogenetic trees were constructed for the sequences identified with both long and short primer sets. Phylogenetic trees were in good agreement with each other and indicated similar communties with both methods. In addition we also evaluated the suitability of primers amplifying SRB from the water samples. However, even though the microbial community analysis with the 16SrDNA gene indicated that SRB were present in the microbial community their amplification with the primers used was not successful. (orig.)

  20. Community-based participatory research and the challenges of qualitative analysis enacted by lay, nurse, and academic researchers.

    Foster, Jennifer W; Chiang, Fidela; Burgos, Rosa I; Cáceres, Ramona E; Tejada, Carmen M; Almonte, Asela T; Noboa, Frank R M; Perez, Lidia J; Urbaez, Marilín F; Heath, Annemarie

    2012-10-01

    There are multiple challenges in adhering to the principles of community-based participatory research (CBPR), especially when there is a wide range of academic preparation within the research team. This is particularly evident in the analysis phase of qualitative research. We describe the process of conducting qualitative analysis of data on community perceptions of public maternity care in the Dominican Republic, in a cross-cultural, CBPR study. Analysis advanced through a process of experiential and conversational learning. Community involvement in analysis provided lay researchers an imperative for improvements in maternity care, nurses a new perspective about humanized care, and academic researchers a deeper understanding of how to create the conditions to enable conversational learning.

  1. Null Models for Everyone: A Two-Step Approach to Teaching Null Model Analysis of Biological Community Structure

    McCabe, Declan J.; Knight, Evelyn J.

    2016-01-01

    Since being introduced by Connor and Simberloff in response to Diamond's assembly rules, null model analysis has been a controversial tool in community ecology. Despite being commonly used in the primary literature, null model analysis has not featured prominently in general textbooks. Complexity of approaches along with difficulty in interpreting…

  2. Factor Analysis and Norms for Parent Ratings on the Aberrant Behavior Checklist-Community for Young People in Special Education.

    Brown, Elaine C.; Aman, Michael G.; Havercamp, Susan M.

    2002-01-01

    Parents of 601 children and adolescents with mental retardation rated their children on the Aberrant Behavior Checklist-Community (ABC). Factor analysis revealed a factor structure similar to the original ABC but without the inappropriate speech factor. Analysis of subject variables revealed main effects for gender, age, and classroom assignment…

  3. Bioconductor workflow for microbiome data analysis: from raw reads to community analyses [version 1; referees: 2 approved

    Callahan, Ben J.; Kris Sankaran; Fukuyama, Julia A.; McMurdie, Paul J.; Holmes, Susan P

    2016-01-01

    High-throughput sequencing of PCR-amplified taxonomic markers (like the 16S rRNA gene) has enabled a new level of analysis of complex bacterial communities known as microbiomes. Many tools exist to quantify and compare abundance levels or microbial composition of communities in different conditions. The sequencing reads have to be denoised and assigned to the closest taxa from a reference database. Common approaches use a notion of 97% similarity and normalize the data by subsampling to equal...

  4. Diversity Analysis of Bacterial Community from Permafrost Soil of Mo-he in China.

    Dan, Dong; Zhang, Dian-Peng; Liu, Wei-Cheng; Lu, Cai-Ge; Zhang, Tao-Tao

    2014-03-01

    The permafrost soil of Mo-he in Northeast China presents a typical cold environment colonized by psychrophilic microorganisms. This study is aimed at assessing the bacterial communities of permafrost soil of Mo-he in China by sequencing the 16S rRNA genes and Mothur analysis. PCR products with universal 16S rRNA gene primers were cloned and partially sequenced, and bacterial identification at the species was performed by comparative analysis with the GenBank/EMBL/DDBJ database. A total of 266 clones were obtained with the average length of 1,050 bp. Mothur analysis showed that the coverage value of clone library was 53.78 %, Shannon diversity (H) was 4.03, Simpson diversity value was 0.018, and 74 operational taxonomic units were generated. Through phylogenetic assignment using BLASTN by more than 97 % similarity, a total of 87 tentative taxa were identified. The majority of bacterial sequences recovered in this study belonged to the Acidobacteria, Proteobacteria, Verrucomicrobia, Bacteroidetes, Chloroflexi and Chlorobi. Among them, Acidobacteria are dominant community, accounting for 30.1 % of total bacteria, followed by Proteobacteria which accounted for 22.2 %. This result reflected the acidic characteristics of the permafrost soil of which pH value was 6.0. Our study indicated that the permafrost soil of Mo-he in China has a high diversity of bacteria and represents a vast potential resource of novel bacteria. As far as we knew, this is the first report on bacterial diversity of permafrost soil of Mo-he in China.

  5. Urban Poor community Access to reproductive Health care in Surabaya. An Equity Analysis Using Spider Web

    Ernawaty Ernawaty

    2015-01-01

    Full Text Available background:Poverty in urban area triggered new problem related with their access to health care services. Heavy burden of life in urban makes health, especially reproductive health, never become first priority for urban poor community. This study is aimed to analyzed equity of urban poor community when accessing the reproductive health care. Methods:This is descriptive study with cross sectional design applied. There were 78 women residents of Penjaringansari II Flats in Surabaya selected by simple random sampling (α=10% as respondents. Penjaringansari II Flats was choosen because it is a slum area that residence by unskilled labours and odd employees. The need fulfillment of respondents in reproductive health care was analyzed by spider web analysis. result: Most of respondents (55.1% were first married before 20 years old. There were 60.5% of them gave birth before 20 years old also, so it belongs to high risk pregnant women. Spider web area for health care of under age married was less than ideal age married which means that under age married urban poor experienced inequity for ANC health services. Approximately 10.3% of respondents had never use contraceptives because they fear of side effects and inhibiton of their husband. conclutions:Better equity shown in the prevention of cervical cancer. Being perceived as the poor who need assistance, free pap smear was often held by Penjaringansari II residents. Poor conditions experienced by a group not only can promote health care inequity, but also promote health care equity. recomendation:Health care equity for urban poor can be pursued through both aid schemes provided by the community or the government.

  6. Standardizing methylation method during phospholipid fatty acid analysis to profile soil microbial communities.

    Chowdhury, Taniya Roy; Dick, Richard P

    2012-02-01

    Phospholipid fatty acid (PLFA) as biomarkers, is widely used to profile microbial communities in environmental samples. However, PLFA extraction and derivatization protocols are not standardized and have widely varied among published studies. Specifically investigators have used either HCl/MeOH or KOH/MeOH or both for the methylation step of PLFA analysis, without justification or research to support either one. It seems likely that each method could have very different outcomes and conclusions for PLFA based studies. Therefore, the objective of this study was to determine the effect of catalyst type for methylation on detecting PLFAs and implications for interpreting microbial profiling in soil. Fatty acid samples extracted from soils obtained from a wetland, an intermittently flooded site, and an adjacent upland site were subjected to HCl/MeOH or KOH/MeOH catalyzed methylation procedures during PLFA analyses. The methylation method using HCl/MeOH resulted in significantly higher concentrations of most PLFAs than the KOH/MeOH method. Another important outcome was that fatty acids with a methyl group (18:1ω,7c 11Me, TBSA 10Me 18:0, 10Me 18:0, 17:0 10Me and 16:0 10Me being an actinomycetes biomarker) could not be detected by HCl/MeOH catalyzed methylation but were found in appreciable concentrations with KOH/MeOH method. From our results, because the HCl/MeOH method did not detect the fatty acids containing methyl groups that could strongly influence the microbial community profile, we recommend that the KOH/MeOH catalyzed transesterification method should become the standard procedure for PLFA profiling of soil microbial communities.

  7. Ammonia biofiltration and community analysis of ammonia-oxidizing bacteria in biofilters.

    Jun, Yin; Wenfeng, Xu

    2009-09-01

    Biological removal of ammonia was investigated using compost and sludge as packing materials in laboratory-scale biofilters. The aim of this study is to characterize the composition of ammonia-oxidizing bacteria (AOB) in two biofilters designed to remove ammonia. Experimental tests and measurements included analysis of removal efficiency and metabolic products. The inlet concentration of ammonia applied was 20-100 mg m(-3). Removal efficiencies of BFC and BFS were in the range of 97-99% and 95-99%, respectively. Periodic analysis of the biofilter packing materials showed ammonia was removed from air stream by nitrification and by the improved absorption of NH(3) in the resultant acidity. Nitrate was the dominant product of NH(3) transformation. Changes in the composition of AOB were examined by using nested PCR, denaturing gradient gel electrophoresis (DGGE) and sequencing of DGGE bands. DGGE analysis of biofilter samples revealed that shifts in the community structure of AOB were observed in the experiment; however, the idle phase did not cause the structural shift of AOB. Phylogenetic analysis revealed the population of AOB showed Nitrosospira sp. remains the predominant population in BFC, while Nitrosomonas sp. is the predominant population in BFS.

  8. Comparative analysis of microbial community between different cathode systems of microbial fuel cells for denitrification.

    Li, Chao; Xu, Ming; Lu, Yi; Fang, Fang; Cao, Jiashun

    2016-01-01

    Two types of cathodic biofilm in microbial fuel cells (MFC) were established for comparison on their performance and microbial communities. Complete autotrophic simultaneous nitrification and denitrification (SND) without organics addition was achieved in nitrifying-MFC (N-MFC) with a total nitrogen (TN) removal rate of 0.35 mg/(L·h), which was even higher than that in denitrifying-MFC (D-MFC) at same TN level. Integrated denaturing gradient gel electrophoresis analysis based on both 16S rRNA and nirK genes showed that Alpha-, Gammaproteobacteria were the main denitrifier communities. Some potential autotrophic denitrifying bacteria which can use electrons and reducing power from cathodes, such as Shewanella oneidensis, Shewanella loihica, Pseudomonas aeruginosa, Starkeya novella and Rhodopseudomonas palustris were identified and selectively enriched on cathode biofilms. Further, relative abundance of denitrifying bacteria characterized by nirK/16S ratios was much higher in biofilm than suspended sludge according to real-time polymerase chain reaction. The highest enrichment efficiency for denitrifiers was obtained in N-MFC cathode biofilms, which confirmed autotrophic denitrifying bacteria enrichment is the key factor for a D-MFC system.

  9. Molecular analysis of bacterial communities in biofilms of a drinking water clearwell.

    Zhang, Minglu; Liu, Wenjun; Nie, Xuebiao; Li, Cuiping; Gu, Junnong; Zhang, Can

    2012-01-01

    Microbial community structures in biofilms of a clearwell in a drinking water supply system in Beijing, China were examined by clone library, terminal restriction fragment length polymorphism (T-RFLP) and 454 pyrosequencing of the amplified 16S rRNA gene. Six biofilm samples (designated R1-R6) collected from six locations (upper and lower sites of the inlet, middle and outlet) of the clearwell revealed similar bacterial patterns by T-RFLP analysis. With respect to the dominant groups, the phylotypes detected by clone library and T-RFLP generally matched each other. A total of 9,543 reads were obtained from samples located at the lower inlet and the lower outlet sites by pyrosequencing. The bacterial diversity of the two samples was compared at phylum and genus levels. Alphaproteobacteria dominated the communities in both samples and the genus of Sphingomonas constituted 75.1%-99.6% of this phylum. A high level of Sphingomonas sp. was first observed in the drinking water biofilms with 0.6-1.0 mg L(-1) of chlorine residual. Disinfectant-resistant microorganisms deserve special attention in drinking water management. This study provides novel insights into the microbial populations in drinking water systems and highlights the important role of Sphingomonas species in biofilm formation.

  10. Community analysis of plant biomass-degrading microorganisms from Obsidian Pool, Yellowstone National Park.

    Vishnivetskaya, Tatiana A; Hamilton-Brehm, Scott D; Podar, Mircea; Mosher, Jennifer J; Palumbo, Anthony V; Phelps, Tommy J; Keller, Martin; Elkins, James G

    2015-02-01

    The conversion of lignocellulosic biomass into biofuels can potentially be improved by employing robust microorganisms and enzymes that efficiently deconstruct plant polysaccharides at elevated temperatures. Many of the geothermal features of Yellowstone National Park (YNP) are surrounded by vegetation providing a source of allochthonic material to support heterotrophic microbial communities adapted to utilize plant biomass as a primary carbon and energy source. In this study, a well-known hot spring environment, Obsidian Pool (OBP), was examined for potential biomass-active microorganisms using cultivation-independent and enrichment techniques. Analysis of 33,684 archaeal and 43,784 bacterial quality-filtered 16S rRNA gene pyrosequences revealed that archaeal diversity in the main pool was higher than bacterial; however, in the vegetated area, overall bacterial diversity was significantly higher. Of notable interest was a flooded depression adjacent to OBP supporting a stand of Juncus tweedyi, a heat-tolerant rush commonly found growing near geothermal features in YNP. The microbial community from heated sediments surrounding the plants was enriched in members of the Firmicutes including potentially (hemi)cellulolytic bacteria from the genera Clostridium, Anaerobacter, Caloramator, Caldicellulosiruptor, and Thermoanaerobacter. Enrichment cultures containing model and real biomass substrates were established at a wide range of temperatures (55-85 °C). Microbial activity was observed up to 80 °C on all substrates including Avicel, xylan, switchgrass, and Populus sp. Independent of substrate, Caloramator was enriched at lower (65 °C) temperatures.

  11. Comparison of DNA extraction methods in analysis of salivary bacterial communities.

    Lazarevic, Vladimir; Gaïa, Nadia; Girard, Myriam; François, Patrice; Schrenzel, Jacques

    2013-01-01

    Culture-independent high-throughput sequencing-based methods are widely used to study bacterial communities. Although these approaches are superior to traditional culture-based methods, they introduce bias at the experimental and bioinformatics levels. We assessed the diversity of the human salivary microbiome by pyrosequencing of the 16S rDNA V1-3 amplicons using metagenomic DNA extracted by two different protocols: a simple proteinase K digestion without a subsequent DNA clean-up step, and a bead-beating mechanical lysis protocol followed by column DNA purification. A high degree of congruence was found between the two extraction methods, most notably in regard to the microbial community composition. The results showed that for a given bioinformatics pipeline, all the taxa with an average proportion >0.12% in samples processed using one extraction method were also detected in samples extracted using the other method. The same taxa tended to be abundant and frequent for both extraction methods. The relative abundance of sequence reads assigned to the phyla Actinobacteria, Spirochaetes, TM7, Synergistetes, and Tenericutes was significantly higher in the mechanically-treated samples than in the enzymatically-treated samples, whereas the phylum Firmicutes showed the opposite pattern. No significant differences in diversity indices were found between the extraction methods, although the mechanical lysis method revealed higher operational taxonomic unit richness. Differences between the extraction procedures outweighed the variations due to the bioinformatics analysis pipelines used.

  12. Comparison of DNA extraction methods in analysis of salivary bacterial communities.

    Vladimir Lazarevic

    Full Text Available Culture-independent high-throughput sequencing-based methods are widely used to study bacterial communities. Although these approaches are superior to traditional culture-based methods, they introduce bias at the experimental and bioinformatics levels. We assessed the diversity of the human salivary microbiome by pyrosequencing of the 16S rDNA V1-3 amplicons using metagenomic DNA extracted by two different protocols: a simple proteinase K digestion without a subsequent DNA clean-up step, and a bead-beating mechanical lysis protocol followed by column DNA purification. A high degree of congruence was found between the two extraction methods, most notably in regard to the microbial community composition. The results showed that for a given bioinformatics pipeline, all the taxa with an average proportion >0.12% in samples processed using one extraction method were also detected in samples extracted using the other method. The same taxa tended to be abundant and frequent for both extraction methods. The relative abundance of sequence reads assigned to the phyla Actinobacteria, Spirochaetes, TM7, Synergistetes, and Tenericutes was significantly higher in the mechanically-treated samples than in the enzymatically-treated samples, whereas the phylum Firmicutes showed the opposite pattern. No significant differences in diversity indices were found between the extraction methods, although the mechanical lysis method revealed higher operational taxonomic unit richness. Differences between the extraction procedures outweighed the variations due to the bioinformatics analysis pipelines used.

  13. Arctic indigenous youth resilience and vulnerability: comparative analysis of adolescent experiences across five circumpolar communities.

    Ulturgasheva, Olga; Rasmus, Stacy; Wexler, Lisa; Nystad, Kristine; Kral, Michael

    2014-10-01

    Arctic peoples today find themselves on the front line of rapid environmental change brought about by globalizing forces, shifting climates, and destabilizing physical conditions. The weather is not the only thing undergoing rapid change here. Social climates are intrinsically connected to physical climates, and changes within each have profound effects on the daily life, health, and well-being of circumpolar indigenous peoples. This paper describes a collaborative effort between university researchers and community members from five indigenous communities in the circumpolar north aimed at comparing the experiences of indigenous Arctic youth in order to come up with a shared model of indigenous youth resilience. The discussion introduces a sliding scale model that emerged from the comparative data analysis. It illustrates how a "sliding scale" of resilience captures the inherent dynamism of youth strategies for "doing well" and what forces represent positive and negative influences that slide towards either personal and communal resilience or vulnerability. The model of the sliding scale is designed to reflect the contingency and interdependence of resilience and vulnerability and their fluctuations between lowest and highest points based on timing, local situation, larger context, and meaning.

  14. Functional characteristics of an endophyte community colonizing rice roots as revealed by metagenomic analysis.

    Sessitsch, A; Hardoim, P; Döring, J; Weilharter, A; Krause, A; Woyke, T; Mitter, B; Hauberg-Lotte, L; Friedrich, F; Rahalkar, M; Hurek, T; Sarkar, A; Bodrossy, L; van Overbeek, L; Brar, D; van Elsas, J D; Reinhold-Hurek, B

    2012-01-01

    Roots are the primary site of interaction between plants and microorganisms. To meet food demands in changing climates, improved yields and stress resistance are increasingly important, stimulating efforts to identify factors that affect plant productivity. The role of bacterial endophytes that reside inside plants remains largely unexplored, because analysis of their specific functions is impeded by difficulties in cultivating most prokaryotes. Here, we present the first metagenomic approach to analyze an endophytic bacterial community resident inside roots of rice, one of the most important staple foods. Metagenome sequences were obtained from endophyte cells extracted from roots of field-grown plants. Putative functions were deduced from protein domains or similarity analyses of protein-encoding gene fragments, and allowed insights into the capacities of endophyte cells. This allowed us to predict traits and metabolic processes important for the endophytic lifestyle, suggesting that the endorhizosphere is an exclusive microhabitat requiring numerous adaptations. Prominent features included flagella, plant-polymer-degrading enzymes, protein secretion systems, iron acquisition and storage, quorum sensing, and detoxification of reactive oxygen species. Surprisingly, endophytes might be involved in the entire nitrogen cycle, as protein domains involved in N(2)-fixation, denitrification, and nitrification were detected and selected genes expressed. Our data suggest a high potential of the endophyte community for plant-growth promotion, improvement of plant stress resistance, biocontrol against pathogens, and bioremediation, regardless of their culturability.

  15. Ethylene removal evaluation and bacterial community analysis of vermicompost as biofilter material.

    Fu, Yuming; Shao, Lingzhi; Liu, Hui; Tong, Ling; Liu, Hong

    2011-08-30

    Biofiltration of ethylene provides an environmentally friendly and economically beneficial option relative to physical/chemical removal, where selection of appropriate bed material is crucial. Here the vermicompost with indigenous microorganisms as bed material was evaluated for ethylene removal through batch test and biofilter experiment. Temporal and spatial dynamics of bacterial community in the vermicompost-biofilter under different ethylene loads were characterized by culture and denaturing gradient gel electrophoresis (DGGE) methods. The results showed that ethylene was effectively degraded by the vermicompost under conditions of 25-50% moisture content and 25-35°C temperature. The vermicompost-biofilter achieved nearly 100% ethylene removal up to an inlet load of 11mg m(-3)h(-1). Local nitrogen lack of the vermicompost in the biofilter was observed over operation time, but the change of pH was slight. DGGE analysis demonstrated that the bacterial abundance and community structure of vermicompost-biofilter varied with the height of biofilter under different ethylene loads. Pseudomonads and Actinobacteria were predominant in the biofilter throughout the whole experiment.

  16. Disturbance, Response, and Persistence in Self-Organized Forested Communities: Analysis of Robustness and Resilience in Five Communities in Southern Indiana

    Forrest D. Fleischman

    2010-12-01

    Full Text Available We develop an analytic framework for the analysis of robustness in social-ecological systems (SESs over time. We argue that social robustness is affected by the disturbances that communities face and the way they respond to them. Using Ostrom's ontological framework for SESs, we classify the major factors influencing the disturbances and responses faced by five Indiana intentional communities over a 15-year time frame. Our empirical results indicate that operational and collective-choice rules, leadership and entrepreneurship, monitoring and sanctioning, economic values, number of users, and norms/social capital are key variables that need to be at the core of future theoretical work on robustness of self-organized systems.

  17. Place-classification analysis of community vulnerability to near-field tsunami threats in the U.S. Pacific Northwest

    Wood, N. J.; Spielman, S.

    2012-12-01

    Near-field tsunami hazards are credible threats to many coastal communities throughout the world. Along the U.S. Pacific Northwest coast, low-lying areas could be inundated by a series of catastrophic tsunamis that begin to arrive in a matter of minutes following a major Cascadia subduction zone (CSZ) earthquake. Previous research has documented the residents, employees, tourists at public venues, customers at local businesses, and vulnerable populations at dependent-care facilities that are in CSZ-related tsunami-prone areas of northern California, Oregon, and the open-ocean coast of Washington. Community inventories of demographic attributes and other characteristics of the at-risk population have helped emergency managers to develop preparedness and outreach efforts. Although useful for distinct risk-reduction issues, these data can be difficult to fully appreciate holistically given the large number of community attributes. This presentation summarizes analytical efforts to classify communities with similar characteristics of community exposure to tsunami hazards. This work builds on past State-focused inventories of community exposure to CSZ-related tsunami hazards in northern California, Oregon, and Washington. Attributes used in the classification, or cluster analysis, fall into several categories, including demography of residents, spatial extent of the developed footprint based on mid-resolution land cover data, distribution of the local workforce, and the number and type of public venues, dependent-care facilities, and community-support businesses. As we were unsure of the number of different types of communities, we used an unsupervised-model-based clustering algorithm and a v-fold, cross-validation procedure (v=50) to identify the appropriate number of community types. Ultimately we selected class solutions that provided the appropriate balance between parsimony and model fit. The goal of the exposure classification is to provide emergency managers with

  18. Molecular analysis of Staphylococcus epidermidis strains isolated from community and hospital environments in China.

    Xin Du

    Full Text Available BACKGROUND: Staphylococcus epidermidis is a common cause of nosocomial infections worldwide. This study analyzed the differences in genetic endowment and clonal lineages with pathogenesis and resistance traits of S. epidermidis isolates collected from community and hospital environments (patients and healthcare staff of the same ecological niche, time period, and geographical location in China. METHODOLOGY/PRINCIPAL FINDINGS: Molecular epidemiology and population analysis showed that nasal colonization rates of S. epidermidis in the community of Shanghai area of China and in healthcare personnel were 44.8% (methicillin-resistant S. epidermidis, MRSE: 17.2% and 61.3% (MRSE: 30.0%, respectively. 86.7% of clinical isolates were MRSE. Among the strains studied, 44 sequence types (STs were identified with 91.7% belonging to clonal complex 2 (CC2. Only 40.8% isolates from patients were also found in healthy individuals. MRSE-ST2-SCCmecIII was the predominant clone in clinical isolates, almost resistant to all antibiotics tested. Biofilm-related genes IS256 and icaA were detected in majority of the predominant clinical MRSE-ST2 clone with a 40.5% biofilm-positive rate. No ST2 isolate was found in community setting. We found a high prevalence of arginine catabolic mobile element (ACME (74.1%. The prevalence of ACME-arc and ACME-opp3 clusters was 71.6% and 32.4%, respectively. Methicillin-sensitive S. epidermidis (MSSE isolates harbored more ACME (83.3% than MRSE isolates (67.7%, and there was no association between ACME and SCCmec types. An association was found between low-level ACME presence and invasive infections. CONCLUSIONS/SIGNIFICANCE: We observed a high level of diversity within S. epidermidis in this study, with CC2 as the dominant clonal complex in both community and hospital settings. Only 40.8% of the isolates from patients were also found in healthy individuals. Contrary to that biofilm formation and multiple antibiotic resistance were

  19. Isolation and Phylogenetic Analysis of Thermophile Community Within Tanjung Sakti Hot Spring, South Sumatera, Indonesia

    Heni Yohandini

    2015-07-01

    Full Text Available A community of thermophiles within Tanjung Sakti Hot Spring (South Sumatera have been cultivated and identified based on 16S ribosomal RNA gene sequence. The hot spring has temperature 80C-91C and pH 7-8. We used a simple method for culturing the microbes, by enriching the spring water with nutrient broth media. Phylogenetic analysis showed that the method could recover microbes, which clustered within four distinct taxonomic groups: Anoxybacillus, Geobacillus, Brevibacillus, and Bacillus. These microbes closely related to Anoxybacillus rupiensis, Anoxybacillus flavithermus, Geobacillus pallidus, Brevibacillus thermoruber, Bacillus licheniformis, and Bacillus thermoamylovorans. The 16S ribosomal RNA gene sequence of one isolate only had 96% similarity with Brevibacillus sequence in GenBank.

  20. A social network analysis of Twitter: Mapping the digital humanities community

    Martin Grandjean

    2016-12-01

    Full Text Available Defining digital humanities might be an endless debate if we stick to the discussion about the boundaries of this concept as an academic “discipline”. In an attempt to concretely identify this field and its actors, this paper shows that it is possible to analyse them through Twitter, a social media widely used by this “community of practice”. Based on a network analysis of 2,500 users identified as members of this movement, the visualisation of the “who’s following who?” graph allows us to highlight the structure of the network’s relationships, and identify users whose position is particular. Specifically, we show that linguistic groups are key factors to explain clustering within a network whose characteristics look similar to a small world.

  1. Measuring and developing Communities of Practice in a blood analysis unit

    Jørgensen, Rasmus; Edwards, Kasper

    2016-01-01

    developing and measuring CoP is lacking. We propose a method to measure and develop CoP and the method is tested in a blood analysis unit at ‘Nordsjællands Hospital’ in Denmark. Material and method: The practice was operationalized narrowly as employees performing a specific maintenance task. A questionnaire...... was developed based on a CoP literature review. Using the ‘think aloud’ method the questionnaire was tested with practitioners investigating if questions were decoded correctly and triggered the desired mental image. CoP level was measured at baseline and at follow-up (seven weeks after the intervention......Introduction: Knowledge sharing is essential to develop operational efficiency and quality. However, knowledge sharing is difficult to achieve due to 24-7 shifts, patient contact and little time for meetings. The theory of communities of practice (CoP) proposes an alternate approach to knowledge...

  2. Social Network Community Detection for DMA Creation: Criteria Analysis through Multilevel Optimization

    Bruno M. Brentan

    2017-01-01

    Full Text Available Management of large water distribution systems can be improved by dividing their networks into so-called district metered areas (DMAs. However, such divisions must be based on appropriated technical criteria. Considering the importance of deeply understanding the relationship between DMA creation and these criteria, this work proposes a performance analysis of DMA generation that takes into account such indicators as resilience index, demand similarity, pressure uniformity, water age (and thus water quality, solution implantation costs, and electrical consumption. To cope with the complexity of the problem, suitable mathematical techniques are proposed in this paper. We use a social community detection technique to define the sectors, and then a multilevel particle swarm optimization approach is applied to find the optimal placement and operating point of the necessary devices. The results obtained by implementing the methodology in a real water supply network show its validity and the meaningful influence on the final result of, especially, elevation and pipe length.

  3. Analysis of Heat Environment Indexes Using Integrated Remote Sensing and Site Measurement Techniques in a Community

    Kun Li; Jian Kang; YeHao Song; Dong Jiang

    2014-01-01

    Remote sensing and on⁃site measurement are used to determine the heat environment within a community, and are compared the differences for heat analysis. The two methods perform differently for various underlying surfaces. The individual methods can detect different aspects of the heat environment, which used in combination are useful for heat island research. The differences in estimated air and surface temperatures are smaller in open space and more obvious for vegetated surfaces. Ventilation does not affect the difference between air and surface temperature in open areas, and the vegetation surface and shading moderates surface temperature more effectively than the water surface; The forest is a type of underlying surface with heat comfortable, in which the feeling of air temperature is much difference to the structure of heat environment that should be survey and detected separately. The two methods can be used to study different aspects of the heat environment, thus forming a comprehensive approach for planners in urban and rural spaces.

  4. Soil-specific limitations for access and analysis of soil microbial communities by metagenomics.

    Lombard, Nathalie; Prestat, Emmanuel; van Elsas, Jan Dirk; Simonet, Pascal

    2011-10-01

    Metagenomics approaches represent an important way to acquire information on the microbial communities present in complex environments like soil. However, to what extent do these approaches provide us with a true picture of soil microbial diversity? Soil is a challenging environment to work with. Its physicochemical properties affect microbial distributions inside the soil matrix, metagenome extraction and its subsequent analyses. To better understand the bias inherent to soil metagenome 'processing', we focus on soil physicochemical properties and their effects on the perceived bacterial distribution. In the light of this information, each step of soil metagenome processing is then discussed, with an emphasis on strategies for optimal soil sampling. Then, the interaction of cells and DNA with the soil matrix and the consequences for microbial DNA extraction are examined. Soil DNA extraction methods are compared and the veracity of the microbial profiles obtained is discussed. Finally, soil metagenomic sequence analysis and exploitation methods are reviewed.

  5. An analysis of a low-energy, low-water use community in Mexico City

    Bermudez Alcocer, Jose Luis

    This study investigated how to determine a potential scenario to reduce energy, water and transportation use in Mexico City by implementing low-energy, low-water use communities. The proposed mixed-use community has multi-family apartments and a small grocery store. The research included the analysis of: case studies, energy simulation, and hand calculations for water, transportation and cost analysis. The previous case studies reviewed include: communities in Mexico City, Mexico, Austin, Texas, Phoenix, Arizona, New York City, New York and San Diego, California in terms of successful low-energy, low-water use projects. The analysis and comparison of these centers showed that the Multifamiliar Miguel Aleman is an excellent candidate to be examined for Mexico City. This technical potential study evaluated energy conserving measures such as low-energy appliances and efficient lighting that could be applied to the apartments in Mexico City to reduce energy-use. The use of the simulations and manual calculations showed that the application of the mixed-use concept was successful in reducing the energy and water use and the corresponding carbon footprint. Finally, this technical potential study showed taking people out of their cars as a result of the presence of the on-site grocery store, small recreation center and park on the ground floor also reduced their overall transportation energy-use. The improvement of the whole community (i.e., apartments plus grocery store) using energy-efficient measures provided a reduction of 70 percent of energy from the base-case. In addition a 69 percent reduction in water-use was achieved by using water-saving fixtures and greywater reuse technologies for the complex. The combination of high-efficiency automobiles and the presence of the on-site grocery store, small recreation center and park potentially reduced the transportation energy-use by 65 percent. The analysis showed an energy cost reduction of 82 percent reduction for

  6. SCEC Community Modeling Environment (SCEC/CME) - Seismic Hazard Analysis Applications and Infrastructure

    Maechling, P. J.; Jordan, T. H.; Kesselman, C.; Moore, R.; Minster, B.; SCEC ITR Collaboration

    2003-12-01

    The Southern California Earthquake Center (SCEC) has formed a Geoscience/IT partnership to develop an advanced information infrastructure for system-level earthquake science in Southern California. This SCEC/ITR partnership comprises SCEC, USC's Information Sciences Institute (ISI), the San Diego Supercomputer Center (SDSC), the Incorporated Institutions for Research in Seismology (IRIS), and the U.S. Geological Survey. This collaboration recently completed the second year in a five-year National Science Foundation (NSF) funded ITR project called the SCEC Community Modeling Environment (SCEC/CME). The goal of the SCEC/CME is to develop seismological applications and information technology (IT) infrastructure to support the development of Seismic Hazard Analysis (SHA) programs and other geophysical simulations. The SHA application programs developed by project collaborators include a Probabilistic Seismic Hazard Analysis system called OpenSHA [Field et al., this meeting]. OpenSHA computational elements that are currently available include a collection of attenuation relationships, and several Earthquake Rupture Forecasts (ERF's). Geophysicists in the collaboration have also developed Anelastic Wave Models (AWMs) using both finite-difference and finite-element approaches. Earthquake simulations using these codes have been run for a variety of earthquake sources. A Rupture Dynamic Model (RDM) has also been developed that couples a rupture dynamics simulation into an anelastic wave model. The collaboration has also developed IT software and hardware infrastructure to support the development, execution, and analysis of SHA programs. To support computationally expensive simulations, we have constructed a grid-based system utilizing Globus software [Kesselman et al., this meeting]. Using the SCEC grid, project collaborators can submit computations from the SCEC/CME servers to High Performance Computers at USC, NPACI and Teragrid High Performance Computing Centers. We have

  7. Bovine Genome Database: supporting community annotation and analysis of the Bos taurus genome

    Childs Kevin L

    2010-11-01

    Full Text Available Abstract Background A goal of the Bovine Genome Database (BGD; http://BovineGenome.org has been to support the Bovine Genome Sequencing and Analysis Consortium (BGSAC in the annotation and analysis of the bovine genome. We were faced with several challenges, including the need to maintain consistent quality despite diversity in annotation expertise in the research community, the need to maintain consistent data formats, and the need to minimize the potential duplication of annotation effort. With new sequencing technologies allowing many more eukaryotic genomes to be sequenced, the demand for collaborative annotation is likely to increase. Here we present our approach, challenges and solutions facilitating a large distributed annotation project. Results and Discussion BGD has provided annotation tools that supported 147 members of the BGSAC in contributing 3,871 gene models over a fifteen-week period, and these annotations have been integrated into the bovine Official Gene Set. Our approach has been to provide an annotation system, which includes a BLAST site, multiple genome browsers, an annotation portal, and the Apollo Annotation Editor configured to connect directly to our Chado database. In addition to implementing and integrating components of the annotation system, we have performed computational analyses to create gene evidence tracks and a consensus gene set, which can be viewed on individual gene pages at BGD. Conclusions We have provided annotation tools that alleviate challenges associated with distributed annotation. Our system provides a consistent set of data to all annotators and eliminates the need for annotators to format data. Involving the bovine research community in genome annotation has allowed us to leverage expertise in various areas of bovine biology to provide biological insight into the genome sequence.

  8. Community characteristics associated with HIV risk among injection drug users in the San Francisco Bay Area: a multilevel analysis.

    Bluthenthal, Ricky N; Do, D Phuong; Finch, Brian; Martinez, Alexis; Edlin, Brian R; Kral, Alex H

    2007-09-01

    Community characteristics have been associated with racial and ethnic health disparities for a wide range of ailments and conditions. Previous research has found that rates of AIDS cases among injection drug users (IDUs) vary by community characteristics. However, few studies have examined whether community characteristics are associated with HIV risk behaviors among IDUs. To address this gap in the literature, we examined the associations between census-tract-level community characteristics and injection-related and sex-related HIV risk behaviors among IDUs in the San Francisco Bay Area. Individual HIV risk behaviors were collected from 4,956 IDUs between 1998 and 2002. Using 2000 US census data, we constructed four census-level community measures: percent African American, percent male unemployment, percent of households that receive public assistance, and median household income. All community variables were measured continuously. Multilevel modeling was used to determine if community characteristics were associated with recent (in the last 6 months) receptive and distributive syringe sharing, multiple sex partners, and unprotected sex risk while controlling for potential individual-level confounders. In bivariate analysis, most of the census-tract-level community characteristics were significantly associated with injection-related HIV risk, while no community characteristics were associated with sex-related risk. However, results from multivariate multilevel models indicate that only percent African American in a census tract was associated with receptive [adjusted odds ratio (AOR) = 0.93; 95% confidence interval (CI) = 0.89, 0.99] and distributive syringe sharing (AOR = 0.94; 95% CI = 0.92, 0.99), net of individual-level characteristics. Accounting for individual-level factors in the multivariate model in the sex-related risk models revealed a significant inverse relationship between percent African American and propensity to engage in unprotected sex (AOR = 0

  9. Improving financial performance by modeling and analysis of radiology procedure scheduling at a large community hospital.

    Lu, Lingbo; Li, Jingshan; Gisler, Paula

    2011-06-01

    Radiology tests, such as MRI, CT-scan, X-ray and ultrasound, are cost intensive and insurance pre-approvals are necessary to get reimbursement. In some cases, tests may be denied for payments by insurance companies due to lack of pre-approvals, inaccurate or missing necessary information. This can lead to substantial revenue losses for the hospital. In this paper, we present a simulation study of a centralized scheduling process for outpatient radiology tests at a large community hospital (Central Baptist Hospital in Lexington, Kentucky). Based on analysis of the central scheduling process, a simulation model of information flow in the process has been developed. Using such a model, the root causes of financial losses associated with errors and omissions in this process were identified and analyzed, and their impacts were quantified. In addition, "what-if" analysis was conducted to identify potential process improvement strategies in the form of recommendations to the hospital leadership. Such a model provides a quantitative tool for continuous improvement and process control in radiology outpatient test scheduling process to reduce financial losses associated with process error. This method of analysis is also applicable to other departments in the hospital.

  10. Back to Basics – The Influence of DNA Extraction and Primer Choice on Phylogenetic Analysis of Activated Sludge Communities

    Albertsen, Mads; Karst, Søren Michael; Ziegler, Anja Sloth

    2015-01-01

    DNA extraction and primer choice have a large effect on the observed community structure in allmicrobial amplicon sequencing analyses. Although the biases are well known, no com- prehensive analysis has been conducted in activated sludge communities. In this study we systematically explored...... and metatranscriptomics. Quantitative fluorescence in situ hybridization was used as a DNA extraction-independent method for qualitative comparison. In general, an effect on the observed community was found on all parameters tested, although bead beating and primer choice had the largest effect. The effect of bead...... the impact of a number of parameters on the observed microbial community: bead beating intensity, primer choice, extracellular DNA removal, and various PCR settings. In total, 176 samples were subjected to 16S rRNA amplicon sequencing, and selected samples were investigated throughmetagenomics...

  11. Back to basics – the influence of DNA extraction and primer choice on phylogenetic analysis in activated sludge communities

    Albertsen, Mads; Karst, Søren Michael; Ziegler, Anja Sloth

    DNA extraction and primer choice have a large effect on the observed community structure in all phylogenetic analyses. Although the biases are well known, no comprehensive analysis have been conducted in activated sludge communities. In this study we investigated the effect of bead beating...... intensity and primer choice on the observed community using 16S rDNA amplicon sequencing. Quantitative fluorescence in situ hybridization (qFISH) was used as a DNA extraction independent method to evaluate the results. The bead beating intensity correlated with cell-wall strength and showed...... that the manufacture recommended settings were insufficient to retrieve a large part of the community. In addition, the in silico “best” primer set was found to greatly underestimate a number of important phyla when compared to qFISH results. The findings underline the need for sample specific and DNA extraction...

  12. A three-scale analysis of bacterial communities involved in rocks colonization and soil formation in high mountain environments.

    Esposito, Alfonso; Ciccazzo, Sonia; Borruso, Luigimaria; Zerbe, Stefan; Daffonchio, Daniele; Brusetti, Lorenzo

    2013-10-01

    Alpha and beta diversities of the bacterial communities growing on rock surfaces, proto-soils, riparian sediments, lichen thalli, and water springs biofilms in a glacier foreland were studied. We used three molecular based techniques to allow a deeper investigation at different taxonomic resolutions: denaturing gradient gel electrophoresis, length heterogeneity-PCR, and automated ribosomal intergenic spacer analysis. Bacterial communities were mainly composed of Acidobacteria, Proteobacteria, and Cyanobacteria with distinct variations among sites. Proteobacteria were more represented in sediments, biofilms, and lichens; Acidobacteria were mostly found in proto-soils; and Cyanobacteria on rocks. Firmicutes and Bacteroidetes were mainly found in biofilms. UniFrac P values confirmed a significant difference among different matrices. Significant differences (P rocks which shared a more similar community structure, while at deep taxonomic resolution two distinct bacterial communities between lichens and rocks were found.

  13. Analysis of the Carnegie Classification of Community Engagement: Patterns and Impact on Institutions

    Driscoll, Amy

    2014-01-01

    This chapter describes the impact that participation in the Carnegie Classification for Community Engagement had on the institutions of higher learning that applied for the classification. This is described in terms of changes in direct community engagement, monitoring and reporting on community engagement, and levels of student and professor…

  14. Public and Tribal Community College Institutional Review Boards: A National Descriptive Analysis

    Ocean, Mia; Hirschi, Melissa

    2016-01-01

    It is currently unknown how many Institutional Review Boards (IRBs) exist at community colleges. This study investigates the percentage of public and Tribal community colleges that have active IRBs. It also examines the potential relationships between states that allow community colleges to confer baccalaureate degrees, or that have articulation…

  15. Community in Three Undergraduate University Science Courses: An Analysis of Student Perception

    Vavala, Robert V.; Namuth-Covert, Deana; Haines, Courtney; Lee, Donald J.; King, James W.; Speth, Carol

    2010-01-01

    Students who feel like part of a classroom community gain more enjoyment and are more academically successful than students who do not feel similar levels of community. This study intended to determine if students in online courses perceive the same level of community as students in face-to-face classes and if outside factors impacted community…

  16. Phylogenetic analysis of microbial communities in different regions of the gastrointestinal tract in Panaque nigrolineatus, a wood-eating fish.

    Ryan McDonald

    Full Text Available The Neotropical detritivorous catfish Panaque nigrolineatus imbibes large quantities of wood as part of its diet. Due to the interest in cellulose, hemi-cellulose and lignin degradation pathways, this organism provides an interesting model system for the detection of novel microbial catabolism. In this study, we characterize the microbial community present in different regions of the alimentary tract of P. nigrolineatus fed a mixed diet of date palm and palm wood in laboratory aquaria. Analysis was performed on 16S rRNA gene clone libraries derived from anterior and posterior regions of the alimentary tract and the auxiliary lobe (AL, an uncharacterized organ that is vascularly attached to the midgut. Sequence analysis and phylogenetic reconstruction revealed distinct microbial communities in each tissue region. The foregut community shared many phylotypes in common with aquarium tank water and included Legionella and Hyphomicrobium spp. As the analysis moved further into the gastrointestinal tract, phylotypes with high levels of 16S rRNA sequence similarity to nitrogen-fixing Rhizobium and Agrobacterium spp. and Clostridium xylanovorans and Clostridium saccharolyticum, dominated midgut and AL communities. However, the hindgut was dominated almost exclusively by phylotypes with the highest 16S rRNA sequence similarity to the Cytophaga-Flavobacterium-Bacteroides phylum. Species richness was highest in the foregut (Chao(1 = 26.72, decreased distally through the midgut (Chao(1 = 25.38 and hindgut (Chao(1 = 20.60, with the lowest diversity detected in the AL (Chao(1 = 18.04, indicating the presence of a specialized microbial community. Using 16S rRNA gene phylogeny, we report that the P. nigrolineatus gastrointestinal tract possesses a microbial community closely related to microorganisms capable of cellulose degradation and nitrogen fixation. Further studies are underway to determine the role of this resident microbial community in Panaque

  17. Community Influences on Married Women's Safer Sex Negotiation Attitudes in Bangladesh: A Multilevel Analysis.

    Jesmin, Syeda S; Cready, Cynthia M

    2016-02-01

    The influence of disadvantaged or deprived community on individuals' health risk-behaviors is increasingly being documented in a growing body of literature. However, little is known about the effects of community characteristics on women's sexual attitudes and behaviors. To examine community effects on married women's safer sex negotiation attitudes, we analyzed cross-sectional data from the 2011 Bangladesh Demographic and Health Surveys on a sample of 15,134 married women in 600 communities. We estimated two multilevel logistic regression models. Model 1, which included only individual-level variables, showed that women's autonomy/empowerment, age, and HIV knowledge had significant associations with their safer sex negotiation attitudes. We did not find any socioeconomic status gradient in safer sex negotiation attitudes at the individual level. Adding community-level variables in Model 2 significantly improved the fit of the model. Strikingly, we found that higher community-level poverty was associated with greater positive safer sex negotiation attitudes. Prevailing gender norms and overall women's empowerment in the community also had significant effects. While research on community influences calls for focusing on disadvantaged communities, our research highlights the importance of not underestimating the challenges that married women in economically privileged communities may face in negotiating safer sex. To have sufficient and equitable impact on married women's sexual and reproductive health, sexual and reproductive health promotion policies and programs need to be directed to women in wealthier communities as well.

  18. Voluntary Participation in Community Economic Development in Canada: An Empirical Analysis

    Laura Lamb

    2011-01-01

    Full Text Available This article is an empirical analysis of an individual's decision to participate in community economic development (CED initiatives in Canada. The objective of the analysis is to better understand how individuals make decisions to volunteer time toward CED initiatives and to determine whether the determinants of participation in CED are unique when compared to those of participation in volunteer activities in general. The dataset employed is Statistics Canada's 2004 Canada Survey of Giving, Volunteering and Participating (CSGVP. To date, there has been no prior econometric analysis of the decision to participate in community economic development initiatives in Canada. Results suggest a role for both public policymakers and practitioners in influencing participation in CED. / Cet article constitue une analyse empirique du processus de prise de décision chez les individus en ce qui a trait à la participation aux initiatives canadiennes de développement économique communautaire (DÉC. Le but de l'analyse est de mieux comprendre la façon dont les individus prennent la décision de consacrer du temps au bénévolat dans les initiatives de DÉC. Elle sert aussi à trancher la question de savoir si les facteurs de participation aux initiatives de développement économique communautaire sont uniques ou communs à la participation à des activités bénévoles en général. Les données employées dans le cadre de cette analyse sont puisées de l'Enquête canadienne sur le don, le bénévolat et la participation effectuée par Statistique Canada en 2004. À ce jour, aucune analyse économétrique n'a été menée sur la décision de participer aux initiatives canadiennes de DÉC. Les résultats suggèrent que les responsables de l'élaboration des politiques ainsi que les praticiens influencent tous deux la participation aux initiatives de DÉC.

  19. Identifying gender-preferred communication styles within online cancer communities: a retrospective, longitudinal analysis.

    Kathleen T Durant

    Full Text Available BACKGROUND: The goal of this research is to determine if different gender-preferred social styles can be observed within the user interactions at an online cancer community. To achieve this goal, we identify and measure variables that pertain to each gender-specific social style. METHODS AND FINDINGS: We perform social network and statistical analysis on the communication flow of 8,388 members at six different cancer forums over eight years. Kruskal-Wallis tests were conducted to measure the difference between the number of intimate (and highly intimate dyads, relationship length, and number of communications. We determine that two patients are more likely to form an intimate bond on a gender-specific cancer forum (ovarian P = <0.0001, breast P = 0.0089, prostate P = 0.0021. Two female patients are more likely to form a highly intimate bond on a female-specific cancer forum (Ovarian P<0.0001, Breast P<0.01. Typically a male patient communicates with more members than a female patient (Ovarian forum P = 0.0406, Breast forum P = 0.0013. A relationship between two patients is longer on the gender-specific cancer forums than a connection between two members not identified as patients (ovarian forum P = 0.00406, breast forum P = 0.00013, prostate forum P = .0.0003. CONCLUSION: The high level of interconnectedness among the prostate patients supports the hypothesis that men prefer to socialize in large, interconnected, less-intimate groups. A female patient is more likely to form a highly intimate connection with another female patient; this finding is consistent with the hypothesis that woman prefer fewer, more intimate connections. The relationships of same-gender cancer patients last longer than other relationships; this finding demonstrates homophily within these online communities. Our findings regarding online communication preferences are in agreement with research findings from person-to-person communication

  20. Identifying Gender-Preferred Communication Styles within Online Cancer Communities: A Retrospective, Longitudinal Analysis

    Durant, Kathleen T.; McCray, Alexa T.; Safran, Charles

    2012-01-01

    Background The goal of this research is to determine if different gender-preferred social styles can be observed within the user interactions at an online cancer community. To achieve this goal, we identify and measure variables that pertain to each gender-specific social style. Methods and Findings We perform social network and statistical analysis on the communication flow of 8,388 members at six different cancer forums over eight years. Kruskal-Wallis tests were conducted to measure the difference between the number of intimate (and highly intimate) dyads, relationship length, and number of communications. We determine that two patients are more likely to form an intimate bond on a gender-specific cancer forum (ovarian P = <0.0001, breast P = 0.0089, prostate P = 0.0021). Two female patients are more likely to form a highly intimate bond on a female-specific cancer forum (Ovarian P<0.0001, Breast P<0.01). Typically a male patient communicates with more members than a female patient (Ovarian forum P = 0.0406, Breast forum P = 0.0013). A relationship between two patients is longer on the gender-specific cancer forums than a connection between two members not identified as patients (ovarian forum P = 0.00406, breast forum P = 0.00013, prostate forum P = .0.0003). Conclusion The high level of interconnectedness among the prostate patients supports the hypothesis that men prefer to socialize in large, interconnected, less-intimate groups. A female patient is more likely to form a highly intimate connection with another female patient; this finding is consistent with the hypothesis that woman prefer fewer, more intimate connections. The relationships of same-gender cancer patients last longer than other relationships; this finding demonstrates homophily within these online communities. Our findings regarding online communication preferences are in agreement with research findings from person-to-person communication preference studies

  1. Genetic Association Analysis under Complex Survey Sampling: The Hispanic Community Health Study/Study of Latinos

    Lin, Dan-Yu; Tao, Ran; Kalsbeek, William D.; Zeng, Donglin; Gonzalez, Franklyn; Fernández-Rhodes, Lindsay; Graff, Mariaelisa; Koch, Gary G.; North, Kari E.; Heiss, Gerardo

    2014-01-01

    The cohort design allows investigators to explore the genetic basis of a variety of diseases and traits in a single study while avoiding major weaknesses of the case-control design. Most cohort studies employ multistage cluster sampling with unequal probabilities to conveniently select participants with desired characteristics, and participants from different clusters might be genetically related. Analysis that ignores the complex sampling design can yield biased estimation of the genetic association and inflation of the type I error. Herein, we develop weighted estimators that reflect unequal selection probabilities and differential nonresponse rates, and we derive variance estimators that properly account for the sampling design and the potential relatedness of participants in different sampling units. We compare, both analytically and numerically, the performance of the proposed weighted estimators with unweighted estimators that disregard the sampling design. We demonstrate the usefulness of the proposed methods through analysis of MetaboChip data in the Hispanic Community Health Study/Study of Latinos, which is the largest health study of the Hispanic/Latino population in the United States aimed at identifying risk factors for various diseases and determining the role of genes and environment in the occurrence of diseases. We provide guidelines on the use of weighted and unweighted estimators, as well as the relevant software. PMID:25480034

  2. Supercritical Fluid Extraction of Quinones from Compost for Microbial Community Analysis

    Ni Luh Gede Ratna Juliasih

    2015-01-01

    Full Text Available Supercritical fluid extraction (SFE was used to extract quinones from compost to monitor the microbial community dynamics during composting. The 0.3 g of dried compost was extracted using 3 mL min−1 of carbon dioxide (90% and methanol (10% at 45°C and 25 MPa for a 30 min extraction time. The extracted quinones were analysed using ultra performance liquid chromatography (UPLC with 0.3 mL min−1 of methanol mobile phase for a 50 min chromatographic run time. A comparable detected amount of quinones was obtained using the developed method and an organic solvent extraction method, being 36.06 μmol kg−1 and 34.54 μmol kg−1, respectively. Significantly low value of dissimilarity index (D between the two methods (0.05 indicated that the quinone profile obtained by both methods was considered identical. The developed method was then applied to determine the maturity of the compost by monitoring the change of quinone during composting. The UQ-9 and MK-7 were predominant quinones in the initial stage of composting. The diversity of quinone became more complex during the cooling and maturation stages. This study showed that SFE had successfully extracted quinones from a complex matrix with simplification and rapidity of the analysis that is beneficial for routine analysis.

  3. Household waste compositional analysis variation from insular communities in the framework of waste prevention strategy plans

    Zorpas, Antonis A., E-mail: antonis.zorpas@ouc.ac.cy [Cyprus Open University, Faculty of Pure and Applied Science, Environmental Conservation and Management, P.O. Box 12794, 2252 Latsia, Nicosia (Cyprus); Lasaridi, Katia, E-mail: klasaridi@hua.gr [Harokopio University, Department of Geography, 70 El. Venizelou, 176 71 Athens, Kallithea (Greece); Voukkali, Irene [Institute of Environmental Technology and Sustainable Development, ENVITECH LTD, Department of Research and Development, P.O. Box 34073, 5309 (Cyprus); Loizia, Pantelitsa, E-mail: irenevoukkali@envitech.org [Institute of Environmental Technology and Sustainable Development, ENVITECH LTD, Department of Research and Development, P.O. Box 34073, 5309 (Cyprus); Chroni, Christina [Harokopio University, Department of Geography, 70 El. Venizelou, 176 71 Athens, Kallithea (Greece)

    2015-04-15

    Highlights: • Waste framework directive has set clear waste prevention procedures. • Household Compositional analysis. • Waste management plans. • Zero waste approach. • Waste generation. - Abstract: Waste management planning requires reliable data regarding waste generation, affecting factors on waste generation and forecasts of waste quantities based on facts. In order to decrease the environmental impacts of waste management the choice of prevention plan as well as the treatment method must be based on the features of the waste that are produced in a specific area. Factors such as culture, economic development, climate, and energy sources have an impact on waste composition; composition influences the need of collecting waste more or less frequently of waste collection and disposition. The research question was to discover the main barriers concerning the compositional analysis in Insular Communities under warm climate conditions and the findings from this study enabled the main contents of a waste management plan to be established. These included advice to residents on waste minimisation, liaison with stakeholders and the expansion of kerbside recycling schemes.

  4. THE ANALYSIS OF SEMI INTENSIVE NATIVE CHICKEN FARMING IN RURAL COMMUNITIES

    E. Wantasen

    2015-04-01

    Full Text Available The study was aimed to determine the income for semi intensive native chicken farming and todetermine the factors influence it. The study was conducted by survey method and direct interview usingquestionnaire to 35 members of farmers group “Poyuyanan” in Poyowa Besar Village, SouthKotamobagu Dstrict North Sulawesi Province. Data were analyzed by using descriptive and quantitativeanalysis using multiple regression analysis of Cobb-Douglass model. The result showed that farmer withan average ownership of 8 hens could obtain income equivalent to 37.9 kg of rice per month. Theregression analysis showed that altogether the dependent variables had effect to income as much 81.2%(R2 = 0.821. Partially variables that could increase farmers’ income were hatching rate, number ofproductive hen, cost of production and number of eggs hatched. Mortality was the only variable thatdecreased farmers’ income. Cost of production in semi intensive native chicken farming which mainlyfor buying feed could increase the production and income for farmers that in turn would support foodavailability of rural communities in Poyowa Besar Villages

  5. Bacterial community analysis of cypermethrin enrichment cultures and bioremediation of cypermethrin contaminated soils.

    Akbar, Shamsa; Sultan, Sikander; Kertesz, Michael

    2015-07-01

    Cypermethrin is widely used for insect control; however, its toxicity toward aquatic life requires its complete removal from contaminated areas where the natural degradation ability of microbes can be utilized. Agricultural soil with extensive history of CM application was used to prepare enrichment cultures using cypermethrin as sole carbon source for isolation of cypermethrin degrading bacteria and bacterial community analysis using PCR-DGGE of 16 S rRNA gene. DGGE analysis revealed that dominant members of CM enrichment culture were associated with α-proteobacteria followed by γ-proteobacteria, Firmicutes, and Actinobacteria. Three potential CM-degrading isolates identified as Ochrobactrum anthropi JCm1, Bacillus megaterium JCm2, and Rhodococcus sp. JCm5 degraded 86-100% of CM (100 mg L(-1) ) within 10 days. These isolates were also able to degrade other pyrethroids, carbofuran, and cypermethrin degradation products. Enzyme activity assays revealed that enzymes involved in CM-degradation were inducible and showed activity when strains were grown on cypermethrin. Degradation kinetics of cypermethrin (200 mg kg(-1)) in soils inoculated with isolates JCm1, JCm2, and JCm5 suggested time-dependent disappearance of cypermethrin with rate constants of 0.0516, 0.0425, and 0.0807 d(-1), respectively, following first order rate kinetics. The isolated bacterial strains were among dominant genera selected under CM enriched conditions and represent valuable candidates for in situ bioremediation of contaminated soils and waters.

  6. The Nanomaterial Registry: facilitating the sharing and analysis of data in the diverse nanomaterial community

    Ostraat ML

    2013-09-01

    Full Text Available Michele L Ostraat, Karmann C Mills, Kimberly A Guzan, Damaris MurryRTI International, Durham, NC, USAAbstract: The amount of data being generated in the nanotechnology research space is significant, and the coordination, sharing, and downstream analysis of the data is complex and consistently deliberated. The complexities of the data are due in large part to the inherently complicated characteristics of nanomaterials. Also, testing protocols and assays used for nanomaterials are diverse and lacking standardization. The Nanomaterial Registry has been developed to address such challenges as the need for standard methods, data formatting, and controlled vocabularies for data sharing. The Registry is an authoritative, web-based tool whose purpose is to simplify the community's level of effort in assessing nanomaterial data from environmental and biological interaction studies. Because the registry is meant to be an authoritative resource, all data-driven content is systematically archived and reviewed by subject-matter experts. To support and advance nanomaterial research, a set of minimal information about nanomaterials (MIAN has been developed and is foundational to the Registry data model. The MIAN has been used to create evaluation and similarity criteria for nanomaterials that are curated into the Registry. The Registry is a publicly available resource that is being built through collaborations with many stakeholder groups in the nanotechnology community, including industry, regulatory, government, and academia. Features of the Registry website (https://www.nanomaterialregistry.org/ currently include search, browse, side-by-side comparison of nanomaterials, compliance ratings based on the quality and quantity of data, and the ability to search for similar nanomaterials within the Registry. This paper is a modification and extension of a proceedings paper for the Institute of Electrical and Electronics Engineers.Keywords: nanoinformatics

  7. Pyrosequencing analysis of the protist communities in a High Arctic meromictic lake: DNA preservation and change

    Sophie eCharvet

    2012-12-01

    Full Text Available High Arctic meromictic lakes are extreme environments characterized by cold temperatures, low nutrient inputs from their polar desert catchments and prolonged periods of low irradiance and darkness. These lakes are permanently stratified with an oxygenated freshwater layer (mixolimnion overlying a saline, anoxic water column (monimolimnion. The physical and chemical properties of the deepest known lake of this type in the circumpolar Arctic, Lake A, on the far northern coast of Ellesmere Island, Canada, have been studied over the last 15 years, but little is known about the lake’s biological communities. We applied high-throughput sequencing of the V4 region of the 18S ribosomal RNA gene to investigate the protist communities down the water column at three sampling times: under the ice at the end of winter in 2008, during an unusual period of warming and ice-out the same year, and again under the ice in mid-summer 2009. Sequences of many protist taxa occurred throughout the water column at all sampling times, including in the deep anoxic layer where growth is highly unlikely. Furthermore, there were sequences for taxonomic groups including diatoms and marine taxa, which have never been observed in Lake A by microscopic analysis. However the sequences of other taxa such as ciliates, chrysophytes, Cercozoa and Telonema varied with depth, between years and during the transition to ice-free conditions. These results imply that there are seasonally active taxa in the surface waters of the lake that are sensitive to depth and change with time. DNA from these taxa is superimposed upon background DNA from multiple internal and external sources that is preserved in the deep, cold, largely anoxic water column.

  8. [Analysis of the probiotic Bifidobacterium and Lactobacillus community in child intestinal flora].

    Jin, Hong-Zhi; Fan, Xiao-Bing; Hang, Xiao-Min; Li, Kun-Bao; Yang, Hong

    2005-08-01

    To investigate the distribution of child intestinal flora and the composition of its key probiotics community, study on intestinal flora of 21 Chinese children (age 2 - 5) was conducted, which included bacteria isolation and counting, 16S rDNA sequencing and homology analysis. For identification of the key probiotics such as Bifidobacterium and Lactobacillus in children feces at the species level, the specific primers Im26/Im3 and L159/L677 for PCR amplification of partial 16S rDNA were used. The results show that the composition of child intestinal flora is was relatively stable and almost same to the intestinal flora of the youth (age 20 - 25). Culture-based approaches show that the key probiotic community in feces at the species level was highly different in composition and numbers from individual to individual. B. longum and B. pseudocatenulatum, which are detected at levels of 10(7) CFU/g (wet) in samples and the detection rates are 90.48% and 85.71% respectively, are believed to be major bifidobacterial species in child intestinal microbiota. In addition, B. adolescentis, B. bifidum, B. infantis and B. thermacidophium have also been found. L. mucosae, L. fermentum, L. salivarius, L. ruminis, L. gasseri and L. plantarum are isolated from the stools. L. mucosae (3.68 log10 CFU/g (wet), detection rate 71.43%) and L. fermentum (3.97 log10 CFU/g (wet), detection rate 52.38%) are two dominant species of Lactobacillus. Study on Chinese child intestinal flora, especially on the compositions and numbers of key probiotics in the feces will be very helpful to the development of effective probiotics in future.

  9. Community perspectives on public health biobanking: an analysis of community meetings on the Michigan BioTrust for Health.

    Thiel, Daniel B; Platt, Tevah; Platt, Jodyn; King, Susan B; Kardia, Sharon L R

    2014-04-01

    Biobanks raise challenges for developing ethically sound and practicable consent policies. Biobanks comprised of dried bloodspots (DBS) left over from newborn screening, maintained for long-term storage, and potential secondary research applications are no exception. Michigan has been a leader in transforming its DBS collection, marketing its biobank of de-identified samples for health research use. The Michigan BioTrust for Health includes approximately 4 million unconsented retrospective samples collected as early as 1984 and prospective samples added since the fall of 2010 with blanket parental consent. We engaged Michigan citizens to ascertain public attitudes, knowledge, and beliefs about the BioTrust and informed consent. A convenience sampling of 393 participants from communities around the state of Michigan (oversampling for minority populations) participated in meetings addressing newborn screening, the BioTrust and informed consent, yielding quantitative and qualitative survey and discussion data. Participants affirmed the principle of voluntary informed participation in research and advocated for greater public awareness of the existence of the BioTrust. Most expressed support for the use of DBS for research and a desire for greater involvement in granting permission for research use. Opinions varied as to which specific research uses were acceptable. Participants indicated a desire for greater engagement, public awareness, and more active decision making on the part of biobank participants and parents. Diversity of opinion over which research areas were deemed acceptable problematizes the blanket consent model that currently applies to the BioTrust's prospective DBS collection and that could become the new norm for research using de-identified data under proposed changes to the Common Rule.

  10. Improvement of DGGE analysis by modifications of PCR protocols for analysis of microbial community members with low abundance.

    Wang, Yong-Feng; Zhang, Fang-Qiu; Gu, Ji-Dong

    2014-06-01

    Denaturing gradient gel electrophoresis (DGGE) is a powerful technique to reveal the community structures and composition of microorganisms in complex natural environments and samples. However, positive and reproducible polymerase chain reaction (PCR) products, which are difficult to acquire for some specific samples due to low abundance of the target microorganisms, significantly impair the effective applications of DGGE. Thus, nested PCR is often introduced to generate positive PCR products from the complex samples, but one problem is also introduced: The total number of thermocycling in nested PCR is usually unacceptably high, which results in skewed community structures by generation of random or mismatched PCR products on the DGGE gel, and this was demonstrated in this study. Furthermore, nested PCR could not resolve the uneven representative issue with PCR products of complex samples with unequal richness of microbial population. In order to solve the two problems in nested PCR, the general protocol was modified and improved in this study. Firstly, a general PCR procedure was used to amplify the target genes with the PCR primers without any guanine cytosine (GC) clamp, and then, the resultant PCR products were purified and diluted to 0.01 μg ml(-1). Subsequently, the diluted PCR products were utilized as templates to amplify again with the same PCR primers with the GC clamp for 17 cycles, and the products were finally subjected to DGGE analysis. We demonstrated that this is a much more reliable approach to obtain a high quality DGGE profile with high reproducibility. Thus, we recommend the adoption of this improved protocol in analyzing microorganisms of low abundance in complex samples when applying the DGGE fingerprinting technique to avoid biased results.

  11. Grid connected integrated community energy system. Phase II: final state 2 report. Cost benefit analysis, operating costs and computer simulation

    1978-03-22

    A grid-connected Integrated Community Energy System (ICES) with a coal-burning power plant located on the University of Minnesota campus is planned. The cost benefit analysis performed for this ICES, the cost accounting methods used, and a computer simulation of the operation of the power plant are described. (LCL)

  12. Multivariate analysis of microbial communities in the River Elbe (Germany) on different phylogenetic and spatial levels of resolution.

    Kloep, Frank; Manz, Werner; Röske, Isolde

    2006-04-01

    The microbial communities of three different habitat types and from two sediment depths in the River Elbe were investigated by fluorescence in situ hybridization at various levels of complexity. Differences in the microbial community composition of free-flowing river water, water within the hyporheic interstitial and sediment-associated bacteria were quantitatively analyzed using domain- and group-specific oligonucleotide probes. Qualitative data on the presence/absence of specific bacterial taxa were gathered using genus- and species-specific probes. The complete data set was statistically processed by univariate statistical approaches, and two-dimensional ordinations of nonmetric multidimensional scaling. The analysis showed: (1) that the resolution of microbial community structures at microenvironments, habitats and locations can be regulated by targeted application of oligonucleotides on phylogenetic levels ranging from domains to species, and (2) that an extensive qualitative presence/absence analysis of multiparallel hybridization assays enables a fine-scale apportionment of spatial differences in microbial community structures that is robust against apparent limitations of fluorescence in situ hybridization such as false positive hybridization signals or inaccessibility of in situ oligonucleotide probes. A general model for the correlation of the phylogenetic depth of focus and the relative spatial resolution of microbial communities by fluorescence in situ hybridization is presented.

  13. Plant community and ecological analysis of woodland vegetation in Metema Area, Amhara National Regional State, Northwestern Ethiopia

    Haile Adamu Wale; Tamrat Bekele; Gemedo Dalle

    2012-01-01

    We studied woodland vegetation in broad-leaved deciduous woodlands of Metema in northwestern Amhara regional state,Ethiopia to determine plant community types and species distribution patterns and their relationships with environmental variables,including altitude,pH,cation exchange capacity,electrical conductivity (EC),and moisture.We used a selective approach with a systematic sampling design.A total of 74 quadrats,each 25m × 25m at intervals of 150-200 m were sampled along the established transect lines.For herbaceous vegetation and soil data collection,five subquadrats each 1m × 1m were established at the four corners and the center of each quadrat.Three community types were identified using TWINSPAN analysis.All three community types showed high diversity (Shannon-Weiner index),the highest in community type Ⅱ at 3.55.The highest similarity coefficient was 0.49 (49%) between community types Ⅱ and Ⅲ,reflecting 0.51 (51%) dissimilarity in their species richness.The canonical correspondence ordination diagram revealed that the distribution pattern of community type Ⅰ was explained by moisture while that of community types Ⅲ and Ⅱ was explained by EC and altitude and moisture,respectively.Altitude was the most statistically significant environmental variable,followed by moisture and EC in determining the total variation in species composition and distribution patterns while pH and cation exchange capacity were non significant.In conclusion,we recommend that any intervention should take into account these three discrete community types and their environmental settings to make the intervention more successful.

  14. Comparing patient and provider perceptions of home- and community-based services: social network analysis as a service integration metric.

    Ryan, David P; Puri, Manveen; Liu, Barbara A

    2013-01-01

    Integrated home- and community-based services (HCBS) for frail seniors require a unique style of teamwork and collaboration. In four case studies, patient perceptions of teamwork and collaboration among their HCBS care providers are compared with those of the providers themselves using network analysis. The degree of coherence between these perceived networks are examined using network analytics, and network visualizations are discussed. The value of network analysis in research on HCBS is considered.

  15. Analysis of phospholipid fatty acids (PLFA) to characterize microbial communities in aquifers

    Green, Christopher T.; Scow, Kate M.

    This paper reviews published applications of lipid-based biochemical techniques for characterizing microbial communities in aquifers and other deep subsurface habitats. These techniques, such as phospholipid fatty acid (PLFA) analysis, can provide information on a variety of microbial characteristics, such as biomass, physiology, taxonomic and functional identity, and overall community composition. In addition, multivariate statistical analysis of lipid data can relate spatial or temporal changes in microbial communities to environmental factors. The use of lipid-based techniques in the study of groundwater microbiology is advantageous because they do not require culturing and can provide quantitative data on entire communities. However, combined effects of physiological and phylogenetic changes on the lipid composition of a community can confound interpretation of the data, and many questions remain about the validity of various lipid techniques. Despite these caveats, lipid-based research has begun to show trends in community composition in contaminated and pristine aquifers that contribute to our understanding of groundwater microbial ecology and have potential for use in optimization of bioremediation of groundwater pollutants. Résumé Ce papier passe en revue les applications des techniques biochimiques basées sur les lipides pour caractériser les communautés microbiennes présentes dans les aquifères et dans les autres habitats souterrains profonds. Ces techniques, telles que l'analyse des acides gras phospholipidiques (PLFA), peuvent fournir des informations sur un ensemble de caractères microbiens, tels que la biomasse, la physiologie, l'identité taxonomique et fonctionnelle, et surtout la composition de la communauté. En outre, l'analyse statistique multivariée des données sur les lipides peut établir les liens entre des changements spatiaux ou temporels dans la communauté microbienne et des facteurs environnementaux. L'utilisation des

  16. Comparative Analysis of Prokaryotic Communities Associated with Organic and Conventional Farming Systems.

    Elizaveta Pershina

    Full Text Available One of the most important challenges in agriculture is to determine the effectiveness and environmental impact of certain farming practices. The aim of present study was to determine and compare the taxonomic composition of the microbiomes established in soil following long-term exposure (14 years to a conventional and organic farming systems (CFS and OFS accordingly. Soil from unclared forest next to the fields was used as a control. The analysis was based on RT-PCR and pyrosequencing of 16S rRNA genes of bacteria and archaea. The number of bacteria was significantly lower in CFS than in OFS and woodland. The highest amount of archaea was detected in woodland, whereas the amounts in CFS and OFS were lower and similar. The most common phyla in the soil microbial communities analyzed were Proteobacteria (57.9%, Acidobacteria (16.1%, Actinobacteria (7.9%, Verrucomicrobia (2.0%, Bacteroidetes (2.7% and Firmicutes (4.8%. Woodland soil differed from croplands in the taxonomic composition of microbial phyla. Croplands were enriched with Proteobacteria (mainly the genus Pseudomonas, while Acidobacteria were detected almost exclusively in woodland soil. The most pronounced differences between the CFS and OFS microbiomes were found within the genus Pseudomonas, which significantly (p<0,05 increased its number in CFS soil compared to OFS. Other differences in microbiomes of cropping systems concerned minor taxa. A higher relative abundance of bacteria belonging to the families Oxalobacteriaceae, Koribacteriaceae, Nakamurellaceae and genera Ralstonia, Paenibacillus and Pedobacter was found in CFS as compared with OFS. On the other hand, microbiomes of OFS were enriched with proteobacteria of the family Comamonadaceae (genera Hylemonella and Hyphomicrobiaceae, actinobacteria from the family Micrococcaceae, and bacteria of the genera Geobacter, Methylotenera, Rhizobium (mainly Rhizobium leguminosarum and Clostridium. Thus, the fields under OFS and CFS did

  17. Communities and beyond: mesoscopic analysis of a large social network with complementary methods

    Tibely, Gergely; Kovanen, Lauri; Kaski, Kimmo; Kertesz, Janos; Saramaki, Jari

    2010-01-01

    Large complex networks show different levels of organization. At the mesoscopic scale communities are considered the most important structures that relate to system function but also other formations like trees or stars may appear. Communities are characterized as groups of nodes with dense internal and loose inter-group connectivity, but beyond this simple notion, even the definition of a community is a controversial issue. Numerous community detection methods have been proposed and assessed either on small empirical networks or larger synthetic benchmarks. However, little is known about their performance on large real-world networks and about the meaningfulness of the community structure they produce. Here we apply three community detection methods, Infomap, the Louvain method, and clique percolation to a large real-world social network based on mobile telephone calls and compare their results. Benchmarks are fabricated to capture only selected aspects of reality, while large empirical networks are much mor...

  18. Systems biology: Functional analysis of natural microbial consortia using community proteomics.

    VerBerkmoes, Nathan C; Denef, Vincent J; Hettich, Robert L; Banfield, Jillian F

    2009-03-01

    We know very little about the metabolic functioning and evolutionary dynamics of microbial communities. Recent advances in comprehensive, sequencing-based methods, however, are laying a molecular foundation for new insights into how microbial communities shape the Earth's biosphere. Here we explore the convergence of microbial ecology, genomics, biological mass spectrometry and informatics that form the new field of microbial community proteogenomics. We discuss the first applications of proteogenomics and its potential for studying the physiology, ecology and evolution of microbial populations and communities.

  19. Waveforms and Sonic Boom Perception and Response (WSPR): Low-Boom Community Response Program Pilot Test Design, Execution, and Analysis

    Page, Juliet A.; Hodgdon, Kathleen K.; Krecker, Peg; Cowart, Robbie; Hobbs, Chris; Wilmer, Clif; Koening, Carrie; Holmes, Theresa; Gaugler, Trent; Shumway, Durland L.; Rosenberger, James L.; Philips, Daisy

    2014-01-01

    The Waveforms and Sonic boom Perception and Response (WSPR) Program was designed to test and demonstrate the applicability and effectiveness of techniques to gather data relating human subjective response to multiple low-amplitude sonic booms. It was in essence a practice session for future wider scale testing on naive communities, using a purpose built low-boom demonstrator aircraft. The low-boom community response pilot experiment was conducted in California in November 2011. The WSPR team acquired sufficient data to assess and evaluate the effectiveness of the various physical and psychological data gathering techniques and analysis methods.

  20. Taxonomic and functional metagenomic analysis of anodic communities in two pilot-scale microbial fuel cells treating different industrial wastewaters.

    Kiseleva, Larisa; Garushyants, Sofya K; Ma, Hongwu; Simpson, David J W; Fedorovich, Viatcheslav; Cohen, Michael F; Goryanin, Igor

    2015-10-06

    The combined processes of microbial biodegradation accompanied by extracellular electron transfer make microbial fuel cells (MFCs) a promising new technology for cost-effective and sustainable wastewater treatment. Although a number of microbial species that build biofilms on the anode surfaces of operating MFCs have been identified, studies on the metagenomics of entire electrogenic communities are limited. Here we present the results of whole-genome metagenomic analysis of electrochemically active robust anodic microbial communities, and their anaerobic digester (AD) sludge inocula, from two pilot-scale MFC bioreactors fed with different distillery wastewaters operated under ambient conditions in distinct climatic zones. Taxonomic analysis showed that Proteobacteria, Bacteroidetes and Firmicutes were abundant in AD sludge from distinct climatic zones, and constituted the dominant core of the MFC microbiomes. Functional analysis revealed species involved in degradation of organic compounds commonly present in food industry wastewaters. Also, accumulation of methanogenic Archaea was observed in the electrogenic biofilms, suggesting a possibility for simultaneous electricity and biogas recovery from one integrated wastewater treatment system. Finally, we found a range of species within the anode communities possessing the capacity for extracellular electron transfer, both via direct contact and electron shuttles, and show differential distribution of bacterial groups on the carbon cloth and activated carbon granules of the anode surface. Overall, this study provides insights into structural shifts that occur in the transition from an AD sludge to an MFC microbial community and the metabolic potential of electrochemically active microbial populations with wastewater-treating MFCs.

  1. Examining experiences of transition, instability and coping for young offenders in the community: A qualitative analysis.

    Heath, Rebecca A; Priest, Helena M

    2016-04-01

    This article explores experiences of transition, instability and coping using a qualitative approach with young offenders within a specialist forensic child and adolescent mental health service (CAMHS). Participants were four young people (aged 14-17 years) on community orders under the supervision of local youth offending teams (YOTs). Semi-structured interviews were conducted and data analysed using an inductive thematic analysis approach. Three main themes were identified: (i) people and places; (ii) growth; and (iii) managing difficult experiences. Findings suggest that young offenders are exposed to a wide range of challenging contextual factors including unpredictable or inadequate home environments, numerous transitions (between family members/foster placements and schools), limited engagement with educational settings and a lack of social support, supporting the findings of Paton et al. Findings also portrayed a sense of participants' 'psychological growth' with development along a trajectory from a young child 'acting out' in response to the environments in which they were living; through a more reflective stage, in which they were able to begin to consider the situations they found themselves in; before reaching a position in which they were able to look beyond their day-to-day circumstances with some hope that their lives could be different in the future. Furthermore, accounts revealed that these young people had a limited range of functional coping strategies and had largely negative experiences of services. Clinical implications and the need for further research developing professionals' understanding of the influence of early experiences on young offenders' behaviour are discussed.

  2. Parallel-META 3: Comprehensive taxonomical and functional analysis platform for efficient comparison of microbial communities.

    Jing, Gongchao; Sun, Zheng; Wang, Honglei; Gong, Yanhai; Huang, Shi; Ning, Kang; Xu, Jian; Su, Xiaoquan

    2017-01-12

    The number of metagenomes is increasing rapidly. However, current methods for metagenomic analysis are limited by their capability for in-depth data mining among a large number of microbiome each of which carries a complex community structure. Moreover, the complexity of configuring and operating computational pipeline also hinders efficient data processing for the end users. In this work we introduce Parallel-META 3, a comprehensive and fully automatic computational toolkit for rapid data mining among metagenomic datasets, with advanced features including 16S rRNA extraction for shotgun sequences, 16S rRNA copy number calibration, 16S rRNA based functional prediction, diversity statistics, bio-marker selection, interaction network construction, vector-graph-based visualization and parallel computing. Application of Parallel-META 3 on 5,337 samples with 1,117,555,208 sequences from diverse studies and platforms showed it could produce similar results as QIIME and PICRUSt with much faster speed and lower memory usage, which demonstrates its ability to unravel the taxonomical and functional dynamics patterns across large datasets and elucidate ecological links between microbiome and the environment. Parallel-META 3 is implemented in C/C++ and R, and integrated into an executive package for rapid installation and easy access under Linux and Mac OS X. Both binary and source code packages are available at http://bioinfo.single-cell.cn/parallel-meta.html.

  3. Comparative Analysis of Prokaryotic Communities Associated with Organic and Conventional Farming Systems.

    Pershina, Elizaveta; Valkonen, Jari; Kurki, Päivi; Ivanova, Ekaterina; Chirak, Evgeny; Korvigo, Ilia; Provorov, Nykolay; Andronov, Evgeny

    2015-01-01

    One of the most important challenges in agriculture is to determine the effectiveness and environmental impact of certain farming practices. The aim of present study was to determine and compare the taxonomic composition of the microbiomes established in soil following long-term exposure (14 years) to a conventional and organic farming systems (CFS and OFS accordingly). Soil from unclared forest next to the fields was used as a control. The analysis was based on RT-PCR and pyrosequencing of 16S rRNA genes of bacteria and archaea. The number of bacteria was significantly lower in CFS than in OFS and woodland. The highest amount of archaea was detected in woodland, whereas the amounts in CFS and OFS were lower and similar. The most common phyla in the soil microbial communities analyzed were Proteobacteria (57.9%), Acidobacteria (16.1%), Actinobacteria (7.9%), Verrucomicrobia (2.0%), Bacteroidetes (2.7%) and Firmicutes (4.8%). Woodland soil differed from croplands in the taxonomic composition of microbial phyla. Croplands were enriched with Proteobacteria (mainly the genus Pseudomonas), while Acidobacteria were detected almost exclusively in woodland soil. The most pronounced differences between the CFS and OFS microbiomes were found within the genus Pseudomonas, which significantly (porganic farming systems.

  4. The Antimicrobial Susceptibility of Klebsiella pneumoniae from Community Settings in Taiwan, a Trend Analysis

    Lin, Wu-Pu; Wang, Jann-Tay; Chang, Shan-Chwen; Chang, Feng-Yee; Fung, Chang-Phone; Chuang, Yin-Ching; Chen, Yao-Shen; Shiau, Yih-Ru; Tan, Mei-Chen; Wang, Hui-Ying; Lai, Jui-Fen; Huang, I-Wen; Lauderdale, Tsai-Ling

    2016-01-01

    Drug-resistant Klebsiella pneumoniae, especially extended-spectrum β-lactamase (ESBL)- and/or AmpC β-lactamase-producing strains, is an emerging problem worldwide. However, few data focusing on drug susceptibility of K. pneumoniae from community is available. In this study, we analyzed 1016 K. pneumoniae isolates from outpatients or those visiting emergency rooms collected during 2002–2012 from Taiwan Surveillance of Antimicrobial Resistance program. Significantly decreased susceptibilities to 3rd generation cephalosporins and ciprofloxacin were found during the study period. By 2012, susceptibility to cefotaxime and ciprofloxacin was 83.6% and 81.6%, respectively. The prevalence of ESBL-producers increased from 4.8% in 2002 to 11.9% in 2012 (P = 0.012), while that of AmpC β-lactamase-producers increased from 0% to 9.5% in the same period (P ESBL and AmpC-β-lactamase-producers by pulsed-field gel electrophoresis and multi-locus sequence typing revealed wide genetic diversity even among the most common sequence type 11 isolates (33.0%). By multivariate analysis, later study year, elderly, and urine isolates were associated with carriage of ESBL genes, while only urine isolates were associated with carriage of AmpC β-lactamase genes. Further studies are needed to determine which antibiotics are reasonable empirical therapy options for patients presenting with severe sepsis that might be caused by K. pneumoniae. PMID:27824151

  5. Viral infection in community-acquired pneumonia: a systematic review and meta-analysis

    Michael Burk

    2016-06-01

    Full Text Available The advent of PCR has improved the identification of viruses in patients with community-acquired pneumonia (CAP. Several studies have used PCR to establish the importance of viruses in the aetiology of CAP. We performed a systematic review and meta-analysis of the studies that reported the proportion of viral infection detected via PCR in patients with CAP. We excluded studies with paediatric populations. The primary outcome was the proportion of patients with viral infection. The secondary outcome was short-term mortality. Our review included 31 studies. Most obtained PCR via nasopharyngeal or oropharyngeal swab. The pooled proportion of patients with viral infection was 24.5% (95% CI 21.5–27.5%. In studies that obtained lower respiratory samples in >50% of patients, the proportion was 44.2% (95% CI 35.1–53.3%. The odds of death were higher in patients with dual bacterial and viral infection (OR 2.1, 95% CI 1.32–3.31. Viral infection is present in a high proportion of patients with CAP. The true proportion of viral infection is probably underestimated because of negative test results from nasopharyngeal or oropharyngeal swab PCR. There is increased mortality in patients with dual bacterial and viral infection.

  6. Microbial community analysis of an aerobic nitrifying-denitrifying MBR treating ABS resin wastewater.

    Chang, Chia-Yuan; Tanong, Kulchaya; Xu, Jia; Shon, Hokyong

    2011-05-01

    A two-stage aerobic membrane bioreactor (MBR) system for treating acrylonitrile butadiene styrene (ABS) resin wastewater was carried out in this study to evaluate the system performance on nitrification. The results showed that nitrification of the aerobic MBR system was significant and the highest TKN removal of approximately 90% was obtained at hydraulic retention time (HRT) 18 h. In addition, the result of nitrogen mass balance revealed that the percentage of TN removal due to denitrification was in the range of 8.7-19.8%. Microbial community analysis based on 16s rDNA molecular approach indicated that the dominant ammonia oxidizing bacteria (AOB) group in the system was a β-class ammonia oxidizer which was identified as uncultured sludge bacterium (AF234732). A heterotrophic aerobic denitrifier identified as Thauera mechernichensis was found in the system. The results indicated that a sole aerobic MBR system for simultaneous removals of carbon and nitrogen can be designed and operated for neglect with an anaerobic unit.

  7. Content-specific network analysis of peer-to-peer communication in an online community for smoking cessation

    Myneni, Sahiti; Cobb, Nathan K.; Cohen, Trevor

    2016-01-01

    Analysis of user interactions in online communities could improve our understanding of health-related behaviors and inform the design of technological solutions that support behavior change. However, to achieve this we would need methods that provide granular perspective, yet are scalable. In this paper, we present a methodology for high-throughput semantic and network analysis of large social media datasets, combining semi-automated text categorization with social network analytics. We apply this method to derive content-specific network visualizations of 16,492 user interactions in an online community for smoking cessation. Performance of the categorization system was reasonable (average F-measure of 0.74, with system-rater reliability approaching rater-rater reliability). The resulting semantically specific network analysis of user interactions reveals content- and behavior-specific network topologies. Implications for socio-behavioral health and wellness platforms are also discussed. PMID:28269890

  8. Macrolides vs. quinolones for community-acquired pneumonia: meta-analysis of randomized controlled trials.

    Skalsky, K; Yahav, D; Lador, A; Eliakim-Raz, N; Leibovici, L; Paul, M

    2013-04-01

    The relative efficacy, safety and ecological implications of macrolides vs. quinolones in the treatment of community-acquired pneumonia (CAP) are debatable. We performed a systematic review and meta-analysis of randomized controlled trials comparing any macrolide vs. any quinolone for the treatment of CAP among adult inpatients or outpatients, as monotherapy or both in combination with a beta-lactam. We did not limit inclusion by pneumonia severity, publication status, language or date of publication. The primary outcomes assessed were 30-day all-cause mortality and treatment failure. Two authors independently extracted the data. Fixed effect meta-analysis of risk ratios (RRs) with 95% confidence intervals was performed. Sixteen trials (4989 patients) fulfilling inclusion criteria were identified, mostly assessing outpatients with mild to moderate CAP. All-cause mortality was not significantly different for macrolides vs. quinolones, RR 1.03 (0.63-1.68, seven trials), with a low event rate (2%). Treatment failure was significantly lower with quinolones, RR 0.78 (0.67-0.91, 16 trials). The definition of failure used in the primary studies was not clearly representative of patients' benefit. Microbiological failure was lower with quinolones, RR 0.63 (0.49-0.81, 13 trials). All adverse events, adverse events requiring discontinuation and any premature antibiotic discontinuation were significantly more frequent with macrolides, mainly on account of gastrointestinal adverse events. Resistance development was not assessed in the trials. Randomized controlled trials show an advantage of quinolones in the treatment of CAP with regard to clinical cure without need for antibiotic modification at end of treatment and gastrointestinal adverse events. The clinical significance of this advantage is unclear.

  9. Molecular analysis of microbial community in a groundwater sample polluted by landfill leachate and seawater

    TIAN Yang-jie; YANG Hong; WU Xiu-juan; LI Dao-tang

    2005-01-01

    Seashore landfill aquifers are environments of special physicochemical conditions (high organic load and high salinity), and microbes in leachate-polluted aquifers play a significant role for intrinsic bioremediation. In order to characterize microbial diversity and look for clues on the relationship between microbial community structure and hydrochemistry, a culture-independent examination of a typical groundwater sample obtained from a seashore landfill was conducted by sequence analysis of 16S rDNA clone library. Two sets of universal 16S rDNA primers were used to amplify DNA extracted from the groundwater so that problems arising from primer efficiency and specificity could be reduced. Of 74 clones randomly selected from the libraries, 30 contained unique sequences whose analysis showed that the majority of them belonged to bacteria (95.9%), with Proteobacteria (63.5%) being the dominant division. One archaeal sequence and one eukaryotic sequence were found as well. Bacterial sequences belonging to the following phylogenic groups were identified: Bacteroidetes (20.3%), β, γ, δ and ε-subdivisions of Proteobacteria (47.3%, 9.5%, 5.4% and 1.3%, respectively), Firmicutes (1.4%), Actinobacteria (2.7%), Cyanobacteria (2.7%). The percentages of Proteobacteria and Bacteroides in seawater were greater than those in the groundwater from a non-seashore landfill, indicating a possible influence of seawater. Quite a few sequences had close relatives in marine or hypersaline environments. Many sequences showed affiliations with microbes involved in anaerobic fermentation. The remarkable abundance of sequences related to (per)chlorate-reducing bacteria (C1RB) in the groundwater was significant and worthy of further study.

  10. Building a Community Infrastructure for Scalable On-Line Performance Analysis Tools around Open|Speedshop

    Miller, Barton

    2014-06-30

    tools targeted at Office of Science Leadership Class computer systems and selected Office of Science application codes. We describe the contributions made by the team at the University of Wisconsin. The project built on the efforts in Open|SpeedShop funded by DOE/NNSA and the DOE/NNSA Tri-Lab community, extended Open|Speedshop to the Office of Science Leadership Class Computing Facilities, and addressed new challenges found on these cutting edge systems. Work done under this project at Wisconsin can be divided into two categories, new algorithms and techniques for debugging, and foundation infrastructure work on our Dyninst binary analysis and instrumentation toolkits and MRNet scalability infrastructure.

  11. Community Colleges and Market Responsiveness: A Conceptual Analysis and Proposed Model

    Adams, Jimmy L.; Edmonson, Stacey L.; Slate, John R.

    2013-01-01

    In this article, we explore the functions of the traditional community college and its expanding mission in regard to its responsiveness to changing economic conditions and workforce development needs. To date, few researchers have specifically addressed market responsiveness in community college settings across the United States. In addition, we…

  12. Refining a Multidimensional Model of Community Adjustment through an Analysis of Postschool Follow-Up Data.

    Thompson, James R.; McGrew, Kevin S.; Johnson, David R.; Bruininks, Robert H.

    2000-01-01

    Survey data were collected on the life experiences and status of 388 young adults with disabilities out of school for 1 to 5 years. Results support a 7-factor model of community adjustment: personal satisfaction, employment-economic integration, community assimilation, need for support services, recreation-leisure integration, social network…

  13. Structure in Community College Career-Technical Programs: A Qualitative Analysis. CCRC Working Paper No. 50

    Van Noy, Michelle; Weiss, Madeline Joy; Jenkins, Davis; Barnett, Elisabeth A.; Wachen, John

    2012-01-01

    Using data obtained from interviews and program websites at Washington community and technical colleges, the authors of this study examine the structure of community college career-technical programs in allied health, business and marketing, computer and information studies, and mechanics and repair. A framework for structure with four…

  14. Sense of Community Belonging and Health in Canada: A Regional Analysis

    Kitchen, Peter; Williams, Allison; Chowhan, James

    2012-01-01

    This article investigates the association between sense of community belonging and health among settlements of different size and across the urban to rural continuum in Canada. Using data from the recent 2007/08 Canadian Community Health Survey (CCHS), the objective is to identify the major health, social and geographic determinants of sense of…

  15. Attitudinal Outcomes of a Multicultural Learning Community Experience: A Qualitative Analysis

    Firmin, Michael W.; Warner, Susan C.; Firmin, Ruth L.; Johnson, Courtney B.; Firebaugh, Stephanie D.

    2013-01-01

    Research investigating the long-term effects of learning communities on students is scarce. This qualitative study focuses on the results of 24 in-depth interviews with students three years after participating in a first year learning community at a private, selective Midwestern university. Interview questions were designed to probe students'…

  16. Participation in Adult Education for Community Development: A Critical Discourse Analysis of "Training for Transformation"

    Krupar, Allyson M.; Prins, Esther

    2016-01-01

    Participation has become so central to adult education for community development that even the World Bank supports participatory programming. This article analyses how participation is conceptualised in "Training for Transformation" (TfT), a Freirean-inspired curriculum used in international community development settings. TfT seeks to…

  17. Comparative analysis of gut microbiota of mosquito communities in central Illinois

    The composition and structure of microbial communities that inhabit the mosquito midguts are poorly understood despite their well-documented potential to impede pathogen transmission. We used MiSeq sequencing of the 16S rRNA gene to characterize the bacterial communities of field-collected populatio...

  18. The Influence of Place-Based Communities on Information Behavior: A Comparative Grounded Theory Analysis

    Gibson, Amelia N.

    2013-01-01

    This study examines the effect of experiential place and local community on information access and behavior for two communities of parents of children with Down syndrome. It uncovers substantive issues associated with health information seeking, government and education-related information access, and information overload and avoidance within the…

  19. A Case Study Analysis of a Constructionist Knowledge Building Community with Activity Theory

    Ang, Chee S.; Zaphiris, Panayiotis; Wilson, Stephanie

    2011-01-01

    This article investigates how activity theory can help research a constructionist community. We present a constructionist activity model called CONstructionism Through ACtivity Theory (CONTACT) model and explain how it can be used to analyse the constructionist activity in knowledge building communities. We then illustrate the model through its…

  20. Onset and Progression of Disruptive Behavior Problems among Community Boys and Girls: A Prospective Longitudinal Analysis

    Farris, Jaelyn R.; Nicholson, Jody S.; Borkowski, John G.; Whitman, Thomas L.

    2011-01-01

    Attention-deficit/hyperactivity disorder, oppositional defiant disorder, and conduct disorder are the most common forms of psychopathology seen among community youth. This study investigated prospective symptomatology of these disruptive behavior disorders from ages 5 though 14 in an at-risk community-based sample of 170 boys and girls born to…

  1. How Are Community Interventions Conceptualized and Conducted? An Analysis of Published Accounts

    Trickett, Edison J.; Espino, Susan Ryerson; Hawe, Penelope

    2011-01-01

    Recent discussions about the conduct of community interventions suggest the importance of developing more comprehensive theorizing about their nature and effects. The present study is an effort to infer how community interventions are theorized by the way they are represented in the peer-reviewed scholarly literature. A coding of a random sample…

  2. Network Analysis of a Virtual Community of Learning of Economics Educators

    Fontainha, Elsa; Martins, Jorge Tiago; Vasconcelos, Ana Cristina

    2015-01-01

    Introduction: This paper aims at understanding virtual communities of learning in terms of dynamics, types of knowledge shared by participants, and network characteristics such as size, relationships, density, and centrality of participants. It looks at the relationships between these aspects and the evolution of communities of learning. It…

  3. Conceptual Analysis for the Strategic and Operational Knowledge Man-agement of a Port Community

    Claudia DURAN

    2012-01-01

    Full Text Available Ports working in a network-community that is composed of a group of associative enterprises and logistic chains require managing their strategic and operational knowledge for achieving the efficiency of their activities at both levels. A conceptual model is presented that allows the development of a strategy for a port community through a strategic planning approach using operational knowledge. The different actors that participate in the community, their roles, and the main processes in which they participate are characterized. Then the vision and the mission of the community, and the strategic objectives in the four perspectives of the Balanced Scorecard: financial, clients, processes, and learning and growth, are defined. Finally, a set of indicators oriented toward the knowledge management of the main actors participating in the community is designed.

  4. A comparative analysis of major Chinese and English online question-answering communities

    WU; Dan; LIU; Yuan; HE; Daqing

    2010-01-01

    This paper compares 12 representative Chinese and English online questionanswering communities(Q&A communities)based on their basic functions,interactive modes,and customized services.An empirical experiment from a comparative perspective was also conducted on them by using 12 questions representing for four types of questions,which are assigned evenly to three different subject fields so as to examine the task performance of these 12 selected online Q&A communities.Our goal was to evaluate those online Q&A communities in terms of their quality and efficiency for answering questions posed to them.It was hoped that our empirical research would yield greater understanding and insights to the working intricacy of these online Q&A communities and hence their possible further improvement.

  5. Social media use by community-based organizations conducting health promotion: a content analysis

    2013-01-01

    Background Community-based organizations (CBOs) are critical channels for the delivery of health promotion programs. Much of their influence comes from the relationships they have with community members and other key stakeholders and they may be able to harness the power of social media tools to develop and maintain these relationships. There are limited data describing if and how CBOs are using social media. This study assesses the extent to which CBOs engaged in health promotion use popular social media channels, the types of content typically shared, and the extent to which the interactive aspects of social media tools are utilized. Methods We assessed the social media presence and patterns of usage of CBOs engaged in health promotion in Boston, Lawrence, and Worcester, Massachusetts. We coded content on three popular channels: Facebook, Twitter, and YouTube. We used content analysis techniques to quantitatively summarize posts, tweets, and videos on these channels, respectively. For each organization, we coded all content put forth by the CBO on the three channels in a 30-day window. Two coders were trained and conducted the coding. Data were collected between November 2011 and January 2012. Results A total of 166 organizations were included in our census. We found that 42% of organizations used at least one of the channels of interest. Across the three channels, organization promotion was the most common theme for content (66% of posts, 63% of tweets, and 93% of videos included this content). Most organizations updated Facebook and Twitter content at rates close to recommended frequencies. We found limited interaction/engagement with audience members. Conclusions Much of the use of social media tools appeared to be uni-directional, a flow of information from the organization to the audience. By better leveraging opportunities for interaction and user engagement, these organizations can reap greater benefits from the non-trivial investment required to use

  6. The Prevalence of Thyroid Nodules and an Analysis of Related Lifestyle Factors in Beijing Communities

    Hua Jiang

    2016-04-01

    Full Text Available Thyroid nodules (TNs have annual increasing trends worldwide, and large-scale investigations on the prevalence of TNs in Beijing communities have not been conducted since the introduction of salt iodization in 1995. We performed a cross-sectional study to determine the prevalence of TNs, their epidemiological characteristics, and their correlation with lifestyle factors. A total of 6324 permanent residents aged 18 years or older (mean age, 52.15 ± 11.58 years from seven representative communities in Beijing were included in the analyses. Once informed consent was obtained, the subjects were asked to complete questionnaires, a physical examination, and thyroid ultrasound. A total of 3100 cases had TNs. The overall prevalence rate was 49.0%, and the age-standardized prevalence was 40.1%, which increased significantly as age increased (p < 0.001. The prevalence was significantly higher in females compared to males (p < 0.001, and it was significantly higher among female current smokers and former smokers compared to non-smokers (p = 0.007. There was no correlation between alcohol consumption and TNs, and there were no significant differences in the prevalence among different groups of taste preference. The prevalence decreased with an increased frequency of seafood intake (p = 0.015 and with higher literacy levels (p < 0.001. The Cochran–Armitage trend test showed that the prevalence significantly increased with decreased physical labor and exercise intensity (p < 0.001, p = 0.009. Logistic regression analysis showed that age (Odds ratio (OR = 1.039 (1.034–1.044, p < 0.001, the female sex (OR = 1.789 (1.527–2.097, Body mass index (BMI (OR = 1.019 (1.005–1.034, and current smoking habits (OR = 1.246 (1.046–1.483 were independent risk factors for TNs. Our findings indicate that there is a high prevalence of TNs in Beijing, with a higher prevalence in females than in males. Moreover, the prevalence increases as age increases. Smoking and

  7. Response of soybean rhizosphere communities to human hygiene water addition as determined by community level physiological profiling (CLPP) and terminal restriction fragment length polymorphism (TRFLP) analysis

    Kerkhof, L.; Santoro, M.; Garland, J.

    2000-01-01

    In this report, we describe an experiment conducted at Kennedy Space Center in the biomass production chamber (BPC) using soybean plants for purification and processing of human hygiene water. Specifically, we tested whether it was possible to detect changes in the root-associated bacterial assemblage of the plants and ultimately to identify the specific microorganism(s) which differed when plants were exposed to hygiene water and other hydroponic media. Plants were grown in hydroponics media corresponding to four different treatments: control (Hoagland's solution), artificial gray water (Hoagland's+surfactant), filtered gray water collected from human subjects on site, and unfiltered gray water. Differences in rhizosphere microbial populations in all experimental treatments were observed when compared to the control treatment using both community level physiological profiles (BIOLOG) and molecular fingerprinting of 16S rRNA genes by terminal restriction fragment length polymorphism analysis (TRFLP). Furthermore, screening of a clonal library of 16S rRNA genes by TRFLP yielded nearly full length SSU genes associated with the various treatments. Most 16S rRNA genes were affiliated with the Klebsiella, Pseudomonas, Variovorax, Burkholderia, Bordetella and Isosphaera groups. This molecular approach demonstrated the ability to rapidly detect and identify microorganisms unique to experimental treatments and provides a means to fingerprint microbial communities in the biosystems being developed at NASA for optimizing advanced life support operations.

  8. Community health orientation of Indian Journal of Endocrinology and Metabolism: A bibliometric analysis of Indian Journal of Endocrinology and Metabolism

    Kaushal, Kanica; Kalra, Sanjay

    2015-01-01

    Background: Endocrine and metabolic diseases especially diabetes have become focus areas for public health professionals. Indian Journal of Endocrinology and Metabolism (IJEM), a publication of Endocrine Society of India, is a peer-reviewed online journal, which covers technical and clinical studies related to health, ethical and social issues in field of diabetes, endocrinology and metabolism. This bibliometric analysis assesses the journal from a community health perspective. Materials and Methods: Every article published in IJEM over a period of 4 years (2011–2014) was accessed to review coverage of community health in the field of endocrinology. Results: Seven editorials, 30 review articles, 41 original articles, 12 brief communications, 20 letter to editors, 4 articles on guidelines and 2 in the section “endocrinology and gender” directly or indirectly dealt with community health aspects of endocrinology. Together these amounted to 17% of all articles published through these 4 years. There were 14 articles on general, 60 pertaining to pancreas and diabetes, 10 on thyroid, 7 on pituitary/adrenal/gonads, 21 on obesity and metabolism and 4 on parathyroid and bone; all community medicine related. Conclusion: Community health is an integral part of the modern endocrinology diabetology and metabolism practice and it received adequate journal space during the last 4 years. The coverage is broad based involving all the major endocrine disorders. PMID:25932398

  9. Microbial community structural analysis of an expanded granular sludge bed (EGSB) reactor for beet sugar industrial wastewater (BSIW) treatment.

    Ambuchi, John Justo; Liu, Junfeng; Wang, Haiman; Shan, Lili; Zhou, Xiangtong; Mohammed, Mohammed O A; Feng, Yujie

    2016-05-01

    A looming global energy crisis has directly increased biomethanation processes using anaerobic digestion technology. However, much knowledge on the microbial community structure, their distribution within the digester and related functions remains extremely scanty and unavailable in some cases, yet very valuable in the improvement of the anaerobic bioprocesses. Using pyrosequencing technique based on Miseq PE 3000, microbial community population profiles were determined in an operated mesophilic expanded granular sludge bed (EGSB) reactor treating beet sugar industrial wastewater (BSIW) in the laboratory scale. Further, the distribution of the organisms in the lower, middle and upper sections within the reactor was examined. To our knowledge, this kind of analysis of the microbial community in a reactor treating BSIW is the first of its kind. A total of 44,204 non-chimeric reads with average length beyond 450 bp were yielded. Both bacterial and archaeal communities were identified with archaea predominance (60 %) observed in the middle section. Bayesian classifier yielded 164 families with only 0.73 % sequences which could not be classified to any taxa at family level. The overall phylum predominance in the reactor showed Firmicutes, Euryarchaeota, Chloroflexi, Proteobacteria and Bacteroidetes in the descending order. Our results clearly demonstrate a highly diverse microbial community population of an anaerobic reactor treating BSIW, with distinct distribution levels within the reactor.

  10. Community health orientation of Indian Journal of Endocrinology and Metabolism: A bibliometric analysis of Indian Journal of Endocrinology and Metabolism

    Kanica Kaushal

    2015-01-01

    Full Text Available Background: Endocrine and metabolic diseases especially diabetes have become focus areas for public health professionals. Indian Journal of Endocrinology and Metabolism (IJEM, a publication of Endocrine Society of India, is a peer-reviewed online journal, which covers technical and clinical studies related to health, ethical and social issues in field of diabetes, endocrinology and metabolism. This bibliometric analysis assesses the journal from a community health perspective. Materials and Methods: Every article published in IJEM over a period of 4 years (2011-2014 was accessed to review coverage of community health in the field of endocrinology. Results: Seven editorials, 30 review articles, 41 original articles, 12 brief communications, 20 letter to editors, 4 articles on guidelines and 2 in the section "endocrinology and gender" directly or indirectly dealt with community health aspects of endocrinology. Together these amounted to 17% of all articles published through these 4 years. There were 14 articles on general, 60 pertaining to pancreas and diabetes, 10 on thyroid, 7 on pituitary/adrenal/gonads, 21 on obesity and metabolism and 4 on parathyroid and bone; all community medicine related. Conclusion: Community health is an integral part of the modern endocrinology diabetology and metabolism practice and it received adequate journal space during the last 4 years. The coverage is broad based involving all the major endocrine disorders.

  11. Geo-ethical dimension of community's safety: rural and urban population vulnerability analysis methodology

    Kostyuchenko, Yuriy; Movchan, Dmytro; Kopachevsky, Ivan; Yuschenko, Maxim

    2016-04-01

    calculate a distribution of losses connected with decision making in land-use is demonstrated. Rural community's vulnerability determines by water availability, quality of soils, effectiveness of land use (including climate change adaptation), intensity of pollutions, crop productivity variations during the period of crop rotation, annual national distribution of crops output, and distance to city centres. It should noted here that "distance to city centres" is not comprehensive indicator of market accessibility in general case: quality and availability of transport infrastructure should be described more detailed on the next stages of analysis. Urban population vulnerability determines by distribution of urban fractures and quality urban environment: density, quality and availability of infrastructure, balance between industrial, residential and recreational zones, effectiveness of urban land use and landscape management, and social policy, particularly, employment. Population density is closely connected with social density, with communications and decision making. Social learning, as the function of social communications, is the way to increase sustainability. Also it possible to say that social sustainability is a function of intensity and efficiency of communications between interlinked and interacted networks in the heterogeneous environment. Therefore the results of study demonstrated that risk management study should includes issues of risk and threats perception, which should be described in framework of appropriate tools and approaches connected with ethical dimension of vulnerability. For instance, problems of accessibility and availability of safety resources in view of social fairness and socio-economic dynamics should be included into future studies in field of risk analysis.

  12. Constructing ecological interaction networks by correlation analysis: hints from community sampling

    WenJun Zhang

    2011-09-01

    Full Text Available A set of methodology for constructing ecological interaction networks by correlation analysis of community sampling data was presented in this study. Nearly 30 data sets at different levels of taxa for different sampling seasons and locations were used to construct networks and find network properties. I defined the network constructed by Pearson linear correlation is the linear network, and the network constructed by quasi-linear correlation measure (e.g., Spearman correlation is the quasi-linear network. Two taxa with statistically significant linear or quasi-linear correlation are determined to interact. The quasi-linear network is more general than linear network.The results reveled that correlation distributions of Pearson linear correlation and partial linear correlation constructed networks are unimodal functions and most of them are short-head (mostly negative correlations and long-tailed (mostly positive correlations. Spearman correlation distributions are either long-head and short-tailed unimodal functions or monotonically increasing functions. It was found that both mean partial linear correlation and mean Pearson linear correlation were approximately 0. The proportion of positive (partial linear correlations declined significantly with the increase in taxa. The mean (partial linear correlation declined significantly with the increase of taxa. More than 90% of network interactions are positive interactions. The average connectance was 9.8% (9.3% for (partial linear correlation constructed network. The parameter λ in power low distribution (L(x=x-λ increased as the decline of taxon level (from functional group to species for the partial linear correlation constructed network. λ is in average 0.8 to 0.9. The number of (positive interactions increased with the number of taxa for both linear and partial linear correlations constructed networks. The addition of a taxon would result in an increase of 0.4 (0.3 interactions (positive

  13. Social Network and Content Analysis of the North American Carbon Program as a Scientific Community of Practice

    Brown, Molly E.; Ihli, Monica; Hendrick, Oscar; Delgado-Arias, Sabrina; Escobar, Vanessa M.; Griffith, Peter

    2015-01-01

    The North American Carbon Program (NACP) was formed to further the scientific understanding of sources, sinks, and stocks of carbon in Earth's environment. Carbon cycle science integrates multidisciplinary research, providing decision-support information for managing climate and carbon-related change across multiple sectors of society. This investigation uses the conceptual framework of com-munities of practice (CoP) to explore the role that the NACP has played in connecting researchers into a carbon cycle knowledge network, and in enabling them to conduct physical science that includes ideas from social science. A CoP describes the communities formed when people consistently engage in shared communication and activities toward a common passion or learning goal. We apply the CoP model by using keyword analysis of abstracts from scientific publications to analyze the research outputs of the NACP in terms of its knowledge domain. We also construct a co-authorship network from the publications of core NACP members, describe the structure and social pathways within the community. Results of the content analysis indicate that the NACP community of practice has substantially expanded its research on human and social impacts on the carbon cycle, contributing to a better understanding of how human and physical processes interact with one another. Results of the co-authorship social network analysis demonstrate that the NACP has formed a tightly connected community with many social pathways through which knowledge may flow, and that it has also expanded its network of institutions involved in carbon cycle research over the past seven years.

  14. Application of nested PCR-DGGE (denaturing gradient gel electrophoresis) for the analysis of ciliate communities in soils.

    Shimano, Satoshi; Sambe, Mitsuo; Kasahara, Yasuhiro

    2012-01-01

    Ciliates play important roles as prey and predators in ecosystems. Changes in the ciliate community can affect the composition and population of microfauna and microflora in ecosystems. To investigate the structure of ciliate communities, we developed a nested PCR-DGGE method, which combines a universal eukaryotic-specific primer set in the first PCR step with a ciliate-specific primer set in the second PCR step, to amplify 18S rRNA genes from ciliates. The 300 bp DGGE fragments generated more bands on the gel than the 600 bp DGGE fragments. Prior to bead beating, DNA extraction of ciliates from soil samples was optimized with a combination of freeze-thaw cycles and ultrasonication. We applied this nested PCR-DGGE method to agricultural soils amended with 0, 120, 300, and 600 t ha⁻¹ year⁻¹ of livestock slurry. The results from the DGGE profiles and principal component analysis (PCA) revealed that the supplement of slurry to soils influenced the ciliate communities. From phylogenetic analysis, 108 DGGE bands were assigned to six classes, which included Spirotrichea and Colpodea, of the subphylum Intramacronucleata, and one class of the subphylum Postciliodesmatophora. These results indicated that a wide variety of taxonomic groups were detected by DGGE profiling. Thus, the nested PCR-DGGE method described here could clearly differentiate between ciliate communities within soil samples and allowed for the phylogenetic identification of these ciliates at the class level.

  15. A diverse bacterial community in an anoxic quinoline-degrading bioreactor determined by using pyrosequencing and clone library analysis.

    Zhang, Xiaojun; Yue, Siqing; Zhong, Huihui; Hua, Weiying; Chen, Ruijia; Cao, Youfang; Zhao, Liping

    2011-07-01

    There is a concern of whether the structure and diversity of a microbial community can be effectively revealed by short-length pyrosequencing reads. In this study, we performed a microbial community analysis on a sample from a high-efficiency denitrifying quinoline-degrading bioreactor and compared the results generated by pyrosequencing with those generated by clone library technology. By both technologies, 16S rRNA gene analysis indicated that the bacteria in the sample were closely related to, for example, Proteobacteria, Actinobacteria, and Bacteroidetes. The sequences belonging to Rhodococcus were the most predominant, and Pseudomonas, Sphingomonas, Acidovorax, and Zoogloea were also abundant. Both methods revealed a similar overall bacterial community structure. However, the 622 pyrosequencing reads of the hypervariable V3 region of the 16S rRNA gene revealed much higher bacterial diversity than the 130 sequences from the full-length 16S rRNA gene clone library. The 92 operational taxonomic unit (OTUs) detected using pyrosequencing belonged to 45 families, whereas the 37 OTUs found in the clone library belonged to 25 families. Most sequences obtained from the clone library had equivalents in the pyrosequencing reads. However, 64 OTUs detected by pyrosequencing were not represented in the clone library. Our results demonstrate that pyrosequencing of the V3 region of the 16S rRNA gene is not only a powerful tool for discovering low-abundance bacterial populations but is also reliable for dissecting the bacterial community structure in a wastewater environment.

  16. Supercritical fluid extraction and ultra performance liquid chromatography of respiratory quinones for microbial community analysis in environmental and biological samples.

    Hanif, Muhammad; Atsuta, Yoichi; Fujie, Koichi; Daimon, Hiroyuki

    2012-03-05

    Microbial community structure plays a significant role in environmental assessment and animal health management. The development of a superior analytical strategy for the characterization of microbial community structure is an ongoing challenge. In this study, we developed an effective supercritical fluid extraction (SFE) and ultra performance liquid chromatography (UPLC) method for the analysis of bacterial respiratory quinones (RQ) in environmental and biological samples. RQ profile analysis is one of the most widely used culture-independent tools for characterizing microbial community structure. A UPLC equipped with a photo diode array (PDA) detector was successfully applied to the simultaneous determination of ubiquinones (UQ) and menaquinones (MK) without tedious pretreatment. Supercritical carbon dioxide (scCO(2)) extraction with the solid-phase cartridge trap proved to be a more effective and rapid method for extracting respiratory quinones, compared to a conventional organic solvent extraction method. This methodology leads to a successful analytical procedure that involves a significant reduction in the complexity and sample preparation time. Application of the optimized methodology to characterize microbial communities based on the RQ profile was demonstrated for a variety of environmental samples (activated sludge, digested sludge, and compost) and biological samples (swine and Japanese quail feces).

  17. Supercritical Fluid Extraction and Ultra Performance Liquid Chromatography of Respiratory Quinones for Microbial Community Analysis in Environmental and Biological Samples

    Koichi Fujie

    2012-03-01

    Full Text Available Microbial community structure plays a significant role in environmental assessment and animal health management. The development of a superior analytical strategy for the characterization of microbial community structure is an ongoing challenge. In this study, we developed an effective supercritical fluid extraction (SFE and ultra performance liquid chromatography (UPLC method for the analysis of bacterial respiratory quinones (RQ in environmental and biological samples. RQ profile analysis is one of the most widely used culture-independent tools for characterizing microbial community structure. A UPLC equipped with a photo diode array (PDA detector was successfully applied to the simultaneous determination of ubiquinones (UQ and menaquinones (MK without tedious pretreatment. Supercritical carbon dioxide (scCO2 extraction with the solid-phase cartridge trap proved to be a more effective and rapid method for extracting respiratory quinones, compared to a conventional organic solvent extraction method. This methodology leads to a successful analytical procedure that involves a significant reduction in the complexity and sample preparation time. Application of the optimized methodology to characterize microbial communities based on the RQ profile was demonstrated for a variety of environmental samples (activated sludge, digested sludge, and compost and biological samples (swine and Japanese quail feces.

  18. Learning Community and Nonlearning Community Students in a Midwestern Community College

    Laanan, Frankie Santos; Jackson, Dimitra Lynette; Stebleton, Michael J.

    2013-01-01

    The research on learning communities has focused primarily on students at four-year colleges and universities. There is a dearth of studies that examine learning communities in community colleges. The purpose of this comparative study was to conduct an analysis of learning community and nonlearning community students in a community college located…

  19. A comparative analysis of ethnomedicinal practices for treating gastrointestinal disorders used by communities living in three national parks (Korea).

    Kim, Hyun; Song, Mi-Jang; Brian, Heldenbrand; Choi, Kyoungho

    2014-01-01

    The purpose of this study is to comparatively analyze the ethnomedicinal practices on gastrointestinal disorders within communities in Jirisan National Park, Gayasan National Park, and Hallasan National Park of Korea. Data was collected through participant observations and indepth interviews with semistructured questionnaires. Methods for comparative analysis were accomplished using the informant consensus factor, fidelity level, and internetwork analysis. A total of 490 ethnomedicinal practices recorded from the communities were classified into 110 families, 176 genera, and 220 species that included plants, animals, fungi, and alga. The informant consensus factor values in the disorder categories were enteritis, and gastralgia (1.0), followed by indigestion (0.94), constipation (0.93), and abdominal pain and gastroenteric trouble (0.92). In terms of fidelity levels, 71 plant species showed fidelity levels of 100%. The internetwork analysis between disorders and all medicinal species are grouped in the center by the four categories of indigestion, diarrhea, abdominal pain, and gastroenteric trouble, respectively. Regarding the research method of this study, the comparative analysis methods will contribute to the availability of orally transmitted ethnomedicinal knowledge. Among the methods of analysis, the use of internetwork analysis as a tool for analysis in this study provides imperative internetwork maps between gastrointestinal disorders and medicinal species.

  20. Diversity in a Polymicrobial Community Revealed by Analysis of Viromes, Endolysins and CRISPR Spacers

    Treangen, Todd J.; Koren, Sergey; Pop, Mihai; Bhaya, Devaki

    2016-01-01

    The polymicrobial biofilm communities in Mushroom and Octopus Spring in Yellowstone National Park (YNP) are well characterized, yet little is known about the phage populations. Dominant species, Synechococcus sp. JA-2-3B'a(2–13), Synechococcus sp. JA-3-3Ab, Chloroflexus sp. Y-400-fl, and Roseiflexus sp. RS-1, contain multiple CRISPR-Cas arrays, suggesting complex interactions with phage predators. To analyze phage populations from Octopus Spring biofilms, we sequenced a viral enriched fraction. To assemble and analyze phage metagenomic data, we developed a custom module, VIRITAS, implemented within the MetAMOS framework. This module bins contigs into groups based on tetranucleotide frequencies and CRISPR spacer-protospacer matching and ORF calling. Using this pipeline we were able to assemble phage sequences into contigs and bin them into three clusters that corroborated with their potential host range. The virome contained 52,348 predicted ORFs; some were clearly phage-like; 9319 ORFs had a recognizable Pfam domain while the rest were hypothetical. Of the recognized domains with CRISPR spacer matches, was the phage endolysin used by lytic phage to disrupt cells. Analysis of the endolysins present in the thermophilic cyanophage contigs revealed a subset of characterized endolysins as well as a Glyco_hydro_108 (PF05838) domain not previously associated with sequenced cyanophages. A search for CRISPR spacer matches to all identified phage endolysins demonstrated that a majority of endolysin domains were targets. This strategy provides a general way to link host and phage as endolysins are known to be widely distributed in bacteriophage. Endolysins can also provide information about host cell wall composition and have the additional potential to be used as targets for novel therapeutics. PMID:27611571

  1. Land use change and landslide characteristics analysis for community-based disaster mitigation.

    Chen, Chien-Yuan; Huang, Wen-Lin

    2013-05-01

    On August 8, 2009, Typhoon Morakot brought heavy rain to Taiwan, causing numerous landslides and debris flows in the Taihe village area of Meishan Township, Chiayi County, in south-central Taiwan. In the Taihe land is primary used for agriculture and land use management may be a factor in the area's landslides. This study explores Typhoon Morakot-induced landslides and land use changes between 1999 and 2009 using GIS with the aid of field investigation. Spot 5 satellite images with a resolution of 2.5 m are used for landslide interpretation and manually digitalized in GIS. A statistical analysis for landslide frequency-area distribution was used to identify the landslide characteristics associated with different types of land use. There were 243 landslides with a total area of 2.75 km(2) in the study area. The area is located in intrinsically fragile combinations of sandstone and shale. Typhoon Morakot-induced landslides show a power-law distribution in the study area. Landslides were mainly located in steep slope areas containing natural forest and in areas planted with bamboo, tea, and betel nut. Land covered with natural forest shows the highest landslide ratio, followed by bamboo, betel nut, and tea. Landslides thus show a higher ratio in areas planted with shallow root vegetation such as bamboo, betel nut, and tea. Furthermore, the degree of basin development is proportional to the landslide ratio. The results show that a change in vegetation cover results in a modified landslide area and frequency and changed land use areas have higher landslide ratios than non-changed. Land use management and community-based disaster prevention are needed in mountainous areas of Taiwan for hazard mitigation.

  2. Metagenomic and metatranscriptomic analysis of microbial community structure and gene expression of activated sludge.

    Ke Yu

    Full Text Available The present study applied both metagenomic and metatranscriptomic approaches to characterize microbial structure and gene expression of an activated sludge community from a municipal wastewater treatment plant in Hong Kong. DNA and cDNA were sequenced by Illumina Hi-seq2000 at a depth of 2.4 Gbp. Taxonomic analysis by MG-RAST showed bacteria were dominant in both DNA and cDNA datasets. The taxonomic profile obtained by BLAST against SILVA SSUref database and annotation by MEGAN showed that activated sludge was dominated by Proteobacteria, Actinobacteria, Bacteroidetes, Firmicutes and Verrucomicrobia phyla in both DNA and cDNA datasets. Global gene expression annotation based on KEGG metabolism pathway displayed slight disagreement between the DNA and cDNA datasets. Further gene expression annotation focusing on nitrogen removal revealed that denitrification-related genes sequences dominated in both DNA and cDNA datasets, while nitrifying genes were also expressed in relative high levels. Specially, ammonia monooxygenase and hydroxylamine oxidase demonstrated the high cDNA/DNA ratios in the present study, indicating strong nitrification activity. Enzyme subunits gene sequences annotation discovered that subunits of ammonia monooxygenase (amoA, amoB, amoC and hydroxylamine oxygenase had higher expression levels compared with subunits of the other enzymes genes. Taxonomic profiles of selected enzymes (ammonia monooxygenase and hydroxylamine oxygenase showed that ammonia-oxidizing bacteria present mainly belonged to Nitrosomonas and Nitrosospira species and no ammonia-oxidizing Archaea sequences were detected in both DNA and cDNA datasets.

  3. Determinants of participation restriction among community dwelling stroke survivors: A path analysis

    Chang Anne M

    2009-09-01

    Full Text Available Abstract Background Apart from promoting physical recovery and assisting in activities of daily living, a major challenge in stroke rehabilitation is to minimize psychosocial morbidity and to promote the reintegration of stroke survivors into their family and community. The identification of key factors influencing long-term outcome are essential in developing more effective rehabilitation measures for reducing stroke-related morbidity. The aim of this study was to test a theoretical model of predictors of participation restriction which included the direct and indirect effects between psychosocial outcomes, physical outcome, and socio-demographic variables at 12 months after stroke. Methods Data were collected from 188 stroke survivors at 12 months following their discharge from one of the two rehabilitation hospitals in Hong Kong. The settings included patients' homes and residential care facilities. Path analysis was used to test a hypothesized model of participation restriction at 12 months. Results The path coefficients show functional ability having the largest direct effect on participation restriction (β = 0.51. The results also show that more depressive symptoms (β = -0.27, low state self-esteem (β = 0.20, female gender (β = 0.13, older age (β = -0.11 and living in a residential care facility (β = -0.12 have a direct effect on participation restriction. The explanatory variables accounted for 71% of the variance in explaining participation restriction at 12 months. Conclusion Identification of stroke survivors at risk of high levels of participation restriction, depressive symptoms and low self-esteem will assist health professionals to devise appropriate rehabilitation interventions that target improving both physical and psychosocial functioning.

  4. Genomic analysis of ST88 community-acquired methicillin resistant Staphylococcus aureus in Ghana

    Buultjens, Andrew H.; Giulieri, Stefano; Owusu-Mireku, Evelyn; Aboagye, Samuel Y.; Baines, Sarah L.; Gonçalves da Silva, Anders; Howden, Benjamin P.; Pluschke, Gerd; Yeboah-Manu, Dorothy

    2017-01-01

    Background The emergence and evolution of community-acquired methicillin resistant Staphylococcus aureus (CA-MRSA) strains in Africa is poorly understood. However, one particular MRSA lineage called ST88, appears to be rapidly establishing itself as an “African” CA-MRSA clone. In this study, we employed whole genome sequencing to provide more information on the genetic background of ST88 CA-MRSA isolates from Ghana and to describe in detail ST88 CA-MRSA isolates in comparison with other MRSA lineages worldwide. Methods We first established a complete ST88 reference genome (AUS0325) using PacBio SMRT sequencing. We then used comparative genomics to assess relatedness among 17 ST88 CA-MRSA isolates recovered from patients attending Buruli ulcer treatment centres in Ghana, three non-African ST88s and 15 other MRSA lineages. Results We show that Ghanaian ST88 forms a discrete MRSA lineage (harbouring SCCmec-IV [2B]). Gene content analysis identified five distinct genomic regions enriched among ST88 isolates compared with the other S. aureus lineages. The Ghanaian ST88 isolates had only 658 core genome SNPs and there was no correlation between phylogeny and geography, suggesting the recent spread of this clone. The lineage was also resistant to multiple classes of antibiotics including β-lactams, tetracycline and chloramphenicol. Discussion This study reveals that S. aureus ST88-IV is a recently emerging and rapidly spreading CA-MRSA clone in Ghana. The study highlights the capacity of small snapshot genomic studies to provide actionable public health information in resource limited settings. To our knowledge this is the first genomic assessment of the ST88 CA-MRSA clone. PMID:28265515

  5. Fear of Crime in Rapidly Changing Rural Communities: A Longitudinal Analysis.

    Krannich, Richard S.; And Others

    1989-01-01

    Finds that, among inhabitants of four small towns in Wyoming and Utah, increased fear of crime was related to rapid community growth, greater criminal victimization experience, and lesser perception of own social integration. Contains 38 references. (SV)

  6. Multi-scale analysis of the European airspace using network community detection.

    Gérald Gurtner

    Full Text Available We show that the European airspace can be represented as a multi-scale traffic network whose nodes are airports, sectors, or navigation points and links are defined and weighted according to the traffic of flights between the nodes. By using a unique database of the air traffic in the European airspace, we investigate the architecture of these networks with a special emphasis on their community structure. We propose that unsupervised network community detection algorithms can be used to monitor the current use of the airspace and improve it by guiding the design of new ones. Specifically, we compare the performance of several community detection algorithms, both with fixed and variable resolution, and also by using a null model which takes into account the spatial distance between nodes, and we discuss their ability to find communities that could be used to define new control units of the airspace.

  7. Multi-scale analysis of the European airspace using network community detection

    Gurtner, Gérald; Cipolla, Marco; Lillo, Fabrizio; Mantegna, Rosario Nunzio; Miccichè, Salvatore; Pozzi, Simone

    2013-01-01

    We show that the European airspace can be represented as a multi-scale traffic network whose nodes are airports, sectors, or navigation points and links are defined and weighted according to the traffic of flights between the nodes. By using a unique database of the air traffic in the European airspace, we investigate the architecture of these networks with a special emphasis on their community structure. We propose that unsupervised network community detection algorithms can be used to monitor the current use of the airspaces and improve it by guiding the design of new ones. Specifically, we compare the performance of three community detection algorithms, also by using a null model which takes into account the spatial distance between nodes, and we discuss their ability to find communities that could be used to define new control units of the airspace.

  8. Social Network Analysis to support interactions in virtual communities for the construction of knowledge

    Elvis Mazzoni

    2005-01-01

    Full Text Available Discussion of approaches to analyze the interactions within virtual communities, shifting from quantity 'interactions assessment of the roles and functions of the individual participants in the process of collaborative construction of knowledge.

  9. Social media use by community-based organizations conducting health promotion: a content analysis

    2013-01-01

    Background: Community-based organizations (CBOs) are critical channels for the delivery of health promotion programs. Much of their influence comes from the relationships they have with community members and other key stakeholders and they may be able to harness the power of social media tools to develop and maintain these relationships. There are limited data describing if and how CBOs are using social media. This study assesses the extent to which CBOs engaged in health promotion use popula...

  10. Social media use by community-based organizations conducting health promotion: a content analysis

    2013-01-01

    Background Community-based organizations (CBOs) are critical channels for the delivery of health promotion programs. Much of their influence comes from the relationships they have with community members and other key stakeholders and they may be able to harness the power of social media tools to develop and maintain these relationships. There are limited data describing if and how CBOs are using social media. This study assesses the extent to which CBOs engaged in health promotion use popular...

  11. Blended Learning and Sense of Community: A Comparative Analysis with Traditional and Fully Online Graduate Courses

    Fred Rovai and Hope Jordan

    2004-08-01

    Full Text Available Blended learning is a hybrid of classroom and online learning that includes some of the conveniences of online courses without the complete loss of face-to-face contact. The present study used a causal-comparative design to examine the relationship of sense of community between traditional classroom, blended, and fully online higher education learning environments. Evidence is provided to suggest that blended courses produce a stronger sense of community among students than either traditional or fully online courses.

  12. Comparative Analysis of the Composition of Intestinal Bacterial Communities in Dastarcus helophoroides Fed Different Diets

    Wang, Wei-Wei; He, Cai; Cui, Jun; Wang, Hai-dong; Li, Meng-Lou

    2014-01-01

    The diversity of the intestinal bacterial communities in Dastarcus helophoroides (Fairmaire) (Coleoptera: Bothrideridae) larvae and adults was assayed by PCR-DGGE to determine whether different artificial diets could influence these bacterial communities. Two diets were used for feeding the larvae and four for the adults. Escherichia, Desemzia, Staphylococcus, Asticcacaulis, Cellvibrio, Aurantimonas, and Planomicrobium were isolated from the gut of the adults, with Escherichia and Staphylococ...

  13. Litter quality versus soil microbial community controls over decomposition: a quantitative analysis

    Cleveland, Cory C.; Reed, Sasha C.; Keller, Adrienne B.; Nemergut, Diana R.; O'Neill, Sean P.; Ostertag, Rebecca; Vitousek, Peter M.

    2014-01-01

    The possible effects of soil microbial community structure on organic matter decomposition rates have been widely acknowledged, but are poorly understood. Understanding these relationships is complicated by the fact that microbial community structure and function are likely to both affect and be affected by organic matter quality and chemistry, thus it is difficult to draw mechanistic conclusions from field studies. We conducted a reciprocal soil inoculum × litter transplant laboratory incubation experiment using samples collected from a set of sites that have similar climate and plant species composition but vary significantly in bacterial community structure and litter quality. The results showed that litter quality explained the majority of variation in decomposition rates under controlled laboratory conditions: over the course of the 162-day incubation, litter quality explained nearly two-thirds (64 %) of variation in decomposition rates, and a smaller proportion (25 %) was explained by variation in the inoculum type. In addition, the relative importance of inoculum type on soil respiration increased over the course of the experiment, and was significantly higher in microcosms with lower litter quality relative to those with higher quality litter. We also used molecular phylogenetics to examine the relationships between bacterial community composition and soil respiration in samples through time. Pyrosequencing revealed that bacterial community composition explained 32 % of the variation in respiration rates. However, equal portions (i.e., 16 %) of the variation in bacterial community composition were explained by inoculum type and litter quality, reflecting the importance of both the meta-community and the environment in bacterial assembly. Taken together, these results indicate that the effects of changing microbial community composition on decomposition are likely to be smaller than the potential effects of climate change and/or litter quality changes in

  14. Patient perspectives on care received at community acupuncture clinics: a qualitative thematic analysis

    2013-01-01

    Abstract Background Community acupuncture is a recent innovation in acupuncture service delivery in the U.S. that aims to improve access to care through low-cost treatments in group-based settings. Patients at community acupuncture clinics represent a broader socioeconomic spectrum and receive more frequent treatments compared to acupuncture users nationwide. As a relatively new model of acupuncture in the U.S., little is known about the experiences o...

  15. Clustering drug-drug interaction networks with energy model layouts: community analysis and drug repurposing

    Lucreţia Udrescu; Laura Sbârcea; Alexandru Topîrceanu; Alexandru Iovanovici; Ludovic Kurunczi; Paul Bogdan; Mihai Udrescu

    2016-01-01

    Analyzing drug-drug interactions may unravel previously unknown drug action patterns, leading to the development of new drug discovery tools. We present a new approach to analyzing drug-drug interaction networks, based on clustering and topological community detection techniques that are specific to complex network science. Our methodology uncovers functional drug categories along with the intricate relationships between them. Using modularity-based and energy-model layout community detection...

  16. [Analysis of the changes of microbial community structure on bio-carrier of recirculating aquaculture systems (RAS)].

    Zhang, Hai-Geng; Ma, Shao-Sai; Li, Qiu-Fen; Fu, Xue-Jun; Zhang, Yan; Qu, Ke-Ming

    2011-01-01

    In order to study the variation of microbial community structure and the mechanism of denitrification on bio-carrier in recirculating aquaculture systems (RAS) during the periods of bio-film formation and operation the systems, traditional microbiological methods were applied to count the quantity of heterotrophic bacteria, ammonia oxidize bacteria and nitrite oxidize bacteria. The amplified products of variable V3 region of bacterial 16S rDNA were separated by using denaturing gradient gel electrophoresis (DGGE). And bacterial community DNA fingerprint was obtained. The sequences retrieved from the DGGE bands were used for homology analysis and construction of phylogenetic tree. It presented a trend that the quantity of the three types of bacteria increased gradually to a top and then fallen slowly to a stable level. The composition of microbial community of bio-carrier was very abundant in all periods, and the Shannon index was 1.53, 1.44, 1.57, 1.08, 1.27 and 1.30, respectively. During different periods, there was a certain shift in the microbial community structure, while the C(s) value (similar index) in two adjacent periods was high, indicating the variation and succession of the microbial community was slow and regular. Several bacteria had an effect on removal of pollutants for farming water and the effluent water quality could meet the requirements of high-density culture. Among them, Proteobacteria and Flavobacteria were main communities. The Nitrosomonas and some other facultative anaerobic bacteria (Flavobacteriaceae bacterium) were identified, which indicated that there may be coexisted pathways of nitrification and denitrification in bio-filter.

  17. Biological oxygen demand optode analysis of coral reef-associated microbial communities exposed to algal exudates

    AK Gregg

    2013-07-01

    Full Text Available Algae-derived dissolved organic matter has been hypothesized to induce mortality of reef building corals. One proposed killing mechanism is a zone of hypoxia created by rapidly growing microbes. To investigate this hypothesis, biological oxygen demand (BOD optodes were used to quantify the change in oxygen concentrations of microbial communities following exposure to exudates generated by turf algae and crustose coralline algae (CCA. BOD optodes were embedded with microbial communities cultured from Montastraea annularis and Mussismilia hispida, and respiration was measured during exposure to turf and CCA exudates. The oxygen concentrations along the optodes were visualized with a low-cost Submersible Oxygen Optode Recorder (SOOpR system. With this system we observed that exposure to exudates derived from turf algae stimulated higher oxygen drawdown by the coral-associated bacteria than CCA exudates or seawater controls. Furthermore, in both turf and CCA exudate treatments, all microbial communities (coral-, algae-associated and pelagic contributed significantly to the observed oxygen drawdown. This suggests that the driving factor for elevated oxygen consumption rates is the source of exudates rather than the initially introduced microbial community. Our results demonstrate that exudates from turf algae may contribute to hypoxia-induced coral stress in two different coral genera as a result of increased biological oxygen demand of the local microbial community. Additionally, the SOOpR system developed here can be applied to measure the BOD of any culturable microbe or microbial community.

  18. Multisubstrate isotope labeling and metagenomic analysis of active soil bacterial communities.

    Verastegui, Y; Cheng, J; Engel, K; Kolczynski, D; Mortimer, S; Lavigne, J; Montalibet, J; Romantsov, T; Hall, M; McConkey, B J; Rose, D R; Tomashek, J J; Scott, B R; Charles, T C; Neufeld, J D

    2014-07-15

    Soil microbial diversity represents the largest global reservoir of novel microorganisms and enzymes. In this study, we coupled functional metagenomics and DNA stable-isotope probing (DNA-SIP) using multiple plant-derived carbon substrates and diverse soils to characterize active soil bacterial communities and their glycoside hydrolase genes, which have value for industrial applications. We incubated samples from three disparate Canadian soils (tundra, temperate rainforest, and agricultural) with five native carbon ((12)C) or stable-isotope-labeled ((13)C) carbohydrates (glucose, cellobiose, xylose, arabinose, and cellulose). Indicator species analysis revealed high specificity and fidelity for many uncultured and unclassified bacterial taxa in the heavy DNA for all soils and substrates. Among characterized taxa, Actinomycetales (Salinibacterium), Rhizobiales (Devosia), Rhodospirillales (Telmatospirillum), and Caulobacterales (Phenylobacterium and Asticcacaulis) were bacterial indicator species for the heavy substrates and soils tested. Both Actinomycetales and Caulobacterales (Phenylobacterium) were associated with metabolism of cellulose, and Alphaproteobacteria were associated with the metabolism of arabinose; members of the order Rhizobiales were strongly associated with the metabolism of xylose. Annotated metagenomic data suggested diverse glycoside hydrolase gene representation within the pooled heavy DNA. By screening 2,876 cloned fragments derived from the (13)C-labeled DNA isolated from soils incubated with cellulose, we demonstrate the power of combining DNA-SIP, multiple-displacement amplification (MDA), and functional metagenomics by efficiently isolating multiple clones with activity on carboxymethyl cellulose and fluorogenic proxy substrates for carbohydrate-active enzymes. Importance: The ability to identify genes based on function, instead of sequence homology, allows the discovery of genes that would not be identified through sequence alone. This

  19. Oral health conditions and frailty in Mexican community-dwelling elderly: a cross sectional analysis

    Castrejón-Pérez Roberto

    2012-09-01

    Full Text Available Abstract Background Oral health is an important component of general well-being for the elderly. Oral health-related problems include loss of teeth, nonfunctional removable dental prostheses, lesions of the oral mucosa, periodontitis, and root caries. They affect food selection, speaking ability, mastication, social relations, and quality of life. Frailty is a geriatric syndrome that confers vulnerability to negative health-related outcomes. The association between oral health and frailty has not been explored thoroughly. This study sought to identify associations between the presence of some oral health conditions, and frailty status among Mexican community-dwelling elderly. Methods Analysis of baseline data of the Mexican Study of Nutritional and Psychosocial Markers of Frailty, a cohort study carried out in a representative sample of people aged 70 and older residing in one district of Mexico City. Frailty was defined as the presence of three or more of the following five components: weight loss, exhaustion, slowness, weakness, and low physical activity. Oral health variables included self-perception of oral health compared with others of the same age; utilization of dental services during the last year, number of teeth, dental condition (edentate, partially edentate, or completely dentate, utilization and functionality of removable partial or complete dentures, severe periodontitis, self-reported chewing problems and xerostomia. Covariates included were gender, age, years of education, cognitive performance, smoking status, recent falls, hospitalization, number of drugs, and comorbidity. The association between frailty and dental variables was determined performing a multivariate logistic regression analysis. Final models were adjusted by socio-demographic and health factors Results Of the 838 participants examined, 699 had the information needed to establish the criteria for diagnosis of frailty. Those who had a higher probability of being

  20. Effect of methamidophos on soil fungi community in microcosms by plate count, DGGE and clone library analysis

    LI Xinyu; ZHANG Huiwen; WU Minna; ZHANG Yan; ZHANG Chenggang

    2008-01-01

    Methamidophos was widely used a pesticide in northern China. The potential influences of methamidophos on soil fungal community in black soil were assessed by plate count, 28S rDNA-PCR-DGGE, and clone library analysis. Three methamidophos levels (50, 150, and 250 mg/kg) were tested in soil microcosms. Results from plate count during a 60-d microcosm experiment showed that high concentrations of methamidophos (250 mg/kg) could significantly stimulate fungal populations. DCGE (denaturing gradient gel electrophoresis) fingerprinting patterns showed a significant difference between the responses of culturable and total fungi communities under the stress of methamidophos. Shannon diversity indices calculated from DGGE profiles indicated that culturable fungi in all microcosms with methamidophos treatment increased after 1 week of incubation. However, the diversity indices of total fungi decreased in the first week, as compared to the stimulation of culturable fungi. At the 8th week, however, all the microcosms treated by methamidophos were similar to the control microcosms in community structure as suggested by the Shannon diversity indices for both culturable and total fungi. In contrast, after 1 week the fungal structure of culturable and unculturable both were disturbed to different extent under the stresses of methamidophos by clustering analysis. Clone sequencing analysis indicated the stimulation of pathogenic and unculturable fungal populations by methamidophos treatment, suggetsing potential risks of plant disease outbreak.

  1. Microbial community analysis of fouled reverse osmosis membranes used in water recycling.

    Ayache, C; Manes, C; Pidou, M; Croué, J P; Gernjak, W

    2013-06-15

    Biofouling on RO membranes has major cost implications in water reclamation. In this study membranes and water samples were collected from a RO pilot-plant operated on two sites to study the differences in microbial communities in order to develop a better understanding of the biofouling. For the two sites studied, the examination of the front membrane of the first stage and the tail membrane of the second stage of the RO train using 16S rRNA gene-based molecular technique showed that bacteria were similar on both stages and no significant effect of the membrane location within the RO train on the biofilm development could be discerned. However, the comparison of the identified bacteria from membrane samples between the two sites showed that each site is specific, leading to a different composition of microbial communities. The different nutrient concentrations in the RO feed water due to the different biological pre-treatments are one potential explanation for the observed differences in the microbial communities. Seasonal variations also play a major role in the development of microbial communities as shown by the significant differences observed between the communities measured in the samples in winter and summer on the second site. The results did not show similarity between the species identified on the RO membranes and in the feed water. Hence, the relationship of microbial community between the water generated during the pre-treatment process and RO membranes is not obvious. From this study, results showed that there is an actual need to investigate the development of microbial communities on membrane surface in real conditions in order to suggest tailored solutions for biofouling control and removal.

  2. Microbial community analysis of fouled reverse osmosis membranes used in water recycling

    Ayache, C.

    2013-06-01

    Biofouling on RO membranes has major cost implications in water reclamation. In this study membranes and water samples were collected from a RO pilot-plant operated on two sites to study the differences in microbial communities in order to develop a better understanding of the biofouling. For the two sites studied, the examination of the front membrane of the first stage and the tail membrane of the second stage of the RO train using 16S rRNA gene-based molecular technique showed that bacteria were similar on both stages and no significant effect of the membrane location within the RO train on the biofilm development could be discerned. However, the comparison of the identified bacteria from membrane samples between the two sites showed that each site is specific, leading to a different composition of microbial communities. The different nutrient concentrations in the RO feed water due to the different biological pre-treatments are one potential explanation for the observed differences in the microbial communities. Seasonal variations also play a major role in the development of microbial communities as shown by the significant differences observed between the communities measured in the samples in winter and summer on the second site. The results did not show similarity between the species identified on the RO membranes and in the feed water. Hence, the relationship of microbial community between the water generated during the pre-treatment process and RO membranes is not obvious. From this study, results showed that there is an actual need to investigate the development of microbial communities on membrane surface in real conditions in order to suggest tailored solutions for biofouling control and removal. © 2013 Elsevier Ltd.

  3. Functional gene array-based analysis of microbial community structure in groundwaters with a gradient of contaminant levels

    Waldron, P.J.; Wu, L.; Van Nostrand, J.D.; Schadt, C.W.; Watson, D.B.; Jardine, P.M.; Palumbo, A.V.; Hazen, T.C.; Zhou, J.

    2009-06-15

    To understand how contaminants affect microbial community diversity, heterogeneity, and functional structure, six groundwater monitoring wells from the Field Research Center of the U.S. Department of Energy Environmental Remediation Science Program (ERSP; Oak Ridge, TN), with a wide range of pH, nitrate, and heavy metal contamination were investigated. DNA from the groundwater community was analyzed with a functional gene array containing 2006 probes to detect genes involved in metal resistance, sulfate reduction, organic contaminant degradation, and carbon and nitrogen cycling. Microbial diversity decreased in relation to the contamination levels of the wells. Highly contaminated wells had lower gene diversity but greater signal intensity than the pristine well. The microbial composition was heterogeneous, with 17-70% overlap between different wells. Metal-resistant and metal-reducing microorganisms were detected in both contaminated and pristine wells, suggesting the potential for successful bioremediation of metal-contaminated groundwaters. In addition, results of Mantel tests and canonical correspondence analysis indicate that nitrate, sulfate, pH, uranium, and technetium have a significant (p < 0.05) effect on microbial community structure. This study provides an overall picture of microbial community structure in contaminated environments with functional gene arrays by showing that diversity and heterogeneity can vary greatly in relation to contamination.

  4. Online Social Support for Patients with Multiple Sclerosis: A Thematic Analysis of Messages Posted to a Virtual Support Community

    Masoumeh Abbasi Shavazi

    2016-07-01

    Full Text Available Background: Currently with the emergence of the Internet, patients have an opportunity to exchange social support online. However, little attention has been devoted to different dimensions of online social support exchanged in virtual support communities for patients with multiple sclerosis (MS. Methods: To provide a rich insight, the aim of this qualitative study was to explore and categorize different dimensions of online social support in messages exchanged in a virtual support community for patients with MS. A total of 548 posted messages created during one year period were selected using purposive sampling to consider the maximum variation sampling. Prior-research-driven thematic analysis was then conducted. In this regard, we used the Cutruna and Suhr’s coding system. The messages that could not be categorized with the used coding system were thematically analyzed to explore new additional social support themes. Results: The results showed that various forms of social support including informational, emotional, network, esteem and tangible support were exchanged. Moreover, new additional social support themes including sharing personal experiences, sharing coping strategies and spiritual support emerged in this virtual support community. Conclusion: The wide range of online social support exchanged in the virtual support community can be regarded as a supplementary source of social support for patients with MS. Future researches can examine online social support more comprehensively considering additional social support themes emerging in the present study.

  5. The current status of community drug testing via the analysis of drugs and drug metabolites in sewage

    Malcolm J. Reid

    2011-12-01

    Full Text Available Over the past few years the analysis of drug residues in sewage has been promoted as a means of estimating the level of drug use in communities. Measured drug residue concentrations in the sewage are used to determine the load (total mass of the drug being used by the entire community. Knowledge of the size or population of the community then allows for the calculation of drug-use relative to population (typically drug-mass/day/1000 inhabitants which facilitates comparisons between differing communities or populations. Studies have been performed in many European countries, including Norway, as well as in the US and Australia. The approach has successfully estimated the use of cocaine, amphetamine, methamphetamine, MDMA, cannabis, nicotine and alcohol. The analysis of biomarkers of drug use in sewage has great potential to support and complement existing techniques for estimating levels of drug use, and as such has been identified as a promising development by the European Monitoring Centre for Drugs and Drug Addiction (EMCDDA; www.emcdda.europa.eu/wastewater-analysis. The approach is not without its challenges, and ongoing collaboration across Europe aims at agreeing upon best-practice and harmonising the methods being used. In Norway development is being performed through the NFR RUSMIDDEL funded DrugMon (www.niva.no/drugmon project that has led to the development of many new techniques, significantly improved our understanding of the uncertainties associated with the approach and allowed the coordination of Europe wide collaboration which has included all important intercalibration exercises. Application of the technique can provide evidence-based and real-time estimates of collective drug use with the resulting data used to improve the much needed estimates of drug use and dependency.

  6. High-throughput nucleotide sequence analysis of diverse bacterial communities in leachates of decomposing pig carcasses

    Seung Hak Yang

    2015-09-01

    Full Text Available The leachate generated by the decomposition of animal carcass has been implicated as an environmental contaminant surrounding the burial site. High-throughput nucleotide sequencing was conducted to investigate the bacterial communities in leachates from the decomposition of pig carcasses. We acquired 51,230 reads from six different samples (1, 2, 3, 4, 6 and 14 week-old carcasses and found that sequences representing the phylum Firmicutes predominated. The diversity of bacterial 16S rRNA gene sequences in the leachate was the highest at 6 weeks, in contrast to those at 2 and 14 weeks. The relative abundance of Firmicutes was reduced, while the proportion of Bacteroidetes and Proteobacteria increased from 3–6 weeks. The representation of phyla was restored after 14 weeks. However, the community structures between the samples taken at 1–2 and 14 weeks differed at the bacterial classification level. The trend in pH was similar to the changes seen in bacterial communities, indicating that the pH of the leachate could be related to the shift in the microbial community. The results indicate that the composition of bacterial communities in leachates of decomposing pig carcasses shifted continuously during the study period and might be influenced by the burial site.

  7. Social capital and adolescent smoking in schools and communities: a cross-classified multilevel analysis.

    De Clercq, Bart; Pfoertner, Timo-Kolja; Elgar, Frank J; Hublet, Anne; Maes, Lea

    2014-10-01

    We sought to determine whether social capital at the individual-, school- and community-level can explain variance in adolescent smoking and accounts for social inequalities in smoking. We collected data as part of the 2005/6 Health Behavior in School-aged Children survey, a nationally representative survey of the health and well-being of high school pupils in Belgium (Flanders). Social capital was assessed by structural and cognitive components of family social capital, a four-factor school social capital scale and a cognitive community social capital scale. We fitted non-hierarchical multilevel models to the data, with 8453 adolescents nested within a cross-classification of 167 schools and 570 communities. Significant variation in adolescent regular smoking was found between schools, but not between communities. Only structural family social capital and cognitive school social capital variables negatively related to regular smoking. No interactions between socio-economic status and social capital variables were found. Our findings suggest that previously observed community-level associations with adolescent smoking may be a consequence of unmeasured confounding. Distinguishing nested contexts of social capital is important because their associations with smoking differ.

  8. Perspective for Aquaponic Systems: “Omic” Technologies for Microbial Community Analysis

    Munguia-Fragozo, Perla; Alatorre-Jacome, Oscar; Rico-Garcia, Enrique; Torres-Pacheco, Irineo; Cruz-Hernandez, Andres; Ocampo-Velazquez, Rosalia V.; Garcia-Trejo, Juan F.; Guevara-Gonzalez, Ramon G.

    2015-01-01

    Aquaponics is the combined production of aquaculture and hydroponics, connected by a water recirculation system. In this productive system, the microbial community is responsible for carrying out the nutrient dynamics between the components. The nutrimental transformations mainly consist in the transformation of chemical species from toxic compounds into available nutrients. In this particular field, the microbial research, the “Omic” technologies will allow a broader scope of studies about a current microbial profile inside aquaponics community, even in those species that currently are unculturable. This approach can also be useful to understand complex interactions of living components in the system. Until now, the analog studies were made to set up the microbial characterization on recirculation aquaculture systems (RAS). However, microbial community composition of aquaponics is still unknown. “Omic” technologies like metagenomic can help to reveal taxonomic diversity. The perspectives are also to begin the first attempts to sketch the functional diversity inside aquaponic systems and its ecological relationships. The knowledge of the emergent properties inside the microbial community, as well as the understanding of the biosynthesis pathways, can derive in future biotechnological applications. Thus, the aim of this review is to show potential applications of current “Omic” tools to characterize the microbial community in aquaponic systems. PMID:26509157

  9. Perspective for Aquaponic Systems: “Omic” Technologies for Microbial Community Analysis

    Perla Munguia-Fragozo

    2015-01-01

    Full Text Available Aquaponics is the combined production of aquaculture and hydroponics, connected by a water recirculation system. In this productive system, the microbial community is responsible for carrying out the nutrient dynamics between the components. The nutrimental transformations mainly consist in the transformation of chemical species from toxic compounds into available nutrients. In this particular field, the microbial research, the “Omic” technologies will allow a broader scope of studies about a current microbial profile inside aquaponics community, even in those species that currently are unculturable. This approach can also be useful to understand complex interactions of living components in the system. Until now, the analog studies were made to set up the microbial characterization on recirculation aquaculture systems (RAS. However, microbial community composition of aquaponics is still unknown. “Omic” technologies like metagenomic can help to reveal taxonomic diversity. The perspectives are also to begin the first attempts to sketch the functional diversity inside aquaponic systems and its ecological relationships. The knowledge of the emergent properties inside the microbial community, as well as the understanding of the biosynthesis pathways, can derive in future biotechnological applications. Thus, the aim of this review is to show potential applications of current “Omic” tools to characterize the microbial community in aquaponic systems.

  10. An integrated metagenome and -proteome analysis of the microbial community residing in a biogas production plant.

    Ortseifen, Vera; Stolze, Yvonne; Maus, Irena; Sczyrba, Alexander; Bremges, Andreas; Albaum, Stefan P; Jaenicke, Sebastian; Fracowiak, Jochen; Pühler, Alfred; Schlüter, Andreas

    2016-08-10

    To study the metaproteome of a biogas-producing microbial community, fermentation samples were taken from an agricultural biogas plant for microbial cell and protein extraction and corresponding metagenome analyses. Based on metagenome sequence data, taxonomic community profiling was performed to elucidate the composition of bacterial and archaeal sub-communities. The community's cytosolic metaproteome was represented in a 2D-PAGE approach. Metaproteome databases for protein identification were compiled based on the assembled metagenome sequence dataset for the biogas plant analyzed and non-corresponding biogas metagenomes. Protein identification results revealed that the corresponding biogas protein database facilitated the highest identification rate followed by other biogas-specific databases, whereas common public databases yielded insufficient identification rates. Proteins of the biogas microbiome identified as highly abundant were assigned to the pathways involved in methanogenesis, transport and carbon metabolism. Moreover, the integrated metagenome/-proteome approach enabled the examination of genetic-context information for genes encoding identified proteins by studying neighboring genes on the corresponding contig. Exemplarily, this approach led to the identification of a Methanoculleus sp. contig encoding 16 methanogenesis-related gene products, three of which were also detected as abundant proteins within the community's metaproteome. Thus, metagenome contigs provide additional information on the genetic environment of identified abundant proteins.

  11. Analysis of the social network development of a virtual community for Australian intensive care professionals.

    Rolls, Kaye Denise; Hansen, Margaret; Jackson, Debra; Elliott, Doug

    2014-11-01

    Social media platforms can create virtual communities, enabling healthcare professionals to network with a broad range of colleagues and facilitate knowledge exchange. In 2003, an Australian state health department established an intensive care mailing list to address the professional isolation experienced by senior intensive care nurses. This article describes the social network created within this virtual community by examining how the membership profile evolved from 2003 to 2009. A retrospective descriptive design was used. The data source was a deidentified member database. Since 2003, 1340 healthcare professionals subscribed to the virtual community with 78% of these (n = 1042) still members at the end of 2009. The membership profile has evolved from a single-state nurse-specific network to an Australia-wide multidisciplinary and multiorganizational intensive care network. The uptake and retention of membership by intensive care clinicians indicated that they appeared to value involvement in this virtual community. For healthcare organizations, a virtual community may be a communications option for minimizing professional and organizational barriers and promoting knowledge flow. Further research is, however, required to demonstrate a link between these broader social networks, enabling the exchange of knowledge and improved patient outcomes.

  12. Microbial Community Analysis of a Single Chamber Microbial Fuel Cell Using Potato Wastewater

    Zhen Li; Rishika Haynes; Eugene Sato; Malcolm Shields; Yoshiko Fujita; Chikashi Sato

    2014-04-01

    Microbial fuel cells (MFCs) convert chemical energy to electrical energy via bioelectrochemical reactions mediated by microorganisms. We investigated the diversity of the microbial community in an air cathode single chamber MFC that utilized potato-process wastewater as substrate. Terminal Restriction Fragment Length Polymorphism (T-RFLP) results indicated that the bacterial communities on the anode, cathode, control electrode, and MFC bulk fluid were similar, but differed dramatically from that of the anaerobic domestic sludge and potato wastewater inoculum. The 16S rDNA sequencing results showed that microbial species detected on the anode were predominantly within the phyla of Proteobacteria, Firmicutes, and Bacteroidetes. Fluorescent microscopy results indicated that there was a clear enhancement of biofilm formation on the anode. Results of this study could help improve understanding of the complexity of microbial communities and optimize the microbial composition for generating electricity by MFCs that utilize potato wastewater.

  13. Metagenomic analysis suggests modern freshwater microbialites harbor a core and distinct microbial community

    Richard Allen White III

    2016-01-01

    Full Text Available Modern microbialites are complex microbial communities that interface with abiotic factors to form carbonate-rich organosedimentary structures whose ancestors provide the earliest evidence of life. Past studies primarily on marine microbialites have inventoried diverse taxa and metabolic pathways, but it is unclear which of these are members of the microbialite community and which are introduced from adjacent environments. Here we control for these factors by sampling the surrounding water and nearby sediment, in addition to the microbialites and use a metagenomics approach to interrogate the microbial community. Our findings suggest that the Pavilion Lake microbialite community profile, metabolic potential and pathway distributions are distinct from those in the neighboring sediments and water. Based on RefSeq classification, members of the Proteobacteria (e.g alpha and delta classes were the dominant taxa in the microbialites, and possessed novel functional guilds associated with the metabolism of heavy metals, antibiotic resistance, primary alcohol biosynthesis and urea metabolism; the latter may help drive biomineralization. Urea metabolism within Pavilion Lake microbialites is a feature not previously associated in other microbialites. The microbialite communities were also significantly enriched for cyanobacteria and acidobacteria, which likely play an important role in biomineralization. Additional findings suggest that Pavilion Lake microbialites are under viral selection as genes associated with viral infection (e.g CRISPR-Cas, phage shock and phage excision are abundant within the microbialite metagenomes. The morphology of Pavilion Lake microbialites changes dramatically with depth; yet, metagenomic data did not vary significantly by morphology or depth, indicating that microbialite morphology is altered by other factors, perhaps transcriptional differences or abiotic conditions. This work provides a comprehensive metagenomic

  14. Democratic school climate and sense of community in school: a multilevel analysis.

    Vieno, Alessio; Perkins, Douglas D; Smith, Thomas M; Santinello, Massimo

    2005-12-01

    This study examines individual- and school-level predictors of sense of community in school among adolescents. Hierarchical linear modeling was used to examine the relationships between individual (demographics, control and monitoring by parents, and perception of democratic school climate), class, and school characteristics (mean democratic school climate, demographics, activities, school size, public/private governance of the school, and facilities) and students' sense of community in the school. Data were analyzed using a three-level model based on 4,092 10- to 18-year-old students nested within 248 classes (across three grade levels: 6th, 8th, and 10th grade level, where the median age was 11, 13, and 15, respectively) in 134 schools in the Veneto region of northeast Italy. Individual and contextual measures of the perception of a democratic school climate, modeled at the individual, class, and school levels simultaneously, were each significant predictor of school sense of community. More parental monitoring and less parental control were also predictive at the individual level. School-level SES predicted between school variation in sense of community, controlling for individual student SES and other student and school-level predictors. School size, facilities (physical spaces resources), level of interaction of the school with the community, public, or private governance, and number of extracurricular activities offered were all nonsignificant. The study demonstrates significant variation in school sense of community at the student, class, and school levels and the important role played by democratic school practices, such as student participation in making rules and organizing events, freedom of expression, and the perceived fairness of rules and teachers, in determining this variable.

  15. Comparison of bacterial community structures in two systems of a sewage treatment plant using PCR-DGGE analysis

    Abd El-Latif Hesham; Rong Qi; MinYang

    2011-01-01

    The combination of PCR amplification of 16S rRNA genes with denaturing gradient gel electrophoresis (DGGE) analysis was used to reveal the compositions and dynamics of bacterial communities in a sewage treatment plant with two systems,i.e.,an anoxicanaerobic-aerobic system (inverted A2O) and an anaerobic-anoxic-aerobic one (conventional A2O) over a period from February to July 2009,during which both systems experienced serious sludge bulking problems.The DGGE patterns showed that there were many common bands in both systems,suggesting the high similarity of bacterial communities of the two systems.Meanwhile,the moving window correlation analysis showed that the two systems experienced different microbial community structure changes during the period,which might be related with the different situations of the occurrence and disappearance of sludge bulking,as being reflected by sludge volume index (SVI) values.Major bands of DGGE patterns of sludge samples were further sequenced.Phylogenetic affiliation indicated that the majority of the sequences obtained were affiliated with Actinobacteria,Firmicutes,Bacteroidetes/Chlorobi group and α- and β-Proteobacteria.Two sequences showed high similarities to typical filamentous bacteria Microthrix parvicella and Nostocoida limicola I,indicating that these bacterial species have been involved in the sludge bulking problems.

  16. RisaAligner software for aligning fluorescence data between Agilent 2100 Bioanalyzer chips: Application to soil microbial community analysis.

    Navarro, Elisabeth; Fabrègue, Olivier; Scorretti, Riccardo; Reboulet, Jérémy; Simonet, Pascal; Dawson, Lorna; Demanèche, Sandrine

    2015-12-01

    Ribosomal Intergenic Spacer Analysis (RISA) is a high-resolution and highly reproducible fingerprinting technique for discriminating between microbial communities. The community profiles can be visualized using the Agilent 2100 Bioanalyzer. Comparison between fingerprints relies upon precise estimation of all amplified DNA fragment lengths; however, size standard computation can vary between gel runs. For complex samples such as soil microbial communities, discrimination by fragment size is not always sufficient. In such cases, the comparison of whole fluorescence data as a function of time (electrophoregrams) is more appropriate. When electrophoregrams [fluorescence = f (time)] are used, and more than one chip is involved, electrophoregram comparisons are challenging due to experimental variations between chips and the lack of correction by the Agilent software in such situations. Here we present RisaAligner software for analyzing and comparing electrophoregrams from Agilent chips using a nonlinear ladder-alignment algorithm. We demonstrate the robustness and substantial improvement of data analysis by analyzing soil microbial profiles obtained with Agilent DNA 1000 and High Sensitivity chips.

  17. Community Energy: Analysis of Hydrogen Distributed Energy Systems with Photovoltaics for Load Leveling and Vehicle Refueling

    Steward, D.; Zuboy, J.

    2014-10-01

    Energy storage could complement PV electricity generation at the community level. Because PV generation is intermittent, strategies must be implemented to integrate it into the electricity system. Hydrogen and fuel cell technologies offer possible PV integration strategies, including the community-level approaches analyzed in this report: (1) using hydrogen production, storage, and reconversion to electricity to level PV generation and grid loads (reconversion scenario); (2) using hydrogen production and storage to capture peak PV generation and refuel hydrogen fuel cell electric vehicles (FCEVs) (hydrogen fueling scenario); and (3) a comparison scenario using a battery system to store electricity for EV nighttime charging (electric charging scenario).

  18. Community collaborations for farmworker health in New York and Maine: process analysis of two successful interventions.

    Earle-Richardson, Giulia; Sorensen, Julie; Brower, Melissa; Hawkes, Lynae; May, John J

    2009-11-01

    We conducted a process evaluation of 2 successful farmworker community-based participatory research intervention development projects (in Maine and New York State). Participant surveys measured satisfaction with the program process. We used qualitative methods to analyze free-text responses. Respondents indicated high satisfaction levels overall. The main concern was long-distance project coordination. Community-based participatory research programs in which (1) the work team defines the target health issue, (2) agricultural employers are meaningfully included, and (3) interventions are carried through to completion, warrant further study.

  19. Analysis of institutional mechanisms that support community response to impacts of floods in the middle-zambezi river basin, Zimbabwe

    Muhonda, P.; Mabiza, C.; Makurira, H.; Kujinga, K.; Nhapi, I.; Goldin, J.; Mashauri, D. A.

    In recent years, the frequency of occurrence of floods has increased in Southern Africa. An increase in the frequency of extreme events is partly attributed to climate change. Floods negatively impact on livelihoods, especially those classified as poor, mainly by reducing livelihood options and also contributing to reduced crop yields. In response to these climatic events, governments within Southern Africa have formulated policies which try to mitigate the impacts of floods. Floods can be deadly, often occurring at short notice, lasting for short periods, and causing widespread damage to infrastructure. This study analysed institutional mechanisms in Mbire District of Zimbabwe which aim at mitigating the impact of floods. The study used both quantitative (i.e. questionnaires) and qualitative (i.e. key informant interviews, focus group discussions and observations) data collection methods. Secondary data such as policy and legislation documents and operational manuals of organisations that support communities affected by disasters were reviewed. Qualitative data was analysed using the thematic approach and social network analysis using UCINET 6. Quantitative data were analysed using SPSS 19.0. The study found out that there exists institutional framework that has been developed at the national and local level to support communities in the study area in response to the impacts of floods. This is supported by various pieces of legislation that are housed in different government departments. However, the existing institutional framework does not effectively strengthen disaster management mechanisms at the local level. Lack of financial resources and appropriate training and skills to undertake flood management activities reduce the capacity of communities and disaster management organisations to effectively mitigate the impacts of floods. The study also found that there are inadequate hydro-meteorological stations to enable accurate forecasts. Even in those cases

  20. Performance of biological phosphorus removal and characteristics of microbial community in the oxic-settling-anaerobic process by FISH analysis

    Jian-fang WANG; Qing-liang ZHAO; Wen-biao JIN; Shi-jie YOU; Jin-na ZHANG

    2008-01-01

    Performance of biological phosphorus removal in the oxic-settling-anaerobic (OSA) process was investigated. Cell staining and fluorescent in situ hybridization (FISH) were used to analyze characteristics and microbial community of sludge.Experimental results showed that phosphorus removal efficiency was near 60% and the amount of biological phosphorus accumulation in aerobic sludge of the OSA system was up to 26.9 mg/g. Biological phosphorus removal efficiency was partially inhibited by carbon sources in the continuous OSA system. Contrasted to the OSA system, biological phosphorus removal efficiency was enhanced by 14% and the average total phosphorus (TP) contents of aerobic sludge were increased by 0.36 mg/g when sufficient carbon sources were supplied in batch experiments. Staining methods indicated that about 35% of microorganisms had typical characteristics of phosphorus accumulating organisms (PAOs). FISH analysis demonstrated that PAOMIX-binding bacteria were predominant microbial communities in the OSA system, which accounted for around 28% of total bacteria.

  1. A longitudinal process analysis of mother-child emotional relationships in a rural Appalachian European American community.

    Bornstein, Marc H; Putnick, Diane L; Suwalsky, Joan T D

    2012-09-01

    This prospective longitudinal study examines emotional relationships in 58 Appalachian mother-child dyads observed at home at 5 and 20 months. Between infancy and toddlerhood, 3 of 4 dimensions of dyadic emotional relationships were stable, and three remained continuous in their mean level. Increasing maternal age was associated with greater maternal sensitivity and structuring and with more responsive and involving children. Marital status and father presence in the home as well as maternal openness, parenting knowledge, investment, and satisfaction accounted for effects of maternal age on dyadic emotional relationships. This longitudinal process analysis provides unique insights into temporal dynamics of mother-child emotional relationships and their determinants in an underserved and underresearched US community. Implications for community-specific interventions are discussed.

  2. A guide to statistical analysis in microbial ecology: a community-focused, living review of multivariate data analyses.

    Buttigieg, Pier Luigi; Ramette, Alban

    2014-12-01

    The application of multivariate statistical analyses has become a consistent feature in microbial ecology. However, many microbial ecologists are still in the process of developing a deep understanding of these methods and appreciating their limitations. As a consequence, staying abreast of progress and debate in this arena poses an additional challenge to many microbial ecologists. To address these issues, we present the GUide to STatistical Analysis in Microbial Ecology (GUSTA ME): a dynamic, web-based resource providing accessible descriptions of numerous multivariate techniques relevant to microbial ecologists. A combination of interactive elements allows users to discover and navigate between methods relevant to their needs and examine how they have been used by others in the field. We have designed GUSTA ME to become a community-led and -curated service, which we hope will provide a common reference and forum to discuss and disseminate analytical techniques relevant to the microbial ecology community.

  3. Integration Of Spa Tio- Temporal Analysis Of Rainfall And Community Information System To Reduce Landslide Risk In Indonesia

    Sudibyakto .

    2013-07-01

    Full Text Available Indonesia is vulnerable to many type of disasters including natural and anthropogenic disasters. Indonesian seasonal rainfall also shows inter annual variation. Sediment-related disaster such as landslide is the mostji-equent disaster occurred and significantly was impacted to natural, human. and social environment. Although. many disaster mitigation e.Oorts have been conducted to reduce disaster risk there are still urgently need to improve the early 1varning .\\~ystem by communicating the risk into local community. Integration qf spatialtemporal analysis qf rainfall and disaster management information !o~vstem would be required to improve the better disaster management in Indonesia. Application of Disaster A1anagement Information System in the study area will presented including evacuation map that used by the local community.

  4. Analysis of denitrifier community in a bioaugmented sequencing batch reactor for the treatment of coking wastewater containing pyridine and quinoline

    Bai, Yaohui; Xing, Rui; Wen, Donghui; Tang, Xiaoyan [Peking Univ., Beijing (CN). Key Lab. of Water and Sediment Sciences (Ministry of Education); Sun, Qinghua [Peking Univ., Beijing (CN). Key Lab. of Water and Sediment Sciences (Ministry of Education); Chinese Center for Disease Control and Prevention, Beijing (China). Inst. of Environmental Health and Related Product Safety

    2011-05-15

    The denitrifier community and associated nitrate and nitrite reduction in the bioaugmented and general sequencing batch reactors (SBRs) during the treatment of coking wastewater containing pyridine and quinoline were investigated. The efficiency and stability of nitrate and nitrite reduction in SBR was considerably improved after inoculation with four pyridine- or quinoline-degrading bacterial strains (including three denitrifying strains). Terminal restriction fragment length polymorphism (T-RFLP) based on the nosZ gene revealed that the structures of the denitrifier communities in bioaugmented and non-bioaugmented reactors were distinct and varied during the course of the experiment. Bioaugmentation protected indigenous denitrifiers from disruptions caused by pyridine and quinoline. Clone library analysis showed that one of the added denitrifiers comprised approximately 6% of the denitrifier population in the bioaugmented sludge. (orig.)

  5. An analysis of topic areas and topic trends in the Community Mental Health Journal from 1965 through 1977.

    Lounsbury, J W; Roisum, K G; Pokorny, L; Sills, A; Meissen, G J

    1979-01-01

    A content analysis of all (N = 604) published articles in the Community Mental Health Journal from 1965 through 1977 was performed (a) to provide a cross-sectional view of the community mental health field, and (b) to identify topic trends over time. Sixty-one content categories were used to classify topic areas. Results revealed major and growing emphases on organizing for the delivery and measuring of the effects of mental health service systems. Topics found to be increasing in relative frequency over time included training, measurement and research methodology, and intervention; those decreasing included planning and needs assessment, therapy, and suicide. Topic areas were compared with key characteristics of the field. Topic trends were interpreted in terms of open systems theory.

  6. MARRIAGE RITUAL TEXT OF BALINESE TRADITIONAL COMMUNITY: AN ANALYSIS OF FUNCTIONAL SYSTEMIC LINGUISTICS

    Putu Sutama

    2012-11-01

    Full Text Available The Marriage Ritual Text of Balinese Traditional Community (Teks Ritual‘Pewiwahan’ Masyarakat Adat Bali, hereon abbreviated to TRPMAB in this dissertationis analyzed in the perspective of linguistic studies using the functional systemic linguistictheory. TRPMAB is a dialogic text containing a discussion, and is terminologicallytermed as a conversational text. It refers to the use of Balinese language (Bahasa Bali,hereon abbreviated to BB in a marriage ritual. There are two inseparable systems in it;they are BB system and social system, which are widely termed as cultural system.The method employed in this study is field method, meaning that the researcherwent directly to the field or to the location where TRPMAP took place. The researcherdirectly took part as both the active and passive participant. In this way, the researchcould observe TRPMAB directly.The population of the study includes all TPRB in Bali. Considering that thepopulation is too wide, then samples were taken to represent all the population. Thesamples total 10 which were obtained from the biggest marriage processions in Bali. Outof the 10 samples, 6 units of text were selected as the corpus of the study. The selectionwas made based on particular criteria including quality. It is this corpus which wasanalyzed to support and examine the hypothesis related to the text analyzed.The analysis of TRPMAB includes: the structure of the texts, the mood, thetransitivity, the theme-rheme and the logical relationship between the clause and theideology. The findings are as follows:(1 TRPMAB is a text which has a number of structural dimensions such as (acultural structure, (b macro structure, that is, the structure related to the situationalcontext made up of field, tenor and mode, (c micro structure, (d structure of meaning,that is, the structure related to the sequence of meanings between the participants withinthe dialogue, and (e the texture, that is, the intact successive relationship

  7. Land Cover Change Community-based Processing and Analysis System (LC-ComPS): Lessons Learned from Technology Infusion

    Masek, J.; Rao, A.; Gao, F.; Davis, P.; Jackson, G.; Huang, C.; Weinstein, B.

    2008-12-01

    The Land Cover Change Community-based Processing and Analysis System (LC-ComPS) combines grid technology, existing science modules, and dynamic workflows to enable users to complete advanced land data processing on data available from local and distributed archives. Changes in land cover represent a direct link between human activities and the global environment, and in turn affect Earth's climate. Thus characterizing land cover change has become a major goal for Earth observation science. Many science algorithms exist to generate new products (e.g., surface reflectance, change detection) used to study land cover change. The overall objective of the LC-ComPS is to release a set of tools and services to the land science community that can be implemented as a flexible LC-ComPS to produce surface reflectance and land-cover change information with ground resolution on the order of Landsat-class instruments. This package includes software modules for pre-processing Landsat-type satellite imagery (calibration, atmospheric correction, orthorectification, precision registration, BRDF correction) for performing land-cover change analysis and includes pre-built workflow chains to automatically generate surface reflectance and land-cover change products based on user input. In order to meet the project objectives, the team created the infrastructure (i.e., client-server system with graphical and machine interfaces) to expand the use of these existing science algorithm capabilities in a community with distributed, large data archives and processing centers. Because of the distributed nature of the user community, grid technology was chosen to unite the dispersed community resources. At that time, grid computing was not used consistently and operationally within the Earth science research community. Therefore, there was a learning curve to configure and implement the underlying public key infrastructure (PKI) interfaces, required for the user authentication, secure file

  8. Understanding Household Connectivity and Resilience in Marginal Rural Communities through Social Network Analysis in the Village of Habu, Botswana

    Grenville D. Barnes

    2012-12-01

    Full Text Available Adaptability is emerging as a key issue not only in the climate change debate but in the general area of sustainable development. In this context, we examine the link between household resilience and connectivity in a rural community in Botswana. We see resilience and vulnerability as the positive and negative dimensions of adaptability. Poor, marginal rural communities confronted with the vagaries of climate change, will need to become more resilient if they are to survive and thrive. We define resilience as the capacity of a social–ecological system to cope with shocks such as droughts or economic crises without changing its fundamental identity. We make use of three different indices of household resilience: livelihood diversity, wealth, and a comprehensive resilience index based on a combination of human, financial, physical, social, and natural capital. Then, we measure the social connectivity of households through a whole network approach in social network analysis, using two measures of network centrality (degree centrality and betweenness. We hypothesize that households with greater social connectivity have greater resilience, and analyze a community in rural Botswana to uncover how different households make use of social networks to deal with shocks such as human illness and death, crop damage, and livestock disease. We surveyed the entire community of Habu using a structured questionnaire that focused on livelihood strategies and social networks. We found that gender, age of household head, and household size were positively correlated with social connectivity. Our analysis indicates that those households that are more socially networked are likely to have a wider range of livelihood strategies, greater levels of other forms of social capital, and greater overall capital. Therefore, they are more resilient.

  9. Influence of commonly used primer systems on automated ribosomal intergenic spacer analysis of bacterial communities in environmental samples.

    Witoon Purahong

    Full Text Available Due to the high diversity of bacteria in many ecosystems, their slow generation times, specific but mostly unknown nutrient requirements and syntrophic interactions, isolation based approaches in microbial ecology mostly fail to describe microbial community structure. Thus, cultivation independent techniques, which rely on directly extracted nucleic acids from the environment, are a well-used alternative. For example, bacterial automated ribosomal intergenic spacer analysis (B-ARISA is one of the widely used methods for fingerprinting bacterial communities after PCR-based amplification of selected regions of the operon coding for rRNA genes using community DNA. However, B-ARISA alone does not provide any taxonomic information and the results may be severely biased in relation to the primer set selection. Furthermore, amplified DNA stemming from mitochondrial or chloroplast templates might strongly bias the obtained fingerprints. In this study, we determined the applicability of three different B-ARISA primer sets to the study of bacterial communities. The results from in silico analysis harnessing publicly available sequence databases showed that all three primer sets tested are specific to bacteria but only two primers sets assure high bacterial taxa coverage (1406f/23Sr and ITSF/ITSReub. Considering the study of bacteria in a plant interface, the primer set ITSF/ITSReub was found to amplify (in silico sequences of some important crop species such as Sorghum bicolor and Zea mays. Bacterial genera and plant species potentially amplified by different primer sets are given. These data were confirmed when DNA extracted from soil and plant samples were analyzed. The presented information could be useful when interpreting existing B-ARISA results and planning B-ARISA experiments, especially when plant DNA can be expected.

  10. Pyrosequence analysis of bacterial communities in aerobic bioreactors treating polycyclic aromatic hydrocarbon-contaminated soil.

    Singleton, David R; Richardson, Stephen D; Aitken, Michael D

    2011-11-01

    Two aerobic, lab-scale, slurry-phase bioreactors were used to examine the biodegradation of polycyclic aromatic hydrocarbons (PAHs) in contaminated soil and the associated bacterial communities. The two bioreactors were operated under semi-continuous (draw-and-fill) conditions at a residence time of 35 days, but one was fed weekly and the other monthly. Most of the quantified PAHs, including high-molecular-weight compounds, were removed to a greater extent in the weekly-fed bioreactor, which achieved total PAH removal of 76%. Molecular analyses, including pyrosequencing of 16S rRNA genes, revealed significant shifts in the soil bacterial communities after introduction to the bioreactors and differences in the abundance and types of bacteria in each of the bioreactors. The weekly-fed bioreactor displayed a more stable bacterial community with gradual changes over time, whereas the monthly-fed bioreactor community was less consistent and may have been more strongly influenced by the influx of untreated soil during feeding. Phylogenetic groups containing known PAH-degrading bacteria previously identified through stable-isotope probing of the untreated soil were differentially affected by bioreactor conditions. Sequences from members of the Acidovorax and Sphingomonas genera, as well as the uncultivated "Pyrene Group 2" were abundant in the bioreactors. However, the relative abundances of sequences from the Pseudomonas, Sphingobium, and Pseudoxanthomonas genera, as well as from a group of unclassified anthracene degraders, were much lower in the bioreactors compared to the untreated soil.

  11. Soil-specific limitations for access and analysis of soil microbial communities by metagenomics

    Lombard, Nathalie; Prestat, Emmanuel; van Elsas, Jan Dirk; Simonet, Pascal

    2011-01-01

    Metagenomics approaches represent an important way to acquire information on the microbial communities present in complex environments like soil. However, to what extent do these approaches provide us with a true picture of soil microbial diversity? Soil is a challenging environment to work with. It

  12. Comparative analysis of the composition of intestinal bacterial communities in Dastarcus helophoroides fed different diets.

    Wang, Wei-Wei; He, Cai; Cui, Jun; Wang, Hai-Dong; Li, Meng-Lou

    2014-01-01

    The diversity of the intestinal bacterial communities in Dastarcus helophoroides (Fairmaire) (Coleoptera: Bothrideridae) larvae and adults was assayed by PCR-DGGE to determine whether different artificial diets could influence these bacterial communities. Two diets were used for feeding the larvae and four for the adults. Escherichia, Desemzia, Staphylococcus, Asticcacaulis, Cellvibrio, Aurantimonas, and Planomicrobium were isolated from the gut of the adults, with Escherichia and Staphylococcus being the main bacterial communities, and the quantities of intestinal bacterial were different in the adults fed different diets. Specifically, the amount of intestinal bacteria from the adults fed different diets had the following ranking according to the major component of the diet: ant powder > darkling beetle pupa powder > cricket powder > silkworm pupa powder. Escherichia, Bacillus, Staphylococcus, Kurthia, Planococcaceae, Ralstonia, Leptothrix, Acinetobacter, and Pseudomonas were isolated from the gut of the larvae. The quantity of intestinal bacteria from the larvae fed the darkling beetle pupae was greater than that from the larvae fed other artificial diets. This study, for the first time, investigated the effect of artificial diets on the bacterial community and the intestinal microbial diversity of D. helophoroides.

  13. One-year reciprocal relationship between community participation and mental wellbeing in Australia: a panel analysis.

    Ding, Ning; Berry, Helen L; O'Brien, Léan V

    2015-03-01

    The links between social capital and mental wellbeing are established but the direction of the social capital-wellbeing relationship is rarely systematically examined. This omission undermines the validity of social capital as a basis for health interventions. The aim of this paper was to explore the short-term (one-year) reciprocal relationship between community participation - an important component of social capital - and mental wellbeing. We used nationally representative Household, Income and Labour Dynamics in Australia (HILDA) Survey data, 2005-11. The HILDA Survey is an annual cohort study from which was extracted a sub-sample of panel data (the same people participating across multiple waves) enabling us to use fixed effects regression methods to model the longitudinal association of mental health and participation controlling for individual heterogeneity. The results showed that better mental wellbeing in one year was generally related to more community participation the next year, while greater past community participation was linked to better mental wellbeing the next year independent of (i) initial mental wellbeing, (ii) multiple potentially confounding factors and (iii) unobserved and time-constant heterogeneity. Political participation was marginally related to worse mental health in both directions. The results also showed that the association between community participation and mental wellbeing the next year is weaker for those with poor initial wellbeing than for initially healthier respondents. Our findings may inform the trial and scientific evaluation of programs aimed at increasing informal social connectedness and civic engagement to promote mental wellbeing.

  14. Financial Aid Tipping Points: An Analysis of Aid and Academic Achievement at a California Community College

    Coria, Elizabeth; Hoffman, John L.

    2016-01-01

    The purpose of this study was to explore relationships between financial aid awards and measures of student academic achievement. Financial aid and academic records for 11,956 students attending an urban California community college were examined and analyzed using simultaneous linear regression and two-way factorial ANOVAs. Findings revealed a…

  15. Continuing Care Retirement Communities: An Analysis of Financial Viability and Health Care Coverage.

    Ruchlin, Hirsch S.

    1988-01-01

    Calculated financial ratios for 109 Continuing Care Retirement Communities (CCRCs). Noted problems with regard to asset productivity, profitability, and equity levels. Found that a risk-spreading charge structure for financing health care needs appeared to exist among CCRCs providing a full-care contract. (Author/ABL)

  16. Typologizing School-Community Partnerships: A Framework for Analysis and Action

    Valli, Linda; Stefanski, Amanda; Jacobson, Reuben

    2016-01-01

    School-community partnerships are currently in the forefront of place-based urban reform efforts. But the literature on these partnerships indicates a variety of models that require different commitments and resources. Through a close review of the literature, we developed a typology of four partnership categories organized from the least to the…

  17. Critiquing the Role of the Community College in Criminal Justice Education: Curriculum Trends and Analysis.

    Meadows, Robert J.

    Based upon a literature review and interviews with selected criminal justice educators, this critique of criminal justice or police education attempts to explore some of the criticisms being leveled against community college criminal justice education and certain issues and trends related to the field that are becoming evident. To place this…

  18. Microbial community analysis of a coastal salt marsh affected by the Deepwater Horizon oil spill.

    Melanie J Beazley

    Full Text Available Coastal salt marshes are highly sensitive wetland ecosystems that can sustain long-term impacts from anthropogenic events such as oil spills. In this study, we examined the microbial communities of a Gulf of Mexico coastal salt marsh during and after the influx of petroleum hydrocarbons following the Deepwater Horizon oil spill. Total hydrocarbon concentrations in salt marsh sediments were highest in June and July 2010 and decreased in September 2010. Coupled PhyloChip and GeoChip microarray analyses demonstrated that the microbial community structure and function of the extant salt marsh hydrocarbon-degrading microbial populations changed significantly during the study. The relative richness and abundance of phyla containing previously described hydrocarbon-degrading bacteria (Proteobacteria, Bacteroidetes, and Actinobacteria increased in hydrocarbon-contaminated sediments and then decreased once hydrocarbons were below detection. Firmicutes, however, continued to increase in relative richness and abundance after hydrocarbon concentrations were below detection. Functional genes involved in hydrocarbon degradation were enriched in hydrocarbon-contaminated sediments then declined significantly (p<0.05 once hydrocarbon concentrations decreased. A greater decrease in hydrocarbon concentrations among marsh grass sediments compared to inlet sediments (lacking marsh grass suggests that the marsh rhizosphere microbial communities could also be contributing to hydrocarbon degradation. The results of this study provide a comprehensive view of microbial community structural and functional dynamics within perturbed salt marsh ecosystems.

  19. Math Readiness of Texas Community College Developmental Education Students: A Multiyear Statewide Analysis

    Abraham, Reni A.; Slate, John R.; Saxon, D. Patrick; Barnes, Wally

    2014-01-01

    In this investigation, we examined the college readiness in math of Texas community college students using archival data from the Texas Higher Education Coordinating Board. Data analyzed were the rate of all first-time in college (FTIC) developmental education students who scored below the Texas college readiness standards in math and the rates of…

  20. The formation of community-based organizations : an analysis of a quasi-experiment in Zimbabwe

    Barr, A.; Dekker, M.; Fafchamps, M.

    2015-01-01

    Previous analyses of the formation and composition of community-based organizations (CBOs) have used cross section data. So, causal inference has been compromised. We obviate this problem by using data from a quasi-experiment in which villages were formed by government officials selecting and cluste

  1. mdRNA-Seq analysis of marine microbial communities from the northern Red Sea

    Hou, Shengwei; Pfreundt, Ulrike; Miller, Dan; Berman-Frank, Ilana; Hess, Wolfgang R.

    2016-01-01

    Metatranscriptomic differential RNA-Seq (mdRNA-Seq) identifies the suite of active transcriptional start sites at single-nucleotide resolution through enrichment of primary transcript 5′ ends. Here we analyzed the microbial community at 45 m depth at Station A in the northern Gulf of Aqaba, Red Sea, during 500 m deep mixing in February 2012 using mdRNA-Seq and a parallel classical RNA-Seq approach. We identified promoters active in situ for five different pico-planktonic genera (the SAR11 clade of Alphaproteobacteria, Synechococcus of Cyanobacteria, Euryarchaeota, Thaumarchaeota, and Micromonas as an example for picoeukaryotic algae), showing the applicability of this approach to highly diverse microbial communities. 16S rDNA quantification revealed that 24% of the analyzed community were group II marine Euryarchaeota in which we identified a highly abundant non-coding RNA, Tan1, and detected very high expression of genes encoding intrinsically disordered proteins, as well as enzymes for the synthesis of specific B vitamins, extracellular peptidases, carbohydrate-active enzymes, and transport systems. These results highlight previously unknown functions of Euryarchaeota with community-wide relevance. The complementation of metatranscriptomic studies with mdRNA-Seq provides substantial additional information regarding transcriptional start sites, promoter activities, and the identification of non-coding RNAs. PMID:27759035

  2. Community analysis of a full-scale anaerobic bioreactor treating paper mill wastewater

    Roest, C.; Heilig, G.H.J.; Smidt, H.; Vos, de W.M.; Stams, A.J.M.; Akkermans, A.D.L.

    2005-01-01

    To get insight into the microbial community of an Upflow Anaerobic Sludge Blanket reactor treating paper mill wastewater, conventional microbiological methods were combined with 16S rRNA gene analyses. Particular attention was paid to microorganisms able to degrade propionate or butyrate in the pres

  3. Analysis of Community Practice Clinical Decision-Making Skills in Pharmacy Students.

    Greer, Marianne L.; Kirk, Kenneth W.

    1988-01-01

    A computerized, simulation-based instrument, consisting of four community practice clinical scenarios, collected information-searching data and the students' decisions. The appropriateness of the decisions, assessed by three clinical judges, and the focus of information search, based on the computer-collected process data, were the dependent…

  4. Community Dental Health Promotion for Children: Integrating Applied Behavior Analysis and Public Health.

    Kramer, Kathryn D.; Geller, E. Scott

    1987-01-01

    The article examines community dental health promotion for children in terms of factors impacting children's dental health (water fluoridation, dental health education, behavior change strategies, use of dental services, and dental phobias). Proposed is a large scale behavior change approach to public dental health which integrates applied…

  5. Community analysis of arbuscular mycorrhizal fungi associated with Ammophila arenaria in Dutch coastal sand dunes

    Kowalchuk, G.A.; De Souza, F.A.; Van Veen, J.A.

    2002-01-01

    A polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) approach for the detection and characterization of arbuscular mycorrhizal fungi (AMF) 18S ribosomal DNA (rDNA) was developed and applied to the study of AMF communities associated with the main sand-stabilizing plant spec

  6. Internationalization Efforts in United States Community Colleges: A Comparative Analysis of Urban, Suburban, and Rural Institutions

    Harder, Natalie J.

    2011-01-01

    With community colleges educating up to one-half of all U.S. undergraduates, more focus on internationalization is warranted in order to ensure student competitiveness in today's global labor pool. This ex post facto study of 2006 survey data from the American Council on Education (ACE) found a low level of internationalization occurring at most…

  7. Analysis of the Cost of Training Residents in a Community Health Center.

    Jones, Timothy F.; And Others

    1995-01-01

    The costs of outpatient training for medical residents in a community health center (CHC) are analyzed, based on a family practice residency of one medical school. The model used a computer spreadsheet program to determine the financial impact of the program on the CHC. Sensitivity analyses determined the effects of changing productivity, nursing…

  8. Hierarchical spatial point process analysis for a plant community with high biodiversity

    Illian, Janine B.; Møller, Jesper; Waagepetersen, Rasmus

    2009-01-01

    A complex multivariate spatial point pattern of a plant community with high biodiversity is modelled using a hierarchical multivariate point process model. In the model, interactions between plants with different post-fire regeneration strategies are of key interest. We consider initially a maximum...

  9. Spatial point process analysis for a plant community with high biodiversity

    Illian, Janine; Møller, Jesper; Waagepetersen, Rasmus Plenge

    A complex multivariate spatial point pattern for a plant community with high biodiversity is modelled using a hierarchical multivariate point process model. In the model, interactions between plants with different post-fire regeneration strategies are of key interest. We consider initially...

  10. Descriptive analysis of individual and community factors among African American youths in urban public housing.

    Nebbitt, Von E; Williams, James Herbert; Lombe, Margaret; McCoy, Henrika; Stephens, Jennifer

    2014-07-01

    African American adolescents are disproportionately represented in urban public housing developments. These neighborhoods are generally characterized by high rates of poverty, crime, violence, and disorganization. Although evidence is emerging on youths in these communities, little is known about their depressive symptoms, perceived efficacy, or frequency of substance use and sex-risk behavior. Further, even less is known about their exposure to community and household violence, their parents' behavior, or their sense of connection to their communities. Using a sample of 782 African American adolescents living in public housing neighborhoods located in four large U.S. cities, this article attempts to rectify the observed gap in knowledge by presenting a descriptive overview of their self-reported depressive symptoms; self-efficacy; frequencies of delinquent and sexual-risk behavior; and alcohol, tobacco, and other drug use. The self-reported ratings of their parents' behavior as well as their exposure to community and household violence are presented. Analytic procedures include descriptive statistics and mean comparisons between genders and across research cities. Results suggest several differences between genders and across research sites. However, results are not very different from national data. Implications for social work practice are discussed.

  11. An Analysis of an Inflammatory Bowel Disease Practise in an Urban Community Hospital

    David Adam

    2000-01-01

    Full Text Available OBJECTIVES: To review an individual community gastroenterologist’s experience with inflammatory bowel disease (IBD. The aspects studied were distribution of disease, need for hospital admission, immunosuppressants, systemic steroids, and surgery and its indications. The incidence of cancer was also reviewed.

  12. Implications of the "My School" Website for Disadvantaged Communities: A Bourdieuian Analysis

    Mills, Carmen

    2015-01-01

    Drawing on the theoretical constructs of Pierre Bourdieu, this article explores implications of the Australian "My School" website for schools located in disadvantaged communities. These implications flow from the legitimisation of certain cultural practices through the hidden linkages between scholastic aptitude and cultural heritage…

  13. Mangrove community in an abandoned brick kiln: A structural and association analysis

    Sumit Manna

    2012-03-01

    Full Text Available Background: The presence of brick kiln along the Hoogly rever sites of lower Bengal is very usual and this phenomenon is not only restricted to India alone but also to the other south Asian countries. The abandoned brick Kiln are important habitat for the formation of mangrove community due to tidal action, loose silty substratum and less anthropogenic interference. In this context, the aim of the present study is to visualize how the structural and association pattern regulate the community dynamics of a mangrove ecosystem. Materials and Methods: The entire study area was divided into 37 units (Quadrats of 27.31 sq m. Structural parameters like density, relative density, abundance, relative abundance, frequency, relative basal area were measured based on vegetation map, prepared through satellite image and ground truthing. Association indices (Ochiai, Dice and Jaccard were measured based on 2X2 contingency/species association table. Results: Out of 10 species under 10 genera and 9 families found in the present habitat, Sonneratia caseolaris is the only mangrove tree species with 155 individuals along with other mangrove associates like Cryptocoryne ciliata, Crinum viviparum, Acanthus ilicifolius and Derris scandens. The high importance value index of Sonneratia caseolaris, Cryptocoryne ciliata, and Crinum viviparum indicated their significant role in community formation. The strong positive association of these 3 species also suggests to help in developing community in stressed environment. Conclusion: Identification of such potential mangrove habitat and study of their community dynamics would be helpful to find out the nature of mangrove establishment for future afforestation programme of threatened mangrove species.

  14. Using Terminal Restriction Fragment Length Polymorphism (T-RFLP) Analysis to Assess Microbial Community Structure in Compost Systems

    Tiquia, Sonia M.

    Terminal restriction fragment length polymorphism (T-RFLP) analysis of PCR-amplified genes is a widely used fingerprinting technique in composting systems. This analysis is based on the restriction endonuclease digestion of fluorescently end-labeled PCR products. The digested product is mixed with a DNA size standard, itself labeled with a distinct fluorescent dye, and the fragments are then separated by capillary or gel electrophoresis using an automated sequencer. Upon analysis, only the terminal end-labeled restriction fragments are detected. An electropherogram is produced, which shows a profile of compost microbial community as a series of peaks of varying height. This technique has also been effectively used in the exploration of complex microbial environments and in the study of bacterial, archaeal, and eukaryal populations in natural habitats.

  15. An Analysis of the Influential Factors in Community Participation of Settlers from Migrant Communities%移民社区居民社区参与影响因素分析

    于波

    2012-01-01

    移民社区同传统社区在形成动力、社区建设模式等方面都存在着差异,这就导致移民社区居民在社区参与中产生了同传统社区居民不同的行动策略和特点。通过对移民社区居民的参与意愿、参与能力、参与内容和参与的制度平台进行考察,可以看到当前移民社区居民社区参与状况的特点,在此基础上,从社区意识、社会资本、社区产生动力以及社区参与的内容和方式四个维度对影响社区居民社区参与状况的主要因素进行了分析,提出改善移民社区居民参与状况的对策。%Disparities that the migrant communities manifest in formation dynamics and mode of community construction and development usually lead to different action strategies and behavioral characteristics on the part of the resettled population groups as compared with those of traditional community groups.A thorough investigation into the participation willingness,participation ability,participation content and the institutionalized platform for participation demonstrated on the part of migrant community groups will help us gain an insight into the overall situation and characteristics of community participation of settlers from migrant communities.Based on these,an analysis of the main factors that influence the community participation of community members is conducted from four dimensions,namely,community consciousness,social capital,community incentives,as well as the content and mode of community participation.Finally,recommendations are proposed regarding the improvement of community participation in migrant communities.

  16. Community Evolution

    Bródka, Piotr; Kazienko, Przemysław

    2016-01-01

    The continuous interest in the social network area contributes to the fast development of this field. The new possibilities of obtaining and storing data facilitate deeper analysis of the entire social network, extracted social groups and single individuals as well. One of the most interesting research topic is the network dynamics and dynamics of social groups in particular, it means analysis of group evolution over time. It is the natural step forward after social community extraction. Having communities extracted, appropriate knowledge and methods for dynamic analysis may be applied in order to identify changes as well as to predict the future of all or some selected groups. Furthermore, knowing the most probably change of a given group some additional steps may be performed in order to change this predicted future according to specific needs. Such ability would be a powerful tool in the hands of human resource managers, personnel recruitment, marketing, telecommunication companies, etc.

  17. High-throughput analysis of ammonia oxidiser community composition via a novel, amoA-based functional gene array.

    Guy C J Abell

    Full Text Available Advances in microbial ecology research are more often than not limited by the capabilities of available methodologies. Aerobic autotrophic nitrification is one of the most important and well studied microbiological processes in terrestrial and aquatic ecosystems. We have developed and validated a microbial diagnostic microarray based on the ammonia-monooxygenase subunit A (amoA gene, enabling the in-depth analysis of the community structure of bacterial and archaeal ammonia oxidisers. The amoA microarray has been successfully applied to analyse nitrifier diversity in marine, estuarine, soil and wastewater treatment plant environments. The microarray has moderate costs for labour and consumables and enables the analysis of hundreds of environmental DNA or RNA samples per week per person. The array has been thoroughly validated with a range of individual and complex targets (amoA clones and environmental samples, respectively, combined with parallel analysis using traditional sequencing methods. The moderate cost and high throughput of the microarray makes it possible to adequately address broader questions of the ecology of microbial ammonia oxidation requiring high sample numbers and high resolution of the community composition.

  18. CoryneRegNet 6.0--Updated database content, new analysis methods and novel features focusing on community demands.

    Pauling, Josch; Röttger, Richard; Tauch, Andreas; Azevedo, Vasco; Baumbach, Jan

    2012-01-01

    Post-genomic analysis techniques such as next-generation sequencing have produced vast amounts of data about micro organisms including genetic sequences, their functional annotations and gene regulatory interactions. The latter are genetic mechanisms that control a cell's characteristics, for instance, pathogenicity as well as survival and reproduction strategies. CoryneRegNet is the reference database and analysis platform for corynebacterial gene regulatory networks. In this article we introduce the updated version 6.0 of CoryneRegNet and describe the updated database content which includes, 6352 corynebacterial regulatory interactions compared with 4928 interactions in release 5.0 and 3235 regulations in release 4.0, respectively. We also demonstrate how we support the community by integrating analysis and visualization features for transiently imported custom data, such as gene regulatory interactions. Furthermore, with release 6.0, we provide easy-to-use functions that allow the user to submit data for persistent storage with the CoryneRegNet database. Thus, it offers important options to its users in terms of community demands. CoryneRegNet is publicly available at http://www.coryneregnet.de.

  19. Analysis of lipophilic pigments from a phototrophic microbial mat community by high performance liquid chromatography

    Palmisano, A. C.; Cronin, S. E.; Des Marais, D. J.

    1988-01-01

    As assay for lipophilic pigments in phototrophic microbial mat communities using reverse phase-high performance liquid chromatography was developed which allows the separation of 15 carotenoids and chloropigments in a single 30 min program. Lipophilic pigments in a laminated mat from a commercial salina near Laguna Guerrero Negro, Baja California Sur, Mexico reflected their source organisms. Myxoxanthophyll, echinenone, canthaxanthin, and zeaxanthin were derived from cyanobacteria; chlorophyll c, and fucoxanthin from diatoms; chlorophyll a from cyanobacteria and diatoms; bacteriochlorophylls a and c, bacteriophaeophytin a, and gamma-carotene from Chloroflexus spp.; and beta-carotene from a variety of phototrophs. Sensitivity of detection was 0.6-6.1 ng for carotenoids and 1.7-12 ng for most chloropigments. This assay represents a significant improvement over previous analyses of lipophilic pigments in microbial mats and promises to have a wider application to other types of phototrophic communities.

  20. Community Detecting and Feature Analysis in Real Directed Weighted Social Networks

    Yao Liu

    2013-06-01

    Full Text Available Real social networks usually have some structural features of the complex networks, such as community structure, the scale-free degree distribution, clustering, "small world" network, dynamic evolution and so on. A new community detecting algorithm for directed and weighted social networks is proposed in this paper. Due to the use of more reference information, the accuracy of the algorithm is better than some of the typical detecting algorithms. And because of the use of heap structure and multi-task modular architecture, the algorithm also got a high computational efficiency than other algorithms. The effectiveness and efficiency of the algorithm is validated by experiments on real social networks. Based on the theories and models of complex networks, the features of the real large social networks are analyzed.

  1. [Analysis of microbial community structure in lactic acid fermentation from kitchen waste].

    Liu, Jian-Guo; Wang, Qun-Hui; Wang, Shuang; Sun, Xiao-Hong; Qiu, Tian-Lei; Li, Huan

    2012-09-01

    In this study, PCR-DGGE was used to analyze the microbial community structure in lactic acid fermentation from kitchen waste. The results showed that with Lactobacillus amylophilus inoculation, both the microbial diversity and lactic acid production in the open fermentation system were higher than those in the sterilized fermentation system. These results indicated that the microbial diversity and the lactic acid production have great correlation in the kitchen waste fermentation system. Through analyzing the sequence of some DNA bands excised from the DGGE gel, it showed that in addition to the inoculation of Lactobacillus amylophilus there were some indigenous lactic acid bacteria, such as Lactobacillus sp., Lactobacillus casei, Lactobacillus plantarum and indigenous hydrolytic bacteria, such as Pseudomonas sp.. These indigenous bacteria can help to promote lactic acid production. PCR-DGGE is feasible for analyzing the dynamic changes of microbial community structure in kitchen waste with complicated composition.

  2. Searching for feminism: an analysis of community psychology literature relevant to women's concerns.

    Angelique, H L; Culley, M R

    2000-12-01

    Articles published in both the American Journal of Community Psychology and Journal of Community Psychology, from their inception in 1973 through 1997, were content analyzed for women relevance, diversity, feminism, and historical change. Overall, 9.8% of the articles reviewed (N = 2,178) were considered women relevant, 4% recognized diversity among women, and 3% were considered feminist. There was an average yearly increase in women-relevant and feminist articles from 7.3 pre-1990 to 11.2 post-1990, and 1.6 pre-1990 to 4.6 post-1990, respectively. Overall, mental health and motherhood were the most addressed content areas. Among feminist articles, gender roles and violence against women were most salient. Race and SES were the most noted issues of diversity in both women-relevant and feminist articles. While an increase in feminist publications by both journals is promising, stereotypes of women and other oppressed groups continue to be perpetuated.

  3. Comparative analysis of two community stressors' long-term mental health effects

    Dew, M.A.; Bromet, E.J.; Schulberg, H.C.

    1987-04-01

    The investigation directly compared the long-term mental health consequences of two community-wide stressors, the Three Mile Island (TMI) nuclear accident and widespread unemployment due to layoff, in demographically comparable samples of women. Results showed a marked degree of similarity in the stressors' effects: Levels of subclinical symptomatology were elevated to similar degrees in each sample during the year following stressor onset, and symptom levels remained elevated in each sample 2 to 3 1/2 years later. Moreover, variables identified as predictors of enduring psychological distress were virtually identical for the two samples. Additional analyses revealed that the mental health status of unemployed husbands mediated the negative psychological effects of layoff on their wives. Implications of these results for understanding the long-term consequences of exposure to community-wide stress are discussed.

  4. 高血压病的社区护理干预分析%Community nursing intervention analysis of hypertension

    徐天红

    2014-01-01

    Objective To analyze the hypertension of community nursing intervention effect. Methods Analysis of 200 cases of patients with high blood pressure the effect of the implementation of community nursing intervention. Results After the intervention effect of the patient's blood pressure levels significantly decreased,compared with before treatment. Conclusion Hypertension,community nursing for hypertension patients,to improve the cognitive and protection consciousness.%目的:分析研究高血压病的社区护理干预实施效果。方法分析研究200例高血压患者实施社区护理干预的效果。结果干预实施后,患者的血压水平明显下降,与治疗前相比有差异。结论高血压病实施社区护理,有利于提高患者对高血压认知以及防护意识,对于提高患者生活质量水平相当重要。

  5. PhyloChip microarray analysis reveals altered gastrointestinal microbial communities in a rat model of colonic hypersensitivity

    Nelson, T.A.; Holmes, S.; Alekseyenko, A.V.; Shenoy, M.; DeSantis, T.; Wu, C.H.; Andersen, G.L.; Winston, J.; Sonnenburg, J.; Pasricha, P.J.; Spormann, A.

    2010-12-01

    Irritable bowel syndrome (IBS) is a chronic, episodic gastrointestinal disorder that is prevalent in a significant fraction of western human populations; and changes in the microbiota of the large bowel have been implicated in the pathology of the disease. Using a novel comprehensive, high-density DNA microarray (PhyloChip) we performed a phylogenetic analysis of the microbial community of the large bowel in a rat model in which intracolonic acetic acid in neonates was used to induce long lasting colonic hypersensitivity and decreased stool water content and frequency, representing the equivalent of human constipation-predominant IBS. Our results revealed a significantly increased compositional difference in the microbial communities in rats with neonatal irritation as compared with controls. Even more striking was the dramatic change in the ratio of Firmicutes relative to Bacteroidetes, where neonatally irritated rats were enriched more with Bacteroidetes and also contained a different composition of species within this phylum. Our study also revealed differences at the level of bacterial families and species. The PhyloChip is a useful and convenient method to study enteric microflora. Further, this rat model system may be a useful experimental platform to study the causes and consequences of changes in microbial community composition associated with IBS.

  6. Building ties: social capital network analysis of a forest community in a biosphere reserve in Chiapas, Mexico

    Luis Rico García-Amado

    2012-09-01

    Full Text Available Governance of the commons depends on the capacity to generate collective action. Networks and rules that foster that collective action have been defined as social capital. However, their causal link is still not fully understood. We use social network analysis to assess social capital, decision-making, and collective action in a forest-based common pool resource management in La Sepultura Biosphere Reserve (Chiapas, Mexico. Our research analyzes the productive networks and the evolution of coffee groups in one community. The network shows some centrality, with richer landholders tending to occupy core positions and poorer landless peasants occupying peripheral ones. This has fostered the community's environmentally oriented development but has also caused internal conflicts. Market requirements have shaped different but complementary productive networks, where organic coffee commercialization is the main source of bridging ties, which has resulted in more connectivity and resilience. Conservation attitudes, along with the institutional setting of the community, have promoted collective action. The unresolved conflicts, however, still leave some concerns about governance in the future.

  7. [Analysis of microbial community variation in the domestication process of sludge in a sulfate-reducing reactor].

    Zeng, Guo-Qu; Jia, Xiao-Shan; Zheng, Xiao-Hong; Yang, Li-Ping; Sun, Guo-Ping

    2014-11-01

    The variations of microbial community in the sludge of sulfate-reducing UASB during domestication period were analyzed by PCR-DGGE technique. The results showed that the diversity of microbial community was strongly related to the sulfate reduction and COD removal performance. The sulfate reduction rate of the reactor was about 95% when the Shannon index of microbial community was higher than 3.45. The preponderant bands in DGGE figure were excised and cloned, and the sequencing analysis indicated there were Firmicutes, Proteobacteria, Deinococcus-Thermus and Chloroflexi in the sludge, which accounted for 50.0%, 28.6% 14.3% and 7.1% of the total sequences of samples, respectively. The anaerobic fermentative bacteria of Clostridium sp. were predominant in the whole domestication period, but the predominant species was changing. Some anaerobic bacteria like Chloroflexi sp. and Geopsychrobacter sp. were detected to be dominant species, which then disappeared along with further domestication, but anaerobic bacteria Geobacter sp. became gradually predominant in the domestication process. Species of Desulfovibrio sp. were detected to be predominant only in the last two phases of domestication.

  8. Ad hoc supervision of general practice registrars as a 'community of practice': analysis, interpretation and re-presentation.

    Clement, T; Brown, J; Morrison, J; Nestel, D

    2016-05-01

    General practice registrars in Australia undertake most of their vocational training in accredited general practices. They typically see patients alone from the start of their community-based training and are expected to seek timely ad hoc support from their supervisor. Such ad hoc encounters are a mechanism for ensuring patient safety, but also provide an opportunity for learning and teaching. Wenger's (Communities of practice: learning, meaning, and identity. Cambridge University Press, New York, 1998) social theory of learning ('communities of practice') guided a secondary analysis of audio-recordings of ad hoc encounters. Data from one encounter is re-presented as an extended sequence to maintain congruence with the theoretical perspective and enhance vicariousness. An interpretive commentary communicates key features of Wenger's theory and highlights the researchers' interpretations. We argue that one encounter can reveal universal understandings of clinical supervision and that the process of naturalistic generalisation allows readers to transfer others' experiences to their own contexts. The paper raises significant analytic, interpretive, and representational issues. We highlight that report writing is an important, but infrequently discussed, part of research design. We discuss the challenges of supporting the learning and teaching that arises from adopting a socio-cultural lens and argue that such a perspective importantly captures the complex range of issues that work-based practitioners have to grapple with. This offers a challenge to how we research and seek to influence work-based learning and teaching in health care settings.

  9. 社区儿童活动场地营建分析%Analysis on Community Children Activity Space Construction

    石晓丽; 王欢; 邱琛; 祖亚会

    2013-01-01

    Outdoor activity is an effective supplement for children to school .Based on the investigation of the ur-ban community parks in Nanjing city ,the importance of community park carrying children's activity space was analyzed .Taking the South Lake Park as an example ,a detailed analysis on children activity field was made . Based on the above ,the design and construction strategy of children activity place in community park was dis-cussed and some proposals were put forward .%  户外活动是儿童校园学习的有效补充,如何营建儿童活动场地以激发儿童心性至关重要。通过对南京市主城区社区公园进行调研,分析了社区公园承载儿童活动场地的重要性。以功能较完善的南京市南湖公园为例,对其儿童活动场所进行具体分析,探讨社区公园儿童活动场所的设计、建设策略,为今后城市公园建设过程中儿童活动空间的设计提出指导性建议。

  10. Bioconductor workflow for microbiome data analysis: from raw reads to community analyses [version 1; referees: 2 approved

    Ben J. Callahan

    2016-06-01

    Full Text Available High-throughput sequencing of PCR-amplified taxonomic markers (like the 16S rRNA gene has enabled a new level of analysis of complex bacterial communities known as microbiomes. Many tools exist to quantify and compare abundance levels or microbial composition of communities in different conditions. The sequencing reads have to be denoised and assigned to the closest taxa from a reference database. Common approaches use a notion of 97% similarity and normalize the data by subsampling to equalize library sizes. In this paper, we show that statistical models allow more accurate abundance estimates. By providing a complete workflow in R, we enable the user to do sophisticated downstream statistical analyses, including both parameteric and nonparametric methods. We provide examples of using the R packages dada2, phyloseq, DESeq2, ggplot2 and vegan to filter, visualize and test microbiome data. We also provide examples of supervised analyses using random forests, partial least squares and linear models as well as nonparametric testing using community networks and the ggnetwork package.

  11. Bioconductor Workflow for Microbiome Data Analysis: from raw reads to community analyses [version 2; referees: 3 approved

    Ben J. Callahan

    2016-11-01

    Full Text Available High-throughput sequencing of PCR-amplified taxonomic markers (like the 16S rRNA gene has enabled a new level of analysis of complex bacterial communities known as microbiomes. Many tools exist to quantify and compare abundance levels or OTU composition of communities in different conditions. The sequencing reads have to be denoised and assigned to the closest taxa from a reference database. Common approaches use a notion of 97% similarity and normalize the data by subsampling to equalize library sizes. In this paper, we show that statistical models allow more accurate abundance estimates. By providing a complete workflow in R, we enable the user to do sophisticated downstream statistical analyses, whether parametric or nonparametric. We provide examples of using the R packages dada2, phyloseq, DESeq2, ggplot2 and vegan to filter, visualize and test microbiome data. We also provide examples of supervised analyses using random forests and nonparametric testing using community networks and the ggnetwork package.

  12. Culture-independent analysis of bacterial communities in hemolymph of American lobsters with epizootic shell disease.

    Quinn, Robert A; Smolowitz, Roxanna; Chistoserdov, Andrei Y

    2013-03-26

    Epizootic shell disease (ESD) of the American lobster Homarus americanus H. Milne Edwards, 1837 is a disease of the carapace that presents grossly as large, melanized, irregularly shaped lesions, making the lobsters virtually unmarketable because of their grotesque appearance. We analyzed the bacterial communities present in the hemolymph of lobsters with and without ESD using nested-PCR of the 16S rRNA genes followed by denaturing gradient gel electrophoresis. All lobsters tested (n = 42) had bacterial communities in their hemolymph, and the community profiles were highly similar regardless of the sampling location or disease state. A number of bacteria were detected in a high proportion of samples and from numerous locations, including a Sediminibacterium sp. closely related to a symbiont of Tetraponera ants (38/42) and a Ralstonia sp. (27/42). Other bacteria commonly encountered included various Bacteroidetes, Pelomonas aquatica, and a Novosphingobium sp. One bacterium, a different Sediminibacterium sp., was detected in 20% of diseased animals (n = 29), but not in the lobsters without signs of ESD (n = 13). The bacteria in hemolymph were not the same as those known to be present in lesion communities except for the detection of a Thalassobius sp. in 1 individual. This work demonstrates that hemolymph bacteremia and the particular bacterial species present do not correlate with the incidence of ESD, providing further evidence that microbiologically, ESD is a strictly cuticular disease. Furthermore, the high incidence of the same species of bacteria in hemolymph of lobsters may indicate that they have a positive role in lobster fitness, rather than in disease, and further investigation of the role of bacteria in lobster hemolymph is required.

  13. Community analysis reveals close affinities between endophytic and endolichenic fungi in mosses and lichens.

    U'ren, Jana M; Lutzoni, François; Miadlikowska, Jolanta; Arnold, A Elizabeth

    2010-08-01

    Endolichenic fungi live in close association with algal photobionts inside asymptomatic lichen thalli and resemble fungal endophytes of plants in terms of taxonomy, diversity, transmission mode, and evolutionary history. This similarity has led to uncertainty regarding the distinctiveness of endolichenic fungi compared with endophytes. Here, we evaluate whether these fungi represent distinct ecological guilds or a single guild of flexible symbiotrophs capable of colonizing plants or lichens indiscriminately. Culturable fungi were sampled exhaustively from replicate sets of phylogenetically diverse plants and lichens in three microsites in a montane forest in southeastern Arizona (USA). Intensive sampling combined with a small spatial scale permitted us to decouple spatial heterogeneity from host association and to sample communities from living leaves, dead leaves, and lichen thalli to statistical completion. Characterization using data from the nuclear ribosomal internal transcribed spacer and partial large subunit (ITS-LSU rDNA) provided a first estimation of host and substrate use for 960 isolates representing five classes and approximately 16 orders, 32 families, and 65 genera of Pezizomycotina. We found that fungal communities differ at a broad taxonomic level as a function of the phylogenetic placement of their plant or lichen hosts. Endolichenic fungal assemblages differed as a function of lichen taxonomy, rather than substrate, growth form, or photobiont. In plants, fungal communities were structured more by plant lineage than by the living vs. senescent status of the leaf. We found no evidence that endolichenic fungi are saprotrophic fungi that have been "entrapped" by lichen thalli. Instead, our study reveals the distinctiveness of endolichenic communities relative to those in living and dead plant tissues, with one notable exception: we identify, for the first time, an ecologically flexible group of symbionts that occurs both as endolichenic fungi and as

  14. Comparative analysis of the fecal bacterial community of five harbor seals (Phoca vitulina).

    Numberger, Daniela; Herlemann, Daniel P R; Jürgens, Klaus; Dehnhardt, Guido; Schulz-Vogt, Heide

    2016-10-01

    The gut microbiota has many beneficial effects on host metabolism and health, and its composition is determined by numerous factors. It is also assumed that there was a co-evolution of mammals and the bacteria inhabiting their gut. Current knowledge of the mammalian gut microbiota mainly derives from studies on humans and terrestrial animals, whereas those on marine mammals are sparse. However, they could provide additional information on influencing factors, such as the role of diet and co-evolution with the host. In this study, we investigated and compared the bacterial diversity in the feces of five male harbor seals (Phoca vitulina). Because this small population included two half-brother pairs, each sharing a common father, it allowed an evaluation of the impact of host relatedness or genetic similarity on the gut microbial community. Fresh feces obtained from the seals by an enema were analyzed by fluorescence in situ hybridization and amplicon sequencing of 16S rRNA genes. The results showed that the bacterial communities in the seals' feces mainly consisted of the phyla Firmicutes (19-43%), Bacteroidetes (22-36%), Fusobacteria (18-32%), and Proteobacteria (5-17%) . Twenty-one bacterial members present in the fecal samples of the five seals contributed an average relative abundance of 93.7 + 8.7% of the total fecal microbial community. Contrary to all expectations based on previous studies a comparison of the fecal community between individual seals showed a higher similarity between unrelated than related individuals.

  15. Integrated metagenomics and network analysis of soil microbial community of the forest timberline

    Junjun Ding; Yuguang Zhang; Ye Deng; Jing Cong; Hui Lu; Xin Sun; Caiyun Yang; Tong Yuan; Van Nostrand, Joy D.; Diqiang Li; Jizhong Zhou; Yunfeng Yang

    2015-01-01

    The forest timberline responds quickly and markedly to climate changes, rendering it a ready indicator. Climate warming has caused an upshift of the timberline worldwide. However, the impact on belowground ecosystem and biogeochemical cycles remain elusive. To understand soil microbial ecology of the timberline, we analyzed microbial communities via 16s rRNA Illumina sequencing, a microarray-based tool named GeoChip 4.0 and a random matrix theory-based association network approach. We selecte...

  16. Community patterns of stigma towards persons living with HIV: A population-based latent class analysis from rural Vietnam

    Pharris, Anastasia

    2011-09-18

    Abstract Background The negative effects of stigma on persons living with HIV (PLHIV) have been documented in many settings and it is thought that stigma against PLHIV leads to more difficulties for those who need to access HIV testing, treatment and care, as well as to limited community uptake of HIV prevention and testing messages. In order to understand and prevent stigma towards PLHIV, it is important to be able to measure stigma within communities and to understand which factors are associated with higher stigma. Methods To analyze patterns of community stigma and determinants to stigma toward PLHIV, we performed an exploratory population-based survey with 1874 randomly sampled adults within a demographic surveillance site (DSS) in rural Vietnam. Participants were interviewed regarding knowledge of HIV and attitudes towards persons living with HIV. Data were linked to socioeconomic and migration data from the DSS and latent class analysis and multinomial logistic regression were conducted to examine stigma group sub-types and factors associated with stigma group membership. Results We found unexpectedly high and complex patterns of stigma against PLHIV in this rural setting. Women had the greatest odds of belong to the highest stigma group (OR 1.84, 95% CI 1.42-2.37), while those with more education had lower odds of highest stigma group membership (OR 0.45, 95% CI 0.32-0.62 for secondary education; OR 0.19, 95% CI 0.10-0.35 for tertiary education). Long-term migration out of the district (OR 0.61, 95% CI 0.4-0.91), feeling at-risk for HIV (OR 0.42, 95% CI 0.27-0.66), having heard of HIV from more sources (OR 0.44, 95% CI 0.3-0.66), and knowing someone with HIV (OR 0.76, 95% CI 0.58-0.99) were all associated with lower odds of highest stigma group membership. Nearly 20% of the population was highly unsure of their attitudes towards PLHIV and persons in this group had significantly lower odds of feeling at-risk for HIV (OR 0.54, 95% CI 0.33-0.90) or of knowing

  17. A for-profit venture marketing research and analysis study conducted for Action for Boston Community Development. [Home repair services

    1987-04-27

    This report is a look at our study to find a for-profit venture for Action for Boston Community Development (ABCD) to establish. Essentially, our study had two stages - find a product or service that appeared to be needed in the market place and that ABCD felt comfortable pursuing, then research and analyze the market for this product or service. The venture selected for complete market research and analysis was home repair services. Our research showed that both an advisory and minor home repair service should be established.

  18. The Financial Analysis of a Modern Scheme for Managing Waste Proposed for the Urban Community Arieş, Cluj County

    Lucia Monica SCORȚAR

    2009-10-01

    Full Text Available This paper presents a scheme for managingwaste, proposed for the urban community of Arieş,Cluj County, in which we are going to show themain activities that should be accomplished withthe support of the local public administration.Based on the analysis of the waste flows, thedemographic trends and the waste generatingtrends, we propose a scheme for managingwaste that has a major investment component,an administrative re-organizing component andan educational one. We suggest a scheme whichincludes advanced techniques and methods fortreating waste. Moreover, we demonstrated thatthe efficiency of the scheme cannot be conceivedoutside a circuit for valorizing and recycling theuseful materials contained in the waste.

  19. A Comparative Analysis of a Community and General Sample of Lesbian, Gay, and Bisexual Individuals.

    Kuyper, Lisette; Fernee, Henk; Keuzenkamp, Saskia

    2016-04-01

    Samples recruited at lesbian, gay, and bisexual (LGB) venues have certain benefits, but a major drawback is that these samples are prone to bias as they only contain LGB participants who visit such venues. Empirical data with regard to the potential differences between LGB community samples and LGB general samples may shed some light on the generalizability of research findings from convenience samples recruited through LGB venues. The current study attempted to contribute to existing knowledge by examining differences in social demographics, sexual orientation, minority stress, and mental health between a convenience sample recruited at LGB venues ("community sample," N = 3,403) and an LGB sample recruited from a general research panel in the Netherlands ("panel sample," N = 1,000). Various differences were found. In general, community participants were younger, reported a more exclusive same-sex sexual orientation, were more open about their sexual orientation, had lower levels of internalized homonegativity, and encountered more negative social reactions on their LGB status. They also reported higher levels of psychological distress and suicidality. The Nagelkerke R (2) of the analyses (which were adjusted for sociodemographic differences) ranged from .08 (suicide plans among men) to .27 (sexual attraction among women). However, while the estimates of sociodemographics, sexual orientation, minority stress, and mental well-being differed, the relationships between these constructs were comparable in both samples. Implications and suggestions for future studies are discussed.

  20. Characterization of Bacterial Communities in Selected Smokeless Tobacco Products Using 16S rDNA Analysis.

    Robert E Tyx

    Full Text Available The bacterial communities present in smokeless tobacco (ST products have not previously reported. In this study, we used Next Generation Sequencing to study the bacteria present in U.S.-made dry snuff, moist snuff and Sudanese toombak. Sample diversity and taxonomic abundances were investigated in these products. A total of 33 bacterial families from four phyla, Actinobacteria, Firmicutes, Proteobacteria and Bacteroidetes, were identified. U.S.-produced dry snuff products contained a diverse distribution of all four phyla. Moist snuff products were dominated by Firmicutes. Toombak samples contained mainly Actinobacteria and Firmicutes (Aerococcaceae, Enterococcaceae, and Staphylococcaceae. The program PICRUSt (Phylogenetic Investigation of Communities by Reconstruction of Unobserved States was used to impute the prevalence of genes encoding selected bacterial toxins, antibiotic resistance genes and other pro-inflammatory molecules. PICRUSt also predicted the presence of specific nitrate reductase genes, whose products can contribute to the formation of carcinogenic nitrosamines. Characterization of microbial community abundances and their associated genomes gives us an indication of the presence or absence of pathways of interest and can be used as a foundation for further investigation into the unique microbiological and chemical environments of smokeless tobacco products.

  1. Characterization of Bacterial Communities in Selected Smokeless Tobacco Products Using 16S rDNA Analysis.

    Tyx, Robert E; Stanfill, Stephen B; Keong, Lisa M; Rivera, Angel J; Satten, Glen A; Watson, Clifford H

    2016-01-01

    The bacterial communities present in smokeless tobacco (ST) products have not previously reported. In this study, we used Next Generation Sequencing to study the bacteria present in U.S.-made dry snuff, moist snuff and Sudanese toombak. Sample diversity and taxonomic abundances were investigated in these products. A total of 33 bacterial families from four phyla, Actinobacteria, Firmicutes, Proteobacteria and Bacteroidetes, were identified. U.S.-produced dry snuff products contained a diverse distribution of all four phyla. Moist snuff products were dominated by Firmicutes. Toombak samples contained mainly Actinobacteria and Firmicutes (Aerococcaceae, Enterococcaceae, and Staphylococcaceae). The program PICRUSt (Phylogenetic Investigation of Communities by Reconstruction of Unobserved States) was used to impute the prevalence of genes encoding selected bacterial toxins, antibiotic resistance genes and other pro-inflammatory molecules. PICRUSt also predicted the presence of specific nitrate reductase genes, whose products can contribute to the formation of carcinogenic nitrosamines. Characterization of microbial community abundances and their associated genomes gives us an indication of the presence or absence of pathways of interest and can be used as a foundation for further investigation into the unique microbiological and chemical environments of smokeless tobacco products.

  2. Clinical data analysis of 19 cases of community-acquired adenovirus pneumonia in immunocompetent adults.

    Yu, Hong-Xia; Zhao, Mao-Mao; Pu, Zeng-Hui; Wang, Yun-Qiang; Liu, Yan

    2015-01-01

    The aim of this study was to investigate the characteristics of clinical manifestations, laboratory tests and imaging changes of community-acquired adenovirus pneumonia in immunocompetent adults. A retrospective study was performed on 19 adult community-acquired adenovirus pneumonia cases in Yantai, whereby the clinical data were collected and analyzed. Of 19 cases, 14 (73.68%) had fever and 17 (89.47%) had cough symptoms. Moreover, 14 cases (73.68%) had normal white blood cell counts, while 11 cases (57.89%) exhibited a reduction in lymphocyte proportion. Among the 19 cases, 17 cases exhibited lesions in a single lung, while 2 cases involved bilateral lungs. The lesions predominantly exhibited ground glass-like changes. The clinical manifestations of adult community-acquired adenovirus pneumonia patients with normal immune functions were mild, with such presenting symptoms as fever, cough, and sputum; most patients did not exhibit high levels of white blood cells or low lymphocyte counts, and the imaging features (ground glass-like effusion) were indicative of single-lung involvement.

  3. Bacterial community analysis during fermentation of ten representative kinds of kimchi with barcoded pyrosequencing.

    Park, Eun-Jin; Chun, Jongsik; Cha, Chang-Jun; Park, Wan-Soo; Jeon, Che Ok; Bae, Jin-Woo

    2012-05-01

    Kimchi, a food made of fermented vegetables, is densely populated by indigenous microorganisms that originate from the raw ingredients under normal conditions. Most microbiological studies on kimchi have been on the most popular dish, baechu-kimchi (Chinese cabbage kimchi). Therefore, relatively little is known about the various other kinds of kimchi (depending on the region, season, main ingredient, starter culture inoculation and recipe). In this study, we collected 100 samples periodically during the fermentation of ten representative kinds of kimchi (including starter-inoculated kimchi) that were stored in the refrigerator (4 °C) during the 30-35 days fermentation period. The multiplex barcoded pyrosequencing of a hypervariable V1-V3 region of the 16S ribosomal RNA (rRNA) gene tagged with sample-specific barcodes for multiplex identifiers was employed for bacterial community profiling. We found that bacterial communities differed between starter-inoculated and non-inoculated kimchi at the early stages of fermentation, but overall there were no significant differences in the late phases. Also, the diversity and richness of bacterial communities varied depending on the various types of kimchi, and these differences could largely be explained by the major ingredients and the manufacture processes of each types of kimchi. This study provides the comprehensive understanding of the factors influencing the biodiversity of the kimchi ecosystem.

  4. Integrated metagenomics and network analysis of soil microbial community of the forest timberline

    Ding, Junjun; Zhang, Yuguang; Deng, Ye; Cong, Jing; Lu, Hui; Sun, Xin; Yang, Caiyun; Yuan, Tong; van Nostrand, Joy D.; Li, Diqiang; Zhou, Jizhong; Yang, Yunfeng

    2015-01-01

    The forest timberline responds quickly and markedly to climate changes, rendering it a ready indicator. Climate warming has caused an upshift of the timberline worldwide. However, the impact on belowground ecosystem and biogeochemical cycles remain elusive. To understand soil microbial ecology of the timberline, we analyzed microbial communities via 16s rRNA Illumina sequencing, a microarray-based tool named GeoChip 4.0 and a random matrix theory-based association network approach. We selected 24 sampling sites at two vegetation belts forming the timberline of Shennongjia Mountain in Hubei Province of China, a region with extraordinarily rich biodiversity. We found that temperature, among all of measured environmental parameters, showed the most significant and extensive linkages with microbial biomass, microbial diversity and composition at both taxonomic and functional gene levels, and microbial association network. Therefore, temperature was the best predictor for microbial community variations in the timberline. Furthermore, abundances of nitrogen cycle and phosphorus cycle genes were concomitant with NH4+-N, NO3--N and total phosphorus, offering tangible clues to the underlying mechanisms of soil biogeochemical cycles. As the first glimpse at both taxonomic and functional compositions of soil microbial community of the timberline, our findings have major implications for predicting consequences of future timberline upshift.

  5. Effectiveness Analysis on the Physical Activity and the Health Benefit of a Community Population Based Program

    JIANG Ying Ying; YANG Zheng Xiong; NI Rong; ZHU You Qun; LI Zhi Yu; YANG Li Chen; ZHAI Yi; ZHAO Wen Hua

    2013-01-01

    Objective To evaluate the community-based health promotion effect of physical activity. Methods The residents aged 18 and above from two communities in Gongshu District of Hangzhou City, Zhejiang province, were randomly selected and recruited for the multi-strategy and comprehensive physical activity intervention. Questionnaire survey, physical check up and blood biochemistry were conducted. Results After this two-year intervention, the time of the participant spent on weekly physical activity of moderate intensity increased from 464 min to 542 min (P<0.05), with an average increase of 78 min. Time spent in walking every week increased from 533 min to 678 min (P<0.05), with an average increase of 145 min. The body weight, waistline, blood pressure and heart rate all reduced significantly (P<0.05);the vital capacity increased significantly (P<0.05); and the related biochemical indicators were also improved. Conclusion Comprehensive and evidence-based physical activity interventions targeting community population can improve the levels of physical activity, related body measurement and biochemical indicators.

  6. Integrated metagenomics and network analysis of soil microbial community of the forest timberline.

    Ding, Junjun; Zhang, Yuguang; Deng, Ye; Cong, Jing; Lu, Hui; Sun, Xin; Yang, Caiyun; Yuan, Tong; Van Nostrand, Joy D; Li, Diqiang; Zhou, Jizhong; Yang, Yunfeng

    2015-01-23

    The forest timberline responds quickly and markedly to climate changes, rendering it a ready indicator. Climate warming has caused an upshift of the timberline worldwide. However, the impact on belowground ecosystem and biogeochemical cycles remain elusive. To understand soil microbial ecology of the timberline, we analyzed microbial communities via 16s rRNA Illumina sequencing, a microarray-based tool named GeoChip 4.0 and a random matrix theory-based association network approach. We selected 24 sampling sites at two vegetation belts forming the timberline of Shennongjia Mountain in Hubei Province of China, a region with extraordinarily rich biodiversity. We found that temperature, among all of measured environmental parameters, showed the most significant and extensive linkages with microbial biomass, microbial diversity and composition at both taxonomic and functional gene levels, and microbial association network. Therefore, temperature was the best predictor for microbial community variations in the timberline. Furthermore, abundances of nitrogen cycle and phosphorus cycle genes were concomitant with NH4(+)-N, NO3(-)-N and total phosphorus, offering tangible clues to the underlying mechanisms of soil biogeochemical cycles. As the first glimpse at both taxonomic and functional compositions of soil microbial community of the timberline, our findings have major implications for predicting consequences of future timberline upshift.

  7. A time-course analysis of four full-scale anaerobic digesters in relation to the dynamics of change of their microbial communities.

    Pycke, B F G; Etchebehere, C; Van de Caveye, P; Negroni, A; Verstraete, W; Boon, N

    2011-01-01

    This study describes the microbial community richness, -dynamics, and -organization of four full-scale anaerobic digesters during a time-course study of 45 days. The microbial community was analyzed using a Bacteria- and Archaea-targeting 16S rRNA gene-based Terminal-Restriction Fragment Length Polymorphism approach. Clustering analysis separated meso- and thermophilic reactors for both archaeal and bacterial communities. Regardless of the operating temperature, each installation possessed a distinct community profile. For both microbial domains, about 8 dominant terminal-restriction fragments could be observed, with a minimum of 4 and a maximum of 14. The bacterial community organization (a coefficient which describes the specific degree of evenness) showed a factor 2 more variation in the mesophilic reactors, compared with the thermophilic ones. The archaeal community structure of the mesophilic UASB reactor was found to be more stable. The community composition was highly dynamic for Bacteria and Archaea, with a rate of change between 20-50% per 15 days. This study illustrated that microbial communities in full-scale anaerobic digesters are unique to the installation and that community properties are dynamic. Converging complex microbial processes such as anaerobic digestion which rely on a multitude of microbial teams apparently can be highly dynamic.

  8. Developing a Referral Protocol for Community-Based Occupational Therapy Services in Taiwan: A Logistic Regression Analysis.

    Mao, Hui-Fen; Chang, Ling-Hui; Tsai, Athena Yi-Jung; Huang, Wen-Ni; Wang, Jye

    2016-01-01

    Because resources for long-term care services are limited, timely and appropriate referral for rehabilitation services is critical for optimizing clients' functions and successfully integrating them into the community. We investigated which client characteristics are most relevant in predicting Taiwan's community-based occupational therapy (OT) service referral based on experts' beliefs. Data were collected in face-to-face interviews using the Multidimensional Assessment Instrument (MDAI). Community-dwelling participants (n = 221) ≥ 18 years old who reported disabilities in the previous National Survey of Long-term Care Needs in Taiwan were enrolled. The standard for referral was the judgment and agreement of two experienced occupational therapists who reviewed the results of the MDAI. Logistic regressions and Generalized Additive Models were used for analysis. Two predictive models were proposed, one using basic activities of daily living (BADLs) and one using instrumental ADLs (IADLs). Dementia, psychiatric disorders, cognitive impairment, joint range-of-motion limitations, fear of falling, behavioral or emotional problems, expressive deficits (in the BADL-based model), and limitations in IADLs or BADLs were significantly correlated with the need for referral. Both models showed high area under the curve (AUC) values on receiver operating curve testing (AUC = 0.977 and 0.972, respectively). The probability of being referred for community OT services was calculated using the referral algorithm. The referral protocol facilitated communication between healthcare professionals to make appropriate decisions for OT referrals. The methods and findings should be useful for developing referral protocols for other long-term care services.

  9. Phylogenetic analysis of atmospheric halotolerant bacterial communities at high altitude in an Asian dust (KOSA) arrival region, Suzu City

    Maki, Teruya, E-mail: makiteru@t.kanazawa-u.ac.jp [College of Science and Engineering, Kanazawa University, Kakuma, Kanazawa, Ishikawa, 920-1192 (Japan); Susuki, Shinzi; Kobayashi, Fumihisa [College of Science and Engineering, Kanazawa University, Kakuma, Kanazawa, Ishikawa, 920-1192 (Japan); Kakikawa, Makiko [Institute of Nature and Environmental Technology, Kanazawa University, Kakuma, Kanazawa, Ishikawa, 920-1192 (Japan); Tobo, Yutaka [Frontier Science Organization, Kanazawa University, Kakuma, Kanazawa, Ishikawa, 920-1192 (Japan); Yamada, Maromu [Faculty of Environmental and Symbiotic Science, Prefectural University of Kumamoto, 3-1-100 Tsukide, Kumamoto 862-8502 (Japan); Higashi, Tomomi [Hygiene, Kanazawa University School of Medicine, 13-1 Takara-machi, Kanazawa, Ishikawa, 920-8640 (Japan); Matsuki, Atsushi; Hong, Chunsang [Frontier Science Organization, Kanazawa University, Kakuma, Kanazawa, Ishikawa, 920-1192 (Japan); Hasegawa, Hiroshi [College of Science and Engineering, Kanazawa University, Kakuma, Kanazawa, Ishikawa, 920-1192 (Japan); Iwasaka, Yasunobu [Frontier Science Organization, Kanazawa University, Kakuma, Kanazawa, Ishikawa, 920-1192 (Japan)

    2010-09-15

    The microbial communities transported by Asian desert dust (KOSA) events have attracted much attention as bioaerosols because the transported microorganisms are thought to influence the downwind ecosystems in Korea and Japan. However, the atmospheric microbial community has not been investigated at high altitude in the KOSA arrival area. In this study, to estimate the viability and diversity of atmospheric halotolerant bacteria, which are expected to resist to various environmental stresses as well as high salinities, bioaerosol samples were collected at 10 and 600 m above the ground within the KOSA arrival area, Suzu City, Japan, during KOSA events. During the sampling period, the particle numbers at 600 m were higher than those at 10 m, suggesting that large particles of aerosol fall from the high altitude of 600 m to the ground surface. The microorganisms in bioaerosol samples grew in media containing up to 15% NaCl concentrations demonstrating the viability of the halotolerant bacteria in bioaerosol samples. The PCR-DGGE analysis using 16S rDNA revealed that the bacterial species in NaCl-amended cultures were similar to the bacteria detected from the genomic DNA directly extracted from the bioaerosol samples. The 16S rDNA sequences of bacterial communities in bioaerosol samples were classified into 4 phylotypes belonging to the Bacilluscereus or Bacillussubtilis group. The bioaerosol samples collected at 600 m included 2 phylotypes belonging to B. subtilis, and one phylotype among all 4 phylotypes was identical between the samples at 10 and 600 m. In the atmosphere at 600 m, the halotolerant bacterial community was expected to remain viable, and the species composition was expected to include a few species of the genus Bacillus. During this investigation period, these atmospheric bacteria may have been vertically transported to the ground surface, where the long-range KOSA particle transport from China is frequently observed.

  10. Effect of dissolved oxygen on elemental sulfur generation in sulfide and nitrate removal process: characterization, pathway, and microbial community analysis.

    Wang, Xiaowei; Zhang, Yu; Zhang, Tingting; Zhou, Jiti

    2016-03-01

    Microaerobic bioreactor treatment for enriched sulfide and nitrate has been demonstrated as an effective strategy to improve the efficiencies of elemental sulfur (S(0)) generation, sulfide oxidation, and nitrate reduction. However, there is little detailed information for the effect and mechanism of dissolved oxygen (DO) on the variations of microbial community in sulfur generation, sulfide oxidation, and nitrate reduction systems. Polymerase chain reaction denaturing gradient gel electrophoresis (PCR-DGGE) was employed to evaluate the variations of microbial community structures in a sulfide oxidation and nitrate reduction reactor under different DO conditions (DO 0-0.7 mg · L(-1)). Experimental results revealed that the activity of sulfide-oxidizing bacteria (SOB) and nitrate-reducing bacteria (NRB) could be greatly stimulated in 0.1-0.3 mg-DO · L(-1). However, when the DO concentration was further elevated to more than 0.5 mg · L(-1), the abundance of NRB was markedly decreased, while the heterotrophic microorganisms, especially carbon degradation species, were enriched. The reaction pathways for sulfide and nitrate removal under microaerobic conditions were also deduced by combining batch experiments with functional species analysis. It was likely that the oxidation of sulfide to sulfur could be performed by both aerobic heterotrophic SOB and sulfur-based autotrophic denitrification bacteria with oxygen and nitrate as terminal electron acceptor, respectively. The nitrate could be reduced to nitrite by both autotrophic and heterotrophic denitrification, and then the generated nitrite could be completely converted to nitrogen gas via heterotrophic denitrification. This study provides new insights into the impacts of microaerobic conditions on the microbial community functional structures of sulfide-oxidizing, nitrate-reducing, and sulfur-producing bioreactors, which revealing the potential linkage between functional microbial communities and

  11. Phenotypic Microdiversity and Phylogenetic Signal Analysis of Traits Related to Social Interaction in Bacillus spp. from Sediment Communities

    Rodríguez-Torres, María Dolores; Islas-Robles, África; Gómez-Lunar, Zulema; Delaye, Luis; Hernández-González, Ismael; Souza, Valeria; Travisano, Michael; Olmedo-Álvarez, Gabriela

    2017-01-01

    Understanding the relationship between phylogeny and predicted traits is important to uncover the dimension of the predictive power of a microbial composition approach. Numerous works have addressed the taxonomic composition of bacteria in communities, but little is known about trait heterogeneity in closely related bacteria that co-occur in communities. We evaluated a sample of 467 isolates from the Churince water system of the Cuatro Cienegas Basin (CCB), enriched for Bacillus spp. The 16S rRNA gene revealed a random distribution of taxonomic groups within this genus among 11 sampling sites. A subsample of 141 Bacillus spp. isolates from sediment, with seven well-represented species was chosen to evaluate the heterogeneity and the phylogenetic signal of phenotypic traits that are known to diverge within small clades, such as substrate utilization, and traits that are conserved deep in the lineage, such as prototrophy, swarming and biofilm formation. We were especially interested in evaluating social traits, such as swarming and biofilm formation, for which cooperation is needed to accomplish a multicellular behavior and for which there is little information from natural communities. The phylogenetic distribution of traits, evaluated by the Purvis and Fritz’s D statistics approached a Brownian model of evolution. Analysis of the phylogenetic relatedness of the clusters of members sharing the trait using consenTRAIT algorithm, revealed more clustering and deeper phylogenetic signal for prototrophy, biofilm and swimming compared to the data obtained for substrate utilization. The explanation to the observed Brownian evolution of social traits could be either loss due to complete dispensability or to compensated trait loss due to the availability of public goods. Since many of the evaluated traits can be considered to be collective action traits, such as swarming, motility and biofilm formation, the observed microdiversity within taxonomic groups might be explained

  12. Utilizing findings from a gender-based analysis to address chronic disease prevention and management among African-American women in a Michigan community.

    Lombard, Wendy; Burke, Jodi; Waddell, Sandra; Franke, Arthur

    2015-08-01

    This research note underscores the importance of including strategies to address gender-based disparities when planning and implementing community health improvement programs. Working in collaboration with the Inkster Partnership for a Healthier Community (IPHC), the National Kidney Foundation of Michigan conducted a gender-based analysis as part of its broader community health needs assessment efforts in Inkster, MI. The findings from these studies revealed significant challenges impacting women that were not being adequately addressed within the community. In response to these findings, the IPHC created a strategic action plan to respond to the highest priority needs by increasing community awareness of and linkages to resources that provide supportive services for low-income African-American women.

  13. Comparative analysis of bacterial communities in a potato field as determined by pyrosequencing.

    Özgül Inceoğlu

    Full Text Available BACKGROUND: Plants selectively attract particular soil microorganisms, in particular consumers of root-excreted compounds. It is unclear to what extent cultivar type and/or growth stage affect this process. METHODOLOGY/PRINCIPAL FINDINGS: DNA-based pyrosequencing was used to characterize the structure of bacterial communities in a field cropped with potato. The rhizospheres of six cultivars denoted Aveka, Aventra, Karnico, Modena, Premiere and Desiree, at three growth stages (young, flowering and senescence were examined, in addition to corresponding bulk soils. Around 350,000 sequences were obtained (5,700 to 38,000 per sample. Across all samples, rank abundance distributions best fitted the power law model, which indicates a community composed of a few highly dominant species next to numerous rare species. Grouping of the sequences showed that members of the Actinobacteria, Alphaproteobacteria, next to as-yet-unclassified bacteria, dominated. Other groups that were consistently found, albeit at lower abundance, were Beta-, Gamma- and Deltaproteobacteria and Acidobacteria. Principal components analyses revealed that rhizosphere samples were significantly different from corresponding bulk soil in each growth stage. Furthermore, cultivar effects were found in the young plant stage, whereas these became insignificant in the flowering and senescence stages. Besides, an effect of time of season was observed for both rhizosphere and bulk soils. The analyzed rhizosphere samples of the potato cultivars were grouped into two groups, in accordance with the allocation of carbon to starch in their tubers, i.e. Aveka, Aventra and Karnico (high versus Premiere and Desiree (low and thus replicates per group were established. CONCLUSIONS: Across all potato cultivars, the young plant stages revealed cultivar-dependent bacterial community structures, which disappeared in the flowering and senescence stages. Furthermore, Pseudomonas, Beta-, Alpha- and

  14. Cannabis use and violence in three remote Aboriginal Australian communities: Analysis of clinic presentations.

    Kylie Lee, K S; Sukavatvibul, Krisakorn; Conigrave, Katherine M

    2015-12-01

    Anecdotal reports have linked cannabis use to violence in some remote Australian Aboriginal communities. We examine the relationship between cannabis use and presentations to local clinics for violence-related trauma at a population level. As part of a larger study, estimates of cannabis and alcohol use status were obtained for 264 randomly selected individuals aged 14-42. These estimates were collected from Aboriginal health workers and respected community informants using a previously validated approach. Clinic records for the sample were audited for physical trauma presentations between January 2004 and June 2006. One in 3 individuals (n = 88/264) presented to the clinic with physical trauma. Of these, the majority (65.9%, n = 58/88) had at least one presentation that was violence-related. Nearly 2 in every 3 of the total presentations for trauma following violence (n = 40/63) involved the use of a weapon. Hunting tools were most often used, followed by wooden or rock implements. Individuals who reported any current cannabis use were nearly 4 times more likely than nonusers to present at least once for violent trauma after adjusting for current alcohol use, age, and sex (OR = 3.8, 95% CI [1.5, 9.8]). Aboriginal individuals in these remote communities experience high rates of physical trauma and violence, often involving weapons. A comprehensive study is needed to explore the association between cannabis and violence. At the same time, an investment in local programmes is needed to address cannabis use and underlying risk factors for substance use and for violence.

  15. Stakeholder Analysis of Community Distribution of Misoprostol in Lao PDR: A Qualitative Study

    Warner, Melissa; Phengsavanh, Alongkone; Sychareun, Vanphanom; Vongxay, Viengnakhone; Rickart, Keith

    2016-01-01

    Background Globally, significant progress has been made in reducing maternal mortality, yet in many low-resource contexts it remains unacceptably high. Many of these deaths are due to postpartum haemorrhage and are preventable with access to essential obstetric care. Where there are barriers to access, maternal deaths could be prevented if community-level misoprostol was available. The purpose of this study was to explore perceptions of stakeholders regarding misoprostol use in the Lao People’s Democratic Republic, a setting with high maternal mortality. Methods Semi-structured interviews were conducted with 35 stakeholders in the capital, Vientiane and in one northern province identified as a site for a possible intervention. The sample included international and national stakeholders involved in policy-making and providing maternal and reproductive health services. Findings Most stakeholders supported a pilot program for community distribution of misoprostol but levels of awareness of the drug’s use in preventing postpartum haemorrhage and level of influence over policy direction varied considerably. Some international organizations, all identified as powerful in influencing policy, were ambivalent about the use of community distribution of misoprostol. Concerns related to the capacity of village health workers or lay people to safely administer misoprostol, whether its distribution would undermine efforts to improve access to safe delivery services and active management of the third stage of labour, the ease with which prescription drugs can be bought over the counter, and technical, logistical, and financial constraints. Conclusion Access to appropriate oxytocic drugs is a matter of health equity. In settings without access to essential obstetrical care, misoprostol represents a viable solution for the prevention of postpartum haemorrhage. Understanding stakeholders’ perspectives and their legitimate concerns on misoprostol can inform interventions in

  16. Adirondack lakes survey: An interpretive analysis of fish communities and water chemistry, 1984--1987

    Baker, J.P. (Baker (Joan P.), Raleigh, NC (USA)); Gherini, S.A.; Munson, R.K. (Tetra Tech, Inc., Pasadena, CA (USA)); Christensen, S.W. (Oak Ridge National Lab., TN (USA)); Driscoll, C.T. (Syracuse Univ., NY (USA)); Gallagher, J. (Adirondack Lakes Survey Corp., Ray Brook, NY (USA)); Newton, R.M. (Smith Coll., Northampton, MA (USA)); Reckhow, K.H. (Duke Univ., Durham, NC (USA)); Schofield, C.L. (Co

    1990-01-01

    The Adirondack Lakes Survey Corporation (ALSC) was formed as a cooperative effort of the New York State Department of Environmental Conservation and the Empire State Electric Energy Research Corporation to better characterize the chemical and biological status of Adirondack lakes. Between 1984 and 1987, the ALSC surveyed 1469 lakes within the Adirondack ecological zone. As a follow-up to the survey, the ALSC sponsored a series of interpretive analyses of the ALSC data base. The primary objectives of these analyses were as follows: Evaluate the influence of mineral acids (from acidic deposition) and nonmineral acids (natural organic acids) on lake pH levels; classify Adirondack lakes according to lake and watershed features expected to influence their responsiveness to changes in acidic deposition; evaluate the sensitivity of Adirondack lakes to changes in environmental conditions, such as changes in mineral acids or dissolved organic carbon concentrations; identify lake characteristics important in explaining the observed present-day status of fish communities in Adirondack lakes, in particular the relative importance of lake acidity; evaluate changes that have occurred over time in Adirondack fish communities and probable causes for these trends by using the available historical data on fish communities in the Adirondacks and the ALSC data base; and determine the degree to which the existing fish resource might be at risk from continued acidic deposition, or might recover if acidity levels were reduced. The basic approach examined relationships observed in the ALSC data base among watershed characteristics, lake chemistry, and fish status. Individual reports are processed separately for the data bases.

  17. Microbial community characterization, activity analysis and purifying efficiency in a biofilter process

    Hong Xiang; Xiwu Lu; Lihong Yin; Fei Yang; Guangcan Zhu; Wuping Liu

    2013-01-01

    The growth and metabolism of microbial communities on biologically activated carbon (BAC) play a crucial role in the purification of drinking water.To gain insight into the growth and metabolic characteristics of microbial communities and the efficiency of drinking water treatment in a BAC filter,we analyzed the heterotrophic plate count (HPC),phospholipid,dehydrogenase,metabolic function and water quality parameters during start-up and steady-state periods.In the start-up process of the filter with natural biofilm colonization,the variation in heterotrophic plate count levels was S-curved.The total phospholipid level was very low during the first 5 days and reached a maximum value after 40 days in the filter.The activity of dehydrogenase gradually increased during the first 30 days and then reached a plateau.The functional diversity of the microbial community in the filter increased,and then reached a relatively stable level by day 40.After an initial decrease,which was followed by an increase,the removal rate of NH4+-N and CODMn became stable and was 80% and 28%,respectively,by day 40.The consumption rate of dissolved oxygen reached a steady level after 29 days,and remained at 18%.At the steady operation state,the levels of HPC,phospholipid,dehydrogenase activity and carbon source utilization had no significant differences after 6 months compared to levels measured on day 40.The filter was shown to be effective in removing NH4+-N,NO2--N,CODMn,UV254,biodegradable dissolved organic carbon and trace organic pollutants from the influent.Our results suggest that understanding changes in the growth and metabolism of microorganisms in BAC filter could help to improve the efficiency of biological treatment of drinking water.

  18. Patterns of Adverse Drug Reactions in Different Age Groups: Analysis of Spontaneous Reports by Community Pharmacists.

    Yun Mi Yu

    Full Text Available To evaluate the clinical manifestations and causative drugs associated with adverse drug reactions (ADRs spontaneously reported by community pharmacists and to compare the ADRs by age.ADRs reported to the Regional Pharmacovigilance Center of the Korean Pharmaceutical Association by community pharmacists from January 2013 to June 2014 were included. Causality was assessed using the WHO-Uppsala Monitoring Centre system. The patient population was classified into three age groups. We analyzed 31,398 (74.9% ADRs from 9,705 patients, identified as having a causal relationship, from a total pool of 41,930 ADRs from 9,873 patients. Median patient age was 58.0 years; 66.9% were female.Gastrointestinal system (34.4%, nervous system (14.4%, and psychiatric (12.1% disorders were the most frequent symptoms. Prevalent causative drugs were those for acid-related disorders (11.4%, anti-inflammatory products (10.5%, analgesics (7.2%, and antibacterials (7.1%. Comparisons by age revealed diarrhea and antibacterials to be most commonly associated with ADRs in children (p < 0.001, whereas dizziness was prevalent in the elderly (p < 0.001. Anaphylactic reaction was the most frequent serious event (19.7%, mainly associated with cephalosporins and non-steroidal anti-inflammatory drugs. Among 612 ADRs caused by nonprescription drugs, the leading symptoms and causative drugs were skin disorders (29.6% and non-steroidal anti-inflammatory drugs (16.2%, respectively.According to the community pharmacist reports, the leading clinical manifestations and causative drugs associated with ADRs in outpatients differed among age groups.

  19. Preparation of fosmid libraries and functional metagenomic analysis of microbial community DNA.

    Martínez, Asunción; Osburne, Marcia S

    2013-01-01

    One of the most important challenges in contemporary microbial ecology is to assign a functional role to the large number of novel genes discovered through large-scale sequencing of natural microbial communities that lack similarity to genes of known function. Functional screening of metagenomic libraries, that is, screening environmental DNA clones for the ability to confer an activity of interest to a heterologous bacterial host, is a promising approach for bridging the gap between metagenomic DNA sequencing and functional characterization. Here, we describe methods for isolating environmental DNA and constructing metagenomic fosmid libraries, as well as methods for designing and implementing successful functional screens of such libraries.

  20. Wisdom Way Solar Village: Design, Construction, and Analysis of a Low Energy Community

    Aldrich, Robb [Consortium for Advanced Residential Buildings (CARB), Norwalk, CT (United States)

    2012-08-01

    This report describes work conducted at the Wisdom Way Solar Village (WWSV), a community of 10 high performance duplexes (20 homes) in Greenfield, MA, constructed by Rural Development, Inc. (RDI). Building America's CARB team monitored temperatures and comfort in several homes during the winter of 2009-2010, and tracked utility bill information from 13 occupied homes. Because of efficient lights, appliances, and conscientious home occupants, the energy generated by the solar electric systems exceeded the electric energy used in most homes.

  1. Longitudinal analysis of virtual community perceptions of cohesion: The role of cooperation, communication, and competition.

    Lyles, Annmarie A; Loomis, Colleen; Mama, Scherezade K; Siddiqi, Sameer; Lee, Rebecca E

    2016-09-14

    Online, virtual group interactions may help adherence to health promotion programs. The purpose of this study was to explore longitudinal relationships among dimensions of group cohesion and group-interaction variables to inform and improve group-based strategies within programs aimed at promoting physical activity in virtual communities. In all, 56 online virtual users completed a group dynamics-based physical activity promotion intervention and assessments of group cohesion and group interaction at baseline and 4 weeks. Friendly competition and cooperation were consistently strong predictors of cohesion. Facilitating a sense of friendly competition and cooperation may increase engagement in physical activity programs by bolstering group cohesion.

  2. Comparative analysis of bacterial community and antibiotic-resistant strains in different developmental stages of the housefly (Musca domestica).

    Wei, Ting; Hu, Jun; Miyanaga, Kazuhiko; Tanji, Yasunori

    2013-02-01

    The housefly (Musca domestica) is an important host for a variety of bacteria, including some pathogenic and antibiotic-resistant strains. To further investigate the relationship between the housefly and the bacteria it harbors, it is necessary to understand the fate of microorganisms during the larval metamorphosis. The major bacterial communities in three developmental stages of the housefly (maggot, pupa, and adult fly) were investigated by a culture-independent method, polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) analysis of 16S rRNA genes. The bacteria that were identified using DGGE analysis spanned phyla Proteobacteria, Firmicutes, and Bacteroidetes. Changes in the predominant genera were observed during the housefly development. Bacteroides, Koukoulia, and Schineria were detected in maggots, Neisseria in pupae, and Macrococcus, Lactococcus, and Kurthia in adult flies. Antibiotic-resistant bacteria were screened using a selective medium and tested for antibiotic susceptibility. Most resistant isolates from maggots and pupae were classified as Proteus spp., while those from adult flies were much more diverse and spanned 12 genera. Among 20 tested strains across the three stages, 18 were resistant to at least two antibiotics. Overall, we demonstrated that there are changes in the major bacterial communities and antibiotic-resistant strains as the housefly develops.

  3. Pre-design and life cycle cost analysis of a hybrid power system for rural and remote communities in Afghanistan

    Mir Sayed Shah Danish

    2014-08-01

    Full Text Available In view of the present situation of the Afghanistan electricity sector, the photovoltaic and diesel generator stand-alone hybrid power system is increasingly attractive for application in rural and remote communities. Thousands of rural communities in Afghanistan depend solely on traditional kerosene for illumination and rarely have access to electricity sources such as DC battery for radio and other small appliances. This study is conducted to offer real-life solution to this problem. The hybrid system is investigated to meet the domestic load demand that is estimated based on the communities’ electricity consumption culture. At first, customary pre-design is pursued. Afterwards, the break-even point and net present value algorithms are applied for economic analysis. That makes this study differ from the previous academic literature. The concepts developed in this study are targeted for a cost-effective hybrid system, which is appropriate for rural and remote residents’ lifestyle change and improvement. Based on the academic research methods, overall analysis procedures can fit as an analogy, especially for developing countries.

  4. Correlation of maple sap composition with bacterial and fungal communities determined by multiplex automated ribosomal intergenic spacer analysis (MARISA).

    Filteau, Marie; Lagacé, Luc; LaPointe, Gisèle; Roy, Denis

    2011-08-01

    During collection, maple sap is contaminated by bacteria and fungi that subsequently colonize the tubing system. The bacterial microbiota has been more characterized than the fungal microbiota, but the impact of both components on maple sap quality remains unclear. This study focused on identifying bacterial and fungal members of maple sap and correlating microbiota composition with maple sap properties. A multiplex automated ribosomal intergenic spacer analysis (MARISA) method was developed to presumptively identify bacterial and fungal members of maple sap samples collected from 19 production sites during the tapping period. Results indicate that the fungal community of maple sap is mainly composed of yeast related to Mrakia sp., Mrakiella sp., Guehomyces pullulans, Cryptococcus victoriae and Williopsis saturnus. Mrakia, Mrakiella and Guehomyces peaks were identified in samples of all production sites and can be considered dominant and stable members of the fungal microbiota of maple sap. A multivariate analysis based on MARISA profiles and maple sap chemical composition data showed correlations between Candida sake, Janthinobacterium lividum, Williopsis sp., Leuconostoc mesenteroides, Mrakia sp., Rhodococcus sp., Pseudomonas tolaasii, G. pullulans and maple sap composition at different flow periods. This study provides new insights on the relationship between microbial community and maple sap quality.

  5. Analysis of oral microbial community and Th17-associated cytokines in saliva of patients with oral lichen planus.

    Wang, Kun; Miao, Tianyu; Lu, Wenxin; He, Jinzhi; Cui, Bomiao; Li, Jiyao; Li, Yan; Xiao, Liying

    2015-03-01

    Oral lichen planus (OLP) is a chronic inflammatory disorder of oral mucosa of unknown cause. Microbial infection and dysimmunity appear to play important roles in its pathogenesis. In this study, differences in genetic profiling of salivary microbial communities in two subtypes of OLP and healthy controls were evaluated by means of PCR-denaturing gradient gel electrophoresis (DGGE). Additionally, ELISA was used to investigate the possible role of Th17 in lesion formation by detecting two related cytokines IL-17 and IL-23 in the saliva of OLP patients. When the DGGE profiles were analyzed, the bacterial populations were found to be significantly less rich in subjects with reticular and erosive OLP than in healthy controls. There was significantly less microbial diversity, as denoted by the Shannon index, in saliva samples from subjects with erosive OLP than in those from healthy controls. Cluster analysis and principal component analysis showed that the DGGE profiles formed distinctly group-specific clusters. Salivary concentrations of IL-17 in subjects with erosive OLP group were significantly higher than in those with reticular OLP and healthy controls. What's more, significantly positive correlations were observed between salivary IL-17 concentrations and disease clinical scores. Microbial richness and diversity was negatively correlated with salivary IL-17 concentrations. These results suggest there is significantly less salivary bacterial diversity and complexity in subjects with OLP han in healthy controls and that the shifted community composition is closely related to an immune cytokine, IL-17.

  6. Community Analysis of Arbuscular Mycorrhizal Fungi in Roots of Poncirus trifoliata and Citrus reticulata Based on SSU rDNA

    Peng Wang

    2014-01-01

    Full Text Available Morphological observation of arbuscular mycorrhizal fungi (AMF species in rhizospheric soil could not accurately reflect the actual AMF colonizing status in roots, while molecular identification of indigenous AMF colonizing citrus rootstocks at present was rare in China. In our study, community of AMF colonizing trifoliate orange (Poncirus trifoliata L. Raf. and red tangerine (Citrus reticulata Blanco were analyzed based on small subunit of ribosomal DNA genes. Morphological observation showed that arbuscular mycorrhizal (AM colonization, spore density, and hyphal length did not differ significantly between two rootstocks. Phylogenetic analysis showed that 173 screened AMF sequences clustered in at least 10 discrete groups (GLO1~GLO10, all belonging to the genus of Glomus Sensu Lato. Among them, GLO1 clade (clustering with uncultured Glomus accounting for 54.43% clones was the most common in trifoliate orange roots, while GLO6 clade (clustering with Glomus intraradices accounting for 35.00% clones was the most common in red tangerine roots. Although, Shannon-Wiener indices exhibited no notable differences between both rootstocks, relative proportions of observed clades analysis revealed that composition of AMF communities colonizing two rootstocks varied severely. The results indicated that native AMF species in citrus rhizosphere had diverse colonization potential between two different rootstocks in the present orchards.

  7. Community-Based HIV-1 Early Diagnosis and Risk Behavior Analysis of Men Having Sex with Men in Hong Kong.

    Liang, Jianguo; Liu, Li; Cheung, Mandy; Lee, Man-Po; Wang, Haibo; Li, Chun-Ho; Chan, Chun-Chung; Nishiura, Kenji; Tang, Xian; Tan, Zhiwu; Peng, Jie; Cheung, Ka-Wai; Yam, Wing-Cheong; Chen, Zhiwei

    2015-01-01

    The increasing prevalence of HIV-1 among men having sex with men (MSM) calls for an investigation of HIV-1 prevalence and incidence in MSM by early diagnosis to assist with early preventive interventions in Hong Kong. The participants were recruited randomly from MSM communities within a one-year period. Rapid HIV Test (RHT) and real-time dried blood spot (DBS)-based quantitative polymerase chain reaction (DBS-qPCR) were used for the early diagnosis of 474 participants. Risk behavior analysis was performed by studying information obtained from the participants during the study period. The HIV-1 prevalence and incident rates in the studied MSM population were 4.01% (19/474) and 1.47% (7/474), respectively. Three infected participants were found at the acute phase of infection by DBS-qPCR. Only 46.4% (220/474) MSM were using condoms regularly for anal sex. HIV infection significantly correlated with unprotected receptive anal sex and syphilis infection. An increased number of infections was found among foreign MSM in Hong Kong. This study is the first to use DBS-qPCR to identify acutely infected individuals in a community setting and to provide both the prevalence and incident rates of HIV-1 infection among MSM in Hong Kong. The risk analysis provided evidence that behavior intervention strengthening is necessary to fight against the increasing HIV-1 epidemic among MSM in Hong Kong and surrounding regions in Asia.

  8. Two-dimensional pattern analysis on dominant species and community in subalpine meadow of Luya Mountain,Shanxi Province,China

    ZHANG Jintun

    2007-01-01

    The spatial pattern analysis of population and community is important to understand community structure and has become one key topic in modern plant ecology.There are many techniques for analyzing one-dimensional pattern in ecological literature.Two-dimensional pattern analysis is better than one-dimensional analysis in the study on community spatial characteristics and structure.However,it is hard to analyze these two-dimensional patterns due to poor effective methodology.The two-dimensional sampling using two transects that meet at right angles was applied to get quadrat data in this work.And then the data from the two transects were analyzed separately by one-dimensional pattern analysis method,two-term local quadrat variance.The length,width,and area of patches at different scales of pattern for populations were obtained from the analysis.For community pattern,detrended correspondence analysis (DCA)was employed to summarize the species information firstly,and then the first DCA axis scores were analyzed to check its pattern.The application of this method to the pattern analysis on dominant populations and community for subalpine meadow (Comm.Polygonum viviparum+Carex rigescens+Kobresia bellardii)in the Luya mountains showed that it could release the characteristics of spatial pattern clearly and was a very effective technique.The method is easy to use and saves time with obvious advantages,compared with the twodimensional pattern analysis methods presented in the literatures.In the study meadow,the patterns of the main dominant species,Polygonum viviparum,Carex rigescens,and Kobresia bellardii,were apparent and comparatively regular in shape with large areas of patches at the same scale compared with other species such as Festuca sp.and Thalictrum petaloideum.There were two or three scales of patterns for each plant population studied.This was related to population features,the interaction with environmental factors,and their dominant position in the community

  9. Incidence of Staphylococcus aureus and analysis of associated bacterial communities on food industry surfaces.

    Gutiérrez, Diana; Delgado, Susana; Vázquez-Sánchez, Daniel; Martínez, Beatriz; Cabo, Marta López; Rodríguez, Ana; Herrera, Juan J; García, Pilar

    2012-12-01

    Biofilms are a common cause of food contamination with undesirable bacteria, such as pathogenic bacteria. Staphylococcus aureus is one of the major bacteria causing food-borne diseases in humans. A study designed to determine the presence of S. aureus on food contact surfaces in dairy, meat, and seafood environments and to identify coexisting microbiota has therefore been carried out. A total of 442 samples were collected, and the presence of S. aureus was confirmed in 6.1% of samples. Sixty-three S. aureus isolates were recovered and typed by random amplification of polymorphic DNA (RAPD). Profiles were clustered into four groups which were related to specific food environments. All isolates harbored some potential virulence factors such as enterotoxin production genes, biofilm formation-associated genes, antibiotic resistance, or lysogeny. PCR-denaturing gradient gel electrophoresis (PCR-DGGE) fingerprints of bacterial communities coexisting with S. aureus revealed the presence of bacteria either involved in food spoilage or of concern for food safety in all food environments. Food industry surfaces could thus be a reservoir for S. aureus forming complex communities with undesirable bacteria in multispecies biofilms. Uneven microbiological conditions were found in each food sector, which indicates the need to improve hygienic conditions in food processing facilities, particularly the removal of bacterial biofilms, to enhance the safety of food products.

  10. Land Rights of Community Forest Plantation Policy: Analysis from an Institutional Perspective

    Bramasto Nugroho

    2012-01-01

    Full Text Available This study aimed to describe the land rights of bussiness permit for timber utilization from community forestplantation (IUPHHK-HTR in Indonesia and to predict its effectiveness based on property rights theory relatedto target group characteristics. Field survey was conducted in November 2008 to April 2009 in Riau and SouthKalimantan Provinces. The results showed that from the property rights theory perspective, the land rights forHTR could be categorized as lease or management rights consisted of rights to exclude, to manage, to use, andto access, without rights to transfer and to bequeath. This suggests that the mechanism of transfer of rights fromthe government to the holder of IUPHHK-HTR as a temporary transfer of rights. As a result, the government needsto regulate a rigid and detailed obligation for IUPHHK-HTR holders that may not be fulfilled by the farmers. Thegranting of permits for a long period (up to 95 years is predicted to lose the meanings, caused of the prohibitionon inheritance of the permits. From these findings it is predicted to reduce the interest of farmers to invest in theHTR.Keywords: land rights, community forest plantation, institutions, property rights, lease/management rights

  11. Perchlorate reduction by hydrogen autotrophic bacteria and microbial community analysis using high-throughput sequencing.

    Wan, Dongjin; Liu, Yongde; Niu, Zhenhua; Xiao, Shuhu; Li, Daorong

    2016-02-01

    Hydrogen autotrophic reduction of perchlorate have advantages of high removal efficiency and harmless to drinking water. But so far the reported information about the microbial community structure was comparatively limited, changes in the biodiversity and the dominant bacteria during acclimation process required detailed study. In this study, perchlorate-reducing hydrogen autotrophic bacteria were acclimated by hydrogen aeration from activated sludge. For the first time, high-throughput sequencing was applied to analyze changes in biodiversity and the dominant bacteria during acclimation process. The Michaelis-Menten model described the perchlorate reduction kinetics well. Model parameters q(max) and K(s) were 2.521-3.245 (mg ClO4(-)/gVSS h) and 5.44-8.23 (mg/l), respectively. Microbial perchlorate reduction occurred across at pH range 5.0-11.0; removal was highest at pH 9.0. The enriched mixed bacteria could use perchlorate, nitrate and sulfate as electron accepter, and the sequence of preference was: NO3(-) > ClO4(-) > SO4(2-). Compared to the feed culture, biodiversity decreased greatly during acclimation process, the microbial community structure gradually stabilized after 9 acclimation cycles. The Thauera genus related to Rhodocyclales was the dominated perchlorate reducing bacteria (PRB) in the mixed culture.

  12. Analysis of Fuel Cell Driven Ground Source Heat Pump Systems in Community Buildings

    Jong-Keun Shin

    2013-05-01

    Full Text Available In the present study, a fuel cell driven ground source heat pump (GSHP system is applied in a community building and heat pump system performance is analyzed by computational methods. Conduction heat transfer between the brine pipe and ground is analyzed by TEACH code in order to predict the performance of the heat pump system. The predicted coefficient of performance (COP of the heat pump system and the energy cost were compared with the variation of the location of the objective building, the water saturation rate of the soil, and the driven powers of the heat pump system. Compared to the late-night electricity driven system, a significant reduction of energy cost can be accomplished by employing the fuel cell driven heat pump system. This is due to the low cost of electricity production of the fuel cell system and to the application of the recovered waste heat generated during the electricity production process to the heating of the community building.

  13. Comparative metagenomic analysis of soil microbial communities across three hexachlorocyclohexane contamination levels.

    Naseer Sangwan

    Full Text Available This paper presents the characterization of the microbial community responsible for the in-situ bioremediation of hexachlorocyclohexane (HCH. Microbial community structure and function was analyzed using 16S rRNA amplicon and shotgun metagenomic sequencing methods for three sets of soil samples. The three samples were collected from a HCH-dumpsite (450 mg HCH/g soil and comprised of a HCH/soil ratio of 0.45, 0.0007, and 0.00003, respectively. Certain bacterial; (Chromohalobacter, Marinimicrobium, Idiomarina, Salinosphaera, Halomonas, Sphingopyxis, Novosphingobium, Sphingomonas and Pseudomonas, archaeal; (Halobacterium, Haloarcula and Halorhabdus and fungal (Fusarium genera were found to be more abundant in the soil sample from the HCH-dumpsite. Consistent with the phylogenetic shift, the dumpsite also exhibited a relatively higher abundance of genes coding for chemotaxis/motility, chloroaromatic and HCH degradation (lin genes. Reassembly of a draft pangenome of Chromohalobacter salaxigenes sp. (∼8X coverage and 3 plasmids (pISP3, pISP4 and pLB1; 13X coverage containing lin genes/clusters also provides an evidence for the horizontal transfer of HCH catabolism genes.

  14. Factors associated with use of community mental health services by schizophrenia patients using multilevel analysis

    Moreno Patricia

    2011-10-01

    Full Text Available Abstract Background Persons with schizophrenia and related disorders may be particularly sensitive to a number of determinants of service use, including those related with illness, socio-demographic characteristics and organizational factors. The objective of this study is to identify factors associated with outpatient contacts at community mental health services of patients with schizophrenia or related disorders. Methods This cross-sectional study analyzed 1097 patients. The main outcome measure was the total number of outpatient consultations during one year. Independent variables were related to socio-demographic, clinical and use of service factors. Data were collected from clinical records. Results The multilevel linear regression model explained 46.35% of the variance. Patients with significantly more contacts with ambulatory services were not working and were receiving welfare benefits (p = 0.02, had no formal education (p = 0.02, had a global level of severity of two or three (four being the most severe (p Conclusions As expected, the variables that explained the use of community service could be viewed as proxies for severity of illness. The most surprising finding, however, was that a group of four psychiatrists was also independently associated with use of ambulatory services by patients with schizophrenia or related disorders. More research is needed to carefully examine how professional support networks interact to affect use of mental health.

  15. The antecedents of identification: a rhetorical analysis of British Muslim activists' constructions of community and identity.

    Hopkins, Nick; Kahani-Hopkins, Vered

    2004-03-01

    This paper takes as its focus the perception of community. This is analysed through reference to the literature concerning the adoption of more inclusive, superordinate social categories. Whilst most research tends to focus on the consequences of these social categories for self and other perception, we focus on their antecedents. These are typically hypothesized to include such issues as the perception of the subordinate groups' common fate and factors affecting their perceptual differentiation (e.g. their similarity and entitativity). However, rather than conceiving of such issues as pre-given antecedent variables, we explore how these issues (and others) are actively constructed in and through discourse. More specifically, we explore how such issues are sites of contestation as activists with different political projects seek to construct quite different versions of the relevant superordinate community identity. Our data are qualitative and are drawn from contemporary debates amongst British Muslims concerning their relations with non-Muslim Britons and non-British Muslims across the globe. A key issue in these deliberations concerns the nature of British Muslims' identity and the superordinate identifications that best facilitate its expression and realization. We suggest that constructions of common fate, similarity, entitativity etc., far from being 'givens', are the means through which different definitions of Muslim identity are constructed and different forms of collective action mobilized.

  16. Analysis of Knowledge Level and Perception on Singkawang City Community towards Generic Medicines

    Forid Morison

    2015-03-01

    Full Text Available Survey data show that the use of generic medicines in Indonesia is relatively very small, which only amounted 7%. This is due to lack of knowledge and poor perceptions towards generic medicines. Knowledge level and perceptions towards generic medicines are inflenced by community characteristics and information resource regarding generic medicines. The aim of this study was to determine the association between community characteristic and information resources with knowledge level and perception towards generic medicines. This study was an analytical survey with cross-sectional descriptive approach on 142 selected respondents who were fulfi inclusion and exclusion criteria. This study was conducted in June 2014 at several randomly selected locations on Singkawang City. The study show that 76 respondents (53.5% had inadequate knowledge and 123 respondents (86.6% had a good perception towards generic medicines. There is signifiant relationship between ethnicity (p=0.000 and information resources (p=0.009 with knowledge level regarding generic medicines at signifiance level of p<0.05. Although good perceptions were noted among the respondents, widespread dissemination of information regarding generic medicines should be continued to increase generic medicines used.

  17. Microbial community in anoxic-oxic-settling-anaerobic sludge reduction process revealed by 454 pyrosequencing analysis.

    Ning, Xinqiang; Qiao, Wenwen; Zhang, Lei; Gao, Xu

    2014-12-01

    Modification of the anoxic-oxic (AO) process by inserting a sludge holding tank (SHT) into the sludge return line forms an anoxic-oxic-settling-anaerobic (A+OSA) process that can achieve a 48.98% sludge reduction rate. The 454 pyrosequencing method was used to obtain the microbial communities of the AO and A+OSA processes. Results showed that the microbial community structures of the 2 processes were different as a result of the SHT insertion. Bacteria assigned to the phyla Proteobacteria and Bacteroidetes commonly existed and dominated the microbial populations of the 2 processes. However, the relative abundance of these populations shifted in the presence of SHT. The relative abundance of Proteobacteria decreased during the A+OSA process. A specific comparison at the class level showed that Sphingobacteria was enriched in the A+OSA process. The result suggested that the fermentative bacteria Sphingobacteria may have key functions in reducing the sludge from the A+OSA process. Uncultured Nitrosomonadaceae gradually became the dominant ammonia-oxidizing bacteria, and the nitrite-oxidizing bacterium Nitrospira was enriched in the A+OSA process. Both occurrences were favorable for stabilized nitrogen removal. The known denitrifying species in the A+OSA process were similar to those in the AO process; however, their relative abundance also decreased.

  18. Hierarchical modeling and inference in ecology: The analysis of data from populations, metapopulations and communities

    Royle, J. Andrew; Dorazio, Robert M.

    2008-01-01

    A guide to data collection, modeling and inference strategies for biological survey data using Bayesian and classical statistical methods. This book describes a general and flexible framework for modeling and inference in ecological systems based on hierarchical models, with a strict focus on the use of probability models and parametric inference. Hierarchical models represent a paradigm shift in the application of statistics to ecological inference problems because they combine explicit models of ecological system structure or dynamics with models of how ecological systems are observed. The principles of hierarchical modeling are developed and applied to problems in population, metapopulation, community, and metacommunity systems. The book provides the first synthetic treatment of many recent methodological advances in ecological modeling and unifies disparate methods and procedures. The authors apply principles of hierarchical modeling to ecological problems, including * occurrence or occupancy models for estimating species distribution * abundance models based on many sampling protocols, including distance sampling * capture-recapture models with individual effects * spatial capture-recapture models based on camera trapping and related methods * population and metapopulation dynamic models * models of biodiversity, community structure and dynamics.

  19. A Foundation of Discourse Analysis: Discourse Community%话语分析的基础:话语共同体

    严明

    2009-01-01

    话语分析,尤其是批评话语分析,已经成为学界研究的热点.但是它的学科目的、分析基础和进一步推进途径等都有待确定.本文以话语共同体为研究对象,从"起源与发展"、"概念"和"特征"三个维度切人,一方面建构话语分析的基础,另一方面构拟话语分析的基本内容,第三方面指出推进话语分析的可能路径.%Discourse analysis, especially critical discourse analysis, has become a hot issue in the research circle of applied linguis-tics. However, its disciplinary purpose, foundations of analysis and future direction for research are yet to be determined. Taking discourse community as its objeet of research which eovers the three dimensions of "origins and developments", "definitions" and "eharaeteristies", this article comes up with the construction of the foundations and basic contents for discourse analysis, on the one hand, and possible paths for promoting discourse analysis, on the other.

  20. Microarray-based analysis of survival of soil microbial community during ozonation

    Wang, Jian; Van Nostrand, Joy D.; He, Zhili; Wu, Liyou; Deng, Ye; Zhang, Xu; Zhou, Jizhong; Li, Guanghe

    2010-05-17

    A 15 h ozonation was performed on bioremediated soil to remove recalcitrant residual oil. To monitor the survival of indigenous microorganisms in the soil during in-situ chemical oxidation(ISCO) culturing and a functional genearray, GeoChip, was used to examine the functional genes and structure of the microbial community during ozonation (0h, 2h, 4h, 6h, 10hand15h). Breakthrough ozonation decreased the population of cultivable heterotrophic bacteria by about 3 orders of magnitude. The total functional gene abundance and diversity decreased during ozonation, as the number of functional genes was reduced by 48percent after 15 h. However, functional genes were evenly distributed during ozonation as judged by the Shannon-Weaver Evenness index. A sharp decrease in gene number was observed in the first 6 h of ozonation followed by a slower decrease in the next 9 h, which was consistent with microbial populations measured by a culture based method. Functional genes involved in carbon, nitrogen, phosphors and sulfur cycling, metal resistance and organic remediation were detected in all samples. Though the pattern of gene categories detected was similar for all time points, hierarchica lcluster of all functional genes and major functional categories all showed a time-serial pattern. Bacteria, archaea and fungi decreased by 96.1percent, 95.1percent and 91.3percent, respectively, after 15 h ozonation. Delta proteobacteria, which were reduced by 94.3percent, showed the highest resistance to ozonation while Actinobacteria, reduced by 96.3percent, showed the lowest resistance. Microorganisms similar to Rhodothermus, Obesumbacterium, Staphylothermus, Gluconobacter, and Enterococcus were dominant at all time points. Functional genes related to petroleum degradation decreased 1~;;2 orders of magnitude. Most of the key functional genes were still detected after ozonation, allowing a rapid recovery of the microbial community after ozonation. While ozone had a large impact on the

  1. Health Quality Analysis of Kaifeng's Community Individuals%开封市社区人群健康素质分析

    贺红梅; 赵艳梅; 刘庆芳; 马玉红; 邢煜君; 张百让; 张宛玉

    2001-01-01

    lack of prevent and cure diseases aknowlege.Conclusion:This study,using community health analysis meth ods,evaluates Kaifeng's community health for population character、conmunity nutrition、child's growing and common diseases,three ways:Coef ticient of burden on young and old in Kaifeng community all are high;The children in Kaifeng have health behaver; Comrmunity individuals health care by themself consciousness is poor.As to this community health situation,we should develop community nutrition prevent and cure common diseases aknowlege education and health care.

  2. Social Network Analysis to Examine Interaction Patterns in Knowledge Building Communities

    Philip, Donald N.

    2010-01-01

    This paper describes use of social network analysis to examine student interaction patterns in a Grade 5/6 Knowledge Building class. The analysis included face-to-face interactions and interactions in the Knowledge Forum[R] Knowledge Building environment. It is argued that sociogram data are useful to reveal group processes; in sociological terms,…

  3. Assessing community-based conservation projects: A systematic review and multilevel analysis of attitudinal, behavioral, ecological, and economic outcomes

    Brooks Jeremy

    2013-01-01

    Full Text Available Abstract Background Community-based conservation (CBC promotes the idea that long-term conservation success requires engaging with, and providing benefits for local communities. Though widespread, CBC projects are not always successful or free of controversy. With criticisms on all sides of the conservation debates, it is critical to have a better understanding of (1 whether CBC is an effective conservation tool, and (2 of the factors associated with the success or failure of CBC projects, and the scale at which these factors operate. Recent CBC reviews have typically examined only a single resource domain, have limited geographic scope, consider only one outcome, or ignore the nested nature of socioecological systems. To remedy these issues, we use a newly coded global comparative database of CBC projects identified by systematic review to evaluate success in four outcome domains (attitudes, behaviors, ecological, economic and explore synergies and tradeoffs among these outcomes. We test hypotheses about how features of the national context (H-NC, project design (H-PD, and local community characteristics (H-CC affect these four measures of success. Methods To add to a sample of 62 projects that we used from previous systematic reviews, we systematically searched the conservation literature using six terms in four online databases. To increase the number of projects for each country in order to conduct a multilevel analysis, we also conducted a secondary search using the Advancing Conservation in a Social Context online library. We coded projects for 65 pieces of information. We conducted bivariate analyses using two-dimensional contingency tables and proportional odds logistic regression and conducted multivariate analyses by fitting reduced form proportional odds logistic regression models that were selected using a forward stepwise AIC approach. Results The primary and secondary searches produced 74 new projects to go along with the 62

  4. Multimorbidity in a Mexican Community: Secondary Analysis of Chronic Illness and Depression Outcomes

    O'Connor, Kathleen; Vizcaino, Maricarmen; Ibarra, Jorge M.; Balcazar, Hector; Perez, Eduardo; Flores, Luis; Anders, Robert L.

    2015-01-01

    The aims of this article are: 1) to examine the associations between health provider-diagnosed depression and multimorbidity, the condition of suffering from more than two chronic illnesses; 2) to assess the unique contribution of chronic illness in the prediction of depression; and 3) to suggest practice changes that would address risk of depression among individuals with chronic illnesses. Data collected in a cross-sectional community health study among adult Mexicans (n= 274) living in a low income neighborhood (colonia) in Ciudad Juárez, Chihuahua, Mexico, were examined. We tested the hypotheses that individuals who reported suffering chronic illnesses would also report higher rates of depression than healthy individuals; and having that two or more chronic illnesses further increased the risk of depression. PMID:26640817

  5. Illumina-based analysis of bacterial community in Khuangcherapuk cave of Mizoram, Northeast India

    Surajit De Mandal

    2015-09-01

    Full Text Available Bacterial community of the Khuangcherapuk cave sediment was assessed by Illumina amplicon sequencing. The metagenome comprised of 533,120 raw reads with an average base quality (Phred score 36.75 and G + C content is 57.61%. A total of 18 bacterial phyla were detected with following abundant genus — Mycobacterium (21.72%, Rhodococcus (7.09%, Alteromonas (1.42%, Holomonas (0.7% and Salinisphaera (0.20%. Majority portion of the sequences (68% is unclassified at the genus level indicating the possibilities for the presence of novel species in this cave. This study reports the cave bacterial diversity from the biodiversity hotspot region of Eastern Himalayas. Metagenome sequence data are available at NCBI under the Bioproject database with accession no. SRP056890.

  6. Metaproteomic Analysis of a Chemosynthetic Hydrothermal Vent Community Reveals Insights into Key-Metabolic Processes

    Steen, I.; Stokke, R.; Lanzen, A.; Pedersen, R.; Øvreås, L.; Urich, T.

    2010-12-01

    In 2005 researchers at the Centre for Geobiology, University of Bergen, Norway, discovered two active vent fields at the southwestern Mohns Ridge in the Norwegian-Greenland Sea. The fields harbours both low-temperature iron deposits and high-temperature white smoker vents. Distinct microbial mats were abundantly present and located in close vicinity to the hydrothermal vent sites. Characteristics of the mat environment were steep physical and chemical gradients with temperatures ranging from 10°C in the top layer to 90°C at 10 cm bsf and high concentrations of hydrogen sulfide and methane. The work presented here focus on the In situ community activities, and is part of an integrated strategy combining metagenomics, metatranscriptomics and metaproteomics to in-depth characterise these newly discovered hydrothermal vent communities. Extracted proteins were separated via SDS-PAGE. Peptides extracted after In-gel tryptic digest was injected into an Ultimate 3000 nanoLC system connected to a linear quadropole ion trap-orbitrap (LTQ-Orbitrap XL) mass spectrometer equipped with a nanoelectrospray ion source. A custom database of open reading frames (ORFs) from the combined metatranscriptome and metagenome datasets was implemented and searched against using Mascot 2.2; the IRMa tool box [1] was used in peptide validation. Validated ORFs were subjected to a Blastp search against Refseq with an E-value cut-off of 0.001. A total of 1097 proteins with ≥ 2 peptides were identified of which 921 gave a hit against Refseq, containing 519 unique proteins. Key enzymes of the sulfur oxidation pathway (sox) were found, which were taxonomically affiliated to Epsilonproteobacteria. In addition, this group actively expressed hydrogenases and membrane proteins involved in aerobic and anaerobic respiratory chains. Enzymes of dissimilatory sulfate-reduction (APS-reductase, AprAB and DsrA2) were found with closest hit to members of the Deltaproteobacteria. These findings indicate an

  7. [Analysis of Microbial Community in the Membrane Bio-Reactor (MBR) Rural Sewage Treatment System].

    Kong, Xiao; Cui, Bing-jian; Jin, De-cai; Wu, Shang-hua; Yang, Bo; Deng, Ye; Zhuang, Guo-qiang; Zhuang, Xu-liang

    2015-09-01

    Uncontrolled release and arbitrary irrigation reuse of rural wastewater may lead to water pollution, and the microbial pathogens could threaten the safety of freshwater resources and public health. To understand the microbial community structure of rural wastewater and provide the theory for microbial risk assessment of wastewater irrigation, microbial community diversities in the Membrane Bio-Reactor (MBR) process for rural wastewater treatment was studied by terminal restriction fragment length polymorphism (T-RFLP) and 16S rDNA gene clone library. Meanwhile, changes of Arcobacter spp. and total bacteria before and after treatment were detected through real-time quantitative PCR. The clone library results showed that there were 73 positive clones included Proteobacteria (91. 80%), Firmicutes (2. 70%), Bacteroidetes (1. 40%), and uncultured bacteria (4. 10%) in the untreated wastewater. The typical pathogenic genus Arcobacter belonging to e-Proteobacteria was the dominant component of the library, accounting for 68. 5% of all clones. The main groups and their abundance in different treatments were significantly distinct. The highest values of species abundance (S), Shannon-Wiener (H) and Evenness (E) were observed in the adjusting tank, which were 43. 0, 3. 56 and 0. 95, respectively. The real-time quantitative PCR results showed that the copy number of Arcobacter spp. was (1. 09 ± 0. 064 0) x 10(11) copies.L-1 in the untreated sewage, which was consistent with the result of 16S rDNA gene clone library. Compared to untreated wastewater, bacterial copy number in the treated effluent decreased 100 to 1 000 times, respectively, suggesting that MBR treatment system could remove the microbial quantity in such scale. In the recycled water, the physicochemical parameters and indicator bacteria met the water quality standard of farmland irrigation. However, further research is needed to estimate the potential health risks caused by residual pathogenic microorganisms in

  8. Community Analysis and Recovery of Phenol-degrading Bacteria from Drinking Water Biofilters.

    Gu, Qihui; Wu, Qingping; Zhang, Jumei; Guo, Weipeng; Wu, Huiqing; Sun, Ming

    2016-01-01

    Phenol is a ubiquitous organic contaminant in drinking water. Biodegradation plays an important role in the elimination of phenol pollution in the environment, but the information about phenol removal by drinking water biofilters is still lacking. Herein, we study an acclimated bacterial community that can degrade over 80% of 300 mg/L phenol within 3 days. PCR detection of genotypes involved in bacterial phenol degradation revealed that the degradation pathways contained the initial oxidative attack by phenol hydroxylase, and subsequent ring fission by catechol 1,2-dioxygenase. Based on the PCR denatured gradient gel electrophoresis (PCR-DGGE) profiles of bacteria from biological activated carbon (BAC), the predominant bacteria in drinking water biofilters including Delftia sp., Achromobacter sp., and Agrobacterium sp., which together comprised up to 50% of the total microorganisms. In addition, a shift in bacterial community structure was observed during phenol biodegradation. Furthermore, the most effective phenol-degrading strain DW-1 that correspond to the main band in denaturing gradient gel electrophoresis (DGGE) profile was isolated and identified as Acinetobacter sp., according to phylogenetic analyses of the 16S ribosomal ribonucleic acid (rRNA) gene sequences. The strain DW-1 also produced the most important enzyme, phenol hydroxylase, and it also exhibited a good ability to degrade phenol when immobilized on granular active carbon (GAC). This study indicates that the enrichment culture has great potential application for treatment of phenol-polluted drinking water sources, and the indigenous phenol-degrading microorganism could recover from drinking water biofilters as an efficient resource for phenol removal. Therefore, the aim of this study is to draw attention to recover native phenol-degrading bacteria from drinking water biofilters, and use these native microorganisms as phenolic water remediation in drinking water sources.

  9. Retrospective analysis towards diagnosis and treatment status of acute myocardial infarction patients in Binhai Community

    Ying Lu; Zhou Zou

    2013-01-01

    Objective:To investigate the features towards diagnosis and treatment status of acute myocardial infarction patients inBinhai community.And to offer some helps towards community hospitals in treatment withAMI patients.Methods:One hundred and twenty oneAMI patients were randomly divided into treatment groups(n=72) and control groups(n=49).Two groups comparative difference was not statistically significant in age,Killip classification, hypertension, diabetes, hyperglycemia, stroke, and drug used after entering the hospital(P all>0.05).The treatment group received the drugs within4 h,Control group received the drugs after4 h.Results:The post infarction angina rate is low in treatment group(4.17%) when compared with control group (18.37%) after entering the hospital.And the death rate is also low in treatment group(1.39%) when compared with control group(10.20%) after entering the hospital.The utilization rates of drugs by recommendation like nitrates, β-receptor blockers, aspirin, clopidogrel, low molecular weight heparin were excellent when compared with situations two decades ago.Traditional Chinese medicine intervention is more popular than before.Conclusions:Low post infarction angina rate and low death rate have the positive correlation with drugs by recommendation and traditionalChinese medicine intervention.AMI patients under emergency thrombolytic therapy can improve the treatment effect, improve the prognosis of patients effectively and accelerate the rehabilitation. hs-cTn detecting techniques will classify the patients rapidly and bring a brilliant future to them.

  10. Community analysis and recovery of phenol-degrading bacteria from drinking water biofilters

    Qihui eGu

    2016-04-01

    Full Text Available Phenol is a ubiquitous organic contaminant in drinking water. Biodegradation plays an important role in the elimination of phenol pollution in the environment, but the information about phenol removal by drinking water biofilters is still lacking. Herein, we study an acclimated bacterial community that can degrade over 80% of 300 mg/L phenol within 3 d. PCR detection of genotypes involved in bacterial phenol degradation revealed that the degradation pathways contained the initial oxidative attack by phenol hydroxylase, and subsequent ring fission by catechol 1,2-dioxygenase. Based on the PCR denatured gradient gel electrophoresis (PCR-DGGE profiles of bacteria from biological activated carbon (BAC, the predominant bacteria in drinking water biofilters including Delftia sp., Achromobacter sp., and Agrobacterium sp., which together comprised up to 50% of the total microorganisms. In addition, a shift in bacterial community structure was observed during phenol biodegradation. Furthermore, the most effective phenol-degrading strain DW-1 that correspond to the main band in DGGE profile was isolated and identified as Acinetobacter sp., according to phylogenetic analyses of the 16S ribosomal ribonucleic acid (rRNA gene sequences. The strain DW-1 also produced the most important enzyme, phenol hydroxylase, and it also exhibited a good ability to degrade phenol when immobilized on GAC. This study indicates that the enrichment culture has great potential application for treatment of phenol-polluted drinking water sources, and the indigenous phenol-degrading microorganism could recover from drinking water biofilters as an efficient resource for phenol removal. Therefore, the aim of this study is to draw attention to recover native phenol-degrading bacteria from drinking water biofilters, and use these native microorganisms as phenolic water remediation in drinking water sources.

  11. Pyrosequencing analysis of microbial communities in hollow fiber-membrane biofilm reactors system for treating high-strength nitrogen wastewater.

    Park, Jung-Hun; Choi, Okkyoung; Lee, Tae-Ho; Kim, Hyunook; Sang, Byoung-In

    2016-11-01

    Wastewaters from swine farms, nitrogen-dealing industries or side-stream processes of a wastewater treatment plant (e.g., anaerobic digesters, sludge thickening processes, etc.) are characterized by low C/N ratios and not easily treatable. In this study, a hollow fiber-membrane biofilm reactors (HF-MBfR) system consisting of an O2-based HF-MBfR and an H2-based HF-MBfR was applied for treating high-strength wastewater. The reactors were continuously operated with low supply of O2 and H2 and without any supply of organic carbon for 250 d. Gradual increase of ammonium and nitrate concentration in the influent showed stable and high nitrogen removal efficiency, and the maximum ammonium and nitrate removal rates were 0.48 kg NH4(+)-N m(-3) d(-1) and 0.55 kg NO3(-)-N m(-3) d(-1), respectively. The analysis of the microbial communities using pyrosequencing analysis indicated that Nitrosospira multiformis, ammonium-oxidizing bacteria, and Nitrobacter winogradskyi and Nitrobacter vulgaris, nitrite-oxidizing bacteria were highly enriched in the O2-based HF-MBfR. In the H2-based HF-MBfR, hydrogenotrophic denitrifying bacteria belonging to the family of Thiobacillus and Comamonadaceae were initially dominant, but were replaced to heterotrophic denitrifiers belonging to Rhodocyclaceae and Rhodobacteraceae utilizing by-products induced from autotrophic denitrifying bacteria. The pyrosequencing analysis of microbial communities indicates that the autotrophic HF-MBfRs system well developed autotrophic nitrifying and denitrifying bacteria within a relatively short period to accomplish almost complete nitrogen removal.

  12. Integrated proteomic and metabolomic analysis of an artificial microbial community for two-step production of vitamin C.

    Qian Ma

    Full Text Available An artificial microbial community consisted of Ketogulonicigenium vulgare and Bacillus megaterium has been used in industry to produce 2-keto-gulonic acid (2-KGA, the precursor of vitamin C. During the mix culture fermentation process, sporulation and cell lysis of B. megaterium can be observed. In order to investigate how these phenomena correlate with 2-KGA production, and to explore how two species interact with each other during the fermentation process, an integrated time-series proteomic and metabolomic analysis was applied to the system. The study quantitatively identified approximate 100 metabolites and 258 proteins. Principal Component Analysis of all the metabolites identified showed that glutamic acid, 5-oxo-proline, L-sorbose, 2-KGA, 2, 6-dipicolinic acid and tyrosine were potential biomarkers to distinguish the different time-series samples. Interestingly, most of these metabolites were closely correlated with the sporulation process of B. megaterium. Together with several sporulation-relevant proteins identified, the results pointed to the possibility that Bacillus sporulation process might be important part of the microbial interaction. After sporulation, cell lysis of B. megaterium was observed in the co-culture system. The proteomic results showed that proteins combating against intracellular reactive oxygen stress (ROS, and proteins involved in pentose phosphate pathway, L-sorbose pathway, tricarboxylic acid cycle and amino acids metabolism were up-regulated when the cell lysis of B. megaterium occurred. The cell lysis might supply purine substrates needed for K. vulgare growth. These discoveries showed B. megaterium provided key elements necessary for K. vulgare to grow better and produce more 2-KGA. The study represents the first attempt to decipher 2-KGA-producing microbial communities using quantitative systems biology analysis.

  13. Integrated proteomic and metabolomic analysis of an artificial microbial community for two-step production of vitamin C.

    Ma, Qian; Zhou, Jian; Zhang, Weiwen; Meng, Xinxin; Sun, Junwei; Yuan, Ying-Jin

    2011-01-01

    An artificial microbial community consisted of Ketogulonicigenium vulgare and Bacillus megaterium has been used in industry to produce 2-keto-gulonic acid (2-KGA), the precursor of vitamin C. During the mix culture fermentation process, sporulation and cell lysis of B. megaterium can be observed. In order to investigate how these phenomena correlate with 2-KGA production, and to explore how two species interact with each other during the fermentation process, an integrated time-series proteomic and metabolomic analysis was applied to the system. The study quantitatively identified approximate 100 metabolites and 258 proteins. Principal Component Analysis of all the metabolites identified showed that glutamic acid, 5-oxo-proline, L-sorbose, 2-KGA, 2, 6-dipicolinic acid and tyrosine were potential biomarkers to distinguish the different time-series samples. Interestingly, most of these metabolites were closely correlated with the sporulation process of B. megaterium. Together with several sporulation-relevant proteins identified, the results pointed to the possibility that Bacillus sporulation process might be important part of the microbial interaction. After sporulation, cell lysis of B. megaterium was observed in the co-culture system. The proteomic results showed that proteins combating against intracellular reactive oxygen stress (ROS), and proteins involved in pentose phosphate pathway, L-sorbose pathway, tricarboxylic acid cycle and amino acids metabolism were up-regulated when the cell lysis of B. megaterium occurred. The cell lysis might supply purine substrates needed for K. vulgare growth. These discoveries showed B. megaterium provided key elements necessary for K. vulgare to grow better and produce more 2-KGA. The study represents the first attempt to decipher 2-KGA-producing microbial communities using quantitative systems biology analysis.

  14. Diel metabolomics analysis of a hot spring chlorophototrophic microbial mat leads to new hypotheses of community member metabolisms

    Young-Mo eKim

    2015-04-01

    Full Text Available Dynamic environmental factors such as light, nutrients, salt, and temperature continuously affect chlorophototrophic microbial mats, requiring adaptive and acclimative responses to stabilize composition and function. Quantitative metabolomics analysis can provide insights into metabolite dynamics for understanding community response to such changing environmental conditions. In this study, we quantified volatile organic acids, polar metabolites (amino acids, glycolytic and citric acid cycle intermediates, nucleobases, nucleosides, and sugars, wax esters, and polyhydroxyalkanoates, resulting in the identification of 104 metabolites and related molecules in thermal chlorophototrophic microbial mat cores collected over a diel cycle in Mushroom Spring, Yellowstone National Park. A limited number of predominant taxa inhabit this community and their functional potentials have been previously identified through metagenomic and metatranscriptomic analyses and in situ metabolisms, and metabolic interactions among these taxa have been hypothesized. Our metabolomics results confirmed the diel cycling of photorespiration (e.g. glycolate and fermentation (e.g. acetate, propionate, and lactate products, the carbon storage polymers polyhydroxyalkanoates, and dissolved gases (e.g. H2 and CO2 in the waters overlying the mat, which were hypothesized to occur in major mat chlorophototrophic community members. In addition, we have formulated the following new hypotheses: 1 the morning hours are a time of biosynthesis of amino acids, DNA, and RNA; 2 photo-inhibited cells may also produce lactate via fermentation as an alternate metabolism; 3 glycolate and lactate are exchanged among Synechococcus and Roseiflexus spp.; and 4 fluctuations in many metabolite pools (e.g. wax esters at different times of day result from species found at different depths within the mat responding to temporal differences in their niches

  15. ABC-VED Analysis of a Drug Store in the Department of Community Medicine of a Medical College in Delhi.

    Anand, T; Ingle, G K; Kishore, J; Kumar, R

    2013-01-01

    A matrix based on coupling of cost (always, better and control) analysis and criticality (vital, essential and desirable) analysis was employed for drug inventory containing 129 items of drug store in the Department of Community Medicine of a Medical College in Delhi. The annual drug expenditure incurred on 129 drug items for the year 2010-2011 was found to be Rs. 4,35,847.85. On always, better and control analysis, 18.6, 24.0 and 57.4% drugs were found to be always, better and control category items, respectively, amounting for 69.1, 20.8 and 10.1% of annual drug expenditure. About 13.2 (17), 38.8 (50) and 48.0% (62) items were found to be vital, essential and desirable category items, respectively, amounting for 18.7, 49.5 and 31.8% of annual drug expenditure. Based on always, better and control-vital, essential and desirable matrix analysis there were 37 (28.68%) items in category I, 53 (41.09%) items in category II and 39 (30.23%) items in category III, amounting for 73.0, 22.2 and 4.8% of annual drug expenditure, respectively. To conclude, scientific inventory management tools are needed to be applied in routine for efficient management of the pharmacy stores as it contributes to not only in improvement in patient care but also judicious use of resources as well.

  16. Project Final Report: Building a Community Infrastructure for Scalable On-Line Performance Analysis Tools around Open|SpeedShop

    Galarowicz, James

    2014-01-06

    In this project we created a community tool infrastructure for program development tools targeting Petascale class machines and beyond. This includes tools for performance analysis, debugging, and correctness tools, as well as tuning and optimization frameworks. The developed infrastructure provides a comprehensive and extensible set of individual tool building components. We started with the basic elements necessary across all tools in such an infrastructure followed by a set of generic core modules that allow a comprehensive performance analysis at scale. Further, we developed a methodology and workflow that allows others to add or replace modules, to integrate parts into their own tools, or to customize existing solutions. In order to form the core modules, we built on the existing Open|SpeedShop infrastructure and decomposed it into individual modules that match the necessary tool components. At the same time, we addressed the challenges found in performance tools for petascale systems in each module. When assembled, this instantiation of community tool infrastructure provides an enhanced version of Open|SpeedShop, which, while completely different in its architecture, provides scalable performance analysis for petascale applications through a familiar interface. This project also built upon and enhances capabilities and reusability of project partner components as specified in the original project proposal. The overall project team’s work over the project funding cycle was focused on several areas of research, which are described in the following sections. The reminder of this report also highlights related work as well as preliminary work that supported the project. In addition to the project partners funded by the Office of Science under this grant, the project team included several collaborators who contribute to the overall design of the envisioned tool infrastructure. In particular, the project team worked closely with the other two DOE NNSA

  17. Evaluation and optimization of nucleic acid extraction methods for the molecular analysis of bacterial communities associated with corroded carbon steel.

    Marty, Florence; Ghiglione, Jean-François; Païssé, Sandrine; Gueuné, Hervé; Quillet, Laurent; van Loosdrecht, Mark C M; Muyzer, Gerard

    2012-01-01

    Different DNA and RNA extraction approaches were evaluated and protocols optimized on in situ corrosion products from carbon steel in marine environments. Protocols adapted from the PowerSoil DNA/RNA Isolation methods resulted in the best nucleic acid (NA) extraction performances (ie combining high NA yield, quality, purity, representativeness of microbial community and processing time efficiency). The PowerSoil RNA Isolation Kit was the only method which resulted in amplifiable RNA of good quality (ie intact 16S/23S rRNA). Sample homogenization and hot chemical (SDS) cell lysis combined with mechanical (bead-beating) lysis in presence of a DNA competitor (skim milk) contributed to improving substantially (around 23 times) the DNA yield of the PowerSoil DNA Isolation Kit. Apart from presenting NA extraction strategies for optimizing extraction parameters with corrosion samples from carbon steel, this study proposes DNA and RNA extraction procedures suited for comparative molecular analysis of total and active fractions of bacterial communities associated with carbon steel corrosion events, thereby contributing to improved MIC diagnosis and control.

  18. A proposed taxonomy of anaerobic fungi (class neocallimastigomycetes suitable for large-scale sequence-based community structure analysis.

    Sandra Kittelmann

    Full Text Available Anaerobic fungi are key players in the breakdown of fibrous plant material in the rumen, but not much is known about the composition and stability of fungal communities in ruminants. We analyzed anaerobic fungi in 53 rumen samples from farmed sheep (4 different flocks, cattle, and deer feeding on a variety of diets. Denaturing gradient gel electrophoresis fingerprinting of the internal transcribed spacer 1 (ITS1 region of the rrn operon revealed a high diversity of anaerobic fungal phylotypes across all samples. Clone libraries of the ITS1 region were constructed from DNA from 11 rumen samples that had distinctly different fungal communities. A total of 417 new sequences were generated to expand the number and diversity of ITS1 sequences available. Major phylogenetic groups of anaerobic fungi in New Zealand ruminants belonged to the genera Piromyces, Neocallimastix, Caecomyces and Orpinomyces. In addition, sequences forming four novel clades were obtained, which may represent so far undetected genera or species of anaerobic fungi. We propose a revised phylogeny and pragmatic taxonomy for anaerobic fungi, which was tested and proved suitable for analysis of datasets stemming from high-throughput next-generation sequencing methods. Comparing our revised taxonomy to the taxonomic assignment of sequences deposited in the GenBank database, we believe that >29% of ITS1 sequences derived from anaerobic fungal isolates or clones are misnamed at the genus level.

  19. Phylogenetic Analysis of Stenotrophomonas spp. Isolates Contributes to the Identification of Nosocomial and Community-Acquired Infections

    Vinicius Godoy Cerezer

    2014-01-01

    Full Text Available Stenotrophomonas ssp. has a wide environmental distribution and is also found as an opportunistic pathogen, causing nosocomial or community-acquired infections. One species, S. maltophilia, presents multidrug resistance and has been associated with serious infections in pediatric and immunocompromised patients. Therefore, it is relevant to conduct resistance profile and phylogenetic studies in clinical isolates for identifying infection origins and isolates with augmented pathogenic potential. Here, multilocus sequence typing was performed for phylogenetic analysis of nosocomial isolates of Stenotrophomonas spp. and, environmental and clinical strains of S. maltophilia. Biochemical and multidrug resistance profiles of nosocomial and clinical strains were determined. The inferred phylogenetic profile showed high clonal variability, what correlates with the adaptability process of Stenotrophomonas to different habitats. Two clinical isolates subgroups of S. maltophilia sharing high phylogenetic homogeneity presented intergroup recombination, thus indicating the high permittivity to horizontal gene transfer, a mechanism involved in the acquisition of antibiotic resistance and expression of virulence factors. For most of the clinical strains, phylogenetic inference was made using only partial ppsA gene sequence. Therefore, the sequencing of just one specific fragment of this gene would allow, in many cases, determining whether the infection with S. maltophilia was nosocomial or community-acquired.

  20. The role of Streptococcus pneumoniae in community-acquired pneumonia among adults in Europe: a meta-analysis.

    Rozenbaum, M H; Pechlivanoglou, P; van der Werf, T S; Lo-Ten-Foe, J R; Postma, M J; Hak, E

    2013-03-01

    The primary objective of this meta-analysis was to estimate the prevalence of adult community-acquired pneumonia (CAP) caused by Streptococcus pneumoniae in Europe, adjusted for possible independent covariates. Two reviewers conducted a systematic literature search using PubMed on English-language articles that involved human subjects with CAP during the period from January 1990 to November 2011 across European countries. A mixed-effects meta-regression model was developed and populated with 24,410 patients obtained from 77 articles that met the inclusion criteria. The model showed that the observed prevalence of S. pneumoniae in CAP significantly varies between European regions, even after adjusting for explanatory covariates, including patient characteristics, diagnostic tests, antibiotic resistance, and health-care setting. The probability of detecting S. pneumoniae was substantially higher in studies that performed more frequently a diagnostic polymerase chain reaction assay compared to all the other diagnostic tests included. Furthermore, S. pneumoniae was more likely to be confirmed as the cause of a CAP in studies with intensive care unit patients as compared to those with hospital- or community-treated patients. This study provides estimates of the average observed prevalence of S. pneumoniae, which could be used for projecting the health and economic benefits of pneumococcal immunization.

  1. Thermophilic hydrogen production from sludge pretreated by thermophilic bacteria: analysis of the advantages of microbial community and metabolism.

    Zheng, He-Shan; Guo, Wan-Qian; Yang, Shan-Shan; Feng, Xiao-Chi; Du, Juan-Shan; Zhou, Xian-Jiao; Chang, Jo-Shu; Ren, Nan-Qi

    2014-11-01

    In this study, the effects of thermophilic bacteria pretreatment and elevated fermentation temperature on hydrogen production from sludge were examined. The highest hydrogen yield of 19.9mlH2g(-1) VSS was achieved at 55°C by using pretreated sludge, which was 48.6% higher than raw sludge without pretreatment, and 28.39% higher than when fermented at 35°C. To explore the internal factors of this superior hydrogen production performance, the microbial community and the metabolism analysis were performed by using high-throughput sequencing and excitation-emission matrix. The pretreated sludge showed better utilization of dissolved organic matter and less inhibition of metabolism, especially at thermophilic condition. The 454 sequencing data indicated that microbial abundance was distinctly reduced and extremely high proportion of hydrogen-producing bacteria was found in the thermophilic community (Thermoanaerobacterium accounted for 93.75%). Thus, the pretreated sludge and thermophilic condition showed significant advantages in the hydrogen production using waste sludge as substrate.

  2. The emergence of community health worker programmes in the late apartheid era in South Africa: An historical analysis.

    van Ginneken, Nadja; Lewin, Simon; Berridge, Virginia

    2010-09-01

    There is re-emerging interest in community health workers (CHWs) as part of wider policies regarding task-shifting within human resources for health. This paper examines the history of CHW programmes established in South Africa in the later apartheid years (1970s-1994) - a time of innovative initiatives. After 1994, the new democratic government embraced primary healthcare (PHC), however CHW initiatives were not included in their health plan and most of these programmes subsequently collapsed. Since then a wide array of disease-focused CHW projects have emerged, particularly within HIV care. Thirteen oral history interviews and eight witness seminars were conducted in South Africa in April 2008 with founders and CHWs from these earlier programmes. These data were triangulated with written primary sources and analysed using thematic content analysis. The study suggests that 1970s-1990s CHW programmes were seen as innovative, responsive, comprehensive and empowering for staff and communities, a focus which respondents felt was lost within current programmes. The growth of these earlier projects was underpinned by the struggle against apartheid. Respondents felt that the more technical focus of current CHW programmes under-utilise a valuable human resource which previously had a much wider social and health impact. These prior experiences and lessons learned could usefully inform policy-making frameworks for CHWs in South Africa today.

  3. Human helminth co-infection: analysis of spatial patterns and risk factors in a Brazilian community.

    Rachel L Pullan

    Full Text Available BACKGROUND: Individuals living in areas endemic for helminths are commonly infected with multiple species. Despite increasing emphasis given to the potential health impacts of polyparasitism, few studies have investigated the relative importance of household and environmental factors on the risk of helminth co-infection. Here, we present an investigation of exposure-related risk factors as sources of heterogeneity in the distribution of co-infection with Necator americanus and Schistosoma mansoni in a region of southeastern Brazil. METHODOLOGY: Cross-sectional parasitological and socio-economic data from a community-based household survey were combined with remotely sensed environmental data using a geographical information system. Geo-statistical methods were used to explore patterns of mono- and co-infection with N. americanus and S. mansoni in the region. Bayesian hierarchical models were then developed to identify risk factors for mono- and co-infection in relation to community-based survey data to assess their roles in explaining observed heterogeneity in mono and co-infection with these two helminth species. PRINCIPAL FINDINGS: The majority of individuals had N. americanus (71.1% and/or S. mansoni (50.3% infection; 41.0% of individuals were co-infected with both helminths. Prevalence of co-infection with these two species varied substantially across the study area, and there was strong evidence of household clustering. Hierarchical multinomial models demonstrated that relative socio-economic status, household crowding, living in the eastern watershed and high Normalized Difference Vegetation Index (NDVI were significantly associated with N. americanus and S. mansoni co-infection. These risk factors could, however, only account for an estimated 32% of variability between households. CONCLUSIONS: Our results demonstrate that variability in risk of N. americanus and S. mansoni co-infection between households cannot be entirely explained by

  4. Microbial community analysis in a long-term membrane-less microbial electrolysis cell with hydrogen and methane production.

    Rago, Laura; Ruiz, Yolanda; Baeza, Juan A; Guisasola, Albert; Cortés, Pilar

    2015-12-01

    A single-chamber microbial electrolysis cell (MEC) aiming at hydrogen production with acetate as sole carbon source failed due to methanogenesis build-up despite the significant amount of 2-bromoethanesulfonate (BES) dosage, 50 mM. Specific batch experiments and a thorough microbial community analysis, pyrosequencing and qPCR, of cathode, anode and medium were performed to understand these observations. The experimental data rebuts different hypothesis and shows that methanogenesis at high BES concentration was likely due to the capacity of some Archaea (hydrogen-oxidizing genus Methanobrevibacter) to resist high BES concentration up to 200 mM. Methanobrevibacter, of the Methanobacteriales order, represented almost the 98% of the total Archaea in the cathode whereas Geobacter was highly abundant in the anode (72% of bacteria). Moreover, at higher BES concentration (up to 200 mM), methanogenesis activity decreased resulting in an increase of homoacetogenic activity, which challenged the performance of the MEC for H2 production.

  5. Creating community action plans for obesity prevention using the ANGELO (Analysis Grid for Elements Linked to Obesity) Framework

    Simmons, A; Mavoa, H M; Bell, A C

    2009-01-01

    prioritized, community-participatory action plans for obesity prevention projects in children and adolescents using the ANGELO (Analysis Grid for Elements Linked to Obesity) Framework. We combined stakeholder engagement processes, the ANGELO Framework (scans for environmental barriers, targeted behaviours......, gaps in skills and knowledge) and workshops with key stakeholders to create action plans for six diverse obesity prevention projects in Australia (n = 3), New Zealand, Fiji and Tonga from 2002 to 2005. Some sites included sociocultural contextual analyses in the environmental scans. Target groups were...... under-5-year-olds (Australia), 4-12-year-olds (Australia) and 13-18-year-olds (all four countries). Over 120 potential behavioural, knowledge, skill and environmental elements were identified for prioritization leading into each 2-day workshop. Many elements were common across the diverse cultural...

  6. Comparative human health risk analysis of coastal community water and waste service options.

    Schoen, Mary E; Xue, Xiaobo; Hawkins, Troy R; Ashbolt, Nicholas J

    2014-08-19

    As a pilot approach to describe adverse human health effects from alternative decentralized community water systems compared to conventional centralized services (business-as-usual [BAU]), selected chemical and microbial hazards were assessed using disability adjusted life years (DALYs) as the common metric. The alternatives included: (1) composting toilets with septic system, (2) urine-diverting toilets with septic system, (3) low flush toilets with blackwater pressure sewer and on-site greywater collection and treatment for nonpotable reuse, and (4) alternative 3 with on-site rainwater treatment and use. Various pathogens (viral, bacterial, and protozoan) and chemicals (disinfection byproducts [DBPs]) were used as reference hazards. The exposure pathways for BAU included accidental ingestion of contaminated recreational water, ingestion of cross-connected sewage to drinking water, and shower exposures to DBPs. The alternative systems included ingestion of treated greywater from garden irrigation, toilet flushing, and crop consumption; and ingestion of treated rainwater while showering. The pathways with the highest health impact included the ingestion of cross-connected drinking water and ingestion of recreational water contaminated by septic seepage. These were also among the most uncertain when characterizing input parameters, particularly the scale of the cross-connection event, and the removal of pathogens during groundwater transport of septic seepage. A comparison of the health burdens indicated potential health benefits by switching from BAU to decentralized water and wastewater systems.

  7. Metagenomic analysis of a permafrost microbial community reveals a rapid response to thaw.

    Mackelprang, Rachel; Waldrop, Mark P; DeAngelis, Kristen M; David, Maude M; Chavarria, Krystle L; Blazewicz, Steven J; Rubin, Edward M; Jansson, Janet K

    2011-11-06

    Permafrost contains an estimated 1672 Pg carbon (C), an amount roughly equivalent to the total currently contained within land plants and the atmosphere. This reservoir of C is vulnerable to decomposition as rising global temperatures cause the permafrost to thaw. During thaw, trapped organic matter may become more accessible for microbial degradation and result in greenhouse gas emissions. Despite recent advances in the use of molecular tools to study permafrost microbial communities, their response to thaw remains unclear. Here we use deep metagenomic sequencing to determine the impact of thaw on microbial phylogenetic and functional genes, and relate these data to measurements of methane emissions. Metagenomics, the direct sequencing of DNA from the environment, allows the examination of whole biochemical pathways and associated processes, as opposed to individual pieces of the metabolic puzzle. Our metagenome analyses reveal that during transition from a frozen to a thawed state there are rapid shifts in many microbial, phylogenetic and functional gene abundances and pathways. After one week of incubation at 5 °C, permafrost metagenomes converge to be more similar to each other than while they are frozen. We find that multiple genes involved in cycling of C and nitrogen shift rapidly during thaw. We also construct the first draft genome from a complex soil metagenome, which corresponds to a novel methanogen. Methane previously accumulated in permafrost is released during thaw and subsequently consumed by methanotrophic bacteria. Together these data point towards the importance of rapid cycling of methane and nitrogen in thawing permafrost.

  8. HydroDesktop as a Community Designed and Developed Resource for Hydrologic Data Discovery and Analysis

    Ames, D. P.

    2013-12-01

    As has been seen in other informatics fields, well-documented and appropriately licensed open source software tools have the potential to significantly increase both opportunities and motivation for inter-institutional science and technology collaboration. The CUAHSI HIS (and related HydroShare) projects have aimed to foster such activities in hydrology resulting in the development of many useful community software components including the HydroDesktop software application. HydroDesktop is an open source, GIS-based, scriptable software application for discovering data on the CUAHSI Hydrologic Information System and related resources. It includes a well-defined plugin architecture and interface to allow 3rd party developers to create extensions and add new functionality without requiring recompiling of the full source code. HydroDesktop is built in the C# programming language and uses the open source DotSpatial GIS engine for spatial data management. Capabilities include data search, discovery, download, visualization, and export. An extension that integrates the R programming language with HydroDesktop provides scripting and data automation capabilities and an OpenMI plugin provides the ability to link models. Current revision and updates to HydroDesktop include migration of core business logic to cross platform, scriptable Python code modules that can be executed in any operating system or linked into other software front-end applications.

  9. Subtype analysis of Blastocystis sp. isolates from asymptomatic individuals in an urban community in the Philippines

    Adao, Davin Edric V.; Dela Serna, Ace O.; Belleza, Maria Luz B.; Bolo, Nicole R.; Rivera, Windell L.

    2016-10-01

    Blastocystis sp. is a commonly reported enteric protistan parasite in faecal specimens with a worldwide distribution afflicting both humans and a wide range of animals. The aim of this study is to characterize the subtypes (STs) of Blastocystis sp. isolates from asymptomatic individuals in an urban community in Pateros, Metro Manila, Philippines. The 600-bp small subunit ribosomal RNA (SSU rRNA) barcoding region of Blastocystis sp. isolates was amplified and sequenced using the primers RD5 and BhRDr. Subtypes were identified by uploading the sequences onto the Basic Local Alignment and Search Tool (BLAST) websites, the Blastocystis Subtype (18S) and Sequence Typing (MLST) Database and by construction of a phylogenetic tree. Twenty-nine (29) out of 35 individuals were detected positive for Blastocystis sp. ST3 is the most common among the three STs detected (65.5%), followed by ST1 (31.0%) and ST4 (3.44%). This study showed that DNA barcoding can serve as a helpful tool to investigate the diversity of Blastocystis sp. in the Philippines.

  10. ASEAN ECONOMIC COMMUNITY 2015: NEEDS ANALYSIS OF UNIVERSITAS INDONESIA’S ENGINEERING STUDENTS

    Lavinia DW Araminta

    2015-07-01

    Full Text Available Prior to the ASEAN Economic Community in the end of 2015, one of the keys for Indonesian engineers to outrank engineers from other ASEAN countries is mastering English language skills. This study aims at analyzing the English needs of undergraduate engineering students at Universitas Indonesia. Questionnaires and semi-structured interviews were used as the data collection methods. The questionnaires were spread to 111 alumni and 150 students from the Faculty of Engineering. The interviews were conducted with HRD from a multinational company, HRD from a local company, three heads of departments, and two lecturers from the Faculty of Engineering. The research reveals that students’ needs of English language learning are considered not as high as their needs of English language use. The recommendation given to the Faculty of Engineering is to conduct an optional course on English for Professional Purposes, and the course is to be handled by professional English teachers helped by the lecturers from the Faculty of Engineering.

  11. Analysis of the community compositions of rhizosphere fungi in soybeans continuous cropping fields.

    Bai, Li; Cui, Jiaqi; Jie, Weiguang; Cai, Baiyan

    2015-11-01

    We used rhizosphere soil sampled from one field during zero year and two years of continuous cropping of high-protein soybean to analyze the taxonomic community compositions of fungi during periods of high-incidence of root rot. Our objectives were to identify the dominant pathogens in order to provide a theoretical basis for the study of pathogenesis as well as control tactics for soybean root rot induced by continuous cropping. A total of 17,801 modified internal transcribed spacer (ITS) sequences were obtained from three different soybean rhizosphere soil samples after zero year and 1 or 2 years of continuous cropping using 454 high-throughput sequencing. The dominant eumycote fungal were identified to be Ascomycota and Basidiomycota in the three soil samples. Continuous cropping of soybean affected the diversity of fungi in rhizosphere soils and increased the abundance of Thelebolus and Mortierellales significantly. Thanatephorus, Fusarium, and Alternaria were identified to be the dominant pathogenic fungal genera in rhizosphere soil from continuously cropped soybean fields.

  12. Microbiological community analysis of vermicompost tea and its influence on the growth of vegetables and cereals.

    Fritz, J I; Franke-Whittle, I H; Haindl, S; Insam, H; Braun, R

    2012-07-01

    Vermicompost, the digestion product of organic material by earthworms, has been widely reported to have a more positive effect on plant growth and plant health than conventional compost. A study was conducted to investigate the effects of different vermicompost elutriates (aerated compost teas) on soils and plant growth. The teas were analyzed by chemical, microbiological, and molecular methods accompanied by plant growth tests at laboratory and field scale. The number of microorganisms in the teas increased during the extraction process and was affected by substrate addition. The vermicompost tea found to increase plant growth best under laboratory tests was applied to cereals (wheat and barley) and vegetables (Raphanus sativus, Rucola selvatica, and Pisum sativum) in a field study. The results revealed no effects of tea application on plant yield; however, sensoric tests indicated an improvement in crop quality. The soils from laboratory and field studies were investigated to detect possible microbial or chemical changes. The results indicated that minor changes to the soil microbial community occurred following tea application by foliar spray in both the laboratory-scale and field-scale experiments.

  13. A retrospective observational analysis to identify patient and treatment-related predictors of outcomes in a community mental health programme

    Green, Stuart A; Honeybourne, Emmi; Chalkley, Sylvia R; Price, Geraint; Bell, Derek; Green, John

    2015-01-01

    Objectives This study aims to identify patient and treatment factors that affect clinical outcomes of community psychological therapy through the development of a predictive model using historic data from 2 services in London. In addition, the study aims to assess the completeness of data collection, explore how treatment outcomes are discriminated using current criteria for classifying recovery, and assess the feasibility and need for undertaking a future larger population analysis. Design Observational, retrospective discriminant analysis. Setting 2 London community mental health services that provide psychological therapies for common mental disorders including anxiety and depression. Participants A total of 7388 patients attended the services between February 2009 and May 2012, of which 4393 (59%) completed therapy, or there was an agreement to end therapy, and were included in the study. Primary and secondary outcome measures Different combinations of the clinical outcome scores for anxiety Generalised Anxiety Disorder-7 and depression Patient Health Questionnaire-9 were used to construct different treatment outcomes. Results The predictive models were able to assign a positive or negative clinical outcome to each patient based on 5 independent pre-treatment variables, with an accuracy of 69.4% and 79.3%, respectively: initial severity of anxiety and depression, ethnicity, deprivation and gender. The number of sessions attended/missed were also important factors identified in recovery. Conclusions Predicting whether patients are likely to have a positive outcome following treatment at entry might allow suitable modification of scheduled treatment, possibly resulting in improvements in outcomes. The model also highlights factors not only associated with poorer outcomes but inextricably linked to prevalence of common mental disorders, emphasising the importance of social determinants not only in poor health but also poor recovery. PMID:25995234

  14. Phylogenetic analysis of a spontaneous cocoa bean fermentation metagenome reveals new insights into its bacterial and fungal community diversity.

    Koen Illeghems

    Full Text Available This is the first report on the phylogenetic analysis of the community diversity of a single spontaneous cocoa bean box fermentation sample through a metagenomic approach involving 454 pyrosequencing. Several sequence-based and composition-based taxonomic profiling tools were used and evaluated to avoid software-dependent results and their outcome was validated by comparison with previously obtained culture-dependent and culture-independent data. Overall, this approach revealed a wider bacterial (mainly γ-Proteobacteria and fungal diversity than previously found. Further, the use of a combination of different classification methods, in a software-independent way, helped to understand the actual composition of the microbial ecosystem under study. In addition, bacteriophage-related sequences were found. The bacterial diversity depended partially on the methods used, as composition-based methods predicted a wider diversity than sequence-based methods, and as classification methods based solely on phylogenetic marker genes predicted a more restricted diversity compared with methods that took all reads into account. The metagenomic sequencing analysis identified Hanseniaspora uvarum, Hanseniaspora opuntiae, Saccharomyces cerevisiae, Lactobacillus fermentum, and Acetobacter pasteurianus as the prevailing species. Also, the presence of occasional members of the cocoa bean fermentation process was revealed (such as Erwinia tasmaniensis, Lactobacillus brevis, Lactobacillus casei, Lactobacillus rhamnosus, Lactococcus lactis, Leuconostoc mesenteroides, and Oenococcus oeni. Furthermore, the sequence reads associated with viral communities were of a restricted diversity, dominated by Myoviridae and Siphoviridae, and reflecting Lactobacillus as the dominant host. To conclude, an accurate overview of all members of a cocoa bean fermentation process sample was revealed, indicating the superiority of metagenomic sequencing over previously used techniques.

  15. Bacterial community analysis in chlorpyrifos enrichment cultures via DGGE and use of bacterial consortium for CP biodegradation.

    Akbar, Shamsa; Sultan, Sikander; Kertesz, Michael

    2014-10-01

    The organophosphate pesticide chlorpyrifos (CP) has been used extensively since the 1960s for insect control. However, its toxic effects on mammals and persistence in environment necessitate its removal from contaminated sites, biodegradation studies of CP-degrading microbes are therefore of immense importance. Samples from a Pakistani agricultural soil with an extensive history of CP application were used to prepare enrichment cultures using CP as sole carbon source for bacterial community analysis and isolation of CP metabolizing bacteria. Bacterial community analysis (denaturing gradient gel electrophoresis) revealed that the dominant genera enriched under these conditions were Pseudomonas, Acinetobacter and Stenotrophomonas, along with lower numbers of Sphingomonas, Agrobacterium and Burkholderia. Furthermore, it revealed that members of Bacteroidetes, Firmicutes, α- and γ-Proteobacteria and Actinobacteria were present at initial steps of enrichment whereas β-Proteobacteria appeared in later steps and only Proteobacteria were selected by enrichment culturing. However, when CP-degrading strains were isolated from this enrichment culture, the most active organisms were strains of Acinetobacter calcoaceticus, Pseudomonas mendocina and Pseudomonas aeruginosa. These strains degraded 6-7.4 mg L(-1) day(-1) of CP when cultivated in mineral medium, while the consortium of all four strains degraded 9.2 mg L(-1) day(-1) of CP (100 mg L(-1)). Addition of glucose as an additional C source increased the degradation capacity by 8-14 %. After inoculation of contaminated soil with CP (200 mg kg(-1)) disappearance rates were 3.83-4.30 mg kg(-1) day(-1) for individual strains and 4.76 mg kg(-1) day(-1) for the consortium. These results indicate that these organisms are involved in the degradation of CP in soil and represent valuable candidates for in situ bioremediation of contaminated soils and waters.

  16. Use of multiple cluster analysis methods to explore the validity of a community outcomes concept map.

    Orsi, Rebecca

    2017-02-01

    Concept mapping is now a commonly-used technique for articulating and evaluating programmatic outcomes. However, research regarding validity of knowledge and outcomes produced with concept mapping is sparse. The current study describes quantitative validity analyses using a concept mapping dataset. We sought to increase the validity of concept mapping evaluation results by running multiple cluster analysis methods and then using several metrics to choose from among solutions. We present four different clustering methods based on analyses using the R statistical software package: partitioning around medoids (PAM), fuzzy analysis (FANNY), agglomerative nesting (AGNES) and divisive analysis (DIANA). We then used the Dunn and Davies-Bouldin indices to assist in choosing a valid cluster solution for a concept mapping outcomes evaluation. We conclude that the validity of the outcomes map is high, based on the analyses described. Finally, we discuss areas for further concept mapping methods research.

  17. Access to medications in the community by patients in a palliative setting. A systems analysis.

    Lucey, M; McQuillan, R; MacCallion, A; Corrigan, M; Flynn, J; Connaire, K

    2008-03-01

    This study performed a systems analysis of the process by which patients under the care of a specialist palliative home care obtained medications, and highlighted factors that delay this process. Systems analysis is the science dealing with analysis of complex, large-scale systems and the interactions within those systems. This study used a mixed-methods approach of questionnaires of general practitioners, pharmacists and patients, and a prospective observational study of delays experienced by patients referred to the home care team over a three-month period. This study found the main factors causing delay to be: medications not being in stock in pharmacies, medications not being available on state reimbursed schemes and inability of patients and carers to courier medications.

  18. Analysis of bacterial communities and bacterial pathogens in a biogas plant by the combination of ethidium monoazide, PCR and Ion Torrent sequencing

    Luo, Gang; Angelidaki, Irini

    2014-01-01

    composition and bacterial pathogens were also studied. Microbial analysis was made by Ion Torrent sequencing of the PCR amplicons from ethidium monoazide treated samples, and ethidium monoazide was used to cleave DNA from dead cells and exclude it from PCR amplification. Both similarity and taxonomic analysis...... showed that the bacterial community composition in the influent was changed after anaerobic digestion. Firmicutes were dominant in all the samples, while Proteobacteria decreased in the biogas reactor compared with the influent. Variations of bacterial community composition in the biogas reactor...

  19. Analysis of the microbial community of the biocathode of a hydrogen-producing microbial electrolysis cell.

    Croese, Elsemiek; Pereira, Maria Alcina; Euverink, Gert-Jan W; Stams, Alfons J M; Geelhoed, Jeanine S

    2011-12-01

    The microbial electrolysis cell (MEC) is a promising system for hydrogen production. Still, expensive catalysts such as platinum are needed for efficient hydrogen evolution at the cathode. Recently, the possibility to use a biocathode as an alternative for platinum was shown. The microorganisms involved in hydrogen evolution in such systems are not yet identified. We analyzed the microbial community of a mixed culture biocathode that was enriched in an MEC bioanode. This biocathode produced 1.1 A m(-2) and 0.63 m3 H2 m(-3) cathode liquid volume per day. The bacterial population consisted of 46% Proteobacteria, 25% Firmicutes, 17% Bacteroidetes, and 12% related to other phyla. The dominant ribotype belonged to the species Desulfovibrio vulgaris. The second major ribotype cluster constituted a novel taxonomic group at the genus level, clustering within uncultured Firmicutes. The third cluster belonged to uncultured Bacteroidetes and grouped in a taxonomic group from which only clones were described before; most of these clones originated from soil samples. The identified novel taxonomic groups developed under environmentally unusual conditions, and this may point to properties that have not been considered before. A pure culture of Desulfovibrio strain G11 inoculated in a cathode of an MEC led to a current development from 0.17 to 0.76 A m(-2) in 9 days, and hydrogen gas formation was observed. On the basis of the known characteristics of Desulfovibrio spp., including its ability to produce hydrogen, we propose a mechanism for hydrogen evolution through Desulfovibrio spp. in a biocathode system.

  20. (Draft) Community air pollution and mortality: Analysis of 1980 data from US metropolitan areas

    Lipfert, F.W.

    1992-11-01

    1980 data from up to 149 metropolitan areas were used to define cross-sectional associations between community air pollution and ``excess`` human mortality. The regression model proposed by Ozkaynak and Thurston (1987), which accounted for age, race, education, poverty, and population density, was evaluated and several new models were developed. The new models also accounted for migration, drinking water hardness, and smoking, and included a more detailed description of race. Cause-of-death categories analyzed include all causes, all ``non-external`` causes, major cardiovascular diseases, and chronic obstructive pulmonary diseases (COPD). Both annual mortality rates and their logarithms were analyzed. Air quality data were obtained from the EPA AIRS database (TSP, SO{sub 4}{sup =}, Mn, and ozone) and from the inhalable particulate network (PM{sub 15}, PM{sub 2.5} and SO{sub 4}{sup =}, for 63{sup 4} locations). The data on particulates were averaged across all monitoring stations available for each SMSA and the TSP data were restricted to the year 1980. The associations between mortality and air pollution were found to be dependent on the socioeconomic factors included in the models, the specific locations included in the data set, and the type of statistical model used. Statistically significant associations were found as follows: between TSP and mortality due to non-external causes with log-linear models, but not with a linear model betweenestimated 10-year average (1980--90) ozone levels and 1980 non-external and cardiovascular deaths; and between TSP and COPD mortality for both linear and log-linear models. When the sulfate contribution to TSP was subtracted, the relationship with COPD mortality was strengthened.

  1. (Draft) Community air pollution and mortality: Analysis of 1980 data from US metropolitan areas

    Lipfert, F.W.

    1992-11-01

    1980 data from up to 149 metropolitan areas were used to define cross-sectional associations between community air pollution and excess'' human mortality. The regression model proposed by Ozkaynak and Thurston (1987), which accounted for age, race, education, poverty, and population density, was evaluated and several new models were developed. The new models also accounted for migration, drinking water hardness, and smoking, and included a more detailed description of race. Cause-of-death categories analyzed include all causes, all non-external'' causes, major cardiovascular diseases, and chronic obstructive pulmonary diseases (COPD). Both annual mortality rates and their logarithms were analyzed. Air quality data were obtained from the EPA AIRS database (TSP, SO[sub 4][sup =], Mn, and ozone) and from the inhalable particulate network (PM[sub 15], PM[sub 2.5] and SO[sub 4][sup =], for 63[sup 4] locations). The data on particulates were averaged across all monitoring stations available for each SMSA and the TSP data were restricted to the year 1980. The associations between mortality and air pollution were found to be dependent on the socioeconomic factors included in the models, the specific locations included in the data set, and the type of statistical model used. Statistically significant associations were found as follows: between TSP and mortality due to non-external causes with log-linear models, but not with a linear model betweenestimated 10-year average (1980--90) ozone levels and 1980 non-external and cardiovascular deaths; and between TSP and COPD mortality for both linear and log-linear models. When the sulfate contribution to TSP was subtracted, the relationship with COPD mortality was strengthened.

  2. Metagenomic analysis of a permafrost microbial community reveals a rapid response to thaw

    MacKelprang, R.; Waldrop, M.P.; Deangelis, K.M.; David, M.M.; Chavarria, K.L.; Blazewicz, S.J.; Rubin, E.M.; Jansson, J.K.

    2011-01-01

    Permafrost contains an estimated 1672????????Pg carbon (C), an amount roughly equivalent to the total currently contained within land plants and the atmosphere. This reservoir of C is vulnerable to decomposition as rising global temperatures cause the permafrost to thaw. During thaw, trapped organic matter may become more accessible for microbial degradation and result in greenhouse gas emissions. Despite recent advances in the use of molecular tools to study permafrost microbial communities, their response to thaw remains unclear. Here we use deep metagenomic sequencing to determine the impact of thaw on microbial phylogenetic and functional genes, and relate these data to measurements of methane emissions. Metagenomics, the direct sequencing of DNA from the environment, allows the examination of whole biochemical pathways and associated processes, as opposed to individual pieces of the metabolic puzzle. Our metagenome analyses reveal that during transition from a frozen to a thawed state there are rapid shifts in many microbial, phylogenetic and functional gene abundances and pathways. After one week of incubation at 5 ??C, permafrost metagenomes converge to be more similar to each other than while they are frozen. We find that multiple genes involved in cycling of C and nitrogen shift rapidly during thaw. We also construct the first draft genome from a complex soil metagenome, which corresponds to a novel methanogen. Methane previously accumulated in permafrost is released during thaw and subsequently consumed by methanotrophic bacteria. Together these data point towards the importance of rapid cycling of methane and nitrogen in thawing permafrost. ?? 2011 Macmillan Publishers Limited. All rights reserved.

  3. Revising the Community of Inquiry Framework for the Analysis of One-to-One Online Learning Relationships

    Stenbom, Stefan; Jansson, Malin; Hulkko, Annelie

    2016-01-01

    In online learning research, the theoretical community of inquiry framework has been used extensively to analyze processes of inquiry among learners and instructors within a community. This paper examines a special case of community of inquiry consisting of only one learner and one instructor. Together they engage in an online coaching discourse…

  4. Black Males in Education: Learning and Achievement. A Summative Community Analysis Response from the Kwanzaa Adult Forum (December 27, 2010)

    Bell, Edward Earl

    2011-01-01

    Background: Educating black males is critical. No longer can the black community blame the school for the academic failure of this population. The black community must address this pervasive issue. Purpose: The purpose for this inquiry was to explore community support and recommendations for educating black males. Setting: The setting took place…

  5. An Analysis of the Effects of Program Structure and Content on Outcomes of Community Leadership Education Programs

    Apaliyah, Godwin Tayese

    2011-01-01

    This study examined community leadership education programs employed in rural communities and organizations of several states to empower both local leaders and residents. In particular, the study investigated the relationships between community leadership education program design and structure (contact hours and content) and six outcome indices of…

  6. A Community Organizing Case Study: An Analysis of Cap-It's Strategy to Prevent the Location of a Toxic Waste Incinerator in Their Community.

    Jacobs, J

    1992-01-01

    With the great proliferation of chemical manufacturing in the past half-century, the dilemma of dealing with the waste produced has become an increasing problem facing communities. One method that is gaining increased acceptance by both government and industry is incineration. Many citizens have formed groups to protest these facilities because of their concerns about health risks, especially exposure to carcinogens. This case study profiles one such group, CAP-IT, a collection of middle-class residents living in a small working-class town and their successful battle to prevent the siting of a hazardous waste incinerator. CAP-IT's strategy will be critiqued using methods advanced by Lee Staples, Nicholas Freudenburg and Kurt Lewin to demonstrate the power of community organizing activities.

  7. The Nanomaterial Registry: facilitating the sharing and analysis of data in the diverse nanomaterial community

    Ostraat ML; Mills KC; Guzan KA; Murry D

    2013-01-01

    Michele L Ostraat, Karmann C Mills, Kimberly A Guzan, Damaris MurryRTI International, Durham, NC, USAAbstract: The amount of data being generated in the nanotechnology research space is significant, and the coordination, sharing, and downstream analysis of the data is complex and consistently deliberated. The complexities of the data are due in large part to the inherently complicated characteristics of nanomaterials. Also, testing protocols and assays used for nanomaterials are diverse and l...

  8. Comparative Analysis of Methanogenic Communities in Different Laboratory-Scale Anaerobic Digesters

    Ayrat M. Ziganshin

    2016-01-01

    Full Text Available Comparative analysis of methanogenic archaea compositions and dynamics in 11 laboratory-scale continuous stirred tank reactors fed with different agricultural materials (chicken manure, cattle manure, maize straw, maize silage, distillers grains, and Jatropha press cake was carried out by analysis of the methyl coenzyme-M reductase α-subunit (mcrA gene. Various taxa within Methanomicrobiales, Methanobacteriaceae, Methanosarcinaceae, Methanosaetaceae, and Methanomassiliicoccales were detected in the biogas reactors but in different proportions depending on the substrate type utilized as well as various process parameters. Improved coverage and higher taxonomic resolution of methanogens were obtained compared to a previous 16S rRNA gene based study of the same reactors. Some members of the genus Methanoculleus positively correlated with the relative methane content, whereas opposite correlations were found for Methanobacterium. Specific biogas production was found to be significantly correlating with Methanosarcinaceae. Statistical analysis also disclosed that some members of the genus Methanoculleus positively correlated with the ammonia level, whereas the prevalence of Methanocorpusculum, Methanobacterium, and Methanosaeta was negatively correlated with this parameter. These results suggest that the application of methanogenic archaea adapted to specific feedstock might enhance the anaerobic digestion of such waste materials in full-scale biogas reactors.

  9. Comparative Analysis of Methanogenic Communities in Different Laboratory-Scale Anaerobic Digesters

    Ziganshin, Ayrat M.; Ziganshina, Elvira E.

    2016-01-01

    Comparative analysis of methanogenic archaea compositions and dynamics in 11 laboratory-scale continuous stirred tank reactors fed with different agricultural materials (chicken manure, cattle manure, maize straw, maize silage, distillers grains, and Jatropha press cake) was carried out by analysis of the methyl coenzyme-M reductase α-subunit (mcrA) gene. Various taxa within Methanomicrobiales, Methanobacteriaceae, Methanosarcinaceae, Methanosaetaceae, and Methanomassiliicoccales were detected in the biogas reactors but in different proportions depending on the substrate type utilized as well as various process parameters. Improved coverage and higher taxonomic resolution of methanogens were obtained compared to a previous 16S rRNA gene based study of the same reactors. Some members of the genus Methanoculleus positively correlated with the relative methane content, whereas opposite correlations were found for Methanobacterium. Specific biogas production was found to be significantly correlating with Methanosarcinaceae. Statistical analysis also disclosed that some members of the genus Methanoculleus positively correlated with the ammonia level, whereas the prevalence of Methanocorpusculum, Methanobacterium, and Methanosaeta was negatively correlated with this parameter. These results suggest that the application of methanogenic archaea adapted to specific feedstock might enhance the anaerobic digestion of such waste materials in full-scale biogas reactors. PMID:28074084

  10. Community contextual predictors of endoscopic colorectal cancer screening in the USA: spatial multilevel regression analysis

    Mobley Lee R

    2010-09-01

    Full Text Available Abstract Background Colorectal cancer (CRC is the second leading cause of cancer death in the United States, and endoscopic screening can both detect and prevent cancer, but utilization is suboptimal and varies across geographic regions. We use multilevel regression to examine the various predictors of individuals' decisions to utilize endoscopic CRC screening. Study subjects are a 100% population cohort of Medicare beneficiaries identified in 2001 and followed through 2005. The outcome variable is a binary indicator of any sigmoidoscopy or colonoscopy use over this period. We analyze each state separately and map the findings for all states together to reveal patterns in the observed heterogeneity across states. Results We estimate a fully adjusted model for each state, based on a comprehensive socio-ecological model. We focus the discussion on the independent contributions of each of three community contextual variables that are amenable to policy intervention. Prevalence of Medicare managed care in one's neighborhood was associated with lower probability of screening in 12 states and higher probability in 19 states. Prevalence of poor English language ability among elders in one's neighborhood was associated with lower probability of screening in 15 states and higher probability in 6 states. Prevalence of poverty in one's neighborhood was associated with lower probability of screening in 36 states and higher probability in 5 states. Conclusions There are considerable differences across states in the socio-ecological context of CRC screening by endoscopy, suggesting that the current decentralized configuration of state-specific comprehensive cancer control programs is well suited to respond to the observed heterogeneity. We find that interventions to mediate language barriers are more critically needed in some states than in others. Medicare managed care penetration, hypothesized to affect information about and diffusion of new endoscopic

  11. Microbial community analysis and bioclogging identification in a Managed Artificial Recharge system.

    Barba, Carme; Folch, Albert; Gaju, Núria; Martínez-Alonso, Maira; Grau, Alba; Sanchez-Vila, Xavier

    2015-04-01

    Managed Artificial Recharge (MAR) is a well-known technique that aims at increasing the aquifer resources while managing its quality. In order to increase water resources in the Barcelona conurbation, an area with significant quantitative and qualitative groundwater disturbances, a MAR facility was built in Sant Vicenç dels Horts, Catalonia, Spain. The system, constructed in 2009 consists of a sedimentation pond that pre-treats the water that is then diverted to the final recharge pond. The facility was originally aimed at increasing the availability of supply water during scarcity periods. Later, it was considered as a good test site to study best infiltration practices regarding water quality evolution. For this purpose, a reactive layer was installed in 2011 at the bottom of the pond. This was composed by organic compost and autochthonous material. Small proportions of iron oxides and clay were added to promote ionic adsorption and exchange. The objective of the layer was to boost microbial activity that would be structured in depth according to the presence of a marked redox profile, thus enhancing the reduction of all organic matter, including a number of recalcitrant compounds. In the last 3 years, site studies were focused on the layer's efficiency (i.e., percentage of organic pollutants degradation). It was found that degradation is occurring despite the infiltration rate has been significantly reduced. In our most recent work, we took a step further in the study of the processes occurring in the facility, and specifically with those related to the presence of the reactive layer. We focused on characterizing microbial communities in the system by combining the sampling of soil in the recharge pond bottom, water of the vadose zone, and groundwater in the aquifer zone from a series of nearby piezometers. Molecular techniques, such as Denaturing Gradient of Gel Electrophoresis (DGGE), were applied to the water and soil samples. This information was matched

  12. The methodology for developing a prospective meta-analysis in the family planning community

    Jacobson Janet C

    2011-04-01

    Full Text Available Abstract Background Prospective meta-analysis (PMA is a collaborative research design in which individual sites perform randomized controlled trials (RCTs and pool the data for meta-analysis. Members of the PMA collaboration agree upon specific research interventions and outcome measures, ideally before initiation but at least prior to any individual trial publishing results. This allows for uniform reporting of primary and secondary outcomes. With this approach, heterogeneity among trials contributing data for the final meta-analysis is minimized while each site maintains the freedom to design a specific trial. This paper describes the process of creating a PMA collaboration to evaluate the impact of misoprostol on ease of intrauterine device (IUD insertion in nulliparous women. Methods After the principal investigator developed a preliminary PMA protocol, he identified potential collaborating investigators at other sites. One site already had a trial underway and another site was in the planning stages of a trial meeting PMA requirements. Investigators at six sites joined the PMA collaborative. Each site committed to enroll subjects to meet a pre-determined total sample size. A final common research plan and site responsibilities were developed and agreed upon through email and face-to-face meetings. Each site committed to contribute individual patient data to the PMA collaboration, and these data will be analyzed and prepared as a multi-site publication. Individual sites retain the ability to analyze and publish their site's independent findings. Results All six sites have obtained Institutional Review Board approval and each has obtained individual funding to meet the needs of that site's study. Sites have shared resources including study protocols and consents to decrease costs and improve study flow. This PMA protocol is registered with the Cochrane Collaboration and data will be analyzed according to Cochrane standards for meta-analysis

  13. Are proton pump inhibitors associated with the development of community-acquired pneumonia? A meta-analysis.

    Giuliano, Christopher; Wilhelm, Sheila M; Kale-Pradhan, Pramodini B

    2012-05-01

    This study was presented at the American College of Chest Physicians meeting in Pittsburgh (PA, USA) in October 2011. The study objective was to evaluate the association of proton pump inhibitors (PPIs) and community-acquired pneumonia (CAP). The design was a meta-analysis of nine case-controlled and cohort studies. 120,863 pneumonia cases from 1987 to 2006 were included in the meta-analysis. PubMed and Ovid Medline were searched from inception through May 2011 by two investigators independently using keywords: PPI, pneumonia, CAP, anti-ulcer, antacid, omeprazole, esomeprazole, lansoprazole, pantoprazole and rabeprazole. This meta-analysis only included case-controlled and cohort studies that were published in full in English and evaluated PPI use and CAP incidence. Studies were excluded if they included the following patients: pediatric, Helicobacter pylori treatment and critically ill. Bibliographies of recent review articles and systematic reviews were hand-searched. Quality of studies was assessed using the Newcastle-Ottawa Quality Assessment Scale. Two investigators independently extracted data into standardized data collection forms that were confirmed by a third investigator. Data were analyzed based on current use of PPIs, duration of PPI use (180 days) and PPI dose (high vs low). Overall association of PPI and CAP was analyzed using the random effects model (Comprehensive Meta analysis(®) Version 2.0). Nine studies met all criteria for the primary outcome. Newcastle-Ottawa Quality Assessment Scale scores ranged from 4 to 8 out of 9. Current use of PPIs (odds ratio [OR]: 1.39; 95% CI: 1.09-1.76), PPI use 180 days (OR: 1.10; 95% CI: 1.00-1.21). In conclusion, patients currently receiving PPIs, particularly <30 days or high dose, showed an association with CAP. Practitioners need to be vigilant about adverse effects of PPIs and consider alternative therapies.

  14. The use of phospholipid fatty acid analysis to measure impact of acid rock drainage on microbial communities in sediments.

    Ben-David, E A; Holden, P J; Stone, D J M; Harch, B D; Foster, L J

    2004-10-01

    The impact of acid rock drainage (ARD) and eutrophication on microbial communities in stream sediments above and below an abandoned mine site in the Adelaide Hills, South Australia, was quantified by PLFA analysis. Multivariate analysis of water quality parameters, including anions, soluble heavy metals, pH, and conductivity, as well as total extractable metal concentrations in sediments, produced clustering of sample sites into three distinct groups. These groups corresponded with levels of nutrient enrichment and/or concentration of pollutants associated with ARD. Total PLFA concentration, which is indicative of microbial biomass, was reduced by >70% at sites along the stream between the mine site and as far as 18 km downstream. Further downstream, however, recovery of the microbial abundance was apparent, possibly reflecting dilution effect by downstream tributaries. Total PLFA was >40% higher at, and immediately below, the mine site (0-0.1 km), compared with sites further downstream (2.5-18 km), even after accounting for differences in specific surface area of different sediment samples. The increased microbial population in the proximity of the mine source may be associated with the presence of a thriving iron-oxidizing bacteria community as a consequence of optimal conditions for these organisms while the lower microbial population further downstream corresponded with greater sediments' metal concentrations. PCA of relative abundance revealed a number of PLFAs which were most influential in discriminating between ARD-polluted sites and the rest of the sites. These PLFA included the hydroxy fatty acids: 2OH12:0, 3OH12:0, 2OH16:0; the fungal marker: 18:2omega6; the sulfate-reducing bacteria marker 10Me16:1omega7; and the saturated fatty acids 12:0, 16:0, 18:0. Partial constrained ordination revealed that the environmental parameters with the greatest bearing on the PLFA profiles included pH, soluble aluminum, total extractable iron, and zinc. The study

  15. Reclaimed spoil heap from an open-cast mine: analysis of meadow communities

    Novak, J.; Hakl, J.; Steklova, J.; Ceska, J.; Dvorakova, E. [Czech University for Life Science Prague, Prague (Czech Republic)

    2008-07-01

    An evaluation of the vegetation on the reclaimed spoil heap of material deposited from the overlaying rock of an open-cast brown coal mine. The application of standard geobotanical research methods with statistical data analysis. Under the present management conditions desirable meadow taxa keep their constancy: the reduction of ruderal and weed species is evident, though statistically insignificant. For the variability of species composition over time, and in particular by the location of releves taken, the strong influence of substrate heterogeneity i.e. (in addition to exposure, humidity etc.) is inferred.

  16. Determinants of the lethality of climate-related disasters in the Caribbean Community (CARICOM): a cross-country analysis.

    Andrewin, Aisha N; Rodriguez-Llanes, Jose M; Guha-Sapir, Debarati

    2015-07-08

    Floods and storms are climate-related hazards posing high mortality risk to Caribbean Community (CARICOM) nations. However risk factors for their lethality remain untested. We conducted an ecological study investigating risk factors for flood and storm lethality in CARICOM nations for the period 1980-2012. Lethality--deaths versus no deaths per disaster event- was the outcome. We examined biophysical and social vulnerability proxies and a decadal effect as predictors. We developed our regression model via multivariate analysis using a generalized logistic regression model with quasi-binomial distribution; removal of multi-collinear variables and backward elimination. Robustness was checked through subset analysis. We found significant positive associations between lethality, percentage of total land dedicated to agriculture (odds ratio [OR] 1.032; 95% CI: 1.013-1.053) and percentage urban population (OR 1.029, 95% CI 1.003-1.057). Deaths were more likely in the 2000-2012 period versus 1980-1989 (OR 3.708, 95% CI 1.615-8.737). Robustness checks revealed similar coefficients and directions of association. Population health in CARICOM nations is being increasingly impacted by climate-related disasters connected to increasing urbanization and land use patterns. Our findings support the evidence base for setting sustainable development goals (SDG).

  17. A community standard for immunogenomic data reporting and analysis: proposal for a STrengthening the REporting of Immunogenomic Studies statement.

    Hollenbach, J A; Mack, S J; Gourraud, P-A; Single, R M; Maiers, M; Middleton, D; Thomson, G; Marsh, S G E; Varney, M D

    2011-11-01

    Modern high-throughput HLA and KIR typing technologies are generating a wealth of immunogenomic data with the potential to revolutionize the fields of histocompatibility and immune-related disease association and population genetic research, much as SNP-based approaches have revolutionized association research. The STrengthening the REporting of Genetic Association studies (STREGA) statement provides community-based data reporting and analysis standards for genomic disease-association studies, identifying specific areas in which adoption of reporting guidelines can improve the consistent interpretation of genetic studies. While aspects of STREGA can be applied to immunogenomic studies, HLA and KIR research requires additional consideration, as the high levels of polymorphism associated with immunogenomic data pose unique methodological and computational challenges to the synthesis of information across datasets. Here, we outline the principle challenges to consistency in immunogenomic studies, and propose that an immunogenomic-specific analog to the STREGA statement, a STrengthening the REporting of Immunogenomic Studies (STREIS) statement, be developed as part of the 16th International HLA and Immunogenetics Workshop. We propose that STREIS extends at least four of the 22 elements of the STREGA statement to specifically address issues pertinent to immunogenomic data: HLA and KIR nomenclature, data-validation, ambiguity resolution, and the analysis of highly polymorphic genetic systems. As with the STREGA guidelines, the intent behind STREIS is not to dictate the design of immunogenomic studies, but to ensure consistent and transparent reporting of research, facilitating the synthesis of HLA and KIR data across studies.

  18. LC/IRMS analysis: A powerful technique to trace carbon flow in microphytobenthic communities in intertidal sediments

    Moerdijk-Poortvliet, Tanja C. W.; Stal, Lucas J.; Boschker, Henricus T. S.

    2014-09-01

    Microphytobenthic communities are important for primary production in intertidal marine sediments. Extracellular polymeric substances (EPS), comprising polysaccharides and proteins, play a key role in the structure and functioning of microphytobenthic biofilms and allow interactions between the benthic microalgae and the associated heterotrophic bacteria. The use of stable isotopes has provided major insights into the functioning of these microbial ecosystems. Until recently, gas chromatography-isotope ratio mass spectrometry (GC/IRMS) was the principal method for compound specific stable isotope analysis in these studies. Liquid chromatography linked to IRMS (LC/IRMS) is a more recently developed technique that broadens the range of compounds that can be targeted, in particular enabling the analysis of 13C in non-volatile, aqueous soluble organic compounds, such as carbohydrates and amino acids. In this paper we present an overview of the possibilities and limitations of the LC/IRMS technique to study metabolic processes in microphytobenthic biofilms consisting of mainly diatoms. With a preliminary in-situ labeling experiment, we show that the biosynthesis of carbohydrates and amino acids in EPS and total carbohydrate and amino acid pools can be determined by LC/IRMS. Water extractable EPS were composed predominantly of carbohydrates, whereas amino acids played a minor role, both in terms of content and production. By using LC/IRMS, we will be able to quantify the biosynthesis of metabolites and, hence, to unravel in detail the metabolic pathways of the transfer of carbon from the diatoms via EPS to the bacteria.

  19. Constructing an AIRS Climatology for Data Visualization and Analysis to Serve the Climate Science and Application Communities

    Ding, Feng; Keim, Elaine; Hearty, Thomas J.; Wei, Jennifer; Savtchenko, Andrey; Theobald, Michael; Vollmer, Bruce

    2016-01-01

    The NASA Goddard Earth Sciences Data and Information Services Center (GES DISC) is the home of processing, archiving, and distribution services for NASA sounders: the present Aqua AIRS mission and the succeeding SNPP CrIS mission. The AIRS mission is entering its 15th year of global observations of the atmospheric state, including temperature and humidity profiles, outgoing longwave radiation, cloud properties, and trace gases. The GES DISC, in collaboration with the AIRS Project, released product from the version 6 algorithm in early 2013. Giovanni, a Web-based application developed by the GES DISC, provides a simple and intuitive way to visualize, analyze, and access vast amounts of Earth science remote sensing data without having to download the data. Most important variables from version 6 AIRS product are available in Giovanni. We are developing a climatology product using 14-year AIRS retrievals. The study can be a good start for the long term climatology from NASA sounders: the AIRS and the succeeding CrIS. This presentation will show the impacts to the climatology product from different aggregation methods. The climatology can serve climate science and application communities in data visualization and analysis, which will be demonstrated using a variety of functions in version 4 Giovanni. The highlights of these functions include user-defined monthly and seasonal climatology, inter annual seasonal time series, anomaly analysis.

  20. Characteristics of Phytoplankton Community Structure During and After a Bloom of the Dinoflagellate Scrippsiella trochoidea by HPLC Pigment Analysis

    WONG Chun-kwan; WONG Chong-kim

    2009-01-01

    A bloom of the dinoflagellate Scrippsiella trochoidea was detected for the first time in inner Tolo Harbor, Hong Kong in 2000. Water samples were collected at eight stations along a transect passing through a red tide patch for microscopic analysis of phytoplankton composition and high-performance liquid chromatography (HPLC) analysis of phytoplankton pigments. During the bloom, the density of dinoflagellates was 1.1×106 cells L-1 within the patch and 8.6×105 cells L-1 outside the patch where the phyto-plankton community was dominated by diatoms. After the bloom the S. trochoidea began to decrease in density and was replaced by diatoms as the dominating bloom-causing organisms at all stations, and the density of dinoflagellates at most stations was less than 1.0×106 cells L-1. The status of S. trochoidea as the causative species of the bloom was indicated by the presence of peridinin, the marker pigment for dinoflagellates. The shift from dinoflagellates to diatoms was marked by the decline of peridinin and the preva-lence of fucoxanthin. Phytoplankton pigment markers also revealed the presence of other minor phytoplankton assemblages such as cryptomonads and blue-green algal.

  1. Adult carrion arthropod community in a tropical rainforest of Malaysia: analysis on three common forensic entomology animal models.

    Azwandi, A; Nina Keterina, H; Owen, L C; Nurizzati, M D; Omar, B

    2013-09-01

    Decomposing carrion provides a temporary microhabitat and food source for a distinct community of organisms. Arthropods constitute a major part of this community and can be utilized to estimate the postmortem interval (PMI) of cadavers during criminal investigations. However, in Malaysia, knowledge of carrion arthropod assemblages and their succession is superficial. Therefore, a study on three types of forensic entomology animal model was conducted from 27 September 2010 to 28 October 2010 in a tropical rainforest at National University of Malaysia, Bangi, Selangor, Malaysia. Over one month collections of arthropods were made on nine animal carcasses: three laboratory rats (Rattus norvegicus, mean weight: 0.508 ± 0.027 kg), three rabbits (Oryctolagus cuniculus, mean weight: 2.538 ± 0.109 kg) and three long tailed macaque (Macaca fascicularis, mean weight: 5.750 ± 0.551 kg). A total of 31,433 arthropods belonging to eight orders and twenty-eight families were collected from all carcasses. Among 2924 of adults flies collected, approximately 19% were calliphorids with Chrysomya megacephala (Fabricius, 1794) being the most abundant. Arthropod taxon richness was lower on rat carcasses compared to that of rabbit and monkey carcasses, and this was more apparent during the first week of decomposition. However, there were no significant differences in Shannon-Weiner index (H'), Simpson dominance index (C) and Pielou's Evenness index (J) between different animal model. The arthropod assemblages associated to animal model were different significantly (p<0.05) while decomposition stage was a significant factor influencing insect assemblages (p<0.05). Analysis on the arthropods succession indicated that some taxa have a clear visitation period while the others, particularly Coleoptera, did not show a clear successional pattern thus require futher insect succession study. Although human bodies were not possible for the succession study, most of the arthropods collected are

  2. How many people have alcohol use disorders?: using the harmful dysfunction analysis to reconcile prevalence estimates in two community surveys

    Jerome C Wakefield

    2014-02-01

    Full Text Available Community prevalence rates of alcohol use disorders (AUDs provided by epidemiological studies using DSM-based diagnostic criteria pose several challenges: the rates appear implausibly high to many epidemiologists; they do not converge across similar studies; and, due to low service utilization by those diagnosed as disordered, they yield estimates of unmet need for services so high that credibility for planning purposes is jeopardized. For example, two early community studies using DSM diagnostic criteria, the Epidemiologic Catchment Area Study (ECA and the National Comorbidity Survey (NCS, yielded lifetime AUD prevalence rates of 14% and 24%, respectively, with NCS unmet need for services 19% of the entire population. Attempts to address these challenges by adding clinical significance requirements to diagnostic criteria have proven unsuccessful. Hypothesizing that these challenges are due to high rates of false positive diagnoses of problem drinking as AUDs, we test an alternative approach. We use the harmful dysfunction (HD analysis of the concept of mental disorder as a guide to construct more valid criteria within the framework of the standard out-of-control model of AUD. The proposed HD criteria require harm and dysfunction, where harm can be any negative social, personal, or physical outcome, and dysfunction requires either withdrawal symptoms or inability to stop drinking. Using HD criteria, ECA and NCS lifetime prevalences converge to much-reduced rates of 6% and 6.8%, respectively. Due to higher service utilization rates, NCS lifetime unmet need is reduced to 3.4%. Service-use and duration comparisons suggest increased diagnostic validity. Moreover, HD criteria eliminate 90% of transient teenage drinking from disorder status. The HD version of the out-of-control model thus potentially resolves the three classic prevalence challenges while offering a more rigorous approach to distinguishing AUDs from problematic drinking.

  3. Evaluation of methods for preparing hydrogen-producing seed inocula under thermophilic condition by process performance and microbial community analysis.

    O-Thong, Sompong; Prasertsan, Poonsuk; Birkeland, Nils-Kåre

    2009-01-01

    Five methods for preparation of hydrogen-producing seeds (base, acid, 2-bromoethanesulfonic acid (BESA), load-shock and heat shock treatments) as well as an untreated anaerobic digested sludge were compared for their hydrogen production performance and responsible microbial community structures under thermophilic condition (60 degrees C). The results showed that the load-shock treatment method was the best for enriching thermophilic hydrogen-producing seeds from mixed anaerobic cultures as it completely repressed methanogenic activity and gave the a maximum hydrogen production yield of 1.96 mol H(2) mol(-1) hexose with an hydrogen production rate of 11.2 mmol H(2) l(-1)h(-1). Load-shock and heat-shock treatments resulted in a dominance of Thermoanaerobacterium thermosaccharolyticum with acetic acid and butyric acid type of fermentation while base- and acid-treated seeds were dominated by Clostridium sp. and BESA-treated seeds were dominated by Bacillus sp. The comparative experimental results from hydrogen production performance and microbial community analysis showed that the load-shock treatment method was better than the other four methods for enriching thermophilic hydrogen-producing seeds from anaerobic digested sludge. Load-shock treated sludge was implemented in palm oil mill effluent (POME) fermentation and was found to give maximum hydrogen production rates of 13.34 mmol H(2) l(-1)h(-1) and resulted in a dominance of Thermoanaerobacterium spp. Load-shock treatment is an easy and practical method for enriching thermophilic hydrogen-producing bacteria from anaerobic digested sludge.

  4. Culture-independent bacterial community analysis of the salty-fermented fish paste products of Thailand and Laos.

    Marui, Junichiro; Boulom, Sayvisene; Panthavee, Wanchai; Momma, Mari; Kusumoto, Ken-Ichi; Nakahara, Kazuhiko; Saito, Masayoshi

    2015-01-01

    A bacterial community analysis, using a culture-independent method (polymerase chain reaction-denaturing gradient gel electrophoresis), detected 17 species of bacteria including species of the genera Tetragenococcus, Lactobacillus, Pediococcus, Weissella Halanaerobium, Clostridium, and Sphingomonas in a traditional salty-fermented fish paste known as pla-ra or pa-daek in Thailand and Laos, which is used as a storage-stable multi-purpose seasoning. The representative genus of lactic acid bacteria seemed to vary in the 10 products collected from Thailand and Laos. Tetragenococci were common in products from central Thailand and Vientiane in Laos which had salinities of not less than 11% and pH values ranging from 5.6 to 6.1. However, lactobacilli were common in products from northern Thailand which had the lowest salinities (8.3-8.6%) and pH values (4.5-4.8) of all the samples examined. Two Lactobacillus and one Tetragenococcus species were detected in one product from northeastern Thailand containing 10% salt. These results suggest that salinity in pla-ra/pa-daek is an important determinant of the representative genus of lactic acid bacteria such as, Tetragenococcus or Lactobacillus. Additionally, differences in the acidity between these two groups seemed to be related to the production of d-/l-lactic acid in the lactic acid bacteria in each product. This is the first study to report a correlation between bacterial community structure and taste components in pla-ra/pa-daek products from various regions. This scientific work on a traditional fermented food will be useful in helping local producers meet differing consumer preferences in various regions.

  5. Metagenome Sequence Analysis of Filamentous Microbial Communities Obtained from Geochemically Distinct Geothermal Channels Reveals Specialization of Three Aquificales Lineages

    Cristina eTakacs-vesbach

    2013-05-01

    Full Text Available The Aquificales are thermophilic microorganisms that inhabit hydrothermal systems worldwide and are considered one of the earliest lineages of the domain Bacteria. We analyzed metagenome sequence obtained from six thermal ‘filamentous streamer’ communities (~40 Mbp per site, which targeted three different groups of Aquificales found in Yellowstone National Park (YNP. Unassembled metagenome sequence and PCR-amplified 16S rRNA gene libraries revealed that acidic, sulfidic sites were dominated by Hydrogenobaculum (Aquificaceae populations, whereas the circumneutral pH (6.5 - 7.8 sites containing dissolved sulfide were dominated by Sulfurihydrogenibium spp. (Hydrogenothermaceae. Thermocrinis (Aquificaceae populations were found primarily in the circumneutral sites with undetectable sulfide, and to a lesser extent in one sulfidic system at pH 8. Phylogenetic analysis of assembled sequence containing 16S rRNA genes as well as conserved protein-encoding genes revealed that the composition and function of these communities varied across geochemical conditions. Each Aquificales lineage contained genes for CO2 fixation by the reverse TCA cycle, but only the Sulfurihydrogenibium populations perform citrate cleavage using ATP citrate lyase (Acl. The Aquificaceae populations use an alternative pathway catalyzed by two separate enzymes, citryl CoA synthetase (Ccs and citryl CoA lyase (Ccl. All three Aquificales lineages contained evidence of aerobic respiration, albeit due to completely different types of heme Cu oxidases (subunit I involved in oxygen reduction. The distribution of Aquificales populations and differences among functional genes involved in energy generation and electron transport is consistent with the hypothesis that geochemical parameters (e.g., pH, sulfide, H2, O2 have resulted in niche specialization among members of the Aquificales.

  6. Cost-Benefit Analysis of Green Infrastructures on Community Stormwater Reduction and Utilization: A Case of Beijing, China

    Liu, Wen; Chen, Weiping; Feng, Qi; Peng, Chi; Kang, Peng

    2016-12-01

    Cost-benefit analysis is demanded for guiding the plan, design and construction of green infrastructure practices in rapidly urbanized regions. We developed a framework to calculate the costs and benefits of different green infrastructures on stormwater reduction and utilization. A typical community of 54,783 m2 in Beijing was selected for case study. For the four designed green infrastructure scenarios (green space depression, porous brick pavement, storage pond, and their combination), the average annual costs of green infrastructure facilities are ranged from 40.54 to 110.31 thousand yuan, and the average of the cost per m3 stormwater reduction and utilization is 4.61 yuan. The total average annual benefits of stormwater reduction and utilization by green infrastructures of the community are ranged from 63.24 to 250.15 thousand yuan, and the benefit per m3 stormwater reduction and utilization is ranged from 5.78 to 11.14 yuan. The average ratio of average annual benefit to cost of four green infrastructure facilities is 1.91. The integrated facilities had the highest economic feasibility with a benefit to cost ratio of 2.27, and followed by the storage pond construction with a benefit to cost ratio of 2.14. The results suggested that while the stormwater reduction and utilization by green infrastructures had higher construction and maintenance costs, their comprehensive benefits including source water replacements benefits, environmental benefits and avoided cost benefits are potentially interesting. The green infrastructure practices should be promoted for sustainable management of urban stormwater.

  7. How Many People have Alcohol Use Disorders? Using the Harmful Dysfunction Analysis to Reconcile Prevalence Estimates in Two Community Surveys

    Wakefield, Jerome C.; Schmitz, Mark F.

    2014-01-01

    Community prevalence rates of alcohol use disorders (AUDs) provided by epidemiological studies using DSM-based diagnostic criteria pose several challenges: the rates appear implausibly high to many epidemiologists; they do not converge across similar studies; and, due to low service utilization by those diagnosed as disordered, they yield estimates of unmet need for services so high that credibility for planning purposes is jeopardized. For example, two early community studies using DSM diagnostic criteria, the Epidemiologic Catchment Area Study (ECA) and the National Comorbidity Survey (NCS), yielded lifetime AUD prevalence rates of 14 and 24%, respectively, with NCS unmet need for services 19% of the entire population. Attempts to address these challenges by adding clinical significance requirements to diagnostic criteria have proven unsuccessful. Hypothesizing that these challenges are due to high rates of false-positive diagnoses of problem drinking as AUDs, we test an alternative approach. We use the harmful dysfunction (HD) analysis of the concept of mental disorder as a guide to construct more valid criteria within the framework of the standard out-of-control model of AUD. The proposed HD criteria require harm and dysfunction, where harm can be any negative social, personal, or physical outcome, and dysfunction requires either withdrawal symptoms or inability to stop drinking. Using HD criteria, ECA and NCS lifetime prevalences converge to much-reduced rates of 6 and 6.8%, respectively. Due to higher service utilization rates, NCS lifetime unmet need is reduced to 3.4%. Service use and duration comparisons suggest that HD criteria possess increased diagnostic validity. Moreover, HD criteria eliminate 90% of transient teenage drinking from disorder status. The HD version of the out-of-control model thus potentially resolves the three classic prevalence challenges while offering a more rigorous approach to distinguishing AUDs from problematic drinking. PMID

  8. Comparison of Rock Varnish Bacterial Communities with Surrounding Non-Varnished Rock Surfaces: Taxon-Specific Analysis and Morphological Description.

    Esposito, Alfonso; Ahmed, Engy; Ciccazzo, Sonia; Sikorski, Johannes; Overmann, Jörg; Holmström, Sara J M; Brusetti, Lorenzo

    2015-10-01

    Rock varnish is a thin layer of Fe and Mn oxyhydroxides with embedded clay minerals that contain an increased Mn/Fe ratio compared to that of the Earth's crust. Even if the study of rock varnish has important implications in several fields, the composition of epilithic bacterial communities and the distribution of taxa on varnish surfaces are still not wholly described. The aim of this study was (i) to identify the bacterial taxa which show the greatest variation between varnish and non-varnish environments, collected from the same rock, and (ii) to describe the morphology of epilithic communities through scanning electron microscopy (SEM). Triplicate samples of rock surfaces with varnish and triplicate samples without varnish were collected from five sites in Matsch Valley (South Tyrol, Italy). The V4 region of 16S rRNA gene was analyzed by Illumina sequencing. Fifty-five ubiquitous taxa have been examined to assess variation between varnish and non-varnish. Cyanobacteria, Chloroflexi, Proteobacteria along with minor taxa such as Solirubrobacterales, Conexibaxter, and Rhodopila showed significant variations of abundance, diversity, or both responding to the ecology (presence/absence of varnish). Other taxa, such as the genus Edaphobacter, showed a more marked spatial variation responding to the sampling site. SEM images showed a multitude of bacterial morphologies and structures involved in the process of attachment and creation of a suitable environment for growth. The features emerging from this analysis suggest that the highly oxidative Fe and Mn-rich varnish environment favors anoxigenic autotrophy and establishment of highly specialized bacteria.

  9. Drought Analysis of Haihe Basin in North China based on the Community Land Model, 1960-2010

    Qin, Y.; Yang, D.; Lei, H.

    2014-12-01

    Drought severity not only depends on weather anomaly, but is also related to terrestrial hydrological condition to a large extent. In this study, we analyzed droughts using indices based on precipitation and soil moisture during the period of 1960-2010 in Haihe basin, which is a typical drought-prone region in North China. The Soil Moisture Drought Severity (SMDS) and Standardized Precipitation Index (SPI) are used to evaluate drought severity. SMDS is calculated based on the monthly soil moisture of upper 50cm from the simulation by Community Land Model (CLM 4.0) and SPI is calculated based on gridded precipitation at 0.05° resolution (5 km × 5 km approximately), which is spatially interpolated from observations. During the last 51 years, 36 severe drought events (affecting areas greater than 20,000 km2 and durations longer than 3 months) have been identified based on SMDS, and 41 drought events identified based on SPI. Results derived from SMDS indicate that there is a significant increasing trend in the drought affected area, and that the drought event occurred in 1999 has the largest affected area. Compared with the drought events derived from SMDS, the events derived from SPI have shorter durations but larger affected areas on average. Although the mean NDVI of the whole basin has been increasing since the 1980s, the two declining periods of 1992-1994 and 1999-2003 show fairly good agreement with the drought events identified in the same periods. Comparison between SMDS and SPI shows the superiority of SMDS for drought assessment in the perspective of terrestrial ecosystem. Keywords: Drought analysis; Standardized Precipitation Index (SPI); Soil Moisture Drought Severity (SMDS); Community Land Model; Haihe basin

  10. Comparative Metagenomic Analysis Of Microbial Communities From Active Layer And Permafrost After Short-Term Thaw

    Vishnivetskaya, T. A.; Chauhan, A.; Saarunya, G.; Murphy, J.; Williams, D.; Layton, A. C.; Pfiffner, S. M.; Stackhouse, B. T.; Sanders, R.; Lau, C. M.; myneni, S.; Phelps, T. J.; Fountain, A. G.; Onstott, T. C.

    2012-12-01

    .Permafrost areas occupy 20-25% of the Earth and extend of 1 km depths. The total number of prokaryotes and their biomass in cold regions are estimated to be 1 x 1030 cells and 140 x1015 g of C, respectively. Thus these environments serve as a reservoir of microbial and biogeochemical activity, which is likely to increase upon thawing. We are currently performing long-term thawing experiments at 4o C on 18, geochemically well-characterized, 1 meter long, intact cores consisting of active-layer (0-70 cm depth) and permafrost, collected from a 7 meter diameter ice-wedge polygon located at the McGill Arctic Research Station on Axel Heiberg Island, Nunavut, Canada. The organic carbon content of these cores averages ~1% at depth but increases to 5.4% in the top 10 cm. The cores were subdivided into four treatment groups: saturated cores (thawed while receiving artificial rain), drained cores (being thawed under natural hydrological conditions), dark cores (thawed under natural hydrological conditions with no light input) and control cores (maintain permafrost table at 70 cm depth). Over the course of 10 weeks the cores were progressively thawed from -4oC to 4oC from the top down to simulate spring thaw conditions in the Arctic. The temperatures at 5 cm, 35 cm, 65 cm, and below the permafrost table in the core were recorded continuously. Pore water and gas samples from 4 depths in each core were collected every two weeks and analyzed for pH, anions, cations, H2, CH4, CO, O2, N2, CO2 and δ13C of CO2. Headspace gas samples were collected weekly and analyzed for the same gases as the pore gases. Sediment sub-samples from the 4 depths were collected and total community genomic DNA (gDNA) was isolated using FastDNA SPIN kit followed by Qiagen column purification. The average yield of gDNA was ~3.5 μg/g of soil for the upper 5 cm active layers and decreased to ~1.5 μg/g of soil in the permafrost. The bacterial 16S copy numbers estimated by real-time quantitative PCR

  11. Psychometric Analysis of a Scale to Assess Norms of Reciprocity of Social Support in Community-Based and Congregation-Based Groups

    Holly C. Pope

    2013-12-01

    Full Text Available Reciprocity, a core component of social capital, is rarely theorized or measured leaving the relationship between reciprocity and health ambiguous. Historically, reciprocity measures have not been used in the context they were designed causing measurement error. This multi-phased study was designed to develop and validate a reciprocity measure for formal and informal groups within communities and congregations as part of a more comprehensive social capital measure. In-depth interviews (n = 72, cognitive interviews (n = 40, and an expert review panel guided item development and selection for content validity. South Carolina residents (n = 500 completed the 10-item Reciprocity of Social Support (RSS Scale during 2008-2010. Construct validity was supported through an exploratory factor analysis (EFA that confirmed a two-factor model for the scale for community- and congregation-based groups. Cronbach’s α values indicated items were highly correlated for community groups and church groups. Psychometric analyses of the RSS Scale support convergent and divergent validity for the community- and congregation-based groups. Mean RSS Scale scores were not statistically different between community- and congregation-based groups. This scale has proven psychometric properties for utilization in future research investigating reciprocity of social support in community- and congregation-based groups and will be useful to examine whether reciprocity (by context and type of group is associated with physical and/or mental health.

  12. Brief Report: Impact of Applied Behaviour Analysis (ABA) on Carer Burden and Community Participation in Challenging Behaviour--Results from a Randomised Controlled Trial

    Hassiotis, A.; Robotham, D.; Canagasabey, A.; Marston, L.; Thomas, B.; King, M.

    2012-01-01

    Background: Applied behaviour analysis (ABA) reduces challenging behaviour in people with intellectual disability. There is interest, however, in whether such interventions reduce carer burden and increase community participation in this group. Methods: A 6-month randomised controlled trial was followed by a longer-term naturalistic follow-up of…

  13. Intervention and societal costs of residential community reintegration for patients with acquired brain injury: a cost-analysis of the Brain Integration Programme

    Heugten, C.M. van; Geurtsen, G.J.; Derksen, R.E.; Martina, J.D.; Geurts, A.C.H.; Evers, S.M.

    2011-01-01

    OBJECTIVE: The objective of this study was to examine the intervention costs of a residential community reintegration programme for patients with acquired brain injury and to compare the societal costs before and after treatment. METHODS: A cost-analysis was performed identifying costs of healthcare

  14. Intercomparison of the community multiscale air quality model and CALGRID using process analysis.

    O'Neill, Susan M; Lamb, Brian K

    2005-08-01

    This study was designed to examine the similarities and differences between two advanced photochemical air quality modeling systems: EPA Models-3/CMAQ and CALGRID/CALMET. Both modeling systems were applied to an ozone episode that occurred along the I-5 urban corridor in western Washington and Oregon during July 11-14, 1996. Both models employed the same modeling domain and used the same detailed gridded emission inventory. The CMAQ model was run using both the CB-IV and RADM2 chemical mechanisms, while CALGRID was used with the SAPRC-97 chemical mechanism. Outputfrom the Mesoscale Meteorological Model (MM5) employed with observational nudging was used in both models. The two modeling systems, representing three chemical mechanisms and two sets of meteorological inputs, were evaluated in terms of statistical performance measures for both 1- and 8-h average observed ozone concentrations. The results showed that the different versions of the systems were more similar than different, and all versions performed well in the Portland region and downwind of Seattle but performed poorly in the more rural region north of Seattle. Improving the meteorological input into the CALGRID/CALMET system with planetary boundary layer (PBL) parameters from the Models-3/CMAQ meteorology preprocessor (MCIP) improved the performance of the CALGRID/CALMET system. The 8-h ensemble case was often the best performer of all the cases indicating that the models perform better over longer analysis periods. The 1-h ensemble case, derived from all runs, was not necessarily an improvement over the five individual cases, but the standard deviation about the mean provided a measure of overall modeling uncertainty. Process analysis was applied to examine the contribution of the individual processes to the species conservation equation. The process analysis results indicated that the two modeling systems arrive at similar solutions by very different means. Transport rates are faster and exhibit

  15. A cost effectiveness analysis within a randomised controlled trial of post-acute care of older people in a community hospital

    O'Reilly, Jacqueline; Lowson, Karin; Young, John; Forster, Anne; Green, John; Small, Neil

    2006-01-01

    Objective To assess the cost effectiveness of post-acute care for older people in a locality based community hospital compared with a department for care of elderly people in a district general hospital, which admits patients aged over 76 years with acute medical conditions. Design Cost effectiveness analysis within a randomised controlled trial. Setting Community hospital and district general hospital in Yorkshire, England. Participants 220 patients needing rehabilitation after an acute illness for which they required admission to hospital. Interventions Multidisciplinary care in the district general hospital or prompt transfer to the community hospital. Main outcome measures EuroQol EQ-5D scores transformed into quality adjusted life years (QALYs), and health and social service costs over six months from randomisation. Results The mean QALY score for the community hospital group was marginally non-significantly higher than that for the district general hospital group (0.38 v 0.35) at six months after recruitment. The mean (standard deviation) costs per patient of the health and social services resources used were similar for both groups: community hospital group £7233 (euros 10 567; $13 341) (£5031), district general hospital group £7351 (£6229), and these findings were robust to several sensitivity analyses. The incremental cost effectiveness ratio for community hospital care dominated. A cost effectiveness acceptability curve, based on bootstrapped simulations, suggests that at a willingness to pay threshold of £10 000 per QALY, 51% of community hospital cases will be cost effective, which rises to 53% of cases when the threshold is £30 000 per QALY. Conclusion Post-acute care for older people in a locality based community hospital is of similar cost effectiveness to that of an elderly care department in a district general hospital. PMID:16861254

  16. Pharmaceutical consultations in community pharmacies: utility of the Roter Interaction Analysis System to study pharmacist-patient communication.

    Cavaco, Afonso; Roter, Debra

    2010-06-01

    Communication is a key issue in the delivery of healthcare services. In the pharmacy context, pharmacist-patient communication may vary from brief counselling episodes to extensive pharmaceutical care consultations. Many community pharmacies have developed practices to facilitate the effective delivery of pharmacy care, in particular to chronic patients, although the nature and extent of the services differ widely from country to country. Diabetes-focused pharmaceutical care is an example highlighting both the opportunities and challenges associated with an expansion of pharmacy services from product dispensing to pharmaceutical consultations. An area of particular challenge of such an expansion of pharmaceutical services is the development of expertise in the delivery of patient-centred pharmaceutical consultations. Although well known to medicine and nursing, patient-centredness has not been routinely incorporated into the training of pharmacists, evaluation of pharmacy practice or conduct of pharmacy-related research. There are few studies of the communication process based on analysis of an objective record such as an audio or video recording and the common perspective is largely a one-way information flow from pharmacist to patient. This has hampered the field's ability to link pharmacy communication to outcomes, including patient adherence and satisfaction with services. An extensive body of communication research on physician-patient interaction, employing the Roter Interaction Analysis System (RIAS), exists and the system presents a potentially useful tool in the pharmacy context. The purpose of this essay is to explore the utility of the RIAS for analysis of pharmacist-patient interaction and its implication for improving patient care and optimizing pharmacy-specific outcomes.

  17. Application of fluorescent microscopy and cascade filtration methods for analysis of soil microbial community

    Ivanov, Konstantin; Pinchuk, Irina; Gorodnichev, Roman; Polyanskaya, Lubov

    2016-04-01

    Methods establishment of soil microbial cells size estimation called from the importance of current needs of research in microbial ecology. Some of the methods need to be improved for more detailed view of changes happen in microbiome of terrestrial ecosystems. The combination of traditional microscopy methods, fluorescence and filtration in addition to cutting-edge DNA analysis gives a wide range of the approaches for soil microbial ecologists in their research questions. In the most of the cases the bacterial cells size is limited of the natural conditions such as lack of nutrients or stress factors due to heterogeneity of soil system. In the samples of soils, lakes and rivers sediments, snow and rain water the bacterial cells were detected minimally of 0.2 microns. We established the combination of the cascade filtration and fluorescent microscopy for complex analysis of different terrestrial ecosystems and various soil types. Our modification based on the use of successively filtered soil suspension for collection of microbes by the membrane pores decrease. Combination with fluorescence microscopy and DNA analysis via FISH method gave the presentation of microbial interactions and review of ecological strategies of soil microorganisms. Humus horizons of primitive arctic soil were the most favorable for bacterial growth. Quantified biomass of soil bacteria depends on the dominance of cells with specific dimensions caused of stress factors. The average bacterial size of different soil varied from 0.23 to 0.38 microns, however in humus horizons of arctic soil we detected the contrast dominance of the bigger bacterial cells sized of 1.85 microns. Fungi in this case contributed to increase the availability of organic matter for bacteria because the fungal mycelium forms the appreciable part of microbial biomass of primitive arctic soil. The dominant content of bigger bacterial cells in forest and fallow soil as well as the opposite situation in arable soils caused

  18. Geo-Chip analysis reveals reduced functional diversity of the bacterial community at a dumping site for dredged Elbe sediment.

    Störmer, Rebecca; Wichels, Antje; Gerdts, Gunnar

    2013-12-15

    The dumping of dredged sediments represents a major stressor for coastal ecosystems. The impact on the ecosystem function is determined by its complexity not easy to assess. In the present study, we evaluated the potential of bacterial community analyses to act as ecological indicators in environmental monitoring programmes. We investigated the functional structure of bacterial communities, applying functional gene arrays (GeoChip4.2). The relationship between functional genes and environmental factors was analysed using distance-based multivariate multiple regression. Apparently, both the function and structure of the bacterial communities are impacted by dumping activities. The bacterial community at the dumping centre displayed a significant reduction of its entire functional diversity compared with that found at a reference site. DDX compounds separated bacterial communities of the dumping site from those of un-impacted sites. Thus, bacterial community analyses show great potential as ecological indicators in environmental monitoring.

  19. The challenge of inclusion in mental health: an analysis of a community center and its work with social bonds

    Sara Ardila-Gómez

    2016-06-01

    Full Text Available Social inclusion is a key component of transformations in mental health care, because it takes into account the benefits of community life for both those with mental illness and the other members of the community. In order to understand the scope of inclusion within mental health, 45 participants of a community center linked to a psychiatric hospital discharge program which explicitly seeks to provide social inclusion were interviewed. The possible changes in social relationships between users and other community members based in their sustained daily interactions in the community center were explored. Results suggest that the building of social bonds, as part of informal support networks, is one of the benefits of attending the community center. Positive changes in ideas regarding people with “mental illness” were also observed, although these ideas seemed to be more connected to the notion of integration than to social inclusion.

  20. Purification of high ammonia wastewater in a biofilm airlift loop bioreactor with microbial communities analysis.

    Qiu, Chunsheng; Zhang, Dandan; Sun, Liping; Wen, Jianping

    2015-01-01

    A 70 m(3) gas-liquid-solid three-phase flow airlift loop bioreactor, in which biofilm attached on granular active carbon carriers, was used for purification of the high ammonia wastewater from bioethanol production. Under the optimum operating conditions, COD and NH4 (+)-N average removal rate of 89.0 and 98.6 % were obtained at hydraulic retention time of 10 h. Scanning electron microscopy was applied for observation of the biofilm formation. High contaminants removal efficiency was achieved by holding high biomass concentration in the reactor due to the attached biofilm over the carriers. The 16S rRNA gene clone library analysis indicated that 68.6 % of the clones were affiliated with the two phyla Bacteroidetes and Proteobacteria, and residual clones clustered with various sequences from uncultured bacteria. The presence of various anoxic/anaerobic bacteria indicated that the oxygen gradient inside the biofilm could provide appropriate micro-environment for nitrogen removal through simultaneous nitrification and denitrification.

  1. A metagenomic analysis displays the diverse microbial community of a vermicomposting system in Uganda

    Anne-Lie Blomström

    2016-11-01

    Full Text Available Background: Vermicomposting is a mesophilic process using earthworms to efficiently and at low cost process large volumes of organic waste. It has been suggested to not only increase soil fertility but also increase biomass of beneficial bacteria while reducing harmful bacteria. The aim of this study was to set up a strategy to investigate and characterise the viral as well as the bacterial composition of a vermicomposting system. Material and methods: The vermicomposting unit used in this study was placed at the Makerere University Agricultural Research Institute Kabanyolo on the outskirts of Kampala, Uganda, and was fed with 80% cattle manure and 20% food waste. On Day 172, the compost was terminated and compost samples were collected from three layers of the unit: the top, the middle and the bottom layer. A metagenomic approach was then applied to characterise the viral and bacterial composition of the vermicomposting system. Results and discussion: A high abundance and diversity of bacteria were identified. Proteobacteria was the largest phyla in the compost (mainly Alpha-, Gamma- and Betaproteobacteria, constituting almost 65% of the bacterial reads in the data sets. DNA samples from several possible pathogenic bacteria, such as Salmonella spp., Escherichia coli, Enterobacter spp., Enterococcus spp. and Clostridium spp, were detected in the vermicompost, suggesting that there might still be harmful bacteria in the vermicast. Phages constituted the main viral group; apart from phages, mainly insect viruses were identified. The only animal or human virus identified was kobuvirus. In summary, metagenomic analysis was shown to be an efficient technology to characterise the microbial composition of vermicast. The data from this study contribute to a better understanding of the microbes present in this kind of composting system and can help determine measures necessary for safe manure handling.

  2. A metagenomic analysis displays the diverse microbial community of a vermicomposting system in Uganda

    Blomström, Anne-Lie; Lalander, Cecilia; Komakech, Allan John; Vinnerås, Björn; Boqvist, Sofia

    2016-01-01

    Background Vermicomposting is a mesophilic process using earthworms to efficiently and at low cost process large volumes of organic waste. It has been suggested to not only increase soil fertility but also increase biomass of beneficial bacteria while reducing harmful bacteria. The aim of this study was to set up a strategy to investigate and characterise the viral as well as the bacterial composition of a vermicomposting system. Material and methods The vermicomposting unit used in this study was placed at the Makerere University Agricultural Research Institute Kabanyolo on the outskirts of Kampala, Uganda, and was fed with 80% cattle manure and 20% food waste. On Day 172, the compost was terminated and compost samples were collected from three layers of the unit: the top, the middle and the bottom layer. A metagenomic approach was then applied to characterise the viral and bacterial composition of the vermicomposting system. Results and discussion A high abundance and diversity of bacteria were identified. Proteobacteria was the largest phyla in the compost (mainly Alpha-, Gamma- and Betaproteobacteria), constituting almost 65% of the bacterial reads in the data sets. DNA samples from several possible pathogenic bacteria, such as Salmonella spp., Escherichia coli, Enterobacter spp., Enterococcus spp. and Clostridium spp, were detected in the vermicompost, suggesting that there might still be harmful bacteria in the vermicast. Phages constituted the main viral group; apart from phages, mainly insect viruses were identified. The only animal or human virus identified was kobuvirus. In summary, metagenomic analysis was shown to be an efficient technology to characterise the microbial composition of vermicast. The data from this study contribute to a better understanding of the microbes present in this kind of composting system and can help determine measures necessary for safe manure handling. PMID:27834174

  3. Metagenomic analysis of microbial community of an Amazonian geothermal spring in Peru.

    Paul, Sujay; Cortez, Yolanda; Vera, Nadia; Villena, Gretty K; Gutiérrez-Correa, Marcel

    2016-09-01

    Aguas Calientes (AC) is an isolated geothermal spring located deep into the Amazon rainforest (7°21'12″ S, 75°00'54″ W) of Peru. This geothermal spring is slightly acidic (pH 5.0-7.0) in nature, with temperatures varying from 45 to 90 °C and continually fed by plant litter, resulting in a relatively high degree of total organic content (TOC). Pooled water sample was analyzed at 16S rRNA V3-V4 hypervariable region by amplicon metagenome sequencing on Illumina HiSeq platform. A total of 2,976,534 paired ends reads were generated which were assigned into 5434 numbers of OTUs. All the resulting 16S rRNA fragments were then classified into 58 bacterial phyla and 2 archaeal phyla. Proteobacteria (88.06%) was found to be the highest represented phyla followed by Thermi (6.43%), Firmicutes (3.41%) and Aquificae (1.10%), respectively. Crenarchaeota and Euryarchaeota were the only 2 archaeal phyla detected in this study with low abundance. Metagenomic sequences were deposited to SRA database which is available at NCBI with accession number SRX1809286. Functional categorization of the assigned OTUs was performed using PICRUSt tool. In COG analysis "Amino acid transport and metabolism" (8.5%) was found to be the highest represented category whereas among predicted KEGG pathways "Metabolism" (50.6%) was the most abundant. This is the first report of a high resolution microbial phylogenetic profile of an Amazonian hot spring.

  4. Social network analysis of micro-blog group virtual communities%微群虚拟社区的社会网络分析

    郭小洁

    2014-01-01

    This paper focuses on the micro-blog group from the perspective of social network analysis. The purpose is to explore the network structure and the mode of communication between members of virtual communities using social network analysis with the help of the analyzing tool UCINET. Then summarizes the structural features of virtual community, discuss the results of the analysis, and give some suggestions for community building on this basis in order to promote the sustainable development of the virtual community.%从社会网络分析的视角看微群,使用社会网络分析方法,借助UCINET软件分析虚拟社区的网络关系,探索其结构以及交流模式,总结虚拟社区的结构特征,对分析结果进行探讨,并在此基础上对社区的建设提出相应的建议,以促进社区的持续性发展。

  5. Depression among Asian-American Adults in the Community: Systematic Review and Meta-Analysis.

    Hee Jun Kim

    Full Text Available In this systematic review, we provide an overview of the literature on depression among Asian-Americans and explore the possible variations in depression prevalence estimates by methodological and demographic factors.Six databases were used to identify studies reporting a prevalence estimate for depression in Asian-American adults in non-clinical settings. Meta-analysis was used to calculate pooled estimates of rates of depression by assessment type. Statistical heterogeneity was assessed for subgroup analyses by gender, age, ethnicity, and other participant characteristics.A total of 58 studies met the review criteria (n = 21.731 Asian-American adults. Heterogeneity across the studies was considerably high. The prevalence of major depression assessed via standardized clinical interviews ranged between 4.5% and 11.3%. Meta-analyses revealed comparable estimated prevalence rates of depression as measured by the Center for Epidemiologic Studies Depression Scale (35.6%, 95% CI 27.6%-43.7% and the Geriatric Depression Scale (33.1%, 95% CI 14.9%-51.3%. Estimates varied by Asian racial/ethnic group and other participant characteristics. Estimates of depression among special populations, which included maternity, caregivers, and homosexuals, were significantly higher than estimates obtained from other samples (58.8% vs 29.3%, p = .003. Estimates of depression among Korean and Filipino-Americans were similar (33.3%-34.4%; however, the estimates were twice as high as those for Chinese-Americans (15.7%; p = .012 for Korean, p = .049 for Filipino.There appears to be wide variability in the prevalence rates of depression among Asian-Americans in the US. Practitioners and researchers who serve Asian-American adults need to be sensitive to the potential diversity of the expression of depression and treatment-seeking across Asian-American subgroups. Public health policies to increase Asian-American access to mental health care, including increased screening

  6. Forest Policy Scenario Analysis: Sensitivity of Songbird Community to Changes in Forest Cover Amount and Configuration

    Robert S. Rempel

    2007-06-01

    Full Text Available Changes in mature forest cover amount, composition, and configuration can be of significant consequence to wildlife populations. The response of wildlife to forest patterns is of concern to forest managers because it lies at the heart of such competing approaches to forest planning as aggregated vs. dispersed harvest block layouts. In this study, we developed a species assessment framework to evaluate the outcomes of forest management scenarios on biodiversity conservation objectives. Scenarios were assessed in the context of a broad range of forest structures and patterns that would be expected to occur under natural disturbance and succession processes. Spatial habitat models were used to predict the effects of varying degrees of mature forest cover amount, composition, and configuration on habitat occupancy for a set of 13 focal songbird species. We used a spatially explicit harvest scheduling program to model forest management options and simulate future forest conditions resulting from alternative forest management scenarios, and used a process-based fire-simulation model to simulate future forest conditions resulting from natural wildfire disturbance. Spatial pattern signatures were derived for both habitat occupancy and forest conditions, and these were placed in the context of the simulated range of natural variation. Strategic policy analyses were set in the context of current Ontario forest management policies. This included use of sequential time-restricted harvest blocks (created for Woodland caribou (Rangifer tarandus conservation and delayed harvest areas (created for American marten (Martes americana atrata conservation. This approach increased the realism of the analysis, but reduced the generality of interpretations. We found that forest management options that create linear strips of old forest deviate the most from simulated natural patterns, and had the greatest negative effects on habitat occupancy, whereas policy options

  7. Building Safer Communities: The Integrated Community Safety Approach

    Fawcett, Ricky Lee; Kerr, Thomas A; Jordan, Steven Albert

    2001-03-01

    This paper discusses an integrated community safety approach to creating safer communities. It defines community broadly to include two categories of community members: “industry” and “neighbors.” Potential community members within the “industry” category include facilities, government/regulators, customers, stockholders, and suppliers. Within the “neighbors” category are towns, cities, counties, states; people/commodity flow systems; news media and special interest groups; environment; and families of employees. Each of these potential community members and its characteristics are discussed. The integrated community safety approach consists of three major activities: (1) define the boundaries of the community; (2) facilitate the sense of community; and (3) address the needs of the community. Defining the boundaries of the community includes determining the geographical and social boundaries; this is accomplished through conducting a hazard analysis and community involvement to identify all of the community members. Facilitating the sense of community includes conducting a capability/needs assessment and continuing community involvement to identify the issues and concerns of community members. Addressing the needs of the community involves master planning to consider safety issues in all community development actions and continuing community education and involvement. The integrated community safety approach is a workable approach for existing industries and their neighbors as well as new projects that industries and their neighbors might be considering. By using this socio-technical approach to integrating industry and all of its neighbors into a safer community, the integrated community safety approach will better assure the viability and safety of industry and its neighbors while maintaining or improving the overall quality of life.

  8. An enhanced anaerobic membrane bioreactor treating bamboo industry wastewater by bamboo charcoal addition: Performance and microbial community analysis.

    Xia, Tian; Gao, Xinyi; Wang, Caiqin; Xu, Xiangyang; Zhu, Liang

    2016-11-01

    In this study, two anaerobic membrane bioreactors (AnMBRs) were operated for 150days to treat bamboo industry wastewater (BIWW), and one of them was enhanced with bamboo charcoal (B-AnMBR). During the steady period, average chemical oxygen demand (COD) removal efficiencies of 94.5±2.9% and 89.1±3.1% were achieved in B-AnMBR and AnMBR, respectively. The addition of bamboo charcoal (BC) increased the amount of biomass and improved the performance of the systems. A higher biogas production and methane yield were also observed in B-AnMBR. Regarding the issue of membrane fouling, BC lowered the soluble microbial product (SMP) content by approximately 62.73mg/L and decreased the membrane resistance, thereby mitigating membrane fouling. Analysis of the microbial communities demonstrated that BC increased the microbial diversity and promoted the activity of Methanosaeta, Methanospirillum, and Methanobacterium, which are dominant in methane production.

  9. Social Analysis of the Benefit of Exclusive Breastfeeding among Muslim Women in Selected Communities in Edo State, Nigeria

    Alenkhe Odianonsen Augustine

    2015-08-01

    Full Text Available Food has always been a means of survival as its nutrient function for the survival of the body system, especially infant that need a proper building of their body system. The first, the best and the most complete nutrient a baby needs is the Breast milk. The act and practice of exclusive Breastfeeding have an advance impact on the child, the mother and the society at large, as the study examines the social analysis of the benefit and hindrances of exclusive breastfeeding among the Muslims in selected communities in Edo State, Nigeria. Social Action theory was used to buttress the benefit of exclusive breastfeeding, 150 Muslim women were interviewed with the aid of a structured questionnaire and an in-depth interview administered face-to face to the respondents. A cluster and purposive sampling technique was utilized and the findings analyzed with the use of Statistical Package for Social Sciences (SPSS 20.0 version. It was discovered that one of the hindrances to exclusive breastfeeding is caused by the health condition f the mother among others, inversely the benefit too numerous one off which is making the children/infant brilliant and healthy. Hence it is recommended that Exclusive Breastfeeding should be encouraged because of its medical/health benefit to both mother and child in both the national and international level for the realization of the Millennium Development Goal strategy by 2015.

  10. Microbial community analysis in a combined anaerobic and aerobic digestion system for treatment of cellulosic ethanol production wastewater.

    Shan, Lili; Yu, Yanling; Zhu, Zebing; Zhao, Wei; Wang, Haiman; Ambuchi, John J; Feng, Yujie

    2015-11-01

    This study investigated the microbial diversity established in a combined system composed of a continuous stirred tank reactor (CSTR), expanded granular sludge bed (EGSB) reactor, and sequencing batch reactor (SBR) for treatment of cellulosic ethanol production wastewater. Excellent wastewater treatment performance was obtained in the combined system, which showed a high chemical oxygen demand removal efficiency of 95.8% and completely eliminated most complex organics revealed by gas chromatography-mass spectrometry (GC-MS). Denaturing gradient gel electrophoresis (DGGE) analysis revealed differences in the microbial community structures of the three reactors. Further identification of the microbial populations suggested that the presence of Lactobacillus and Prevotella in CSTR played an active role in the production of volatile fatty acids (VFAs). The most diverse microorganisms with analogous distribution patterns of different layers were observed in the EGSB reactor, and bacteria affiliated with Firmicutes, Synergistetes, and Thermotogae were associated with production of acetate and carbon dioxide/hydrogen, while all acetoclastic methanogens identified belonged to Methanosaetaceae. Overall, microorganisms associated with the ability to degrade cellulose, hemicellulose, and other biomass-derived organic carbons were observed in the combined system. The results presented herein will facilitate the development of an improved cellulosic ethanol production wastewater treatment system.

  11. Segregation analysis of apolipoprotein A1 levels in families of adolescents: A community-based study in Taiwan

    Su Ta-Chen

    2006-01-01

    Full Text Available Background Apolipoprotein (Apo A1 is a protective factor for cardiovascular events. This study aimed to perform complex segregation analyses of Apo A1 levels in families of adolescents systematically ascertained from the junior high school students in a rural community. Both siblings and parents of the adolescent probands were recruited for the study. Apo A1 concentrations were measured by turbidimetric immunoassay methods. After adjustment for gender, age, body mass index, smoking and drinking status, residual values of Apo A1 were subjected to subsequent analyses. Results Significant mother-father and parent-offspring correlations were found. Commingling analyses indicated that a four-component distribution model was needed to account for the Apo A1 variation. Segregation analysis using regressive models revealed that the best-fit model of Apo A1 was a model of environmental effect plus familial correlation (heritability = 23.9%, in which a significant mother-father correlation existed. Models containing major gene effect could be rejected. Conclusion These results suggest that variations of Apo A1 levels in the normal range, especially during adolescence, are likely to be influenced by multiple factors without significant contribution from major genes.

  12. Pastoral power in the community pharmacy: A Foucauldian analysis of services to promote patient adherence to new medicine use.

    Waring, Justin; Latif, Asam; Boyd, Matthew; Barber, Nick; Elliott, Rachel

    2016-01-01

    Community pharmacists play a growing role in the delivery of primary healthcare. This has led many to consider the changing power of the pharmacy profession in relation to other professions and patient groups. This paper contributes to these debates through developing a Foucauldian analysis of the changing dynamics of power brought about by extended roles in medicines management and patient education. Examining the New Medicine Service, the study considers how both patient and pharmacist subjectivities are transformed as pharmacists seek to survey patient's medicine use, diagnose non-adherence to prescribed medicines, and provide education to promote behaviour change. These extended roles in medicines management and patient education expand the 'pharmacy gaze' to further aspects of patient health and lifestyle, and more significantly, established a form of 'pastoral power' as pharmacists become responsible for shaping patients' self-regulating subjectivities. In concert, pharmacists are themselves enrolled within a new governing regime where their identities are conditioned by corporate and policy rationalities for the modernisation of primary care.

  13. Analysis of wastewater as a new approach to determine the amount of drugs intake by local communities. A review

    Marta Boroń

    2014-09-01

    Full Text Available Qualitative and quantitative analysis of wastewater in terms of the amount of illegal drugs and their metabolites is a modern method of research, which is considered to be an objective and effective way to determine the amount of substances taken and excreted by humans. The results obtained in a real time allow for a quick identification of the quantitative and qualitative changes of the drugs intake. Such approach allows to estimate the daily intake of the drug by the local communities in terms of cities, countries and even the continent. Most often the estimation refers to the intake of the following drugs: cocaine, amphetamine, methamphetamine, ecstasy and cannabis. The wastewater`s monitoring provides information on the dynamics of the drug level changes depending on the weekday, and the general trend in a year. Retrospective estimation of drug intake carries errors, dependent from sampling, sewer system tightness, the stability of the analytes and mixtures of the wastewater itself but remains objective by providing very valuable information for the institutions struggling with drug crime.

  14. Calcium Carbonate Precipitation by Bacillus and Sporosarcina Strains Isolated from Concrete and Analysis of the Bacterial Community of Concrete.

    Kim, Hyun Jung; Eom, Hyo Jung; Park, Chulwoo; Jung, Jaejoon; Shin, Bora; Kim, Wook; Chung, Namhyun; Choi, In-Geol; Park, Woojun

    2016-03-01

    Microbially induced calcium carbonate precipitation (CCP) is a long-standing but re-emerging environmental engineering process for production of self-healing concrete, bioremediation, and long-term storage of CO2. CCP-capable bacteria, two Bacillus strains (JH3 and JH7) and one Sporosarcina strain (HYO08), were isolated from two samples of concrete and characterized phylogenetically. Calcium carbonate crystals precipitated by the three strains were morphologically distinct according to field emission scanning electron microscopy. Energy dispersive X-ray spectrometry mapping confirmed biomineralization via extracellular calcium carbonate production. The three strains differed in their physiological characteristics: growth at alkali pH and high NaCl concentrations, and urease activity. Sporosarcina sp. HYO08 and Bacillus sp. JH7 were more alkali- and halotolerant, respectively. Analysis of the community from the same concrete samples using barcoded pyrosequencing revealed that the relative abundance of Bacillus and Sporosarcina species was low, which indicated low culturability of other dominant bacteria. This study suggests that calcium carbonate crystals with different properties can be produced by various CCP-capable strains, and other novel isolates await discovery.

  15. Energy Engineering Analysis. Cutler Army Community Hospital and Associated Facilities, Fort Devens, Massachusetts. Volume 1 - executive summary. Final Submittal report

    NONE

    1985-10-01

    In February 1980, the Corps of Engineers, Norfolk District, initiated Contract No. DACA65-80-C-0003 with Reynolds, Smith and Hills, Architects-Engineers-Planners, Inc. of Jacksonville, Florida. This contract called for the performance of Energy Engineering Analysis Programs (EEAP) at three U.S. Army installations: Fort Devens, Massachusetts; Letterkenny Army Depot, Pennsylvania; and Seneca Army Depot, New York. The objective of these programs was the identification, evaluation and development of programming documents for energy conservation projects which meet the criteria of the Army`s Energy Conservation Investment Program (ECIP) and other funding mechanisms. The basic contract was modified by the Corps of Engineers several times to include additional increments of energy-related studies at each of the three installations. Work performed thus far for Fort Devens has included the following increments: A - ECIP`s for buildings and processes; B - ECIP`s for utilities and energy distribution systems and EMCS; C - Solar and renewable energy systems; D - Wood-Fired Steam Generation Plant; E - Coal conversion; and G - Projects identified in Increments A B that did not meet ECIP criteria In order to fulfill expanded requirements of the Army Facilities Energy Plan, the Corps of Engineers extended the contract with RSH to include a detailed energy audit of the Cutler Army Community Hospital and Associated Facilities at Fort Devens, Massachusetts. The Associated Facilities are the Vail Dental Clinic and the Oral Health Center. The energy audit consists of a field survey, analysis of energy conservation opportunities, and development of 1391`s and other programming documents for qualifying projects.

  16. 16S rRNA-based PCR-DGGE analysis of actinomycete communities in fields with continuous cotton cropping in Xinjiang, China.

    Zhang, Wei; Long, XuanQi; Huo, XiangDong; Chen, YiFeng; Lou, Kai

    2013-08-01

    The purpose of this study was to examine the variations in the microbial community structure of soil actinomycetes in fields with continuous cropping of cotton in Xinjiang Autonomous Region, China. Soil samples were collected from four depths in fields with 7-year continuous cotton cropping. The community structure of soil actinomycetes was examined using the 16S rRNA-based polymerase chain reaction-density gradient gel electrophoresis (PCR-DGGE) techniques. The microbial diversity indices of the soil samples from different depths generally decreased along with the period of continuous cotton cropping. When the period of continuous cropping of cotton reached 5 years, the diversity indices rose again and gradually stabilized at a level slightly lower than that of soils with original ecology (i.e., 0-year cotton cropping). Cluster analysis showed that at the 1-20-cm depth, the actinomycete community structure of the soil subjected to 1-year cotton cropping was similar to that of soil subjected to 0-year cotton cropping, whereas that of soils after 3-year continuous cotton cropping showed high similarity. At the 21-40-cm depth, the actinomycete community structure showed various changes but generally recovered to its original pattern after repeated fluctuations. Principal component analysis showed that at the 1-30-cm depth, the actinomycete community structure varied similarly regardless of the period of continuous cotton cropping. In contrast, there were no clear actinomycete community structure variation trends at the 31-40-cm soil depth. Homology comparison of sequences recovered from the DGGE bands showed that the obtained sequences shared similarities >88 %. Alignment with the known homologous sequences indicated a lack of microorganisms related to soil-borne cotton diseases. Continuous cotton cropping exerted significant influences on the community structure of soil actinomycetes in Xinjiang Autonomous Region, which were largely determined by the soil depth and

  17. Systems level insights into alternate methane cycling modes in a freshwater lake via community transcriptomics, metabolomics and nano-SIMS analysis

    Lidstrom, Mary E. [Univ. of Washington, Seattle, WA (United States); Chistoserdova, Ludmila [Univ. of Washington, Seattle, WA (United States); Kalyuzhnaya, Marina G. [Univ. of Washington, Seattle, WA (United States); Orphan, Victoria J. [California Inst. of Technology (CalTech), Pasadena, CA (United States); Beck, David A. [Univ. of Washington, Seattle, WA (United States)

    2014-08-07

    The research conducted as part of this project contributes significantly to the understanding of the microbes and their activities involved in methane metabolism in freshwater lake sediments and in the environment in a more global sense. Significant new insights have been gained into the identity of the species that are most active in methane oxidation. New concepts have been developed based on the new data on how these organisms metabolize methane, impacting not only environmental microbiology but also biotechnology, including biotechnology of next generation biofuels. Novel approaches have been developed for studying functional microbial communities, via holistic approaches, such as metagenomics, metatrancriptomics and metabolite analysis. As a result, a novel outlook has been obtained at how such communities operate in nature. Understanding methane-oxidizing communities in lakes and other environments is of significant benefit to the public, in terms of methane emission mitigation and in terms of potential biotechnological applications.

  18. Follow-up of Students Who Entered Montgomery Community College Fall 1970. A Preliminary Analysis of Student Goals.

    Gell, Robert L.

    As part of a statewide followup study of all students who entered a community college in the fall of 1970, a questionnaire was mailed in April 1974 to the 3,615 students who had entered Montgomery Community College in fall 1970. Twenty percent of the questionnaires were nondeliverable; thus, 2,890 students received the questionnaire, and of these,…

  19. Community Schools. ACSA School Management Digest, Series 1, Number 15. ERIC/CEM Research Analysis Series, Number 42.

    Schofield, Dee

    Utilizing material in the ERIC network, this paper briefly investigates the theory, history, and current state of community schools. Planning guidelines for alternative uses of school facilities are discussed and some examples are given of effective shared facilities. Financial requirements for starting a community school and possible sources of…

  20. Mobilizing Ideas in Knowledge Networks: A Social Network Analysis of the Human Resource Management Community 1990-2005

    Henneberg, Stephan C.; Swart, Juani; Naude, Peter; Jiang, Zhizhong; Mouzas, Stefanos

    2009-01-01

    Purpose: The purpose of this paper is to show the role of social networks in mobilizing how actors both impact and are impacted on by their colleagues. It seeks to compare the human resource management (HRM) academic community with two other comparable communities, and to identify those groups that are seen to work closely together.…